Transcript from February 20, 2003 3:00-3:30 PM Eastern

Copyright © by International Society for Complexity, Information, and Design 2003.

*This is a post-chat Q&A session with biochemist Dr. James Shapiro from the University of Chicago. You can read the actual transcript by clicking here.

Masciarelli
Here is a totally wild question for Mr. Shapiro or others:

micah
This is a less formal discussion...

micah
no moderation takes place...

micah
so as soon as you ask the question it will appear.

James Shapiro
Nonetheless, we can hope it will not be immoderate!

Kirk
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.

Kirk
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

Yaakov
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 correctly

Masciarelli
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 to input?

James Shapiro
Yaakov, you get the message. Evolution, yes, Randomness and gradualism, only in the fine-tuning after the heavy lifting has been done.

phil
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

MyKell
I don't think this is an attack on NeoDarwinism as much as it is broadening of the concept

newchurchguy
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?

James Shapiro
Phil, I think the key problem is to get genuinely new inventions in evolution. This clearly happens. Otherwise we are back with the homunculus and preformationism.

cougar
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?

andrewc
Dr Shapiro, in a sexually reproducing being how does the computed information get transferred to the propagating machinery?

MyKell
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

James Shapiro
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.

cougar
Dr. Shapiro, do you have any comments on Stuart Kauffman's work?

MyKell
oh yeah, that's a good one cougar

James Shapiro
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.

andrewc
Thank you Dr. Shapiro

James 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."

James Shapiro
I'm taking a quick break. I'll be back shortly if there is more to discuss.

joy
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.

bertvan
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?

Kirk
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.

James Shapiro
I just got back and am not able to keep up with all the questions. Could I please ask everyone to put them again?

micah
I was just going to comment on that....you can all see why we need a moderator;-)

cougar
Hmm. Cellular computation and decision-making.... How is this accomplished?

James Shapiro
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.

micah
being a philosopher, I've got to ask this question...

Masciarelli
3 or 4 folks have all asked Q's that seem to drive at this issue: "Are cells making choices?" "Are they *thinking*?"

joy
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?

micah
Do you see the functionality of living systems as reflective of some fundamental or as emergent...

bertvan
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 of reality?

James Shapiro
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.

micah
re: masciarelli, and if the cells are "making decisions" does this reflect on the ability of matter to organize itself at some fundamental level?

James Shapiro
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 amazingly so.

James Shapiro
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.

James Shapiro
Micah, living organisms are self-organizing systems. That's probably why we call them "organisms."

micah
great, I agree.

James Shapiro
Self-organization, growth and assimilation are fundamental properties of life: "sucking order out of the environment" was Schroedinger's description of it.

micah
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.

James Shapiro
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.

cougar
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?

James Shapiro
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.

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Copyright © by International Society for Complexity, Information, and Design 2003.