[] strong IDSO

[Mikhail.Prokopenko]

Hi Russ and all,

 

The paper I mentioned earlier

    M. Piraveenan, D. Polani, M. Prokopenko. Emergence of Genetic Coding: an Information-theoretic Model, in F. Almeida e Costa, L. M. Rocha, E. Costa, I. Harvey, A. Coutinho (eds). Advances in Artificial Life: 9th European Conference on Artificial Life (ECAL-2007), Lisbon, Portugal, September 10-14, Lecture Notes in Artificial Intelligence, vol. 4648, pp. 42-52, Springer, Berlin, 2007.

 

cab be d/loaded from

http://www.ict.csiro.au/staff/mikhail.prokopenko/Publications/Agents/ct7.pdf

I should clarify that this paper is not intended as a statement on IDSO at all, but attempts to crudely model possible emergence of proto-symbols (rudimentary genes) that capture dynamics of an object (a rudimentary cell) within its environment.

 

Russ, you make an interesting distinction that "the genes themselves generally don't encode those regularities", but rather "just generate proteins that result in light skin, which correspond to certain facts about nature where those genes evolved". If, say, y is a gene, and h(y) is the protein that corresponds to some regularity in nature - let's ignore the trivialisation of the functional form h(.) for the moment - then wouldn't one be able to say that gene y itself also corresponds to this regularity?  ...and maybe even encodes it in some way?

 

Thanks,

Mikhail

 

---

From: Abbott, Russ
Sent: Thursday, 22 November 2007 3:41 PM
To: Boschetti, Fabio (CMAR, Floreat)
Cc: Prokopenko, Mikhail (ICT Centre, North Ryde); Lafusa, Antonio; IDSO-CSIRO
Subject: Re: starting IDSO discussions: weak and strong IDSO

Hi,

I can't resist jumping in here.

Mikhail's original statement was, I gather, in support, for example, of Adami's claim that "the evolutionary process extracts valuable information and stores it in the genes." That seems quite true. Genes do seem to do that sort of thing. That claim, though doesn't say that everything that happens in nature (or in man-made systems like sodaplay) involves the explicit encoding and passing of information.

Furthermore, it seems that even strong IDSO is an example of weak IDSO in the sense that genes do not store information about the world. Yes, one can say that certain genes evolved to correspond to certain regularities in nature. But the genes themselves generally don't encode those regularities. Genes for, say, light skin that evolved in higher latitudes don't say anything about the length of the day or the strength of the sun. They just generate proteins that result in light skin, which correspond to certain facts about nature where those genes evolved.

So I'd like to request that we attempt to clarify a bit what the issue is that's being discussed.

-- Russ

[Russ Abbott]

Thanks, I'll have a look at the paper. 

Regarding your question:

If, say, y is a gene, and h(y) is the protein that corresponds to some regularity in nature ... then wouldn't one be able to say that gene y itself also corresponds to this regularity?

It seems to me that neither the gene nor the protein typically corresponds to some regularity in nature. In my original message I should have said "is advantageous given some regularity in nature" instead of "corresponds to some regularity in nature." 

Pardon the following fairly long discussion.

The example I used was skin color.  I freely admit to not being an expert in the field. The Wikipedia article (and I don't claim that Wikipedia is always a reliable source) paints a fairly complex picture of the relationship between genes, skin color, latitude, etc. One of the basic mechanisms (it claims) is that like chimpanzees, humans had light skin under our fur. When we lost our fur, dark skin became essential in those parts of the world where the sun was brightest as a way to protect against skin cancer. The genetic configuration for dark skin (lots of melanin) is apparently fairly specific. Any mutation results in significantly lighter skin, which tends to be disadvantageous for survival in the hot sun of Africa. According to this theory, the environment selected for dark skin, not light skin. When that environmental pressure wasn't present, mutation wasn't so disadvantageous, and lighter skin survived.  In addition, lighter skin is advantageous for the production of vitamin D.

So the cartoon version of this is that there is a gene for skin color.  One specific DNA sequence produces dark skin; all other versions produce lighter skin. Dark skin is advantageous where the sun is hot and strong (because of the skin cancer connection). Light skin is advantageous where the sun is weak (because of the vitamin D connection). Both of these connections are correlated with the strength of the sun. But neither of them is directly connected. That is, dark skin with weak sun is OK if you have another source of vitamin D (as the article says the Inuit do). Light skin with strong sun is OK if you have lots of fur (as our primate ancestors did).

So I think it's a stretch to say that either a gene or the protein it produces records information about the environment. It's much more complex than that.

And even if it were more directly connected (without the fur or the other sources of vitamin D), the gene controls the production of melanin. Assume that's all it does.  (It's probably even more complex than that.) The amount of melanin has the effect of making the skin "lighter" or "darker." But why does that matter? It matters because that affects how the skin will respond to sunlight. But isn't that backwards? Light colors reflect sunlight, and dark colors accept it. In this case, though melanin acts as a sun (UV) block rather than as a reflective color. So the more melanin, the less sun.  But:

• Do we care how the specific configuration of nucleic acids produces lots of melanin and other configurations produce less? Or is that a level of abstraction that we can ignore?
  
• Do we care about the mechanism whereby melanin acts as a sun block? Or is that another level of abstraction that we can ignore? 
  
• And finally, do we care about what happens when UV rays are blocked or not blocked , i.e., the biological mechanisms that produce skin cancer and vitamin D? Or is that still  another level of abstraction we can ignore? 

As you know, I'm all in favor of understanding nature in terms of emergent phenomena.  So some of these mechanisms may be subsumed under the mantle of emergence, and we may be able to talk about them as levels of abstraction.  But even so, it seems to me that there is probably significantly more to be said than that genes (or the proteins they produce) encode specific regularities about the environment.

Having gone this far, I would say that it probably makes more sense to understand genes and the proteins they generate as part of a larger collection of mechanisms that working together produce useful (or not-so-useful) results.  Nature typically works that way; it builds new stuff on top of existing stuff.  So if one has a genetic mechanism that results in some functionality, that functionality may be incorporated into some other functionality if the new functionality turns out to be useful.

This view would propose to look at biological mechanisms as increasingly complex levels of abstraction. Some of those levels of abstraction produce functionality in the world. Others produce internal functionality. The overall effect result is that beings with certain functionalities survive better in certain environments.

For example, being able to extract oxygen from water is good if you live in the water, and being able to use oxygen in the atmosphere is good if you live in an atmosphere with oxygen. It's not so much that genes encode information about the environment; it's that genes provide certain functionalities, which are useful in certain environments.

Again, apologies for the length of this post. I got carried away.

-- Russ

On Nov 23, 2007 12:21 AM, <Mikhail.Prokopenko@...> wrote:

Hi Russ and all,

 

The paper I mentioned earlier

    M. Piraveenan, D. Polani, M. Prokopenko. Emergence of Genetic Coding: an Information-theoretic Model, in F. Almeida e Costa, L. M. Rocha, E. Costa, I. Harvey, A. Coutinho (eds). Advances in Artificial Life: 9th European Conference on Artificial Life (ECAL-2007), Lisbon, Portugal, September 10-14, Lecture Notes in Artificial Intelligence, vol. 4648, pp. 42-52, Springer, Berlin, 2007.

 

cab be d/loaded from

http://www.ict.csiro.au/staff/mikhail.prokopenko/Publications/Agents/ct7.pdf

I should clarify that this paper is not intended as a statement on IDSO at all, but attempts to crudely model possible emergence of proto-symbols (rudimentary genes) that capture dynamics of an object (a rudimentary cell) within its environment.

 

Russ, you make an interesting distinction that "the genes themselves generally don't encode those regularities", but rather "just generate proteins that result in light skin, which correspond to certain facts about nature where those genes evolved". If, say, y is a gene, and h(y) is the protein that corresponds to some regularity in nature - let's ignore the trivialisation of the functional form h(.) for the moment - then wouldn't one be able to say that gene y itself also corresponds to this regularity?  ...and maybe even encodes it in some way?

 

Thanks,

Mikhail

 

---

From: Abbott, Russ
Sent: Thursday, 22 November 2007 3:41 PM
To: Boschetti, Fabio (CMAR, Floreat)
Cc: Prokopenko, Mikhail (ICT Centre, North Ryde); Lafusa, Antonio; IDSO-CSIRO
Subject: Re: starting IDSO discussions: weak and strong IDSO

Hi,

I can't resist jumping in here.

Mikhail's original statement was, I gather, in support, for example, of Adami's claim that "the evolutionary process extracts valuable information and stores it in the genes." That seems quite true. Genes do seem to do that sort of thing. That claim, though doesn't say that everything that happens in nature (or in man-made systems like sodaplay) involves the explicit encoding and passing of information.

Furthermore, it seems that even strong IDSO is an example of weak IDSO in the sense that genes do not store information about the world. Yes, one can say that certain genes evolved to correspond to certain regularities in nature. But the genes themselves generally don't encode those regularities. Genes for, say, light skin that evolved in higher latitudes don't say anything about the length of the day or the strength of the sun. They just generate proteins that result in light skin, which correspond to certain facts about nature where those genes evolved.

So I'd like to request that we attempt to clarify a bit what the issue is that's being discussed.

-- Russ

--
-- Russ Abbott
_____________________________________________
Professor, Computer Science
California State University, Los Angeles
o Check out my blog at http://russabbott.blogspot.com/

[Mikhail.Prokopenko]

Hi Russ and all,

 

I agree, of course, that genotype-phenotype relationship is not a simple X = f(Y) relationship :)  And emergence plays a role in the process: I completely agree that "there is probably significantly more to be said than that genes (or the proteins they produce) encode specific regularities about the environment." 

 

Russ argued that

---------

Nature typically works that way; it builds new stuff on top of existing stuff.  So if one has a genetic mechanism that results in some functionality, that functionality may be incorporated into some other functionality if the new functionality turns out to be useful.

This view would propose to look at biological mechanisms as increasingly complex levels of abstraction. Some of those levels of abstraction produce functionality in the world. Others produce internal functionality. The overall effect result is that beings with certain functionalities survive better in certain environments. 

---------

 

This may be a good representation. If we are to learn from Nature (and I don't mean bio-mimetics) we have to start somewhere. Information Theory may be one good tool that transcends simple X = f(Y) relationships (read: simple correlations), and captures the [probably nested] relationships leading to functionality. For example, one could attempt to measure mutual information I(X;Y) between *gene sequences* X and *functional behaviours* Y - without specifying or even assuming a precise relationship f between and Y. It could be said that genes (or the proteins they produce) encode *information* RATHER THAN specific regularities about the environment! 

 

If we assume that a) environment has a "statistical structure", b) agents' genome has a "statistical structure", c) agent's dynamics/functionality in the environment have "statistical structure", then What's the information dynamics among these (and other conceivable) abstraction levels, is a valid question, I think.

In short, the view you advocated (increasingly complex levels of abstraction), as far as I understand, is not at odds with IDSO.

 

I'm curious if "neutral emergence" view (Andrew Weeks, Susan Stepney, Fiona Polack)

http://www-users.cs.york.ac.uk/susan/bib/ss/nonstd/rand07.pdf

is related to this thread?  Susan, would you like to comment on this?

 

Cheers,

Mikhail

P.S. I'm still using IDSO but happy to switch to "information-mediated" rather than "information-driven" at any time when we reach a consensus :)

 

---

From: Abbott, Russ
Sent: Saturday, 24 November 2007 6:25 AM
To: Prokopenko, Mikhail (ICT Centre, North Ryde)
Cc: IDSO-CSIRO
Subject: Re: [IDSO] strong IDSO

Thanks, I'll have a look at the paper. 

Regarding your question:

If, say, y is a gene, and h(y) is the protein that corresponds to some regularity in nature ... then wouldn't one be able to say that gene y itself also corresponds to this regularity?

It seems to me that neither the gene nor the protein typically corresponds to some regularity in nature. In my original message I should have said "is advantageous given some regularity in nature" instead of "corresponds to some regularity in nature." 

Pardon the following fairly long discussion.

The example I used was skin color.  I freely admit to not being an expert in the field. The Wikipedia article (and I don't claim that Wikipedia is always a reliable source) paints a fairly complex picture of the relationship between genes, skin color, latitude, etc. One of the basic mechanisms (it claims) is that like chimpanzees, humans had light skin under our fur. When we lost our fur, dark skin became essential in those parts of the world where the sun was brightest as a way to protect against skin cancer. The genetic configuration for dark skin (lots of melanin) is apparently fairly specific. Any mutation results in significantly lighter skin, which tends to be disadvantageous for survival in the hot sun of Africa. According to this theory, the environment selected for dark skin, not light skin. When that environmental pressure wasn't present, mutation wasn't so disadvantageous, and lighter skin survived.  In addition, lighter skin is advantageous for the production of vitamin D.

So the cartoon version of this is that there is a gene for skin color.  One specific DNA sequence produces dark skin; all other versions produce lighter skin. Dark skin is advantageous where the sun is hot and strong (because of the skin cancer connection). Light skin is advantageous where the sun is weak (because of the vitamin D connection). Both of these connections are correlated with the strength of the sun. But neither of them is directly connected. That is, dark skin with weak sun is OK if you have another source of vitamin D (as the article says the Inuit do). Light skin with strong sun is OK if you have lots of fur (as our primate ancestors did).

So I think it's a stretch to say that either a gene or the protein it produces records information about the environment. It's much more complex than that.

And even if it were more directly connected (without the fur or the other sources of vitamin D), the gene controls the production of melanin. Assume that's all it does.  (It's probably even more complex than that.) The amount of melanin has the effect of making the skin "lighter" or "darker." But why does that matter? It matters because that affects how the skin will respond to sunlight. But isn't that backwards? Light colors reflect sunlight, and dark colors accept it. In this case, though melanin acts as a sun (UV) block rather than as a reflective color. So the more melanin, the less sun.  But:

• Do we care how the specific configuration of nucleic acids produces lots of melanin and other configurations produce less? Or is that a level of abstraction that we can ignore?
  
• Do we care about the mechanism whereby melanin acts as a sun block? Or is that another level of abstraction that we can ignore? 
  
• And finally, do we care about what happens when UV rays are blocked or not blocked , i.e., the biological mechanisms that produce skin cancer and vitamin D? Or is that still  another level of abstraction we can ignore? 

As you know, I'm all in favor of understanding nature in terms of emergent phenomena.  So some of these mechanisms may be subsumed under the mantle of emergence, and we may be able to talk about them as levels of abstraction.  But even so, it seems to me that there is probably significantly more to be said than that genes (or the proteins they produce) encode specific regularities about the environment.

Having gone this far, I would say that it probably makes more sense to understand genes and the proteins they generate as part of a larger collection of mechanisms that working together produce useful (or not-so-useful) results.  Nature typically works that way; it builds new stuff on top of existing stuff.  So if one has a genetic mechanism that results in some functionality, that functionality may be incorporated into some other functionality if the new functionality turns out to be useful.

This view would propose to look at biological mechanisms as increasingly complex levels of abstraction. Some of those levels of abstraction produce functionality in the world. Others produce internal functionality. The overall effect result is that beings with certain functionalities survive better in certain environments.

For example, being able to extract oxygen from water is good if you live in the water, and being able to use oxygen in the atmosphere is good if you live in an atmosphere with oxygen. It's not so much that genes encode information about the environment; it's that genes provide certain functionalities, which are useful in certain environments.

Again, apologies for the length of this post. I got carried away.

-- Russ

On Nov 23, 2007 12:21 AM, <Mikhail.Prokopenko@...> wrote:

Hi Russ and all,

 

The paper I mentioned earlier

    M. Piraveenan, D. Polani, M. Prokopenko. Emergence of Genetic Coding: an Information-theoretic Model, in F. Almeida e Costa, L. M. Rocha, E. Costa, I. Harvey, A. Coutinho (eds). Advances in Artificial Life: 9th European Conference on Artificial Life (ECAL-2007), Lisbon, Portugal, September 10-14, Lecture Notes in Artificial Intelligence, vol. 4648, pp. 42-52, Springer, Berlin, 2007.

 

cab be d/loaded from

http://www.ict.csiro.au/staff/mikhail.prokopenko/Publications/Agents/ct7.pdf

I should clarify that this paper is not intended as a statement on IDSO at all, but attempts to crudely model possible emergence of proto-symbols (rudimentary genes) that capture dynamics of an object (a rudimentary cell) within its environment.

 

Russ, you make an interesting distinction that "the genes themselves generally don't encode those regularities", but rather "just generate proteins that result in light skin, which correspond to certain facts about nature where those genes evolved". If, say, y is a gene, and h(y) is the protein that corresponds to some regularity in nature - let's ignore the trivialisation of the functional form h(.) for the moment - then wouldn't one be able to say that gene y itself also corresponds to this regularity?  ...and maybe even encodes it in some way?

 

Thanks,

Mikhail

 

---

From: Abbott, Russ
Sent: Thursday, 22 November 2007 3:41 PM
To: Boschetti, Fabio (CMAR, Floreat)
Cc: Prokopenko, Mikhail (ICT Centre, North Ryde); Lafusa, Antonio; IDSO-CSIRO
Subject: Re: starting IDSO discussions: weak and strong IDSO

Hi,

I can't resist jumping in here.

Mikhail's original statement was, I gather, in support, for example, of Adami's claim that "the evolutionary process extracts valuable information and stores it in the genes." That seems quite true. Genes do seem to do that sort of thing. That claim, though doesn't say that everything that happens in nature (or in man-made systems like sodaplay) involves the explicit encoding and passing of information.

Furthermore, it seems that even strong IDSO is an example of weak IDSO in the sense that genes do not store information about the world. Yes, one can say that certain genes evolved to correspond to certain regularities in nature. But the genes themselves generally don't encode those regularities. Genes for, say, light skin that evolved in higher latitudes don't say anything about the length of the day or the strength of the sun. They just generate proteins that result in light skin, which correspond to certain facts about nature where those genes evolved.

So I'd like to request that we attempt to clarify a bit what the issue is that's being discussed.

-- Russ

--
-- Russ Abbott
_____________________________________________
Professor, Computer Science
California State University, Los Angeles
o Check out my blog at http://russabbott.blogspot.com/

[Sara Mitri]

* Apologies for multiple postings *

================================================
CALL FOR PAPERS

IEEE CEC 2009 - Special Session on "Evolutionary Robotics"
Trondheim, Norway, 18th-21st of May, 2009

http://lis.epfl.ch/specialsessions/CEC09/
http://lis.epfl.ch/specialsessions/CEC09/CFP.pdf

Paper submission deadline: 1st of November 2008
================================================

ORGANISERS

Patricia A. Vargas (University of Sussex)
Sabine Hauert (EPFL-Lausanne)
Dario Floreano (EPFL-Lausanne)
Phil Husbands (University of Sussex)

DESCRIPTION

Evolutionary Robotics (ER) aims to apply evolutionary computation
techniques, inspired by Darwin's principle of selective reproduction
of the fittest, to automatically design the control and/or hardware of
both real and simulated autonomous robots.

Having an intrinsic interdisciplinary character, ER is being employed
towards the development of many fields of research, among which we can
highlight neuroscience, cognitive science, evolutionary biology and
robotics. Hence the objective of this special session is to assemble a
set of high-quality original contributions that reflect and advance
the state-of-the-art in the area of Evolutionary Robotics, with an
emphasis on the cross-fertilization between ER and the aforementioned
research areas, ranging from theoretical analysis to real-life
applications.

Topics of interest include (but are are not restricted to):

* Evolution of robots which display minimal cognitive behaviour,
learning, memory, spatial cognition, adaptation or homeostasis.

* Evolution of neural controllers for robots, aimed at giving an
insight to neuroscientists or advancing control structures.

* Evolution of communication, cooperation and competition, using
robots as a research platform.

* Co-evolution and the evolution of collective behaviour.

* Evolution of morphology in close interaction with the environment,
giving rise to self-reconfigurable, self-designing, self-healing and
self-reproducing robots or humanoid and walking robots.

* Evolution of robot systems aimed at real-world applications as in
aerial robotics, space exploration, industry, search and rescue, robot
companions, entertainment and games.

* Evolution of controllers on board real robots or the real-time
evolution of robot hardware.

* Novel or improved algorithms for the evolution or robot systems.

* The use of evolution for the artistic exploration of robot design.

PAPER SUBMISSION

Submissions should follow the guidance given on the IEEE CEC 2009
conference website: http://www.cec-2009.org/submission.shtml. When
submitting, please select the special session on "Evolutionary
Robotics". All submissions will be peer-reviewed with the same
criteria used for other contributed papers. All accepted papers will
be included in the published conference proceedings.

POST CONFERENCE BOOK PUBLICATION

Authors of the best selected paper from among those accepted for the
"Evolutionary Robotics" session will be invited to submit an extended
version for review for possible publication as a chapter in the
forthcoming book "The Horizons of Evolutionary Robotics" edited by
Patricia A. Vargas, Ezequiel Di Paolo, Inman Harvey and Phil Husbands
(target publisher MIT Press).

IMPORTANT DATES:

Paper Submission:.........................November 01, 2008
Notification of Acceptance:...........January 16, 2009
Camera-Ready Submission:........February 16, 2009

------------------------------------------
Sabine Hauert
Laboratory of Intelligent Systems
EPFL, Switzerland
http://lis.epfl.ch
Phone: [phone]
Email: sabine.hauert@...
------------------------------------------