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Author
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Topic: Alternative to RM&NS
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Berthajane Vandegrift
Member
Member # 272
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posted 18. May 2002 05:17
Endogenous Adaptive Mutagenesis is even simpler than RM&NS. It views life as intelligently organized systems, rather than fortuitous collections of pieces. Mechanisms of EAM consist of all the mechanisms by which living systems change and adapt to their environments and ways of life. Biological change takes place in individual, living, adaptable, environmentally-sensitive organisms -- not in a genome. Adaptive changes in living organisms are readily documented. Such adaptive change may not be reflected in the genome for many generations, until the adaptation has proved to be a permanent part of the organism. (If an organism has the ability to repair random mutations to its genome, it surely has the ability to incorporate a permanently effective behavior or trait into its genome.) Changes to more plastic organs, such as the central nervous system and brain might never be inherited genetically. Evidence for (but not proof of) EAM will consist of:
1. Evidence that behaviors and instincts are inherited epigenetically.
2. Evidence of Lamarckian type inheritance. Not assaults upon the organism, such as cutting the tails off mice for a few generations, but long-term, purposeful, adaptive change purposefully achieved by the phenotype.
3. Evidence of adaptive change taking place in an organism before being reflected in the genome.
4. Evidence of environmentally directed mutation.
5. Evidence that “junk DNA” is not junk, but raw material the genome uses to reflect adaptations achieved by the phenotype. (perhaps acquired by horizontal transfer.)
6. Evidence of cellular intelligence and communication – or evidence of any conscious or non-conscious intelligent behavior occurring in a biological system.
7. Evidence that truly random mutations in the genome can sometimes be corrected by the organism.
8. Evidence of all mechanisms by which individual organisms are able to change and adjust to their environment, not randomly but intelligently and purposefully.
9. Evidence of co-evolution, dramatizing the implausibility of numerous fortuitous “random mutations” occurring accidentally and simultaneously.
10. Evidence against the one-gene-one-trait assumption.
11. Evidence that human “genetic engineering” can sometimes be intelligently reversed or corrected by the organism.
Additions to this list are easy and fun to think of – once you make the transition to thinking of evolution occurring in a living biological system -- not in a genome.
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warren_bergerson
Member
Member # 262
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posted 18. May 2002 08:43
BerthaJane,
Your EAM appears to be very similar to what I call adaptive change or the adaptive paradigm(AP?). I would agree that EAM, or ‘evolutionary change’ consists "of all the mechanisms by which living systems change and adapt to their environments and ways of life".
Whether the details or right or wrong, I have attempted to take the EAM concept a couple of steps further. First, I am speculating or hypothesizing that all the different adaptive change process and mechanisms associated with life forms fit a single logical structure called the adaptive paradigm. Second, I am hypothesizing that the adaptive paradigm is, or can be expressed as a ‘set of complex causal relationships’. Third, I am hypothesizing that an ideal, optimal or efficient form of this set of causal relationships can be expressed or modeled by a specific ‘logic machine program’ called a Life Force Simulator(LFS). Finally, I am proposing a ‘hard science’ theory of adaptive change of the form "Under ideal conditions, adaptive change in intelligent/biological systems occurs as defined by the LFS". [I am not trying to change the subject here, I simply want to clarify where I am coming from]
The form of EAM or AP that I have studied extensively is human decision making. Humans make 1000’s of complex decisions every day, and the logic used in decision making must be continually modified to adapt to changing environmental conditions. Human decision making turns out to be excellent subject to study how ‘intelligence is used to generate adaptive change". [Again, I am just providing some background for my comments on the nature of EAM.]
I know there is a lot of AI work going on in the area of decision making. My analysis involves two major departures from the work being done in AI. First, my analysis is based on observing and modeling how individuals make individual decisions. Second, I separated 1)how an individual makes a decision from 2)how an individual changes how a decision is made. It will be recognized that ‘modeling how I will make decision X today’ is very different from the traditional AI approach of trying "to model how a group of people will make decision X over the next 50 years".
Early on I found there was a fairly simple, standardized technique that could be used to model the logic used to make any ‘conscious’ decision( not a very difficult task if you are only looking the model the logic used by one person at one point in time.). Applying this technique to actual decision making produced the result one would have expected. Different individuals use different logic to make the same decision and the same individual uses different decision making logic at different times. A totally expected result.
What was unexpected, and relevant (finally) to the discussion here, is that the different forms of decision making logic used were, for the most part, all ‘adaptive’ or appropriate for the individual making the decision and conditions under which the individual was making the decision. This suggests that humans use relatively simple logic in making decisions, but we have a very powerful ability to modify or adapt that logic to the specific conditions applicable to an individual at a point in time. In AI terminology, human decision making involves a dynamic, and rapidly changing and very localized, fitness landscape.
To finally get back EAM, I think you are right to assert that life involves ‘intelligently organized systems’ .. in.. ‘which living systems change and adapt to their environments’. My analysis, in support of your assertion, suggests that we can observe, analyze, and model many of those adaptive processes.
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James A. Barham
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Member # 50
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posted 18. May 2002 09:18
I would like to second everything Berthajane has to say about Endogenous Adaptive Mutagenesis, and merely supply some references.
Although much of Berthajane's list consists of a program for the future, there is already considerable empirical support for much of it.
The key reference is Lynn Helena Caporale (ed.), Molecular Strategies in Biological Evolution (Annals of the New York Academy of Sciences, vol. 870), NY Acad. Sci., 1999.
This volume is filled with careful empirical studies demonstrating the goal-directed manipulation of the genome by the cell, and the possible consequences for phylogenesis.
The other crucial works (that I know of---if anyone knows of others, please let me know!) are, of course, those of Barry G. Hall, "Adaptive Mutagenesis: A Process That Generates Almost Exclusively Beneficial Mutations," Genetica, 1998, 102/103: 109--125; and
James A. Shapiro, "Genome Organization, Natural Genetic Engineering and Adaptive Mutation," Trends in Genetics, 1997, 13: 98--104, and "A Twenty-first Century View of Evolution," Journal of Biological Physics, 2002, 28: 1--20 (available on his web site). He also has a great article in the Caporale volume.
Finally, there is the more theoretical but I think very important work of Richard von Sternberg, "Genomes and Form: The Case for Teleomorphic Recursivity," in J.L.R. Chandler and G. Van de Vijver (eds.), Closure: Emergent Organizations and Their Dynamics (Annal. NY Acad. Sci., vol. 901), NY Acad. Sci., 2000, pp. 224--236.
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