Science9

Complex Adaptive Systems                     John H. Miller & Scott E. Page        Mar 2009
The Green Fuse                                       John Harte                                         Apr 2009
The Invention of Air                                Steven Johnson                                 May 2009
A Short History of Nearly Everything     Bill Bryson                                       May 2009


Complex Adaptive Systems      John H. Miller & Scott E. Page        Mar 2009
            Subtitle:  An Introduction to Computational Models of Social Life

Part I Introduction  
C1  Introduction  The authors believe that the first writing on complexity in the social sciences go back to Adam Smith's The Wealth of Nations (1776) which was one of the earliest and most cohesive discussions of the topic.  They focus on his concept of an "invisible hand" leading agents into paths where no agent specifically aimed at.  (Perhaps our goal is to make visible the invisible?)  

"The tools and ideas emerging from complex systems research complement existing approaches, and they should allow us to build much better theories about the world when they are carefully integrated with existing techniques."  

"Kenneth Boulding summarized science as consisting of 'testable and partially tested fantasies about the real world.'  The science of complex systems is not a new way of doing science but rather one in which new fantasies can be indulged."

C2  Complexity in Social Worlds  "When a distinguished but elderly scientists states that something is possible, he is almost certainly right.  When he states that something is impossible, he is very probably wrong."  Arthur C. Clarke, Report on Planet Three

"In a complicated world, the various elements that make up the system maintain a degree of independence from one another.  Thus, removing one such element (which reduces the level of complication) does not fundamentally alter the system's behavior. . .  Complexity arises when the dependencies among the elements become important.  In such a system, removing one such element destroys system behavior. . ."

In a complicated world, scientists traditionally try to reduce it to its atomic elements so as best to study them.  Using these same tools to study complex systems fails because it becomes impossible to reduce the system without killing it.  (OK now, a human is a complex system, if you remove the heart, brain, etc. it kills the system / human.  But what if you chop off a little finger, or perhaps the whole hand - with appropriate care the human / system survives - with excellent care the little finger or hand can be reattached.  Therefore a human is not a complex system - or did someone miss something?)

The Standing Ovation problem.  Do you treat all performers as the same?  Do you treat all audience members as appreciating the performance the same?  Do you assume that all audience members are seated at 4th row center or are some behind a piller?  Do some audience members attend with like-minded friends and some come in with a whole crowd of complete strangers?  Do you allow variance in your model?  Bees cooling a hive: variability of response to temperature can keep a hive at a more even temperature.  Feedback, positive and negative.  

The authors make the point that formal modeling usually proceeds by developing mathematical models derived from first principles.  This results in very clean and stark models that can be useful but it works best for static, homogeneous, equilibrating worlds.  This does not work well in dynamic worlds.  How complex is the system we hope to model?  How robust is it?  How is variability in agents handled?  How does the system handle heterogeneity?  Can the model handle niche behavior?  How are the actions of the agents controlled?  How is information about the status of the system processed and how is it used by the agents?  

Part II  Preliminaries  
C3  Modeling  "For every complex problem, there is a solution that is simple, neat and wrong."  H. L. Mencken

The authors point out that good models are similar to maps.  They must present the important relationships while leaving out a lot of unnecessary details.  They must also be easily understandable to others.  They must allow us to predict key features of the world and also enable us to discover new phenomena.  They point out that even though we can model a portion of the world at one level we do not necessarily have the ability to model the higher level portions of the world which seemingly depend on the features of the lower level.  

C4  On Emergence  He intends only his own gain, and he is in this, as in many other cases, led by an invisible hand to promote an end which was no part of his intention.  --  Adam Smith, Wealth of Nations

Any sufficiently advancced technology is indistinguishable from magic.  --  Arthur C. Clarke, Profiles of the Future.

They begin the discussion of emergence with an image composed of pixels.  Up close it is hard to abstract the underlyng image from the individual pixels.  As the number of pixels increase or you step back further the image becomes more obvious.  They discuss the Law of Large Numbers and the Central Limit Theorem and how the mean becomes more obvious as the number of samples increase.  They also discuss the types of transformations (or disorganizations) and how they effect our ability to recognize the underlying pixelated image.  Feedback and organized complexity.  

Part III  Computational Modeling  
C5  Computation as Theory  For centuries houses were build by their occupants, possibly with help from skilled neighbors.  Their design followed the "tried and true" or whims of the occupants.  Some of them fell down.  With the rise of standardized supplies (2X4's) lessened creativity and collapse.  Advanced engineering allows us to create very fanciful homes with a very small liklihood of collapse.  With luck our ability to handle social problems is beginning to follow this model with computational models.  Our theories should be kept separate from the tools used to derive them and different tools are good for different things.  The discuss the difference between computation in theory and using computation as theory.  It is not necessary to use a computer for the computation, it is just generally easier.  They discuss several of the objections to computation as theory:
  1. Computations Build in Their Results  In part this is correct, a model can never go beyond the capabilities of the modeling tool.  It is our job as modelers to build models that are capable of emergent or complex behavior.

  2. Computations Lack Discipline  They do not have the rigid structure of mathematical models but they have the capability of handling problems that are incapable of solution by purely mathematical means.

  3. Computational Models are Only Approximations to Specific Circumstances  All models are approximations.  Modelers must make them as applicable to as many circumstances as possible.

  4. Computational Models are Brittle  By this they mean that slight changes in the model can cause dramatically different results.  They discuss Active Nonlinear Testing (sometimes called sensativity analysis) which can reveal where the model is likely to break down.

  5. Computational Models Are Hard to Test  Simplistic mathematical models often give precise results.  This is more a function of an inadequate model than precise predictions.  Many compututational models use randomly generated probabilities which will naturally result in answers which cluster around a mean instead of a single prediction.  

  6. Computational Models Are Hard to Understand  Math models are impossible to understand if you do not have the appropriate mathematical background.  If the computer model is expressed in understandable code then any suitably educated user can understand it.  
C6  Why Agent-Based Objects?  Much of this chapter contrasts agent-based object modeling with traditional mathematical tools.  One of the important points about any theoretical tool is its trade-off between flexibility and precision.  Mathematical tools offer the highest of precision.  Verbal descriptions (like Smith's Wealth of Nations) offer very low precision but great flexibility.  Flexibility is defined as capturing a wide class of behaviors, precision is exactly defining the elements of a model.  Between the two options above (math vs verbal) you end up with one or the other.  Computational models can offer very high degrees of both.  

The simplest way to discuss this issue is a table comparing traditional (mathematical) models and agent-based (computational) models.  
Traditional (math) tools Agent-Based (computation) tools
Very Precise May be precise, very flexible
Little process in model May incorporate a great deal of process
Aimed at optimization Agents (portions of model) may vary in parameters
Typically static Comp. model allow for dynamic systems
Homogeneous Heterogeneous
Moderate scalability 1, 2, inf High scalability  1, 2, ... , N
Deterministic results are equal Both exactly repeatable or statistically resample
Typically study only end state Can study the process of the phenomena
Cost is rising Model creation expensive, running model cheap
Many (most) areas have been explored Excellent and cost effective theory development

Part IV  Models of Complex Adaptive Social Systems The authors wish to understand the behavior of both the agents in the system and of the system itself.  They want the models to be as simple and accessable as possible.  They also use as many techniques as possible to demonstrate the range of analytic possibilities.

C7  A Basic Framework  As an aid in exploring systems the authors draw a parallel with the Eightfold Path from Buddhism.  
  1. Right View:  What is the information that an agent (element of a model) receives from the system?  In the real world agents have access to huge amounts of information but all of this is never used, there is always some selection process.  What information is selected so that it can be acted upon?  
  2. Right Intention:  What are the goals of the agents?  They may be explicit or they may be inferred from the situation.  Also the system as a whole may have goals. 
  3. Right Speech:  What information is passed between agents?  Is the information passed passively (the other agents "observe" the agent or is there some sort of explicit communication channel?
  4. Right Action:  What interactions occur among the agents?  Do these actions only occur among "friends" or "neighbors" or do they effect other agents at a distance?  Do the agents act simultaneously or do they act asynchronously?  Are these actions delayed or do they occur immediatly?  Is there an ordering of action - do some agents have to wait for others?
  5. Right Livelihood:  How to the actions of other agents effect an individual agent?  
  6. Right Effort:  What sort of processing (rules) do agents use to determine their actions?
  7. Right Mindfulness:  How much "mental" processing do agents use in determining their actions?  This ranges from the very simple (generate a random number) to complex analysis.
  8. Right Concentration:  This is the focus of the model.  The model must be sufficiently complex to capture the phenomenon of interest without burying the user in unneeded details.  
They demonstrate some of this framework by using the Forest Fire Model.  This is a very simple model of a forest with a single tree (optionally) in each cell with rules and probabilities of a lightning strike, a fire propagating from one tree to another, and trees growing.  

C8  Complex Adaptive Social Systems in One Dimension  They start off with a very simple system, a world in which agents live in a circle atop a large atoll with agents 1 through N.  The first model is a cellular atomata (think a simplified Game of Life).  The basis for the rules are simple (status of self and neighbors) so they are "social" cellular automata.  Then they discuss a number of different sets of rules and explore the results.  This area of the book I got from the library has a number of double printed pages which makes reading quite difficult.  

C9  Social Dynamics  Slightly more complex systems.  In the previous chapter the agents did not move and reacted only to their neighbors.  In this chapter the agents may move in their environment thus changing their surroundings.  Examples include the "segregation" problem where similar agents have the option of moving to areas with more or less of their "own kind", the "beach" problem where agents may choose to use a limited facility (the beach), a mainly mathematical discussion of the formation of groups, and network problems where the size, shape, and interconnectedness of the network is studied.  The emphasis here is more on final configuration and math models than on the development and specification of the model.

C10  Evolving Automata  A mostly philosophical chapter.  They start out with automata, Moore machines, properly designed automata that can emulate any computation, representation of faces given a limited number of designs for eyes, noses, etc., the Prisoners Dilemma, 2 X 2 games, and communication between agents.

C11  Some Fundamentals of Organizational Decision Making  Some discussions of bit-wise calculations and their use in making decisions.  They define an organization as a group of agents that accept binary information and transform into a single bit of data which in essence says "Yes" or "No".  I had a great deal of difficulty in relating this to any sort of real-world problem.  

Part V  Conclusions  
C12  Social Science in Between  More talk, not much more information.

Epilogue  The world is complex when you wish to study complicated stuff.  
Appendixes  

A  An Open Agenda for Complex Adaptive Social Systems  The appendix asks a series of questions (or in the first case - a problem) and discusses each.  

They are 1) Whither Complexity 2) What does it take for a system to exhibit complex behavior? 3) Is there an objective basis for recognizing emergence and complexity? 4) Is there a mathematics of complex adaptive social systems? (my opinion, Yes, computational models) 5) What mechanisms exist for tuning the performance of complex systems? 6) Do productive complex systems have unusual properties?  7) Do social systems become more complex over time? (they seem to think so - but only over short periods in America - not Africa, etc.) 8) What makes a system robust?  9) Causality in complex systems?  10) When does coevolution work?  11) When does updating matter?  (synchronous vs. asynchronous updating)  12 When does heterogeneity matter?  13) How sophisticated must agents be before they are interesting?  (this is where the authors and I have the greatest divergence.)  14) What are the equivalence classes of adaptive behavior?  15) When does adaptation lead to optimization and equilibrium?  16) How important is communication to complex adaptive social systems?  17) How do decentralized market equilibrate?  (making the invisible hand visible)  18) When do organizations arise?  19) What are the origins of social life?  

B  Practices for Computational Modeling  A list of a number of computing practices that should help promote quality science in computational modeling.  

1) Keep the model simple.  2) Focus on the science, not the computer.  3) The old computer test.  Write the program as though it will run on an old, slow computer, this is a way of enforcing rules 1 and 2.  4) Avoid black boxes.  Avoid large blocks of code that are very difficult for consumers of the model to understand.  All portions of the code that are relevant to the model should be well documented.  5) Nest your models.  If there are simpler models that work for portions of the model and are well known they should be included in the larger model for at least a portion of the time so that the behavior of the model can be compared with known results.  6) Have tunable dials.  Include methods of altering portions of the model so that its behavior can be evaluated in simpler conditions.  7) Construct flexible frameworks.  Design the model in such a way that it can be easily modified to change conditions to test new questions that were not anticipated by the researcher.  8) Create multiple implementations.  Several ways of doing this, have the model written by several groups of programmers independently, make sure that probability distributions, etc. can be easily modified.  9) Check the parameters.  This could be called a sensitivity analysis or by using automated procedures like Active Nonlinear Tests (ANTs).  10) Document the code.  11) Know the source of random numbers (and make sure that they are adequate).  12) Beware of debugging bias.  Evaluate the code and the results to validate the model not the results.  13) Write good code.  There are several suggestions for writing computer code.  a- all projects involve trade offs, the model accuracy should be very high  b- the majority of the time should be spent on the design  c- correct errors quickly, they become much more costly as time passes  d- there are great differences in programmer ability, make sure that the programmers are up to the task.  14) Avoid false precision (significant digit problem).   15) Distribute your code (make it available on the web).  16) Keep a lab notebook.  17)  Prove your results (perhaps - try to disprove your results).  18) Reward the right things.  The important feature is the quality and simplicity of the model, the quality of the experimental design, and the new insights gained.  Other features should be reported elsewhere.

There is a 6 page bibliography and a 3 page index.  Specific notes are in the text.

This is a book that I would have liked to have read when I was in graduate school in the early 1960's.  It would have been timely and filled with information that I thought was valuable.  For a book published in 2007 it seemed hopelessly old fashioned and out of date.  To say that this is a book aimed at graduate students tells me that their undergraduate education is sorely lacking as it completely ignores the very sophisticated modeling that has been done in the last 40 years.  I was extremely disappointed.

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The Green Fuse                            John Harte                     Apr 2009
            Subtitle:  An Ecological Odyssey

Prologue  The word "fuse" has three main meanings.  The first is a safety device that pops when the circuits are overloaded.  The canary in a mine is an example in a biological system.  Unfortunately for our problems with the world climate we don't have any elevator to escape the mine.

The second meaning for "fuse" is a slow-burning device used to ignite explosives.  We have certainly been lighting enough fuses, we just don't know which will be the first to destructively explode.

The third meaning is to combine, unite, join.  We certainly come together in trying to solve our problems.  We need to realize that all elements of the earth are interrelated and we need to take many things into consideration if we are to successfully survive the coming centuries.  

C1  A Walk up Hidden Creek  Hidden Creek is a small creek off Brooks Lake which feeds the Brooks River which feeds Naknek Lake which feeds the Naknek River which runs into Bristol Bay which is off SW Alaska.  The author and a graduate student went there to evaluate the nitrogen flows in the area.  It turns out that each element recycles about 90% of the nitrogen and that most of the nitrogen entering the system comes from nitrogen fixating blue green algae in lichen.  He tells a fascinating story of how each species and element uses, modifies, and returns nitrogen and other nutrients to the entire ecosystem.  He also points out many other factors which influence life in the area.  One of these is arctic haze which is primarily caused by pollution from transportation and factories in Eurasia.  This causes the arctic to warm several degrees and the pollutants often are deposited on lichen and they are concentrated when animals eat lichen.  

C2  . . . And Down the River of Grass Again a brief description of the many and complex relationships between the life forms and the geographic features of south Florida - from Lake Okeechobee south to the ocean.  In 1969 the author was invited to join a team of scientists to evaluate the construction of a supersonic jetport west of Miami.  The gist of their evaluation was that the jetport itself would not be much of a problem but the surrounding area which would undoubtedly be built up would be of major impact.  To build housing large areas of the swamps would have to be drained and this would reduce the water available.  All of the current water pushing down forces water out through natural channels in the rock where it slowly flows into the Atlantic.  Without this pressure the Atlantic Ocean would flow into these channels and salt water would replace fresh water.  Wells drilled into this aquifer would then begin pumping up salt water destroying the water supply for hundreds of thousands of people including the city of Miami.  Between this analysis and the realization that supersonic jet liners would not be profitable the jetport was never built and larger areas were set aside aside as natural areas.  There is an extensive discussion of the ecological services provided by swamps and marshes.

C3  An Island in the Alpine Archipelago  The salamanders of Galena Mountain in the Colorado Rockies.  They are located in the Mexican Cut Preserve which is very close to the Rocky Mountain Biological Laboratory.  The question that the author and several of his graduate students asked was: Is acid rain responsible for the poor reproduction found in the salamander populations of this area?  The answer was a qualified, Yes.  It is certainly not the only problem that the salamanders face and some of these can reduce reproduction but acid rain certainly causes problems and is almost certainly a contributor.  One of his students came up with a method of predicting how much effect acid rain will have on specific lakes.  This should help in explaining how much effect acid rain will have on salamander populations.

C4  Sage Hill: Chaos and Continuity  Harte describes the camp, the area, and some of the people in the neighborhood of Sage Hill, which in the early 1950's was home to a boys camp where he spent many summers.  

C5  The Greatest Show on Earth  The great diversity of life on earth.  He describes several locations on earth that he has observed, and the sights and sounds associated with each.  He describes three general kinds of biodiversity, habitat diversity, genetic diversity, and species diversity.  

Habitat diversity is very straight forward.  There are many different habitats on earth and each is home to many different species that live in them.  If a particular habitat is destroyed then the species that live there can no longer survive in that place.  If enough similar habitats are destroyed then the species that require that habitat can no longer survive and will become extinct.  

Genetic diversity is primarily a function of the number of small populations of a given species that in the area.  By definition all members of a species can interbreed with any other member of the species.  Practically speaking any individual in a species only breeds with members of the small population in their geographic area.  Each population has a slightly different genetic endowment from other populations.  Species with only one population (like the California condor) are more at risk than species with many populations.  If major environmental change occurs it is more likely that species with many populations will have one or more that can easily adapt to the new environment.

Species diversity is a measure of how many different species coexist in an area.  Tropical rain forests have many more species than extremely harsh environments like the polar regions.  The loss of a single species in a rain forest would hardly be noticed but the loss of a species like the emperor penguins in Antarctica would be noticed almost immediately.  

He discusses some of the ways that major extinction events can happen.  The first mentioned is a large meteorite like the dinosaur killer of 65mya.  The second is rain forest destruction.  This causes problems because trees transpire moisture which raises and creates clouds, clouds reflect more light - without the clouds the earth heats up.  When trees transpire moisture moisture they cool the air.  Also when trees are cut much of the wood is burned or decays which releases CO2 into the air.  He goes on to discuss the benefits of many individual species associated with forests.  If the forests were destroyed these, and others not yet identified, would be destroyed also.  

C6  Between the Devil and the Deep Blue Sea  Coral reefs.  Coral polyps build "houses" in geometric structures which slowly grow larger as new layers are added.  Inside the bodies of the polyps live microscopic algae cells.  The algae and the polyps live in a symbiotic relationship, each producing some of what the other requires to live.  The chapter contains a description of many different factors of importance about coral reefs.  He goes into considerable detail about El Niño and La Niña, how they are created and what effects they have in the world.  

C7  The Sinister Side of Synergy  The author's trip to the Tibetan Plateau and the Ngolog people who live there.  The average elevation is approximately 3 miles above sea level - almost 16,000 ft.  Some people think that the elevation of this plateau, which was very active around 20 mya was a major cause of the series of ice ages that began about this time and are still continuing.  Three reasons have been proposed for this.  Since the elevation is so high it is covered with snow and ice for much of the year, this increases the albedo, decreasing the amount of solar heating.  A second reason is that the huge mass blocks and changes the winds for much of the northern hemisphere.  A third is that the plateau is made up of carbonate rock (sea shells) and when acid rain from natural sources - which is composed of carbonic acid (CO2 + H2O) - falls on the mountains it is neutralized very rapidly forming calcium carbonate.  This rapidly precipitates when the rivers empty into the sea.  Over hundreds of thousands of years this decreases the amount of CO2 in the air which reduces the greenhouse effect cooling the earth.  

The synergy part of the title refers to the effect that humans have on the environment.  In an effort to pacify the Ngolog tribes the Chinese are paying them to kill wild animals and paying them to raise sheep degrading the soil through overgrazing.  He discusses many other initiatives of the Chinese that are very damaging to the environment.  He criticizes the "fuzzy thinking" of the Gaia Hypothesis of James Lovelock but I think his vision here is much too narrow.  He is evaluating it as a physics hypothesis and not as a teaching device.  Lovelock can convince many people to be more ecologically minded through his semi-mystical Gaia construct but Harte's books have reached very few people and they are out of print.  Lovelock was targeting a different group of people which he reached very well.

Epilogue  The epilogue is philosophy, not science - unless you are talking of the philosophy-science of George Lakoff.  I did like his argument for limiting population growth.  He agrees that people are a good thing and one should maximize the number of people on the planet.  He just doesn't want all of them here at the same time.  He leaves it unsaid that a greatly overpopulated earth would loose much of this population from hunger, thirst, war, and disease caused by overcrowding.  

One of my criticisms of some political books is that they are "Bad people doing bad things." books.  This book is much more intelligently written but it is designed to convince the people who are already convinced that the facts given are already true.  When I compare this book with the people who need to be convinced - I fear that they would look at the book and say that it is too dry and scientific and just not read more than the first few pages.  To write a book that grabs people and convinces them of "inconvenient truths" is a very difficult task.  I wish I knew of a technique that would work every time, I wish many other authors knew this technique.  

The references are contained within footnotes.  There is a four page index.  Since much of the book is based on his personal journeys he does not make use of external references.

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The Invention of Air                                Steven Johnson                                 May 2009
            Subtitle: A Story of Science, Faith, Revolution, and The Birth of America

Prologue  The Vortex  In the spring of 1794 the hundred-odd passengers on board the merchant ship Samson were presented with a view of four distinct waterspouts at the same time.  Among these passengers were Joseph Priestley and his wife Mary.  Among the other sights that they saw were "some fine mountains of ice, flying fishes, porpoises, whales, and sharks".  Along the way Priestley measured the temperature of the Gulf Stream just as his good friend Benjamin Franklin had done 20 years earlier.  Both men were fleeing persecution if not death in England because of their political view and both were among the most revered scientists of their day.  

The author makes an interesting point regarding Priestley's importance to the founders of America.  John Adams and Thomas Jefferson had become bitter rivals as politicians but after retiring they engaged in a deep friendship of letter writing to each other.  They wrote 165 letters back and forth, of these Benjamin Franklin is mentioned 5 times, George Washington is mentioned 3 times, Alexander Hamilton only 2 times while Joseph Priestley, an Englishman who only spent 10 years in America was mentioned 52 times.

C1  The Electricians  December 1765 London  A young Joseph Priestley had come to a meeting of the Honest Whigs.  They were a small group of freethinkers and self described "Electricians" who came together every two weeks to eat, drink, and talk.  Priestley was born into an extended family of religious nonconformists, he had become an ordained minister, started a boys school, wrote his first book, The Rudiments of English Grammar, and became interested in electricity.  Along the way he would help found Unitarianism.  He came to this meeting with a proposal.  He offered to write a popular book explaining electrical phenomena.  In short they took Priestley up on his proposal, they assisted him by giving him notes and commenting on his work.  Within about 15 months he had produced a 700 page book, 500 pages describing previous work and 200 pages of his own experiments.  Following publication the book circulated around the world and became one of the principle texts on electricity for almost 100 years.  

The author takes a detour into the philosophy of science, probability, Hegel, Marx, Thomas Kuhn, Earth System Science, etc.  

Following the success of his book on electricity he was offered a ministry in Leeds.  Even though the church was much larger his teaching responsibilities were much less.  Upon moving there they discovered that the official residence was being repaired so the Priestleys took residence for a short while in a house on Meadow Lane which bordered on the Jakes and Nell brewery.  Being curious, Priestley investigated and in a short while he was a constant visitor.  Carbon dioxide, which was then called "fixed" or "metaphitic" air had been discovered only 12 years earlier and he soon began conducting experiments with the carbon dioxide that bubbled out of the vats.  He was soon caught up in the study of gases and he spent much of the next ten years in researching gases.

C2  Rose and Nightshade  August 1771 Leeds  One of the experimental techniques that he used was to place a candle in a sealed jar and see how long it took to go out or put a small animal in the jar and see how long until it died.  Then he tried the same experiment with a small plant of mint - it didn't die.  And when he put a candle or a mouse in with the mint, the candle or mouse took longer before it died.  He conducted many such experiments, laying much of the groundwork for the discovery of oxygen, and when he presented his work to the Royal Society they awarded him the Copley Medal, the most prestigious scientific prize of its day, in 1772.

In 1773 he moved to Wiltshire with Lord Shelburne as as a sponsor.  He was given a much larger house with a very large and well supported laboratory area.  One of his new instruments was a very large (12" diameter) magnifying glass.  He heated up many substances in sealed jars.  One of whicy was mercury calx (or mercury oxide).  This yielded a gas which was even more powerful at keeping candles or mice alive than plants.  Others had actually produced oxygen before Priestley and Priestley discussed his findings with Antoine Lavoisier, and Lavoisier with his superior scales and measurement techniques renamed the "phlogisticated" air Oxygen and described it much more effectively.  Unfortunately Priestley was an adherent to phlogiston theory which kept him from fully understanding what he had discovered.  

In March of 1775 Benjamin Franklin realized that he had to return to America.  He spent his last day in London with Priestley.  

C3  Intermezzo: An Island of Coal  300 Million B.C. Pangaea  A brief description of the Carboniferous Age, when most of the worlds coal deposits were accumulated.  Oxygen levels climbed to 35% of the atmosphere and many giant species of plants and animals were found.  Discussion of oxygen levels, the Gaia Hypothesis, energy (from coal), and how the events in Priestley's life made it possible for him to do what he did;

C4  The Wild Gas  July 1791 Birmingham  Paul Revere's ride took place while Franklin was en-route to America and when Franklin landed he quickly penned a letter to Priestley in which he said that he had made a major discovery (probably the discovery of the "gulph stream") but from then on their correspondence was mainly taken over by political matters.  

Priestley gave Lavoisier ideas about the chemistry of combustion, Lavoisier was appointed head of the French Royal Gunpowder and Saltpeter Administration and with is advise on chemistry the French produced gunpowder that was half again as powerful as British gunpowder.  Franklin negotiated a secret pact with the French that supplied 200 tons of their gunpowder to the Continental Army (about 5 times as much as the Americans had before the war started.  By 1779 more than 800 tons had been imported.  

By 1779 Lord Shelburne had remarried, his second wife did not like the middle-class sensibilities of the Priestleys, and Lord Shelburne was planning on returning to government (he negotiated the close of the Revolutionary War with Franklin), and Priestley was becoming politically active in favor of America, so the Priestleys were no longer welcome around the Shelburne residence.  The Priestley family moved to Birmingham.  There Priestley became associated with the Lunar Society, similar to the Honest Whigs, but whose members included Wilkinson, Wedgwood, Boulton, James Watt, and Erasmus Darwin.  These people supported him financially and he "consulted" regarding scientific matters.  

On April 19, 1786 while John Adams was ambassador to London he met Priestley and became friends.  

In his first productive period, Priestley wrote and experimented with electricity, during his second he focused on chemistry, during his third, while consulting on chemistry with members or the Lunar Society he wrote extensively on politics and religion.  It is well known that Jefferson read and was very much influenced by Priestley's History of the Corruptions of Christianity as well as some of his other works.  The religious establishment in England was not amused by Priestley's works.  

In 1789 and 1790 feelings against Priestley became more and more hostile.  Then on July 14, 1791 they reached a climax.  Several meeting halls where Priestley and others were supposed to have met were burned and the mob then went to Priestley's home.  This was then burned and all of his notes and experimental apparatus was destroyed.  Priestley and his family fled to London.  Then in August 1792 the French granted Priestley an honorary citizenship (this didn't help at all),  his son emigrated to Pennsylvania in October 1793 and in the spring of 1794 Joseph and Mary Priestley set sail for America.  Samuel Taylor Coleridge wrote a short poem mourning his loss to England.  

C5  A Comet in the System  February 1804 Northumberland, Pennsylvania  On June 4, 1794 Priestley arrived in New York.  Vice President John Adams invited him to live in Boston.  The New York papers, scientific, and religious societies welcomed him.  When he moved to Philadelphia he was welcomed there, he had tea several times with President Washington and became good friends with Benjamin Rush.  

Unfortunately the new world was not kind to the Priestley's.  After a warm and happy arrival in December 1795 their son Harry died.  Mary had not been well and she died in September 1796.  Priestley's sermons had become controversial and politicians started avoiding him because of the controversy.  He became good friends with Jefferson and politically attacked Adam's policies.  

Priestley wrote little in a scientific theme after this but he continued his political and religious writing.  He continued to get in trouble with the authorities and was considered for arrest under the Alien and Sedition Acts but President John Adams refused to allow him to be arrested.  He published four new volumes of his General History of the Christian Church in 1803 but then his health began to fail.  He died on February 5, 1804.  As mentioned in the beginning, Priestley had a great influence in the thought of arguably 3 of the 4 most important figures in the American Revolution, Franklin, Adams, and Jefferson and he was well acquainted with the fourth, Washington.  He was well known to George III in England and to the government of France as well as the scientific world and many religious figures.  

The book has 8 pages of notes, a bibliography of 9 pages, and a 14 page index.

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A Short History of Nearly Everything     Bill Bryson                May 2009

Introduction  A very brief introduction to the book mentioning atoms, life, chemistry, species, extinction, the age of the earth, his introduction to science and why he wrote the book.

Part I  LOST IN THE COSMOS    They're all in the same plane.  They're all going around in the same direction. . . . . It's perfect, you know.  It's gorgeous.  It's almost uncanny.  --  Astronomer Geoffrey Marcy describing the solar system.

C1  How to Build a Universe  Imagine a proton, it is really very small.  Now imagine it shrunk to a billionth of it's size.  Now imagine about an ounce of matter stuffed into that space.  Or alternatively imagine all of the matter in the universe stuffed into the same space.  Then imagine a Big Bang!  Depending upon your theory that is the magnitude of the Big Bang.  Now wait about 13.7 billion years until 1965 until two radio astronomers (Penzias and Wilson) have a problem.  Their antenna keeps coming up with a hiss and they can't get rid of it.  The upshot is that they won the Nobel Prize for hearing the echoes of the Big Bang.  

I have one problem with this chapter, ". . . you will never be able to grasp just how tiny . . . is a proton . . .", ". . . there's more space than you can imagine . . ."  Actually I (and many others) can.  Or at least if you can truly grasp any number larger than "the magic number 7 +/- 2" which is about what the average human can readily perceive in a single short glance of a number of things (dots, cows, houses, etc.)  I can compare or do arithmetic with these numbers just as I can with 17 and 38.  So if I can say I understand these, I can be said to understand the very big or very small numbers.  One person's lack of ability to comprehend something does not imply my lack of that ability.  This is also one of the arguments that is used against evolution.  It is false.

C2  Welcome to the Solar System  The discovery of Pluto's moon, the discovery of Pluto.  The Oort cloud, Proxima Centauri, the Drake equation, things a long way out there.

C3  The Reverend Evan's Universe  Rev. Robert Evans is a quiet and cheerful semiretired minister in Australia who is probably the worlds best finder of supernovae.  A discussion of supernovae.  The creation of the earth about 4.6 billion years ago and the creation of the moon about 100 million years later.  

Part II  THE SIZE OF THE EARTH  Nature and Nature's laws lay hid in night; God said, Let Newton be! and all was light.  --  Alexander Pope  

C4  The Measure of Things  Newton's law of gravitation (F=G*m*m' / r*r), the shape of the earth, the invention of calculus, Halley vs. (Newton vs. Hooke), problems with measuring the shape of the earth, Mason and Dixon, Henry Cavendish and the weight of the earth.

C5  The Stone-Breakers  James Hutton and the beginnings of geology.  Hutton was a brilliant man but he was an absolutely terrible communicator, either writing or speaking.  Hutton had a good friend, John Playfair, who, five years after Hutton's death, published a book explaining Hutton's work.  Other early students of geology, Murchison, Lyell, Parkinson, Buckland, Agassiz.  Early attempts at establishing the age of the earth.  Lord Kelvin and his estimates of the age of the earth, ranging from 400 million years to 24 million years.  

C6  Science Red in Tooth and Claw  The description of the first dinosaur bone, 1787.  Disagreements between American and European scientists about living species and fossils.  The realization that fossils could be used to date geological formations.  The petty rivalries that occupied so much time and caused so many heart aches among the fossil hunters of the 1800's, both in Europe and America.  

C7  Elemental Matters  The rise of chemistry.  The use of urine as raw material for phosphorus.  Karl Scheele and the discovery of chlorine, fluorine, manganese, barium molybdenum, tungsten, nitrogen, and oxygen - and how he was never credited with the discovery of any of them.  Priestley and Lavoisier, Count von Rumford, Humphry Davy (potassium, sodium, magnesium, calcium, strontium, and aluminum).  The uniform naming of elements and the table of elements devised by Mendeleev.  The discovery of radioactivity.  Becquerel and the Curies.  Rutherford and the discovery of half-life.  

Part III  A NEW AGE DAWNS   A physicist is the atoms' way of thinking of atoms.  --  Anonymous

C8  Einstein's Universe The chapter is roughly broken into three parts, Max Plank is the focus of the first, Einstein the second, and Edwin Hubble the third.  Plank was the first to propose quantum theory.  Other people mentioned were J. Willard Gibbs and Michelson and Morley.  Hubble was a brilliant scholar and superb athlete.  He was also an inveterate liar and had a huge ego.  He was able to combine others discoveries with his own observations and begin the science of distance measurement in astronomy.  He is credited with the discovery and effective use of red shift.

C9  The Mighty Atom  The modern story of the atom starts with John Dalton.  Dalton was born in 1766.  At the age of 12 he was hired to teach school and he maintained this type of employment throughout his life.  His major work, A New System of Chemical Philosophy, was published in 1808.  His work was of primarily philosophical interest until Einstein described Brownian movement in 1905.  Some other people that follow his lead were Ernest Rutherford, Hantaro Nagaoka, Neils Bohr, and Wolfgang Pauli.

C10  Getting the Lead Out  Thomas Midgley, Jr.  In his productive career he developed tetraethyl lead and chlorofluorocarbons, two of the most dangerous air pollutants of the twentieth century.  The perfection of radioactive dating.  The struggle to remove lead and CFC's from the atmosphere.  

C11  Muster Mark's Quarks  Cloud chambers, atom smashers, and the discovery of subatomic particles.  New models of the atom and of space-time.  Superstring theory.  The determination of the age of the universe - approximately 13.7 billion years as of the time this book was published.

C12  The Earth Moves  One of the last acts that Albert Einstein did was to write a foreword to a book on geology.  It was very complementary, unfortunately it was also badly timed.  One of the main themes of the book was that the continents were fixed and that the idea that they moved was ludicrous.  Plate tectonics, as it would become know as, was first proposed in 1908.  It was roundly criticized but over the years more and more inconvenient facts kept cropping up.  Not every fact supports plate tectonics but as a working theory it seems to best fit all the available facts.  Obviously more is going on but that remains to be explained.

Part IV  DANGEROUS PLANET  The history of any one part of the Earth, like the life of a soldier, consists of long periods of boredom and short periods of terror.  -  British geologist Derek V. Ager  

C13  Bang!  The mystery of the strange earth below Manson, Iowa.  Instead of the usual limestone for that area it is composed of "crystalline clast breccia with a melt matrix" and "overturned ejecta flap".  The water contained in it is also odd, most Iowa water is very hard and Manson water is naturally soft, almost like rainwater.  A discussion of the threat and results of meteorite strikes on the Earth.  The Manson crater was thought to be the cause of the dinosaur extinctions but it was later found to be 9 million years early and much too small.  

The chapter goes on to discuss the cultural geology of meteor strikes (geologists didn't believe in them until their noses were rubbed into the mess), some of the major names (Shoemaker, Levy, the Alvarez's), and the problem that paleontologists had (they also didn't believe in them).  Back to the Manson crater - it has been unfortunately bulldozed and filled in by glaciers over the last 2.5 million years - you can's see anything of it.

C14  The Fire Below  A brief description of Ashfall Fossil Beds State Park in Nebraska.  About 12 million years ago a huge volcanic eruption in Idaho buried the area, and many animals, under 10 feet of volcanic ash.  It then goes on to a description of earthquakes, the movement of magma, etc. in the earth, and moving on to volcanoes and a comparison of other volcanoes with Mt. St. Helens.

C15  Dangerous Beauty  It wasn't until the 1960's that it was realized that almost the entire area of Yellowstone Park is the caldera of a huge volcano, the same "volcano" that blew up 12 million years ago to dump the ash in Nebraska.  The volcano is the surface manifestation of a "hot spot" that has been moving into, then through Idaho, and now into Wyoming for millions of years.  The chapter ends with a description of some of the life that survives in some of the volcanic pools and hot springs of Yellowstone.

Part V  LIFE ITSELF  The more I examine the universe and study the details of its architecture, the more evidence I find that the universe in some sense must have known we were coming.  --  Freeman Dyson

C16  Lonely Planet
 As far as we know, humans can only live on one planet and even on that one planet there are very exacting limits as to where we can live.  A long, and somewhat irrelevant discussion of the activities of John Scot and J. B. S. Haldane, an English father and son team who studied the effects of varying pressures and constituent gases of the atmosphere and how they effected humans.  Its a wonder that they both didn't kill themselves.  

The author then discusses how well humans are adapted to life on earth as it is and how little it would have to change to make human life impossible.  He does mention that humans have adapted to life in our own little niche and that other forms of life have adapted to very different niches.  Perhaps the most important point is that life adapts to whatever situation that is available to it.

C17  Into the Troposphere  A quick discussion of the gases and fluids that surround the sphere that we call the earth.  The four parts of the atmosphere (troposphere, stratosphere, mesosphere, and ionosphere [or thermosphere]).  A brief discussion of the science of the atmosphere and the effect on humans of processes in the atmosphere.  An even briefer discussion of the oceans and global warming.  

C18  The Bounding Main  A lot of information about the exploration and what we know about the seas and life in them.  It is all at a fairly superficial or "Ge Whiz" level.  

C19  The Rise of Life  The Urey-Miller experiment in which they passed electrical discharges through a mixture of water and gases.  The author discusses the conditions necessary to create life but he seems to be arguing from a somewhat Creationist or Intelligent Design point of view.  He needs to read Dawkins, Climbing Mount Improbable or Wills & Bada, The Spark of Life.  He spends too much time on the improbable discussion and not enough on the possible discussion.  The rest of the chapter is quite good, especially the discussion of how oxygen became an important constituent of the atmosphere.

C20  Small World  Bacteria, viruses, and other small things.  Bacteria were probably the first life forms that we would recognize on earth.  They have been found in pretty much every environment on earth other than molten lava.  One estimate says that if you were to take all the bacteria living under the surface of the earth and dump them on the surface they would cover the earth to a depth of five feet.  It is only recently that science has recognized the incredible numbers and the diversity of bacterial species.

C21  Life Goes On  Fossil formation.  The author discuses how fantastically unlikely it is for any given organism to be fossilized and then be found.  One estimate is that less than one species in ten thousand has made it into the fossil record, other estimate it as closer to one species in 120,000.  Trilobites and the Burgess Shale.  The discovery of Precambrian fossils in Australia and England.  The discovery of two other Cambrian fossil sites.  The debate over the Cambrian explosion.  

C22  Good-bye to All That  Some life is fast moving, some is very, very slow.  Patches of lichen in Antarctica a foot in diameter may well be thousands of years old.  For the first 3 billion years or so of life on earth there was very little obvious change.  Then perhaps about 700 million years ago considerably larger life forms appeared and the race was on.  The evolution of the many types of life is explored as well as a number of the major extinction events.  It would almost seem that many smaller species would be sitting around waiting and then when a major extinction event happened they would be ready to explode, rapidly taking over the niches that the larger and older species had left behind.  He makes four points about life: life wants to be; life doesn't always want to be much;life from time to time goes extinct; and life goes on.  

C23  The Richness of Being  Taxonomy, and the institutions that support it.  A visit to the Natural History Museum in London, the obsession the Linnaeus had with sexual nomenclature, the problems with establishing the forms and terminology for naming things.  Why do we have so much trouble in naming and describing our fellow travelers on this journey through life?  1) Most living things are small and easily overlooked.  2) We don't look in the right places (many -most- of the species in the world live where educated white people don't live).  3) There aren't enough specialists.  4) The world is a really big place.

C24  Cells  We briefly bounce around the human body and consider the smallest elements of life that compose a human.  Lots of types of cells are considered, a fertilized egg becomes a baby after about forty-seven doublings and a few losses.  A briefer discussion of Hooke and Leeuwenhoek and a few of their contemporaries.  

C25  Darwin's Singular Notion  A brief biography of Charles Darwin.  How Darwin was urged to drop Origin of Species and write about pigeons, his birth and early education, his voyage on the Beagle, his delays in writing anything about his findings for over 20 years when he finally published,  Alfred Russel Wallace, Gregor Mendel, and the controversy over his ideas which have not lessened in over 150 years since their publication.

C26  The Stuff of Life  How many parents, grandparents, ggrandparents, gggrandparents, etc. do we have?  At 20 generations we have 1,048,576, at 25 generations 33,554,432, at 30 generations 1,073,741,824 and earlier than that it just plain old gets ridiculous.  Obviously there is a lot of incest going on - although much of it is fairly remote incest - 20th cousins etc.  The discovery of Chromosomes, fruit flies, DNA and RNA, the controversy and bad behavior of those involved in the discovery of the structure of DNA, and a brief discussion of how the body creates proteins.  

Part VI  THE ROAD TO US  Descended from the apes!  My dear, let us hope that it is not true, but if it is, let us pray that it will not become generally known.  --  Remark attributed to the wife of the Bishop of Worchester after Darwin's theory of evolution was explained to her.

C27  Ice Time  In April 1815 Mount Tambora exploded in Indonesia.  It was the largest recorded explosion in history.  1816 became known as the year without summer because of the global cooling caused by the smoke and ash in the atmosphere.  Perhaps this event began to symbolize, although not recognized at the time, that the climate of the earth was not a constant.  Throughout the years of the century more and more evidence surfaced and began to be recognized that climate had been different in the past, and especially glaciers had a major effect on the surface of the earth.  The effect of changes in the Earth's orbit from elliptical to circular, mountain building, and changes in the chemical composition of the atmosphere have on the climate (temperature) of the earth.  

C28  The Mysterious Biped  A description of the search for ancient man.  The Dutch Dubois was the first person to set out to find ancient man, and he did it in a very unlikely spot, Sumatra, and then switched over to Java where his team discovered a skullcap in 1891.  Previous to this a few Neanderthal fossils had been discovered by accident.  In 1924 Raymond Dart was sent a skull of a child from the Taung area.  The Peking Man was discovered in China but the bones were lost in WW II.  Following the war in the 1950's the race to discover ancient man was on.  It was not a well regulated race.  Many racers, many large egos, many contradictory explanation, but information and bones were collected.  There are still many controversies but progress is being made.

C29  The Restless Ape  Toolmaking.  There are three basic ways of studying the human past.  The first is fossils of modern day humans and their ancestors (and cousins), the second is tools, and the third is genetics.  The previous chapter covered older fossils, say between 5 mya to 1.5 mya.  This chapter discusses fossils younger than 1.5 my and then starts discussing tools.  The first tools date from 1.5 mya.  Between roughly 1.5 my and about 20,000 years ago both fossil remains and tools become very controversial.  The closer one gets to the modern era the more the bulk of the fossils and the tools resemble modern humans but there is a great deal of overlap and no clear consensus of how modern species of man changed from the ancient species.  The tools are also confusing.  The DNA record is equally confused.  There are clear linkages showing up but we don't have enough samples and we don't have the knowledge to interpret all the findings.  

C30  Good-bye  In the early 1680's Newton wrote his Principia and the last Dodo was killed on Mauritius.  Why it is important to bring Newton into this discussion I don't know, but the Dodo is mentioned because it was the first really well documented extinction to make it into the written record.  Since then many different species of plants, birds, animals, etc. have been clearly killed to extinction by humans.  Before then it is abundantly clear that many species have become extinct when confronted with humans.  

The book has 37 pages of notes, 11 pages of bibliography, and a 16 page index.

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