from February 20, 2003 3:00-3:30 PM Eastern
Copyright © by
International Society for Complexity, Information, and Design 2003.
is a post-chat Q&A session with biochemist Dr. James
the University of Chicago. You can read the actual transcript by clicking
Here is a totally wild question for Mr. Shapiro or others:
This is a less formal discussion...
no moderation takes place...
so as soon as you ask the question it will appear.
Nonetheless, we can hope it will not be immoderate!
Re. the immune system point that Dr. Shapiro mentioned. The information
to perform the necessary iterations is already written into the genome.
Successful shuffling can only occur within this system. What follows
is a short excerpt from a paper I am currently writing.
An example of using existing information to produce new information
is the process that produces the antigen receptor proteins necessary
to detect a host of pathogen molecules. Different DNA segments encoding
these receptors are essentially excised, shuffled, and recombined
to produce a very large variety of forms. The system of cutting and
pasting includes a RAG protein complex for cutting, and another complex
for joining, which includes the five core proteins Ku70, Ku80, DNA-Pkcs,
Xrcc4 and DNA ligase IV (Ma et al., 2002). Given the existing functional
information in the DNA segments and the system for cutting and pasting,
new functional information can be produced. One of the principle
contributors to the discussion after Claude Shannon’s paper
was Leon Brillouin. Brillouin pointed out that the total information
required to produce a functional sequence or configuration, is composed
of two parts (Brillouin, 1951). Part A is “the part corresponding
to the technical organization of the system of transmission
Hi James, It seems to me that what you are saying throws out Darwinian(or
NeoDarwinian) theory of evolution as the "major" means
of evolution of life on Earth and now this 21st century evolution
sees a much more elegant and orgerly mechanism to induce a guided
development of life when needed. Do I understand your propositions
My wild question: Jim wrote: "cells are capable of altering their
genomes in non-random but not rigidly specified or pre-determined ways." Could
this mean that cells are making 'choices' about how to react, adjust & develop
Yaakov, you get the message. Evolution, yes, Randomness and gradualism,
only in the fine-tuning after the heavy lifting has been done.
For Prof. Shapiro Spetner has suggested that much of what passes for
evolution is response to stress by expression of information already
present in the genome. Is he positing something similar to what you
presented? Phil Skell
I don't think this is an attack on NeoDarwinism as much as it is broadening
of the concept
Thanks, Dr. Shapiro. When you answered Micah's question it was revealing.
If I understood you correctly, you separate information from detection
from information that is instructions. Do you see all information
from observation as different than information that is a response?
Phil, I think the key problem is to get genuinely new inventions in
evolution. This clearly happens. Otherwise we are back with the homunculus
Hi James. Sorry I've missed most of this chat, and I know little about
your... propositions. Are you implying that evolution is directed,
that in some cases the evolution of life can be toward some purpose?
Dr Shapiro, in a sexually reproducing being how does the computed information
get transferred to the propagating machinery?
Dr. Shapiro I want to follow up Glenn's question about speciation.
Can natural genetic engineering help answer the question about the
evolutionary gap between man and the last common ape ancestor
I don't really separate information into categories. The cell is of
necessity a highly interactive environment. If you look at my paper
on the web site, you'll see how I deal with information processing
in sugar utilization by bacteria.
Dr. Shapiro, do you have any comments on Stuart
oh yeah, that's a good one cougar
Andrew, this has to do with how the germ line develops, and that has
major implications for how new populations with new genome organizations
can appear. Again, I have to refer you to my papers or to a later
email correspondence on this issue.
Thank you Dr. Shapiro
I think we need to include functionality in our understanding of biological
complexity. That's why I like to think of it in terms of cellular
computation and decision-making, not just "emergence."
I'm taking a quick break. I'll be back shortly if there is more to
Hello, Dr. Shapiro. Sorry I'm late (business)! I would like to know
if in your modeling you have taken into consideration the computational
theories of consciousness, such as the Penrose-Hameroff microtubule
model. I guess I'd like to know if you see room for cells themselves
to be the selectors as well as the mutators. Thanks.
Dr Shapiro, does the indetermancy of quantum theory imply that the
potential "decision making" exists in inanimate matter,
is a part of basic aspect of reality?
Re. immune system shuffling, I don't know if my question was posted
or noticed, but the information for the system to perform the necessary
iterations is already written into the genome and successful shuffling
can only occur within that system.An example of using existing information
to produce new information is the process that produces the antigen
receptor proteins necessary to detect a host of pathogen molecules.
Different DNA segments encoding these receptors are essentially excised,
shuffled, and recombined to produce a very large variety of forms.
The system of cutting and pasting includes a RAG protein complex
for cutting, and another complex for joining, which includes the
five core proteins Ku70, Ku80, DNA-Pkcs, Xrcc4 and DNA ligase IV
(Ma et al., 2002). Given the existing functional information in the
DNA segments and the system for cutting and pasting, new functional
information can be produced.
I just got back and am not able to keep up with all the questions.
Could I please ask everyone to put them again?
I was just going to comment on that....you can all see why we need
Hmm. Cellular computation and decision-making.... How is this accomplished?
Kirk, the amazing thing about the immune system is that it converts
finite information to infinite variety. That illustrates the tremendous
power of natural genetic engineering. It is not clear to me that
we yet fully comprehend the meaning of this in our thinking about
genomes or evolution.
being a philosopher, I've got to ask this question...
3 or 4 folks have all asked Q's that seem to drive at this issue: "Are
cells making choices?" "Are they *thinking*?"
Dr. Shapiro, my question was to whether or not you have examined and
considered the computational theories of consciousness, including
the Penrose-Hameroff microtubule model. Is there room in cells for
them to be selectors as well as mutators?
Do you see the functionality of living systems as reflective of some
fundamental or as emergent...
you mention a "decision making ability" of the cells. Does
the indetermancy of quantum theory imply that the potential for decision
making was there in inanimate matter, and is therefore a basic aspect
Cougar, through the operation of distributed molecular networks. Dennis
Bray and others have written about the computational properties of
cellular networks. There is a good book by Gerheart and Kirschner
that touches on this subject. The general field of "signal transduction" really
constitutes the study of how cells process information,. Last year's
Nobel Prize went to pioneers in the study of the computational network
that regulate the cell cycle. It's all over molecular biology.
re: masciarelli, and if the cells are "making decisions" does
this reflect on the ability of matter to organize itself at some fundamental
Bertvan, I think this operates far beyond the level of quantum indeterminacy.
Indeed, the interactive, cooperative nature of biological circuits
makes them reliable and subject to a lot of stochastic variation
or to chaotic transitions. They have to be reliable, and they are
I have to correct myself. Biological networks are NOT subject to stochastic
variation. They use feedback and "checkpoints" to make
sure that things come out right and are not left to chance.
Micah, living organisms are self-organizing systems. That's probably
why we call them "organisms."
great, I agree.
Self-organization, growth and assimilation are fundamental properties
of life: "sucking order out of the environment" was Schroedinger's
description of it.
but do we see this functional capacity elsewhere in nature? some have
speculated for example that there is an intrinsic teleological property
in all matter and that life was inevitable. My sense is that we see
a strong demarcation between the organization of matter in life and
the organization of matter otherwise.
Masciarelli, cells are making decisions all the time. Each cell cycle
involves millions of biochemical events. It's a huge task keeping
this from going out of control. Again, the study of the cell cycle
is central to our understanding of this decision-making process.
OK, molecular networks have computational properties. Complex
systems seem to have inherent natural order. How does this connect to the
ongoing evolution of the system?
Cougar, your question goes to the heart of the issue. The ability of
cells to rewrite their hereditary information and their ability to
regulate that process are fundamental to what I think of as a 21st
Century view of evolution. We know a lot about the molecular mechanisms
involved. Our understandinbg of the computational processes involved
are the weak point.
to the chat transcript with James Shapiro.
Copyright © by
International Society for Complexity, Information, and Design 2003.