The Quark & Jaguar, Gell-Mann; Table of Contents

The Quantum Universe
10 Simplicity and Randomness
11 A Contemporary View of QM & classical approximation
12 Quantum Mechanics
13 Quarks and the Standard Model
14 Superstring Theory
15 Time's Arrow: Forward and Backward Time

Selection & Fitness
16 Biological Evolution
17 From Learning to creative thinking
18 Superstition & Skepticism
19 Adaptive and maladaptive schemes
20 Machines that learn or simulate learning

Diversity & Sustainability
21 Diversities Under Threat
22 Transitions to a more sustainable world
23 Afterword

Biological Evolution is selection

"One crucial mistake made by those who claim a contradiction between that law [Second Law of Thermodynamics] and biological evolution lies in looking only at what happens to certain organisms and not taking into account the environment of those organisms."

"The flow of energy through a system (absorption of energy from the sun) can produce local order (earth, lake, pond, or aquarium)."

"…the influence of information from the terrestrial environmental must be taken into account."

"A population of a given organism is then evolving in the presence of a consistent environment. As time goes on, the population tends to become better adapted to its environment, since different genotypes within the population compete with one another and some are more successful than others in creating phenotypes that survive and reproduce" (236)

"Consequently a kind of discrepancy between the environment and the organism is gradually reduced."

"the rather difficult problem of living in that hot, acidic, sulfurous environment was solved when the Earth was young. The extremophiles (bacteria) reached a kind of steady state, something like an evolutionary equilibrium with their surroundings." (237)

"Most natural environments are more dynamic,"

Coevolving species
"the cluster of genotypes that that characterizes each species, can be regarded as a schema that includes a description of many of the other species and how they are likely to react to different forms of behavior."

"An ecological community consists then , of a great many species all evolving models of other species' habits and how to cope with them."

Cecropia tree of the Amazon Rain forest is coevolving with a species of stinging ant that lives within the tree ( An acacia in Africa has the same relationship)
"Such a situation of symbiosis must have been produced by a substantial period of coevolution."
"the evolution of two species adapting to each other."

"Many species evolve together in an ecological community, with nonliving surroundings that gradually (or even rapidly) alter with time. (238)

"In an ecological community, the process of mutual adjustment through evolution is an aspect of that aging. Biological evolution is part of the winding down process by which the informational gap between the potential (genotype) and the actual (phenotype) tends to be reduced."

"Biological evolution .... often exhibits the phenomenon of punctuated equilibrium'."

What causes the often rapid changes amid enduringly profound periods of stasis?

1: "widespread changes in the physicochemical environment."
2: biological accumulation of "genetic drift" affords a change in the phenotype
3: "Gateway Events" (240)

a. pre-biotic chemosynthesis
b. biotic

origins of the eukaryotic cell from the amalgam of prokaryotic cells
endosymbiosis
autotroph & heterotroph hypotheses (241)

c. [not mentioned] poly-ploidy
the doubling of the number of chromosomes in the cells (plants)
some life cycles include haploid & diploid phases

"In entering the realm opened up by the gateway event, an organism acquires new and very significant regularities, which raise it to a higher level of complexity."

"In the evolution of an ecological community for an economy or a society, opportunities for increased complexity keep arising, as they do in biological evolution, and the result is a tendency for the maximum complexity to drift upward." (241)

"Cooperation leading to aggregation can be effective." (242)
The trend toward higher complexity --- may be inexorable

"The opening of a critical gateway results in an explosion of ecological niches, the filling of which may well look as if it were caused by a drive toward greater complexity."

"Our effect on the biosphere is so profound and our ability to transform life will soon be so great that the future of life on Earth really does depend in large part on crucial choices made by our species."

"-- it looks as if the role of natural biological evolution in the foreseeable future will be secondary…to the role of human culture and its evolution." (246)

Learning to creative thinking

"A successful new theoretical idea …alters & extends the existing body of theory to allow for observational facts…"

"Sometimes a correct idea, when first proposed and accepted, is given too narrow an interpretation. In a sense its possible implications are not taken seriously enough. Then either the original proponent of that idea or some other theorist has to return to it, taking it more seriously than when it was originally put forward, so that its full significance can be appreciated." (261)

Siry examples:
1798, T. Malthus "artificial selection" -> 1855 Darwin "natural selection"
1679, F. Sylvius; "tubercles" -> 1882, Germ theory: tuberculosis
1798, Adam Seybert, marshes' necessity -> 1961, Odum "productive"
"I=1" not "I = 5/2"

"the explanation of strange particle decay that arose through that slip of the tongue proved to be correct." (263)

"we each had found a contradiction between the established way of doing things and something we needed to accomplish"

Helmholtz
"saturation" do the readings & immerse in details
"incubation" associating beyond the boundaries
"illumination" (264) escaping from a basin of attraction

Fitness landscapes

the mathematical formulation that describes adaptive behavior with respect to other adaptive creatures

"a complex adaptive system functions best in a situation intermediate between order & disorder."

“The landscape is very complicated, with numerous pits (local maxima of fitness’) of widely varying depths.” (249)

see Gell-Mann, p. 250.

Transference <§>
Note: genotype is equivalent to the number on the dice
phenotype is equivalent of the pattern you create by connecting the outcomes.

“An extreme form of the selfish gene phenomenon can occur in what is called “segregation distortion.” (251)

“That is more in line with the notion of a complex adaptive system, in which the schema (in this case the genome) is tested in the real world (…by means of the phenotype) rather than directly. (251)

Individual (reproduction and survival) & Inclusive (close relatives) Fitness:
“A fascinating case in which ordinary individual fitness and inclusive fitness both seem to be involved is the so-called altruistic behavior of certain species of birds.”

Mexican or gray-breasted jay
scrub jay of the Oak-scrub habitat of (dry {aquifer recharge} sand hills) Florida

“Nesting territories in the oak scrub are large (on the order of thirty acres), fiercely defended, and not easy to come by.”

Even when fitness is a useful concept, it is still a bit circular. Evolution favors the survival of the fittest, and the fittest are those who survive or whose close relatives survive.” (252)

“Why sex then?
What are males really good for?”
A) crossing over
B) parasite protection

“comparative uniformity of a population produced by parthenogenesis.”

“The mingling of chromosomes contributed by father and mother and also the process of crossing over allow all sorts of new combinations to occur among the offspring, forcing the parasites to cope with a wide variety of hosts, presenting different body chemistry, different habitats, and so forth. As a result the enemies have trouble and the hosts are safer.” (253)

dispersal as a strategy to compensate for having dispensed with sex (rotifers in moss bogs)

At what level of complexity is selection taking place?

Just as the maps above suggest there are different sizes of landscape portions, by analogy we may make the following comparisons between the diagram of a region's many sub-regions and organisms as follows:

level of organization

A landscape

A creature

Initial catchment area genes form traits

Secondary sub-watershed basin chromosomes carry genes

Tertiary watershed cells possess chromosomes

Quaternary tributary basin or sub-basin organs are made of cells

Whole entire river system an individual or entitre body

Supra-whole a complete continent individuals make up a population

crossing over occurs with reproduction {mitotic = division; meiotic = reduction division)
reproduction works on individuals
individuals survive or die (fitness) {life expectancy}

“these [crossing over] advantages accrue to the population”

(page, 255.)

populations (gene pool {genotypes & phenotypes}) have differential survival rates
species (many populations over time) evolve, coevolve or become extinct
ecosystems are a collection of co-adapting species

Two strategists in ecological succession: “R” & “K”
r strategist employs asexual reproduction, increasing rapidly, pioneer species
k strategist employs sexuality to replace the “r” strategist once ecological conditions stabilize

Death, Reproduction, and Population in Biology

“The death of organisms is one of the more dramatic manifestations of the second law of thermodynamics.”
common to all complex adaptive systems
“the interplay between death and reproduction is at the forefront of the adaptive process.”
“fitness…is connected with population size” (255)
schemata
genotype (256)

“Biological evolution, with its emphasis on death and population, is fairly efficient in the long term at filling ecological niches as they arise.” (257)

“Always exploring, seeking out opportunities, experimenting with novelty, the complex adaptive system tries out increases in complexity and occasionally discovers gateway events that open up the possibility of whole new structures, including new kinds of complex adaptive systems. Given enough time, the likelihood of the evolution of intelligence would seem to be high.”

Deception by mimicry is well known”
sentinel species

“The sentinels warn the others by a special call of approaching birds that may turn out to be raptors.” “fake alarm often permitted the sentinel to grab a succulent morsel”

15% = 1/{2(þ)} = 1/ {3.1416 X 2}{10} = 15.708% (p. 259)

Small Steps & Large Changes

“In our discussion of gateway events, we listed some examples of developments in biological evolution that look like enormous jumps, but we also pointed out that those are rare occurrences at one end of a whole spectrum of changes of various magnitudes, the small changes at the other end of the spectrum being much more common.”

“the phenomenon of ‘punctuated equilibrium,’ the comparatively sudden changes can have several different origins.” (260)

1
“physiochemical environment that alters selection pressures significantly”

2
“Another is the result of ‘drift.’ in which neutral mutations, ones that do not disturb the viability of the phenotype gradually lead to a kind of instability in the genotype.”

“in this situation, one mutation or just a few can make a significant difference to the organism and prepare the way for a cascade of changes in a variety of other species as well.”

“Sometimes small changes set off gateway events, often biochemical in character, that open up whole new realms of life forms.”“Nothing is invented out of whole cloth.”

Skepticism

"In contrast to the distinctive selection pressures that characterize the scientific enterprise (at least science at its best), very different kinds of selection have also affected the evolution of theoretical ideas on the same subjects that now form the province of science." (275)
"An example is provided by the appeal to authority, independent of comparison with nature."
1661 "Nullius in verba" motto of the Royal Society -- "Don't believe in anyone's words" instead "'experimental philosophy' which is now called science."
sympathetic magic responds to
"selection pressures quite different from the comparison of predictions with observation."
"partnership of observation {jaguar} and theory {quark}." (275)

Adaptive and maladaptive schemes

"Adaptation takes place on at least three different levels, and that sometimes causes confusion in the use of the term. (292)

1) direct adaptation (thermostat)
no change in the "prevailing schemata"
2) competition among various schemata for primary influence on behavior
change in the prevailing schemata vis a vis other schemata (293)
3) The third level of adaptation is the Darwinian survival of the fittest.
extinction of the prevailing schemata

"The three levels of adaptation take place, generally speaking, on different time scales. An existing dominant schema may be translated into action right away, within days or months. A revolution in the hierarchy of schemata is generally associated with a longer time scale, although the culminating events may come swiftly. Extinction of societies usually take place at still longer intervals of time." (294)

1) translation (send troops to Bosnia to keep the peace settlement)
convert marshlands from occasional grazing to diked farmland
2) revolution (abolition of serfdom & slavery)
realize marshes' necessity in their native condition as productive
3) extinction (Mayan collapse; 10th century, Anasazi; 12th cent)
siltation of the river Meander ended Ephesus as a viable port

Language: reflects all three types of adaptive behavioral time frames:
"child's acquisition of language represents a complex adaptive system in operation"
descent of human languages from the Indo-European root
"biological evolution produced the capacity of human beings(Homo sapiens sapiens) to communicate by means of languages of the modern type." (294)
"When considering the evolution of grammar, it is important to take the various levels of adaptation into account."
"In studying evolution of any complex adaptive system, it is essential to try to pick apart these three strands: the basic rules, frozen accidents, and the selection of what is adaptive. And of course the basic rules may themselves look like frozen accidents when viewed on a cosmic scale of space and time." (295)

"What are some of the conditions that permit maladaptive schemata to survive?"

External Selection Pressures:

(296)

1) reinforcement of the authoritative position of key individuals

(Lord Kelvin vis a vis Darwin)

2) maintenance of social cohesion
3) imposition of a structure of false order on disconnected facts …can provide a degree of comfort
4) illusion of understanding and mastery
5) "the selfish scheme" -- "a pattern is its own reward"

"success in describing nature" is what is adaptive in science
success in engineering "applied science" --"controlling nature for some human purpose"
"Nevertheless, such selection pressures play critical roles in the evolution of cultural DNA." (296)

"In the domain of biological evolution, where selection normally takes place at the phenotypic level, there may be, …exceptional cases where it acts directly on the germ cells: 'a truly selfish gene' promoting. for sperm carrying it, the successful fertilization of an egg, even though the gene may not be helpful, and could even be harmful , to the developing organism."

(297)

The role played by influential individuals, or dominant characters

"the character and ideas -- of individuals -- are critical to the success or failure of the enterprise."

TQM -- "strictures on the internal pressures exerted by managers"

are people rewarded for agreement with managerial whims or what is good for the corporation because it satisfies and retains customer loyalty?
menageries acting as "selfish genes" causing selection of favorites -

- "quis custodiet ipsos custodiet" problem
peter principle of promoting adaptive schemata until they reach the level at which they are no longer promotable."

"the breeding of animals and plants for human use."

“Darwin repeatedly referred to them [plant and animal breeding] ... under the rubric of ‘artificial selection’ with which natural selection can be compared and contrasted.”

page 300.

Windows of Maturation
Time scales for the persistence of maladaptive schemata:

Machines

"Computers can function as complex adaptive systems."

"So far, most such designs or programs have depended on imitating a simplified picture of how some living complex adaptive system works."
digital (home PC) "bits (0 or 1) that is supposed to indicate if the 'neuron' is firing or not."

Analog (hooked up with patch cords) machines where the initial computers, large and slow.

"neural net, which can be implemented either with software or hardware."

(307)

Feedback as a sort of circuitry or wetware:

positive or "+" excite the other, or subsequent response.
negative or "–" if it inhibits the second or subsequent response.

(308)

"Supervision allows fitness to be defined, in terms of the amount of difference between the correct pronunciation of a text and the pronunciation resulting from the schema."

"As usual when fitness is well defined, he learning process consists of exploring valleys on a fitness landscape. If the fitness is also steadily increasing, so that the height keeps decreasing, then the problem of getting stuck in a shallow depression when there are deep pits nearby crops up as always and can be ameliorated by introducing moisture"

"Such random changes in the schema resemble those proposed to jog the mind out of a rut when one is seeking a creative idea. As usual there is an optimum level of noise (interference)."

Genetic Algorithms as a Complex Adaptive System

Diversity

Biological and cultural evolution

He argues that "higher levels of complexity " lead to the … the generation of new types" of organisms and organizations.

"We have examined how simple rules, including an orderly initial condition, together with the operation of chance, have produced the wonderful complexities of the universe."
(329)

"Over long periods of time, they distill out of their experience remarkable amounts of information, characterized by both complexity and depth."

"it is crazy to squander in a few decades much of the rich biological diversity

"that has evolved over billions of years."
(338)

Sustainability

inseparable from concern about the future of the biosphere as a whole …linked with virtually every aspect of the human future." (345)

"However, there is also a growing need for specialization to be supplemented by integration." (345)

Afterword

"all of the alternative coarse grained histories form a branching tree, or 'garden of forking paths,' called a quasi classical domain. " (368)

evolution of complex adaptive systems such as biota, human culture & organizations

"Thus the process of adaptation of the schemata leads only approximately to 'adaptive' results for the systems. 'Maladaptive' schemata can occur as well." (369)

"The nearly 4 billion years of biological evolution on Earth have distilled, by trial and error, a gigantic amount of information about different ways for organisms to live, in the presence of one another, in the biosphere. " (374)

"Both biological and cultural diversity are now severely threatened and working for their preservation is a critical task." (374-75)

"universalizing, scientific, secular culture,"

& homogecene ecological communities

"The conservation of nature, safeguarding as much biological diversity as possible, is urgently required….the need to accomplish a set of interlinked transitions to a more sustainable situation during the course of the next century."
"but it is worthwhile to construct models of the future …"

(375)

"the main function of the book is to stimulate thought and discussion."

(367)

Adaptation, evolution and learning are all aspects of the winding down of the universe.

(372)