[BiO BB] Wolfram's Cellular Automata

James Freeman jmfreeman at attbi.com
Fri Dec 20 00:07:15 EST 2002

Hi Parthav,

This might seem a little off topic, but what the heck. Reading the book 
A New Kind of Science will help following this thread.

Parthav Jailwala wrote:

> Hi James,
> You are putting a great effort to program an automaton in perl. Keep 
> it up.
Thanks, I hope that means you tried it and it worked :).

> However, in his book, Wolfram claims (doesn't prove) that many 
> biological mechanisms (including human disease manifestations) can be 
> explained using automatons. How far do you agree or believe in this 
> theory. I feel that biological processes and nature are not that 
> simplistic and will still require classical newtonian 
> physics/math/chemistry to explain its complexities.
What I get out of the book is that there is random data or any 
complexity in a system that can come from two sources, randomness or 
complexity fed to a system, or randomness or complexity in the nature of 
the system itself. Randomness is defined as incompressibility or 
equivalently you have to run the system to know what will happen there 
is no predicting in advance. Systems which are not simply repeating or 
nested patterns are all of the same class and computationally 
equivalent, and probably able to support universal computation, given 
the right input. Simple rules can lead to extremely complicated 
outcomes, and what seems difficult (the patterns on the side of a 
seashell e.g.) can be generated by very simple automata. Automata can 
produce patterns complicated enough for any definition of complexity you 
might throw at it and Wolfram goes quite a ways in showing that. Can 
automata be made that model complex biological behavior? Lindenmayer's L 
systems are computationally equivalent to some automata and go quite a 
way in modeling plant growth and other biological systems. More is 
possible, I am sure, but I made this module for myself to learn and 
explore in my spare time and I hope it is some use to you and others.

Warmest Regards,


> Any thought on this ? Any others wish to air their thoughts? Wolfram 
> is making a remarkable (and startling) theory here, so it will help 
> all of us to share our thoughts on it and satisfy our intellectual 
> curiosities.
> thanks
> parthav jailwala
> James Freeman <jmfreeman at attbi.com> wrote:
>     Hi Folks,
>     If any of you have any spare time over the holidays and are
>     interested
>     in Cellular Automata as shown in Steven Wolfram's book: A New Kind of
>     Science.
>     I have made a Perl module which implements one dimensional
>     non-totalistic cellular automata that can be found at:
>     http://search.cpan.org/author/JMFREEMAN/Cellular-Automata-Wolfram-1.1/
>     This may seem off topic, but there are some interesting phenotypes
>     which
>     can be modeled with cellular automata, and it is a very interesting
>     topic in its own right.
>     See:
>     http://www.wolframscience.com/
>     for more details.
>     Warmest Regards,
>     Jim
>     -- 
>     Bioinformatics Consultant
>     jmfreeman at attbi.com
I am always doing that which I can not do, in order that I may
>     learn how to do it.

>     - Pablo Picasso
>     _______________________________________________
>     Bi O_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
>     https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> ---------------------------------------------------------------------------------------- 
> If you would lift me up you must be on higher ground.
> Ralph Waldo Emerson 1803-1882, American Poet
> ---------------------------------------------------------------------------------------- 
> Parthav Jailwala,Analyst/Project Programmer,Max McGee National Centre 
> for Juvenile Diabetes,Pediatrics(Endocrinology), Medical College of 
> Wisconsin, Milwaukee, WI. Ph : 414-456-8269,E-mail : pjailwal at mcw.edu, 
> Alternate E-mail : pajailwala at yahoo.com
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Bioinformatics Consultant
jmfreeman at attbi.com

I am always doing that which I can not do, in order that I may learn how to do it.

- Pablo Picasso

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