Darwin emerges
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Darwin emerges

Summary
Desmond & Moore paint a picture of Charles Darwin's life, expanded from his own highlights:
Following our summary of their main points, RSS is Rob's Strategy Studio frames the details from the perspective of complex adaptive system (CAS)
This page introduces the complex adaptive system (CAS) theory frame.  The theory provides an organizing framework that is used by 'life.'  It can be used to evaluate and rank models that claim to describe our perceived reality.  It catalogs the laws and strategies which underpin the operation of systems that are based on the interaction of emergent agents.  It highlights the constraints that shape CAS and so predicts their form.  A proposal that does not conform is wrong. 

John Holland's framework for representing complexity is outlined.  Links to other key aspects of CAS theory discussed at the site are presented. 
theory

 
Darwin
In Adrian Desmond & James Moore's biography 'Darwin', Charles Darwin, two prior generations of his family and his children; are presented in the context of their proximate environment.  

Catching a Falling Christian
Erasmus Darwin, Charles's paternal grandfather, was a free thinking intellectual and successful doctor based in Lichfield.  He was part of the Unitarian Lunar Society, a
This page discusses the benefits of geographic clusters of agents and resources at the center of a complex adaptive system (CAS). 
geographic cluster
of the industrial elite, a counter culture to the entrenched Anglican hierarchy, that formed around Boulton & Watt, was an innovative maker of marine and stationary steam engines based in Birmingham, England.  It was founded in 1775 by the inventor James Watt & manufacturer Matthew Boulton.  The business leveraged Watt's patented design of a steam engine with a separate condenser, which made the product much more fuel efficient than Newcomen's earlier design.  Most of the parts were initially sourced from other producers until the development of their Smethwick Foundry in 1795. 
's innovative is the economic realization of invention and combinatorial exaptation.  It operates across all CAS, being supported by genetic and cultural means.  Creativity provides the mutation and recombination genetic operators for the cultural process.  While highly innovative, monopolies: AT&T, IBM; usually have limited economic reach, constraining productivity.  This explains the use of regulation, or even its threat, that can check their power and drive the creations across the economy. 
business in Birmingham after the invention of the steam engine uses heat to generate steam to do mechanical work.  They have an external combustion source that burns wood or coal.  Early instances include Newcomen's stationary beam atmospheric engine, and Boulton and Watt's more efficient beam engine.  The steam engine was later used in railroads. 
by Newcomen was an ironmonger and Baptist lay preacher who invented the first practical fuel burning engine, the atmospheric engine in 1712 to support pumping water from a Cornish tin mine.  The network of Baptists supported the deployment of Newcomen steam engines. 
and Watt was a chemist, mechanical engineer and inventor of an efficient steam engine design.  He needed the wealth, skilled iron workers and manufacturing expertise of Matthew Boulton to fully innovate the engine into the market.  While less prolific than Newcomen's earlier engine, the Boulton and Watt product was far more fuel efficient, and supported the emergenceof a geographic cluster of the first industrial revolution.  Watt was born in Greenock Scotland, on the 19 January 1736, to a well educated forceful mother, Agnes Muirhead, and shipright, ship owner and contractor, James Watt, who were Presbyterians and Covenanters.  James was educated at home by his mother before attending Greenock Grammar School where he demonstrated a talent for mathematics.  He initially worked for his father and then, having learned to make instruments in London, became a mathematical instrument maker in Glasgow.  He was able to support the University of Glasgow's astronomical instruments and setup a workshop there.  Interested in the thermodynamics of heat and steam he experimented with the concepts and studied the design of the Newcomen engine.  Having repaired a model for the university he showed that it performed poorly because much of the energy was used in heating the engine cylinder before it was cooled to condense the steam.  Watt patented a modification of a separate condensor where the temperature could be maintained. 


Josiah Wedgwood, the pottery baron, was Charles's maternal grandfather, and was another leader of the Lunar Society. 

The Lunar Society's theology was developed by philosopher, chemist & theologian, Joseph Priestley, who had been focused on developing a religion of universal happiness and souls that were not immortal, came to Birmingham in 1780, and influenced three generations of Wedgwoods and Darwins.  Anglicanism was actively hostile to the ideas of Unitarianism after the French and American revolutions. 

Charles's stern father, Robert, is revealed to be an empathic is the capability to relate to another person from their perspective.  It is implemented by spindle neurons.  Empathy towards others is controlled by the right-hemisphere supramarginal gyrus.  Empathy is context dependently mediated by estrogen.  It develops over time: Piaget's preoperational stage includes rudimentary empathy, Theory of mind supports the development; initially feeling someone's pain as one integrated being, then for them and eventually as them.  In adults, when someone else is hurt the anterior cingulate cortex, amygdala & insula activates projecting [scapegoating] to the vmPFC.  If the pain is physical the PAG activates and motor neurons for the area where the other person was injured.  The intertwining of the ACC amygdala & insula in adults results in attribution of fault even when there is none which can make it hard to step in and actually help.  But in seven-year-olds the activation is concrete: PAG and sensory & motor cortexes with minimal coupling to the rudimentary vmPFC.  In older children the vmPFC is coupled to limbic structures.  Ten to twelve year olds abstract empathy to classes of people.  Brizendine asserts young girls develop empathy earlier than boys, because their evolved greater neuronal investment in communication and emotion networks.  Year old girls are much more responsive to the distress of other people than boys are.  At 18 months girls are experiencing infantile puberty.  By adolescence the vmPFC is coupled to theory of mind regions and intentional harm induces disgust via the amygdala.  Sapolsky explains adolescent boys are utilitarian and tend to accept inequality more than girls do.  But both sexes accept inequality as the way it is.  Sociopaths do not develop empathy.   and highly valued PCP is a Primary Care Physician.  PCPs are viewed by legislators and regulators as central to the effective management of care.  When coordinated care had worked the PCP is a key participant.  In most successful cases they are central.  In certain Medicare ACO models (Pioneer) PCPs are committed to achieve meaningful use requirements.  Working against this is the: replacement of diagnostic skills by technological solutions, low FFS leverage of the PCP compared to specialists, demotivation of battling prior authorization for expensive treatments. 
.  Charles was borne on 12 February 1809, when his mother Susannah, oldest daughter of Josiah, was 43.  His mother ensured that all her children attended Unitarian Sunday school

Charles, being five or more years younger than his siblings, struggled for attention and learned to amuse himself, collecting and hording: shells, 'stamps,' birds' eggs, minerals; hoping for praise, exploring books in his father's library, plants in the greenhouse, and fishing for hours in the river. 

Charles education began at home, where he and his sister Catherine competed for the affection of older sister Caroline who coached them.  Charles was boisterous, mischievous and an attention-seeker, hoping for praise.  At age eight Charles was sent by his mother to attend day school with Unitarian preacher and school teacher George Case. 

When Susannah died, in July 1818, weakened by childbirth and living with Robert, ten year old Charles was cared for by his elder sisters.  In September 1818, Charles started attending Shrewsbury School as a boarder, joining his brother Erasmus

The school was headed by Reverend Samuel Butler, and had gained a national reputation for excellence.  The core education focus was classics: reading, writing & dissecting Latin & Greek languages; learned rote which Charles loathed.  Verse-making was used as a creative outlet, which Charles & his friends generated by patching together pieces from a 'grand collection of old verses.'  Charles spent lots of
Carlo Rovelli resolves the paradox of time. 
Rovelli initially explains that low level physics does not include time:
  • A present that is common throughout the universe does not exist
  • Events are only partially ordered.  The present is localized
  • The difference between past and future is not foundational.  It occurs because of state that through our blurring appears particular to us
  • Time passes at different speeds dependent on where we are and how fast we travel
  • Time's rhythms are due to the gravitational field
  • Our quantized physics shows neither space nor time, just processes transforming physical variables. 
  • Fundamentally there is no time.  The basic equations evolve together with events, not things 
Then he explains how in a physical world without time its perception can emerge:
  • Our familiar time emerges
    • Our interaction with the world is partial, blurred, quantum indeterminate
    • The ignorance determines the existence of thermal time and entropy that quantifies our uncertainty
    • Directionality of time is real but perspectival.  The entropy of the world in relation to us increases with our thermal time.  The growth of entropy distinguishes past from future: resulting in traces and memories
    • Each human is a unified being because: we reflect the world, we formed an image of a unified entity by interacting with our kind, and because of the perspective of memory
    • The variable time: is one of the variables of the gravitational field.  With our scale we don't register quantum fluctuations, making space-time appear determined.  At our speed we don't perceive differences in time of different clocks, so we experience a single time: universal, uniform, ordered; which is helpful to our decisions

time
reading, enjoying Shakespeare and Byron's poetry.  Butler demanded hard work with the goal of building disciplined young men. 

Charles continued to build collections of plants and insects, which he gathered on long solitary walks.  He loved reading Reverend C. C. Clarke's Wonders of the World, developing a vision of distant trips to tropical islands and South American landscapes.  And Desmond & Moore explain, his need to please, required that he learned the names of all he captured because the older boys, he played with and looked up to, all knew these details, required knowledge when every upper-class drawing-room had a cabinet of curios. 

Erasmus, with Charles in tow, built a chemistry lab, at their home, an idea which was likely inspired by the Wedgwood's understanding and use of chemistry to develop their pottery. 

Dr. Robert decided that Erasmus should follow him into medicine.  He selected King's college, Cambridge, for his medical education, which would provide him with the perspective of an Anglican, upper class, English gentleman, to align him with the status is a publically accepted, signal that one possesses assets: wealth, beauty, talent, expertise, access & trust of powerful people; to be able to help others. 
and expectations of his future clients

Charles meanwhile had learned to shoot game, which he found invigorating.  But he was demotivated at Shrewsbury School, underachieving and so a problem for his father.  Dr. Robert's solution was to remove Charles from school in 1825 and send him, starting in 1826, aged 17, to Edinburgh to learn medicine.  And Erasmus was able to accompany him, since he could intern at the hospital in Edinburgh to complete his medical qualifications

The Northern Athens
Unfortunately, Charles was sickened at the sight of blood and unimpressed with the lackluster professors teaching medicine.  But Edinburgh, had a great library, where Charles & Erasmus read voraciously, and was a haven for revolutionary Continental ideas, discussed at extra-mural schools situated around the university, which introduced Charles to the leading edge of scientific thought: Natural history including evolutionary theories and debunking of religious orthodoxy, advanced geology, traveling in South American rain forests & paleontology. 

Sea-Mats & Seditious Science
Charles, accepted by the Edinburgh elite since he was Erasmus Darwin's grandson, was introduced to new ideas, emotionally aligned with his prior interests, by various mentors who also sponsored him to various societies:
  • William Browne, who studied madness and attacked Church doctrine, who sponsored Charles, aged 17, to join Robert Jameson's Plinian society in Nov 1826
  • William Greg, who promoted humans being evolved from other animals
  • John Coldstream, who shared Charles interest in exploring the shores for sponges, corals & sea-pens
  • Robert Grant, evolutionist & renound sponge expert, who pushed Darwin to read the works of Lamarck and his colleagues and promoted Darwin's discoveries alongside his own
    • Grant generated 20 ground breaking papers on sponges, in the Edinburgh journals in 1826 & 1827 which resulted in a Europe wide reputation for this work.  
    • Grant asserted all animals shared similar organs, and demonstrated the pancreas he had discovered in a mollusc.  This was a notion that threatened Creationism, which viewed each animal designed by God to perfectly match its niche. 
    • Darwin under instruction helped Grant, carefully observing larvae of molluscs and sea-mats, and stalked sea-pens.  He admired the approach and made observations himself, noting that the black peppercorn-like bodies found inside oyster shells, were the eggs of a skate leech.  Grant promoted Darwin's discovery in a presentation to the Wernerian Natural History Society.  
  • Conservatives were aghast at the godless philosophy, seeing it as subversive, still worried by the threat of revolution coming to Great Britain; Charles had to rationalize the various ideas of these dissident scientists and the reactionary response. He was helped by attending popular geology lectures which aligned with his interest in chemistry and agreement with Grandfather Erasmus's ideas. 
Charles's advisors told him to attend Regius Professor of Natural History, Robert Jameson's practical geology course.  It covered mineralogy and meteorology, geology, and natural history, and a series of lectures on the 'Origin of the Species of Animals.'  Jameson also held practicals three times a week in 'his museum,' where he explained exhibits: minerals, and sequences of rock strata and how to read them.  And his field trips showed his students, rocks in situ and how to keep records of the flora and fauna, which Desmond & Moore note was seen as most important by the East India Company.  The company recommended attendance to its training military surgeons and engineers. 

Charles left Edinburgh and abandoned his father's proposed choice of a career in medicine. 

Anglican Orders
Desmond & Moore explain that Dr. Robert's goal was to place Charles in a profession.  Having failed at medicine he hatched a plan to make Charles an Anglican vicar, another role that was a pillar of the community.  Charles was sent to Cambridge, in 1828, just turning 19, to learn theology. His father would invest in an auctioned parish that Charles could then takeover.  As a leader of the parish, Charles would be able to hunt and socialize with the other wealthy parishioners. 

Charles, agreed to the plan, brushed up on the classics that he had found tedious at school, and read some introductory divinity books.  Early in 1828, Erasmus, who was set to take his Bachelor of Medicine exam in Cambridge and Charles, headed to the town, which was controlled by the all-powerful university and Anglican church.  The university was an Anglican institution.  Almost all college heads, most professors and Fellows had taken holy orders.  Half the graduates would enter the Church.  The university was a key node in England's law & order.  The university proctors were setup to spy on the students.  Erasmus told Charles: keep the college curfew, no fighting or dueling, remain sober in public, never be seen with girls, and always wear a cap and gown.  The university had its own court.  The Vice-Chancellor had autocratic powers over the gowns and town's people. 

The head proctor was Reverend Adam Sedgwick, a professor of Geology.  He was Vice-President of the Geological Society of London, and passionately devoted to research on the most ancient and little-known stratified rocks.  He had great attention to detail that was helpful in both roles. 

Charles, and the rest of the students, were sucked into unique Cambridge approved extra-mural activities: Dining clubs, Outdoor sports, conversation clubs, Union Debating Society, The Apostles; with Charles focused on collecting beetles, along with most of the nation and Charles's relatives.  It required Charles to scrutinize their structure and habits and reading manuals including world-leader on invertebrates, Lamarck.  Charles attended Friday dinner with Cambridge Botany professor Reverend John Henslow to discuss natural history.  Charles was happy with his father's proposal: the Church was the place to be. 

Paradise & Punishment
But this focus started to undermine his core studies, leaving him baffled by mathematics.  He dedicated
Carlo Rovelli resolves the paradox of time. 
Rovelli initially explains that low level physics does not include time:
  • A present that is common throughout the universe does not exist
  • Events are only partially ordered.  The present is localized
  • The difference between past and future is not foundational.  It occurs because of state that through our blurring appears particular to us
  • Time passes at different speeds dependent on where we are and how fast we travel
  • Time's rhythms are due to the gravitational field
  • Our quantized physics shows neither space nor time, just processes transforming physical variables. 
  • Fundamentally there is no time.  The basic equations evolve together with events, not things 
Then he explains how in a physical world without time its perception can emerge:
  • Our familiar time emerges
    • Our interaction with the world is partial, blurred, quantum indeterminate
    • The ignorance determines the existence of thermal time and entropy that quantifies our uncertainty
    • Directionality of time is real but perspectival.  The entropy of the world in relation to us increases with our thermal time.  The growth of entropy distinguishes past from future: resulting in traces and memories
    • Each human is a unified being because: we reflect the world, we formed an image of a unified entity by interacting with our kind, and because of the perspective of memory
    • The variable time: is one of the variables of the gravitational field.  With our scale we don't register quantum fluctuations, making space-time appear determined.  At our speed we don't perceive differences in time of different clocks, so we experience a single time: universal, uniform, ordered; which is helpful to our decisions

time
in the holidays to seeing his girlfriend Fanny Owen.  And he visited his brother Erasmus, returning from a trip to Europe in London, where Reverend Hope, a Shropshire beetle collector, gave him an introduction with the leading collectors of beetles.  Erasmus showed him round the highlights of scientific London: the Royal Institution, Linnean society, Zoological gardens ... over 5 days, including a meeting with Robert Grant, now at London University. 

Returning to Cambridge, and alone, Charles lost focus, as in Edinburgh, feeling that he was not moved by the Holy Spirit, or his studies, and was warned by his tutor that he was ill prepared for the preliminary exam.  And his enthusiasm for beetles was waning, and ignoring his brother's advice he took to drinking and partying with a wilder set of students.  It took a major demonstration of punishment of trouble-making free thinkers, Taylor and Carlile, and associated innocents, by the university authorities, to snap Charles out of his profligate ways. 

While in Shropshire for the holidays, Charles went entomologizing with Hope in North Wales, but his lip became enflamed and he had to return to his father and sisters for care.  But he was energized when he read his name in print, a credit in Stephens's Illustrations of British Entomology.  He visited his cousin but returned to see Erasmus, happily pensioned off from medicine, by his father who determined that Charles's brother was too frail to cope with the stress is a multi-faceted condition reflecting high cortisol levels.  Dr. Robert Sapolsky's studies of baboons indicate that stress helps build readiness for fight or flight.  As these actions occur the levels of cortisol return to the baseline rate.  A stressor is anything that disrupts the regular homeostatic balance.  The stress response is the array of neural and endocrine changes that occur to respond effectively to the crisis and reestablish homeostasis. 
  • The short term response to the stressor
    • activates the amygdala which: Stimulates the brain stem resulting in inhibition of the parasympathetic nervous system and activation of the sympathetic nervous system with the hormones epinephrine and norepinephrine deployed around the body, Activates the PVN which generates a cascade resulting in glucocorticoid secretion to: get energy to the muscles with increased blood pressure for a powerful response.  The brain's acuity and cognition are stimulated.  The immune system is stimulated with beta-endorphin and repair activities curtail.  In order for the body to destroy bacteria in wounds, pro-inflammatory cytokines increase blood flow to the area.  The induced inflammation signals the brain to activate the insula and through it the ACC.  But when the stressor is
  • long term: loneliness, debt; and no action is necessary, or possible, long term damage ensues.  Damage from such stress may only occur in specific situations: Nuclear families coping with parents moving in.  Sustained stress provides an evolved amplifier of a position of dominance and status.  It is a strategy in female aggression used to limit reproductive competition.  Sustained stress:
    • Stops the frontal cortex from ensuring we do the harder thing, instead substituting amplification of the individual's propensity for risk-taking and impairing risk assessment! 
    • Activates the integration between the thalamus and amygdala. 
      • Acts differently on the amygdala in comparison to the frontal cortex and hippocampus: Stress strengthens the integration between the Amygdala and the hippocampus, making the hippocampus fearful. 
      • BLA & BNST respond with increased BDNF levels and expanded dendrites persistently increasing anxiety and fear conditioning. 
    • Makes it easier to learn a fear association and to consolidate it into long-term memory.  Sustained stress makes it harder to unlearn fear by making the prefrontal cortex inhibit the BLA from learning to break the fear association and weakening the prefrontal cortex's hold over the amygdala.  And glucocorticoids decrease activation of the medial prefrontal cortex during processing of emotional faces.  Accuracy of assessing emotions from faces suffers.  A terrified rat generating lots of glucocorticoids will cause dendrites in the hippocampus to atrophy but when it generates the same amount from excitement of running on a wheel the dendrites expand.  The activation of the amygdala seems to determine how the hippocampus responds. 
    • Depletes the nucleus accumbens of dopamine biasing rats toward social subordination and biasing humans toward depression. 
    • Disrupts working memory by amplifying norepinephrine signalling in the prefrontal cortex and amygdala to prefrontal cortex signalling until they become destructive.  It also desynchronizes activation in different frontal lobe regions impacting shifting of attention.  
    • Increases the risk of autoimmune disease (Jan 2017) 
  • During depression, stress inhibits dopamine signalling.  
  • Strategies for stress reduction include: Mindfulness. 
of the profession.  Erasmus, twenty-five, planned to settle in London, with a spare bed for Charles when he visited. 

The Man Who Walks With Henslow
Charles returned to Cambridge, attended tutorials, and became a fixture again at Professor Henslow's naturalist Friday evening parties. 

Charles, and the other divinity students were nearing their second year examinations, and he aimed to get a pass, by immersing himself in the ancient languages.  And he found Paley's Evidences of Christianity fascinating, so logical he learned it by heart.  And it was reflected in the operation of Cambridge.  Charles passed the examination and oral well enough to have completed his courses. 

Charles, often moody when feeling ignored by his friends, decided Fanny was finished with him, and so doubled down on professor Henslow's friendship.  Charles obvious expertise in collecting plants and beetles helped justify the professor's interest in him.  He was clearly the favorite pupil at Henslow's lectures.  Henslow's ideas were in conflict with Grant's but Charles kept the conflict to himself.  He was becoming an expert field naturalist and priest, with Henslow as his
The agents in complex adaptive systems (CAS) must model their environment to respond effectively to it.  Evolution's schematic operators and Samuel modeling together support the indirect recording of past successes and their strategic use by the current agent to learn how to succeed in the proximate environment. 
model
.  He was called to Fanny's parents, who let him know that Fanny was engaged to John Hill. 

Every Man For Himself
Charles returned to Cambridge, to prepare for his final exams.  Friday evening with Professor Henslow and his wife, was his only distraction from study.  And he was fortunate that Henslow gave him private tuition in mathematics and theology.  He would be examined on Paley's Principles of Moral and Political Philosophy, and the Evidences.  But Paley's justification for sovereign and state was expediency, he asserted every man must judge for themselves, which now that France had revolted once more, seemed out of tune, presenting a dilemma for the examination.  Charles stayed in Cambridge over Christmas, cramming, before sitting the week of exams: Homer, Virgil, Paley's Evidences, Paley's Moral & Political Philosophy, Locke's Essay concerning Human Understanding, mathematics; which he passed, ranking 10th out of 178 who passed.  He was awarded the BA, and became inexplicably depressed is a debilitating episodic state of extreme sadness, typically beginning in late teens or early twenties. This is accompanied by a lack of energy and emotion, which is facilitated by genetic predisposition - for example genes coding for relatively low serotonin levels, estrogen sensitive CREB-1 gene which increases women's incidence of depression at puberty; and an accumulation of traumatic events.  There is a significant risk of suicide: depression is involved in 50% of the 43,000 suicides in the US, and 15% of people with depression commit suicide.  Depression is the primary cause of disability with about 20 million Americans impacted by depression at any time.  There is evidence of shifts in the sleep/wake cycle in affected individuals (Dec 2015).  The affected person will experience a pathological sense of loss of control, prolonged sadness with feelings of hopelessness, helplessness & worthlessness, irritability, sleep disturbances, loss of appetite, and inability to experience pleasure.  Michael Pollan concludes depression is fear of the past.  It affects 12% of men and 20% of women.  It appears to be associated with androgen deprivation therapy treatment for prostate cancer (Apr 2016).  Chronic stress depletes the nucleus accumbens of dopamine, biasing humans towards depression.  Depression easily leads to following unhealthy pathways: drinking, overeating; which increase the risk of heart disease.   It has been associated with an aging related B12 deficiency (Sep 2016).  During depression, stress mediates inhibition of dopamine signalling.  Both depression and stress activate the adrenal glands' release of cortisol, which will, over the long term, impact the PFC.  There is an association between depression and additional brain regions: Enlarged & more active amygdala, Hippocampal dendrite and spine number reductions & in longer bouts hippocampal volume reductions and memory problems, Dorsal raphe nucleus linked to loneliness, Defective functioning of the hypothalamus undermining appetite and sex drive, Abnormalities of the ACC.  Mayberg notes ACC area 25: serotonin transporters are particularly active in depressed people and lower the serotonin in area 25 impacting the emotion circuit it hubs, inducing bodily sensations that patients can't place or consciously do anything about; and right anterior insula: which normally generates emotions from internal feelings instead feel dead inside; are critical in depression.  Childhood adversity can increase depression risk by linking recollections of uncontrollable situations to overgeneralizations that life will always be terrible and uncontrollable.  Sufferers of mild autism often develop depression.  Treatments include: CBT which works well for cases with below average activity of the right anterior insula (mild and moderate depression), UMHS depression management, deep-brain stimulation of the anterior insula to slow firing of area 25.  Drug treatments are required for cases with above average activity of the right anterior insula.  As of 2010 drug treatments: SSRIs (Prozac), MAO, monoamine reuptake inhibitors; take weeks to facilitate a response & many patients do not respond to the first drug applied, often prolonging the agony.  By 2018, Kandel notes, Ketamine is being tested as a short term treatment, as it acts much faster, reversing the effect of cortisol in stimulating glutamate signalling, and because it reverses the atrophy induced by chronic stress.   Genomic predictions of which treatment will be effective have not been possible because: Not all clinical depressions are the same, a standard definition of drug response is difficult;.  His residency required Charles to stay in Cambridge until June.  Charles was convinced he wanted to be a clerical naturalist or professor like Henslow, who had first travelled, broadened his education, got married and then taken holy orders.  This vision suggested reading broadly: Charles read Paley's Natural Theology, which asserted life was so well designed, there had to be a designer, Paley's proof of God.  He read Herschel's Preliminary Discourse on the Study of Natural Philosophy - giving him a burning zeal for science, and Humboldt's Personal Narrative - a seven volume description of a trip to South America. 

Henslow concluded that Charles needed detailed training in geology, from the man that had taught him - Professor Adam Sedgwick.  Henslow formerly introduced Charles to him, explaining the trip's goal and Sedgwick agreed to his tuition.  Charles was allowed to attend his lectures and go with him on a geological tour in the summer.  Charles found the lectures fascinating, and although he new little about the subject, his desire to please drove him to work hard.  He helped Sedgwick solve a puzzle hidden in the Welsh hills, and at the same time learned geological expertise first hand from a master, and fell in love with the subject. 

Charles now had a vision for his future, and a mission: a month long trip to the Canaries, with Henslow and other scientists; so he requested permission from his father, who agreed to fund the trip.  Visiting Erasmus in London, Charles was made aware of the political crisis that led the King, William IV, to dissolve parliament, but Charles could only get emotional about visiting the Canary Islands.  As he worked on the plans, circumstances changed.  His partners dropped out and he was offered the opportunity to participate instead in a round the world trip. 

1831-1836

My Final Exit
The Admiralty was planning a two-year survey of coastal South America, and the ship's commanding officer, Captain Robert FitzRoy, was in need of a gentleman companion, to provide company that should stop him going crazy from the isolation of command.  FitzRoy had captured some Fuegians on a previous trip and after presenting them to the King was now intending to take them back to their homeland.  While Charles's father worried that this proposal was a demonstration of Charles's aimless preoccupation with enjoying himself, he was swayed by Jos. Wedgwood, who asserted:
  • A global voyage would do Charles the world of good
  • It would shape his character
  • It might well ready him for a profession; 'Natural History ... is very suitable to a Clergyman.'
  • It will make him a man of enlarged curiosity
  • The voyage was a golden opportunity to see 'men and things.' 
  • The admiralty would look after him well. 
Desmond & Moore note Charles was now well prepared for his monumental creative act.  "He was well qualified scientifically, and perfectly so socially.  Jameson's Edinburgh course, as luck would have it, had catered for colonial travellers.  He had learned to identify minerals and disentangle strata, and Sedgewick had fired up his feeling for the subjectGrant had given him the best instruction in Britain on lowly sea life.  Darwin had worked his way round Lamarck's systematics and the latest insect identification guides.  And what he lacked in experience he made up for in enthusiasm.  He could shoot, skin, and stuff, and Henslow had topped his training off with a grounding in botany.  He was, as Henslow said, 'amply qualified for collecting, observing & noting,' and that is what counted." they write. 

FitzRoy transforms the Beagle, rebuilding it with the most advanced equipment. 

A Chaos of Delight
They set off with the Beagle headed for Madeira & Tenerife.  Darwin, now nearly 23 in early 1832, struggles to get his sea legs, but while he fails to stand he spends
Carlo Rovelli resolves the paradox of time. 
Rovelli initially explains that low level physics does not include time:
  • A present that is common throughout the universe does not exist
  • Events are only partially ordered.  The present is localized
  • The difference between past and future is not foundational.  It occurs because of state that through our blurring appears particular to us
  • Time passes at different speeds dependent on where we are and how fast we travel
  • Time's rhythms are due to the gravitational field
  • Our quantized physics shows neither space nor time, just processes transforming physical variables. 
  • Fundamentally there is no time.  The basic equations evolve together with events, not things 
Then he explains how in a physical world without time its perception can emerge:
  • Our familiar time emerges
    • Our interaction with the world is partial, blurred, quantum indeterminate
    • The ignorance determines the existence of thermal time and entropy that quantifies our uncertainty
    • Directionality of time is real but perspectival.  The entropy of the world in relation to us increases with our thermal time.  The growth of entropy distinguishes past from future: resulting in traces and memories
    • Each human is a unified being because: we reflect the world, we formed an image of a unified entity by interacting with our kind, and because of the perspective of memory
    • The variable time: is one of the variables of the gravitational field.  With our scale we don't register quantum fluctuations, making space-time appear determined.  At our speed we don't perceive differences in time of different clocks, so we experience a single time: universal, uniform, ordered; which is helpful to our decisions

time
reading: Humboldt's Personal Narrative (again), and Lyell's principles of Geology.  Lyell pictures the world slowly shifting, in disagreement with Sedgwick who asserted cataclysmic shifts.  When the Beagle anchors in the Cape Verde Islands, Darwin investigates the island of St. Jago.  He notices a line of compressed shells and corals 30 feet above sea level.  Charles concludes that St. Jago has risen out of the sea.  And there was no sign of catastrophic damage, in line with Lyell's proposals. 

When the Beagle reaches Bahia, Brazil, Charles is able to see a rain forest first hand, allowing Humboldt's stories to come alive.  He listened to the sounds, and gathered flowers and beetles, inducing a state of rapture.  In the town Charles was disgusted to observe the use of slave labor. 

In Rio, Charles went inland with a group of British adventurers, and observed: conical ants' nests 12 feet tall, egrets, vampire bats drinking the blood of horses, orchids and cabbage palms.  And he saw firsthand the torment of slave families, separated and sold, as punishments by their owners.  He was there for weeks trapping, preserving and writing correspondence about the animals and plants to Henslow and the geology to Cousin William Darwin Fox.  The Beagle entertained visits from all the great men who were passing through Rio, and as a gentleman naturalist Charles was included in the socializing by FitzRoy.  The Beagle's Surgeon-naturalist, Robert McCormick, quit and shipped home, unhappy to live in Darwin's shadow. 

As the Beagle sailed south to Tierra Del Fuego, the weather turned treacherous, and Charles was once again nauseous, and read, Milton's Paradise Lost, 'trapped' in his hammock.  He was inspired by the book's vision of a prehistoric world torn by titanic struggle.  Darwin's collecting of species followed his Edinburgh interests: reproduction in encrusting sea-mats, movement in sea-pens - there are many feeding polyps but only one ovary which incited his thinking about individuality.  And he collected fossils in a race with a French naturalist, also scouring the area.  These caused Charles to think about the way the fossils had formed. 

Charles read news relayed by his family: Tory Lords had finally allowed the reform bill to pass, dampening calls for revolution and leaving William IV on the thrown.  Cholera was sweeping the country. He also received a new book: Lyell's next volume; which asserted that species were adapted to their birth spot, and did not evolve. 

Troubled Spirits from Another World
In December 1832 as the Beagle charted the east coast of South America Charles investigated the shifting geology, archeology and nature of the continent and Falkland Islands.  Over the year in which he turned 25, Charles noted:

Shaken Foundations
By 10th March 1834, the Beagle returned to the Falkland Islands.  The British navy had taken the islands and then left the British settlers with a Union Flag but no arms.  The Argentine people celebrated a revolt that killed the few British settlers.  The British navy returned, and with the Beagle's marines restored control to Britain.  Charles, imagining the islands as a strategic station within Britain's mercantile operations, concluded that they should have built a fort like the Spanish typically did. 

In the mail from the UK there were positive words from Henslow which raised Charles's spirits.  Darwin and other readers on the Beagle were fascinated by the pamphlets by Martineau, who justified the new draconian 'poor law ended relief for all but the destitute.  Accepting Malthus at face value, the poor were judged a burden, breeding too much and putting society at risk.  Now a vast saving would be made, and it was argued by the Whig intelligencia that this would make the poor more self-reliant.  But the law was designed to encourage the poor to compete for jobs, decreasing labor costs and expanding profits. 
' based on Malthus, Thomas Robert Malthus was an English cleric, East India Company economist and scholar.  He described the geometrical expansion of populations supported by sufficient resources and the population's subsequent collapse as the land used to grow the resources became fully deployed.  Initially concerned by England's leaders' fears of a French style revolution and disagreeing with William Godwin's visions of utopian progress and the idea of the Noble Savage, he argued for harsh treatment of the unemployed poor, denouncing charity.  Subsequently he softened his position accepting that emigration, education, and celibacy could constrain the impact of exponential population growth.  He socialized with the Wedgwood and Darwin families.  His ideas influenced Charles Darwin. 


Charles was ill for a month.  During that period FitzRoy was scalded by the Admiralty for profligate acts in purchasing a second ship.  He collapsed and resigned his commission.  But within a few days he had been convinced by his officers to tear up the resignation and continue with the charting trip. 

Darwin had seen enough to reject many of the scientific theories he had been taught.  He had puzzled over the life force, which from his observation of apples, appeared to be shared by a tree's cuttings, wondering if all would die when the initiator died.  That might explain the puzzling deaths of all the giant sloths.  But after observing an earthquake and volcanic eruption in Chile he reassessed everything. 

Charles mentally pulled together the contributing discoveries: his observations disagreed with Lamarck's classification of corals, the giant sloths were wiped out, but the environment around the fossil remains contained the remnants of sea creatures that still existed in Charles's life.  The earthquake he experienced had pushed the proximate environment up a bit and he had been able to show it was related to volcanic activity - Lyell was right about the slow transition: even if this undermined the Biblical 40 day flood; but Darwin now disagreed with Lyell's climatic theory, and he felt the earth had a thin crust above molten rock.  Charles concluded that vast spans of
Carlo Rovelli resolves the paradox of time. 
Rovelli initially explains that low level physics does not include time:
  • A present that is common throughout the universe does not exist
  • Events are only partially ordered.  The present is localized
  • The difference between past and future is not foundational.  It occurs because of state that through our blurring appears particular to us
  • Time passes at different speeds dependent on where we are and how fast we travel
  • Time's rhythms are due to the gravitational field
  • Our quantized physics shows neither space nor time, just processes transforming physical variables. 
  • Fundamentally there is no time.  The basic equations evolve together with events, not things 
Then he explains how in a physical world without time its perception can emerge:
  • Our familiar time emerges
    • Our interaction with the world is partial, blurred, quantum indeterminate
    • The ignorance determines the existence of thermal time and entropy that quantifies our uncertainty
    • Directionality of time is real but perspectival.  The entropy of the world in relation to us increases with our thermal time.  The growth of entropy distinguishes past from future: resulting in traces and memories
    • Each human is a unified being because: we reflect the world, we formed an image of a unified entity by interacting with our kind, and because of the perspective of memory
    • The variable time: is one of the variables of the gravitational field.  With our scale we don't register quantum fluctuations, making space-time appear determined.  At our speed we don't perceive differences in time of different clocks, so we experience a single time: universal, uniform, ordered; which is helpful to our decisions

time
were the keys to achieving all the transformations.  But, as science undermined the legitimacy of religous doctrine, Darwin wondered what would keep the masses from demanding more in this life?

Colonial Life
The Beagle docked in Valparaiso in March 1835, and then sailed on to be refitted in Coquimbo, before the 18 month period sailing back to England. 26 year old Charles sets out on two expeditions to explore the Andes: the first from Valparaiso via Santiago, the second from Coquimbo.  During the first he finally stood on the continental divide looking across the valleys.  While there were no plants or birds he found fossil shells in the rocks.  Trekking between the two main ridges of the Andes his team was inundated with locusts and attacked at night by blood sucking inch long Vinchuca bugs.  But Darwin also came across a grove of petrified trees at 7,000 ft.  This evidence drove Darwin to assert:
  • The land then on the Atlantic shore sank,
  • The luxuriant tropical forest was drowned, buried in sand and silt thousands of feet thick, resulting in compressed rock that crystalized the wood. 
  • Then lava overflowed it. 
  • Finally the continent slowly rose out of the ocean leaving the trees and shells high in the mountains. 

The refurbished Beagle sailed to Lima, which was not safe.  Confined to the ship, Charles linked his geological theory to Lyell's undulating crust: proposing that the continents were rising and so the Pacific floor was sinking.  He hypothesized that the Pacific coral islets should be sinking and the coral would be forming in the warm light shallow sea land interface as the mountain top descended. 

The Beagle started its homeward stretch:
  • They visited the Galapagos archipelago: frying hot volcanic islands, with turtles in the bays, giant tortoises on the islands, along with seaweed eating lizards, tame hawks, mockingbirds that Charles trapped and chronicled, noting the island where they were killed, ugly flowers, many volcanoes.  Many seed-eating finches were present but Darwin did not even note which ones were native to which island, assuming they all came from the mainland.  Similarly he had ignored the tortoises, cheerfully eating the bodies and allowing the Beagle's cook to throw the distinctive carapaces overboard. 
  • Then Tahiti.  Here Darwin was pleased to see the civilizing influence of the Christian missions on the formerly violent natives.  He canoed out to the coral reef, marveling at how the tiny creatures had built the mountainous rings around the island. 
  • In New Zealand the natives seemed fearsome and warlike and Darwin viewed them as just above Fuegans on the 'ladder of civilization' ascending to Europeans.  But due to its history as an English prison colony, the English population appeared even worse to Charles. 
  • Charles was impressed when the Beagle arrived at Sydney Cove, Australia, with its well-stocked shops, trading ships, warehouses and wool.  Built on the cheap labor of indentured workers, Australia was generating huge profits from its trading operations, but had little intellectual life, contradicting his grandfather Erasmus's predictions. Charles, is made welcome in the homes of the leaders of Sydney.  The aboriginals he met were good natured, but he could see they were being dispossessed of their lands.  In Tasmania almost all had been exterminated and the few that remained had been placed on an island.  And the marsupials were suffering from the introduction of sheep farming.  He did not see the differences between mammals and marsupials as contradicting Paley's argument 'from one perfect design to one perfect designer.' 
Temples of Nature
The Beagle began its return.  It would sale from Australia, to the coral atoll, structures formed by polyps when the sea bed is near enough to the ocean surface that the Sun's rays can penetrate.  As the sea bed descends slowly new layers of coral are deposited keeping the top of the coral within range of the Sun light.  Over time a coral tower or atoll forms.  In warm & acidic seas the atolls collapse.   Cocos Islands in the Indian Ocean.  Then on to Mauritius, and Simon's Bay at the Cape of Good Hope, where Charles visited Cape Town.  From there they sailed to the volcanic rock St Helena.  Then FitzRoy decided to check his longitudinal measurements and set sail back to Brazil!  Only in August did they set off for home again.  They obtained stores at St Jago in September, and more in Terceira in the Azores.  From there they set off for Falmouth via Land's End.  Notable events included:
  • The Cocos Islands coral atoll, structures formed by polyps when the sea bed is near enough to the ocean surface that the Sun's rays can penetrate.  As the sea bed descends slowly new layers of coral are deposited keeping the top of the coral within range of the Sun light.  Over time a coral tower or atoll forms.  In warm & acidic seas the atolls collapse.   was of interest to the British Navy.  Darwin's theory held.  Darwin looked at a variety of corals with a microscope.  He became convinced that the lowest animals and plants had a common starting point, aligning with Grant.  
  • In Cape Town, FitzRoy & Charles visited Sir John Herschel, who talked about Lyell's gradually evolving landscapes, and may have noted the analogy to the mystery of successive appearance of new species on the earth.  Mail came bringing news that Henslow had published Darwin's letters - making Charles the talk of society for 6 months. 
  • On St Helena, he noted how the island had been taken over by invasive plants.  And he was able to look at the noted fossil shells found at 2000 ft., which had been used as evidence of the recent raising of the island from the sea.  Darwin judged the shells to be land shells and so they were not in conflict with Lyell and Charles views about gradual shifts in geology. 
  • As the Beagle sailed, with Charles, as always, sea sick and confined, he reflected on the trip and began an assessment.  He carefully catalogued his collections.  The notes show him still puzzling over how animals, brought to islands by pirates, along with the Galapagos mockingbirds, could have rapidly specialized to their local environment.  He wondered what 'species' really meant.  Herschel's comment became increasingly prescient.  Darwin realized he now had a collection and experiences that would require him to be in a position to coordinate further studies.  He wrote Henslow to help him become a fellow of the Geological Society.  He asked Erasmus to help him join a Gentleman's club.  Other friends had already got him membership of the Entomological Society.  And he was developing huge numbers of questions from the details of the trip.  And developed an approach of taking a trend and extrapolating it from its origins to big outcomes - based on an accumulation of tiny changes: everything natural, gradual and slow. 
  • His shifting ideas raised his interest in natural science and undermined his interest in being a clergyman.  
  • He still maintained his Eurocentric ideas about scales of humanity: Fuegens, Maoris, Tahitians, Gauchos, and finally British colonists.  

1836-1842

A Peacock Admiring His Tail
Desmond & Moore note the shift in England Darwin experienced on his return:  Reform bill has empowered the Whig manufacturers and undermined the land-owner Tory hierarchy, Whig government's New Poor law ended relief for all but the destitute.  Accepting Malthus at face value, the poor were judged a burden, breeding too much and putting society at risk.  Now a vast saving would be made, and it was argued by the Whig intelligencia that this would make the poor more self-reliant.  But the law was designed to encourage the poor to compete for jobs, decreasing labor costs and expanding profits. 
applied Malthus, Thomas Robert Malthus was an English cleric, East India Company economist and scholar.  He described the geometrical expansion of populations supported by sufficient resources and the population's subsequent collapse as the land used to grow the resources became fully deployed.  Initially concerned by England's leaders' fears of a French style revolution and disagreeing with William Godwin's visions of utopian progress and the idea of the Noble Savage, he argued for harsh treatment of the unemployed poor, denouncing charity.  Subsequently he softened his position accepting that emigration, education, and celibacy could constrain the impact of exponential population growth.  He socialized with the Wedgwood and Darwin families.  His ideas influenced Charles Darwin. 
's ideas: to force the poor to emigrate, work for lower wages, Live on courser food; backed by 155 new barracks near the industrial centers; while they follow Darwin as he explores how to push his collection of 'New World' plants and animals to geologists, botanists and zoologists in Cambridge and London who are already overwhelmed by the other collections flowing back from the empire.  His naturalist mentors in Cambridge: Henslow, Sedgwick; provided introductions to the dons of London-science who were building the great collections at the national museums and zoo and supported his fellowship to the societies. 

Darwin's achievements are accepted by his family: his father gives him the capital to establish financial independence enabling Charles to become a self-financing naturalist investigator; which supports his shift from being: insecure, flustered, directionless; to confident, earnest; able to challenge authority.  He saw the value of Henslow's contemplative life for him.  But for now he gravitated towards the intellectuals: geologists to whom he presented his coral atoll, structures formed by polyps when the sea bed is near enough to the ocean surface that the Sun's rays can penetrate.  As the sea bed descends slowly new layers of coral are deposited keeping the top of the coral within range of the Sun light.  Over time a coral tower or atoll forms.  In warm & acidic seas the atolls collapse.   theory building on the ideas of Lyell (2, 3) - who typed the giant llama fossil helping Darwin see the importance of locality, and Darwin fended off critics; leveraged Tory Richard Owen to deploy his collections.  He still hated the aggressive arguments between the zoologist old guard and Grant's radicals wanting English science to use the French approach. 

Darwin's Galapagos bird collection were cataloged and analyzed by John Gould, who realized they included a sub-collection that were all ground finches, with drastically different beaks!  His research report made the newspapers making him and Darwin objects of popular conversation. 

Reforming Nature
Desmond & Moore review the creative adjacent possible to which Charles had returned:
Charles used the huge treasury grant to dispense patronage, becoming pay and taskmaster, to create Zoology

Tearing Down the Barriers
Charles was accepted into the leadership of the London scientific societies.  But he also secretly started Zoonomia - notebook 'B', the contents of which he only discussed with his brother Eras, since it was where he explored transmutation through written monologues and musings.  He had decided to follow his Grandfather's path.  The decision was of huge consequence:


Mental Rioting
Darwin explored the mechanism of variation.  In notebook 'C' he detailed talks with pigeon-fanciers, dog breeders, and landowning farmers about how they selected for traits they desired in their animals.  William Yarrell provided facts on domestic varieties, crosses, hybrids, and foreign escapees.  Yarell had explained about crossing farmyard stock, stressing how older established breeds always dominate the hybrid offspring.  Charles did not yet see a connection between breeding dogs and livestock and nature's actions, but was beginning to question his assumption that wild variants were born ready adapted.  He worried that selecting was unnatural.  Eventually he realized the erroneous idea of natural perfection derived from Paley's justification for the power hierarchy.  Instead, only some offspring would be a good fit.  And he realized that fit depended on the proximate environment, so nothing was always perfect. 

Darwin observed that humans were also self-selectors, favoring certain traits.  So they were part of nature's process too.  Desmond & Moore stress how the notebooks show Darwin repeatedly recording brilliant flashes of understanding but then moving on to other topics of interest, that might conflict: fitness and proximate environment replaced by Lamarck's ideas of altering habits to match the shifting environment, which had the attraction of being goal-oriented.  Charles explored Lamarck's proposals even though Lyell & Sedgwick ridiculed them.  Charles became convinced evolution explained every aspect of animal, including human, physiology and
The complexity of behavior is explored through Sapolsky developing scenarios of our best and worst behaviors across time spans, and scientific subjects including: anthropology, psychology, neuroscience, sociology.  The rich network of adaptive flows he outlines provides insights and highlight challenges for scientific research on behavior. 

Complex adaptive system (CAS) theory builds on Sapolsky's details highlighting the strategies that evolution has captured to successfully enter niches we now occupy. 

behavior
.  The
Computational theory of the mind and evolutionary psychology provide Steven Pinker with a framework on which to develop his psychological arguments about the mind and its relationship to the brain.  Humans captured a cognitive niche by natural selection 'building out' specialized aspects of their bodies and brains resulting in a system of mental organs we call the mind. 

He garnishes and defends the framework with findings from psychology regarding: The visual system - an example of natural selections solutions to the sensory challenges of inverse modeling of our environment; Intensions - where he highlights the challenges of hunter gatherers - making sense of the objects they perceive and predicting what they imply and natural selections powerful solutions; Emotions - which Pinker argues are essential to human prioritizing and decision making; Relationships - natural selection's strategies for coping with the most dangerous competitors, other people.  He helps us understand marriage, friendships and war. 

These conclusions allow him to understand the development and maintenance of higher callings: Art, Music, Literature, Humor, Religion, & Philosophy; and develop a position on the meaning of life. 

Complex adaptive system (CAS) modeling allows RSS to frame Pinker's arguments within humanity's current situation, induced by powerful evolved amplifiers: Globalization, Cliodynamics, The green revolution and resource bottlenecks; melding his powerful predictions of the drivers of human behavior with system wide constraints.  The implications are discussed. 

mind
must depend on the brain.  Observing an orang-utan supported his views and helped push man off Paley's pedestal.  As he continued to gather evidence and ideas, he realized Sir John Sebright's pamphlet provided the key on nature picking & choosing: sickly offspring were cut off before they could breed; and stressed the sexual struggle driving out the weakest from the competition.  Charles explored facial expressions.  And he included studies of censored works. 

Charles continued to manage the Zoology and write Geology, eating up his
Carlo Rovelli resolves the paradox of time. 
Rovelli initially explains that low level physics does not include time:
  • A present that is common throughout the universe does not exist
  • Events are only partially ordered.  The present is localized
  • The difference between past and future is not foundational.  It occurs because of state that through our blurring appears particular to us
  • Time passes at different speeds dependent on where we are and how fast we travel
  • Time's rhythms are due to the gravitational field
  • Our quantized physics shows neither space nor time, just processes transforming physical variables. 
  • Fundamentally there is no time.  The basic equations evolve together with events, not things 
Then he explains how in a physical world without time its perception can emerge:
  • Our familiar time emerges
    • Our interaction with the world is partial, blurred, quantum indeterminate
    • The ignorance determines the existence of thermal time and entropy that quantifies our uncertainty
    • Directionality of time is real but perspectival.  The entropy of the world in relation to us increases with our thermal time.  The growth of entropy distinguishes past from future: resulting in traces and memories
    • Each human is a unified being because: we reflect the world, we formed an image of a unified entity by interacting with our kind, and because of the perspective of memory
    • The variable time: is one of the variables of the gravitational field.  With our scale we don't register quantum fluctuations, making space-time appear determined.  At our speed we don't perceive differences in time of different clocks, so we experience a single time: universal, uniform, ordered; which is helpful to our decisions

time
.  But he squeezed in a trip to Glen Roy to observe the parallel roads.  He concluded they were old sea beaches, formed at sea-level before the land rose in three stages. 

Observing Eras and Martineau, Darwin reviews the pros and cons of marriage, and begins to consider his interest in cousin Emma and what future role to pursue. 

The risk, is an assessment of the likelihood of an independent problem occurring.  It can be assigned an accurate probability since it is independent of other variables in the system.  As such it is different from uncertainty. 
of his work on transmutation, which he subsequently termed descent, played on his constitution.  England's sedition and blasphemy laws were designed to conserve the Anglican power hierarchy, a hierarchy which Charles admired, and he had seen the laws applied

Marriage & Malthusian Respectability
Charles asked his father for advice on marriage to his first cousin Emma Wedgwood.  He was warned not to discuss his religious views since Darwins' and Wedgwoods' ideas differed on the subject.  Charles ignored his father, being very open with Emma when they sat and talked.  She was always subsequently concerned but accepted his proposal.  They married setup by the families with capital is the sum total nonhuman assets that can be owned and exchanged on some market according to Piketty.  Capital includes: real property, financial capital and professional capital.  It is not immutable instead depending on the state of the society within which it exists.  It can be owned by governments (public capital) and private individuals (private capital).  , an income stream, and everyone's blessings.  The couple moved into a rental property in London's Gower Street: Charles an elite Whig naturalist with a weak constitution and Emma adopting the position of his nurse. 

Charles kept up the editing and writing activities, having to do more himself: Owen was distracted when his mother died and Gould went to Tasmania. 

Charles was made a fellow of the Royal Society, still an elitist clique in 1840.  And he sat in as the leadership of the Geologists planned, forced out and celebrated the expulsion of Grant for his openly Lamarckian and evolutionist views.  But in private Darwin explored the positivist philosophy is a philosophical and sociological position based on the primacy of empirical data which is supported by experimental testing and adaptation of current theory, advocated by Comte. 
of Comte, and adopted it in his thinking.  He abandoned Lamarck's goal based ideas preferring: random change, Malthusian, Thomas Robert Malthus was an English cleric, East India Company economist and scholar.  He described the geometrical expansion of populations supported by sufficient resources and the population's subsequent collapse as the land used to grow the resources became fully deployed.  Initially concerned by England's leaders' fears of a French style revolution and disagreeing with William Godwin's visions of utopian progress and the idea of the Noble Savage, he argued for harsh treatment of the unemployed poor, denouncing charity.  Subsequently he softened his position accepting that emigration, education, and celibacy could constrain the impact of exponential population growth.  He socialized with the Wedgwood and Darwin families.  His ideas influenced Charles Darwin. 
competition's alignment with Whig philosophy and action, and nature's Poor Law ended relief for all but the destitute.  Accepting Malthus at face value, the poor were judged a burden, breeding too much and putting society at risk.  Now a vast saving would be made, and it was argued by the Whig intelligencia that this would make the poor more self-reliant.  But the law was designed to encourage the poor to compete for jobs, decreasing labor costs and expanding profits. 
like selection process.  Charles liked the alignment of his ideas with advanced Whig social thinking.  The Chartists pushed back against the Whig's lack of charity to the poor.  Charles leveraged the Unitarian's view of God working through laws that drove the operation of physics including nature, but worried about the acceptability, to the elite, of no Free Will is the subjective assessment of one's ability to make decisions and perform independent actions.  Philosophers note that causal chains linking physical phenomena with conscious decisions would undermine the idea of independent free will.  RSS views the architecture of CAS agency as requiring indirect associations between phenomena and agent's models.  Evolution captures these associations within the genetic structures of the emergent agents, removing any epistemological or complementarity constraints.  Sapolsky concludes that this evolved agency severely limits the potential contribution of free will.  

Charles extended descent to include morality, sexual, parental & social instinct: concluding from studies of human statistics about law-like behavior of populations, they evolved to support
Peter Turchin describes how major pre-industrial empires developed due to effects of geographic boundaries constraining the empires and their neighbors' interactions.  Turchin shows how the asymmetries of breeding rates and resource growth rates results in dynamic cycles within cycles.  After the summary of Turchin's book complex adaptive system (CAS) theory is used to augment Turchins findings. 
cohesion of the troop
; and saw a linkage between primate and human emotional are low level fast unconscious agents distributed across the brain and body which associate, via the amygdala and rich club hubs, important environmental signals with encoded high speed sensors, and distributed programs of action to model: predict, prioritize guidance signals, select and respond effectively, coherently and rapidly to the initial signal.  The majority of emotion centered brain regions interface to the midbrain through the hypothalamus.  The cerebellum and basal ganglia support the integration of emotion and motor functions, rewarding rhythmic movement.  The most accessible signs of emotions are the hard to control and universal facial expressions.  Emotions provide prioritization for conscious access given that an animal has only one body, but possibly many cells, with which to achieve its highest level goals.  Because of this emotions clash with group goals and are disparaged by the powerful.  Evolutionary psychology argues evolution shaped human emotions during the long period of hunter-gatherer existence in the African savanna.  Human emotions are universal and include: Anger, Appreciation of natural beauty, Disgust, Fear, Gratitude, Grief, Guilt, Happiness, Honor, Jealousy, Liking, Love, Rage, Romantic love, Lust for revenge, Passion, Sadness, Self-control, Shame, Sympathy, Surprise; and the sham emotions and distrust induced by reciprocal altruism. 
expressions.  He started 'M' notebooks on the wider consequences of descent.  He could replace Plato's preexisting soul is an ancient concept that was eternal according to Plato.  In his cave analogy he promotes the ideal and the sensory which highlights the dualism of soul and body.  The soul was eternal - being simple, pure and generated by the creator.  Bodies were associated with souls by gods at birth.  Epicurus argued that souls were constructed from atoms, were complex and died.  CAS theory likens:
  • 'souls' to schematic strings, and 'bodies' to organisms, and
  • 'souls' to the mind's well known entities: amygdala, insula etc, and the 'bodies' to the percepts & representations that the well known entities become conscious hubs for; which agrees in part with both positions. 
as the foundation of good and evil with evolution's plan.  Brougham's description of a parasitic is a long term relationship between the parasite and its host where the resources of the host are utilized by the parasite without reciprocity.  Often parasites include schematic adaptations allowing the parasite to use the hosts modeling and control systems to divert resources to them or improve their chance of reproduction: Toxoplasma gondii.   wasp laying its eggs in a caterpillar: where long after the wasp died the offspring will obtain a benefit; helped Charles see that instincts must develop by chance events that are conserved because they were useful.  He reviewed his own feelings are subjective models: sad, glad, mad, scared, surprised, and compassionate; of the organism and its proximate environment, including ratings of situations signalled by broadly distributed chemicals and neural circuits.  These feelings become highly salient inputs, evolutionarily associated, to higher level emotions encoded in neural circuits: amygdala, and insula.  Deacon shows James' conception of feeling can build sentience.  Damasio, similarly, asserts feelings reveal to the conscious mind the subjective status of life: good, bad, in between; within a higher organism.  They especially indicate the affective situation within the old interior world of the viscera located in the abdomen, thorax and thick of the skin - so smiling makes one feel happy; but augmented with the reports from the situation of the new interior world of voluntary muscles.  Repeated experiences build intermediate narratives, in the mind, which reduce the salience.  Damasio concludes feelings relate closely and consistently with homeostasis, acting as its mental deputies once organisms developed 'nervous systems' about 600 million years ago, and building on the precursor regulatory devices supplied by evolution to social insects and prokaryotes and leveraging analogous dynamic constraints.  Damasio suggests feelings contribute to the development of culture:
  • As motives for intellectual creation: prompting detection and diagnosis of homeostatic deficiencies, identifying desirable states worthy of creative effort.
  • As monitors of the success and failure of cultural instruments and practices
  • As participants in the negotiation of adjustments required by the cultural process over time 
regarding Emma.  He wrote in notebook after notebook and grouped the facts under sub laws. 

The Dreadful War
Desmond & Moore tell how Charles marriage to first cousin Emma Wedgwood was immediately clouded by the death of Charles's sister Caroline's six-week-old baby Sophie.  The knowledge that Caroline and Josiah, Emma's brother, were also first cousins added to their concerns.  Emma also worried that Charles's skepticism about Christianity would leave him dammed.  And his vomiting and migraines were increasing.  He avoided company, preferring to stay with Emma. 

Charles was studying how horticulture was performed.  He noted their leverage of chance peculiarities.  Darwin was by now convinced that hardier seedlings could only be produced by chance.  He corresponded with farmers and started a 'Questions & Experiments' notebook, with ideas that would have been viewed as bizarre by contemporaries.  But few of his questions were answered, with the recipients typically overwhelmed by his carefully designed requests. 

Charles was growing less comfortable with the Malthusian, Thomas Robert Malthus was an English cleric, East India Company economist and scholar.  He described the geometrical expansion of populations supported by sufficient resources and the population's subsequent collapse as the land used to grow the resources became fully deployed.  Initially concerned by England's leaders' fears of a French style revolution and disagreeing with William Godwin's visions of utopian progress and the idea of the Noble Savage, he argued for harsh treatment of the unemployed poor, denouncing charity.  Subsequently he softened his position accepting that emigration, education, and celibacy could constrain the impact of exponential population growth.  He socialized with the Wedgwood and Darwin families.  His ideas influenced Charles Darwin. 
management of the poor, he had read about on the Beagle.  He watched a society gripped by economic is the study of trade between humans.  Traditional Economics is based on an equilibrium model of the economic system.  Traditional Economics includes: microeconomics, and macroeconomics.  Marx developed an alternative static approach.  Limitations of the equilibrium model have resulted in the development of: Keynes's dynamic General Theory of Employment Interest & Money, and Complexity Economics.  Since trading depends on human behavior, economics has developed behavioral models including: behavioral economics. 
depression.  The poor were starving, and reduced to emigrating or marching in protest.  De Candolle, who had first proposed the idea of nature's 'war' came to dinner - the contest was paramount, leaving many losers of the Malthusian battle.  Added to the Galapagos revealed properties of isolation, this war allowed Darwin to see a way forward. 

Darwin thought about moral provides rules for identifying right from wrong.  It develops in stages with children using play to work out rules of appropriate behavior.  Kohlberg's 1950s experiments using children led him to conclude moral judgement is a cognitive process that develops in three stages.  Sapolsky raises issues with the framework: Its a model, It does not apply to other cultures, Intuition & emotion are as significant as cognition, Moral reasoning doesn't predict moral actions; and notes the capacity of the frontal cortex to regulate emotions and behavior is far more predictive.  The marshmallow test, performed on three to six year olds, actually predicted their subsequent SAT scores at high school, social success and lack of aggression, and forty years on more PFC activation during a frontal task and a lower BMI!  Jonathan Haidt argues people's moral decisions are rationalizations rather than using reasoning. 
faculties.  Hensleigh's father-in-law had asserted they were inborn.  Darwin agreed but added they must have emerged from herding and bonding instincts that were useful in strengthening relations in the ancestral troop. 

Charles's Journal of the voyage was published, and his friends and leading scientists praised the book: Humboldt wrote it was one of the most remarkable travelogues published.  But it was soon clear that a theorist like Darwin would struggle for acceptance in a time when data gathering was fashionable.  This made him fearful about revealing his developing theory of evolution.  His friend Owen would be horrified.  And so Charles struggled with the inner conflict.  Eventually he gave in and told Lyell, who concluded that the theory undermined the biological basis of his Principles of Geology (2), and turned away from Darwin.  Charles was working on a book describing his Zoology and had just published a theory of coral reefs, structures formed by polyps when the sea bed is near enough to the ocean surface that the Sun's rays can penetrate.  As the sea bed descends slowly new layers of coral are deposited keeping the top of the coral within range of the Sun light.  Over time a coral tower or atoll forms.  In warm & acidic seas the atolls collapse.  .  He wrote a 35 page coherent sketch of the evolutionary theory with sub-headings: Natural Selection resulted from overpopulation and competition, Life developed with a tree-like geneology of common parents, Island colonization, diversification, unity of plan reflecting common inheritance; and strategy of grand laws showing the power of the omniscient Creator.  But he knew it was blasphemy to the parsons and heresy to the geologists.  He would not publish the evolutionary theory.  It could be misused. 

Chartists were demanding universal suffrage, but Parliament rejected the call.  Rioting ensued and was constrained by the army.  The revolutionaries were aligned with an evolution based on socialist ideals.  Ideas of monkey ancestry would have been capitalized on, and Charles would have then been ridiculed by his friends.  Charles wanted to move Emma, and first son William Erasmus, to the country from Gower St.  Charles made copious notes of the newborn's facial expressions including first signs of anger is an emotion which protects a person who has been cheated by a supposed friend.  When the exploitation of the altruism is discovered, Steven Pinker explains, the result is a drive for moralistic aggression to hurt the cheater.  Anger is mostly experienced as a rapid wave that then quickly dissipates.  When it is repressed, for example by a strong moral sense (superego), it can sustain, inducing long term stress. 
, fear is an emotion which prepares the body for time sensitive action: Blood is sent to the muscles from the gut and skin, Adrenalin is released stimulating: Fuel to be released from the liver, Blood is encouraged to clot, and Face is wide-eyed and fearful.  The short-term high priority goal, experienced as a sense of urgency, is to flee, fight or deflect the danger.  There are both 'innate' - really high priority learning - which are mediated by the central amygdala and learned fears which are mediated by the BLA which learns to fear a stimulus and then signals the central amygdala.  Tara Brach notes we experience fear as a painfully constricted throat, chest and belly, and racing heart.  The mind can build stories of the future which include fearful situations making us anxious about current ideas and actions that we associate with the potential future scenario.  And it can associate traumatic events from early childhood with our being at fault.  Consequent assumptions of our being unworthy can result in shame and fear of losing friendships.  The mechanism for human fear was significantly evolved to protect us in the African savanna.  This does not align perfectly with our needs in current environments: U.S. Grant was unusually un-afraid of the noise or risk of guns and trusted his horses' judgment, which mostly benefited his agency as a modern soldier. 
, pleasure is the outcome of the dopamine reward system, argues UCSF professor Robert Lustig.  He, like the early Christians, contrasts [addiction oriented] pleasure with serotonin driven happiness & contentment. 
and reason.  The Darwin's found a former parsonage in Down, near Farnborough in Kent which they purchased for 2,000 pounds.  As troops battled the starving Chartist poor the Darwin's left London for the peace of Down. 

1842-1851

The Extreme Verge of the World
Desmond & Moore detail Charles's flight from London society to Down in north Kent, still geographically close by but with no infrastructural connections.  Charles added a defensive wall and a mirror so he could identify visitors as they approached from his study.  The house was modified leaving the family in the upper floors and Charles at a distance, quiet in the study. 

Tragedy hit the family twice.  Soon after the move, in Oct. 1842, Emma gave birth to their third child, Mary Eleanor, but she was sickly and died within a month.  And in July 1843 Emma's father, Josiah, who was like his wife already demented is a classification of memory impairment, constrained feelings and enfeebled or extinct intellect.  The most common form for people under 60 is FTD.  Dementia has multiple causes including: vascular disease (inducing VCI) including strokes, head trauma, syphilis and mercury poisoning for treating syphilis, alcoholism, B12 deficiency (Sep 2016), privation, Androgen deprivation therapy (Oct 2016), stress, Parkinson's disease, Alzheimer's disease, and prion infections such as CJD and kuru.  The condition is typically chronic and treatment long term (Laguna Honda ward) and is predicted by Stanley Prusiner to become a major burden on the health system.  It may be possible to constrain the development some forms of dementia by: physical activity, hypertension management, and ongoing cognitive training.  Dementia appears to develop faster in women than men.  , died. 

Charles theories about Glen Roy were disputed by Louis Agissiz, who credibly argued the parallel roads were formed by the action of glaciers. 

Charles offered his collection of plants from Tierra del. Fuego and Southern Patagonia to Joseph Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
, a ship's surgeon and botanist, who had been on a similar four year trip with Capt. Ross's Antarctic expedition, and was the son of the Director of Kew Gardens, Sir William Hooker.  This kindness would later develop into an important friendship. 

Charles discussed classifications of species with George Waterhouse, who had described the Beagle's mammals.  But their approaches differed:
  • Charles, seeing the implications of descent, proposed to build a tree of connections between the species.  He felt if all the individuals could still be traced they would all be connected with gradual changes being observed. 
  • Waterhouse was aiming for nature to be symbolically represented with spiritual man shown to be the 'standard of perfection.'  He was excellent at describing each specimen.  He felt Darwin was brow beating him and so, ignored and resented the position Charles took. 

Murder
Charles decided to share the conclusions of the secret evolution essay with Joseph Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
: Looking at the collection of fossils he had gathered in South America and Galapagos life, he was forced to conclude species are not immutable, Isolation allowed species to pick niches and over time would specialize into them; but it was risky.  He hardly knew the man.  And it went against Anglican doctrine were developed in the reigns of Henry VIII of England and Elizabeth I by 1571, to define the doctrine of the Church of England, providing a position for Anglicanism relative to the Catholic Church and dissident Protestants.  They provided constraints against following Catholic reactionaries and Protestant reformers who threatened the monarchical power structure. 
& abandoned all Darwin's important friends, just as they were being threatened by Lamarckian evolutionists, demanding French style revolution against the English power hierarchy.  



Illformed Little Monsters
Charles had one Galapagos barnacle are a highly variable group related to crabs and shrimps.  At Hooker's suggestion Darwin studied barnacles for many years to dive deeply and broadly into the origin of species.  Milne-Edwards showed the archetypal crustacean had twenty-one segments.  Darwin believed this primitive shrimp-like creature provided a vision of the common ancestor of crabs, lobsters, and barnacles.  Everything visible externally in barnacles was equivalent to the first three segments of a crab's head, extensively modified and enlarged to fit the rest of the 14 body segments inside.  The feet could protrude to strain food from the water.  Many barnacles are a large female with minute males clinging to their shells.  Desmond & Moore explain Darwin was fascinated by Arthrobalanus where the male was a 'mere bag, lined by a few muscles, enclosing an eye,' antennae, and a gigantic sexual organ, with no vestige of the other fourteen segments of a normal barnacle body.  Their life-cycle includes free-swimming larva with part of the original crustacean's reproductive organs modified to secrete cement, through ducts opening at the tip of the antennae.  The cement glues the larva to a rock where the adult remains inverted. 
left to describe.  It was a tiny parasite of Concholepas. 

Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
helped with the micro-dissections.  But he also commented on a book 'On Species' by Frederic Gerard, arguing that no one should theorize on species without studying many in depth.  The assertion led Charles to seek more data to defend his theory on the origin of species.  He would dive deep into barnacles. 

Charles starts his detailed barnacles study, calling in huge collections from his network of collectors.  Charles looks more closely at the tiny parasites is a long term relationship between the parasite and its host where the resources of the host are utilized by the parasite without reciprocity.  Often parasites include schematic adaptations allowing the parasite to use the hosts modeling and control systems to divert resources to them or improve their chance of reproduction: Toxoplasma gondii.   he has been discarding in prior studies and discovers that some are tiny parasitic male barnacles, attached to the larger female or hermaphrodyte barnacle.  In each case the active male organs are provided by the parasites. 

Hooker, leaves on a trip to India as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens. 

Al Diabolo
Charles is struggling with a bad stomach, which limits his attendance of the council of the geological society.  His secret work on evolution, even with a Malthusian, Thomas Robert Malthus was an English cleric, East India Company economist and scholar.  He described the geometrical expansion of populations supported by sufficient resources and the population's subsequent collapse as the land used to grow the resources became fully deployed.  Initially concerned by England's leaders' fears of a French style revolution and disagreeing with William Godwin's visions of utopian progress and the idea of the Noble Savage, he argued for harsh treatment of the unemployed poor, denouncing charity.  Subsequently he softened his position accepting that emigration, education, and celibacy could constrain the impact of exponential population growth.  He socialized with the Wedgwood and Darwin families.  His ideas influenced Charles Darwin. 
core & capitalist roots would be seen as traitorous, which adds to his stress is a multi-faceted condition reflecting high cortisol levels.  Dr. Robert Sapolsky's studies of baboons indicate that stress helps build readiness for fight or flight.  As these actions occur the levels of cortisol return to the baseline rate.  A stressor is anything that disrupts the regular homeostatic balance.  The stress response is the array of neural and endocrine changes that occur to respond effectively to the crisis and reestablish homeostasis. 
  • The short term response to the stressor
    • activates the amygdala which: Stimulates the brain stem resulting in inhibition of the parasympathetic nervous system and activation of the sympathetic nervous system with the hormones epinephrine and norepinephrine deployed around the body, Activates the PVN which generates a cascade resulting in glucocorticoid secretion to: get energy to the muscles with increased blood pressure for a powerful response.  The brain's acuity and cognition are stimulated.  The immune system is stimulated with beta-endorphin and repair activities curtail.  In order for the body to destroy bacteria in wounds, pro-inflammatory cytokines increase blood flow to the area.  The induced inflammation signals the brain to activate the insula and through it the ACC.  But when the stressor is
  • long term: loneliness, debt; and no action is necessary, or possible, long term damage ensues.  Damage from such stress may only occur in specific situations: Nuclear families coping with parents moving in.  Sustained stress provides an evolved amplifier of a position of dominance and status.  It is a strategy in female aggression used to limit reproductive competition.  Sustained stress:
    • Stops the frontal cortex from ensuring we do the harder thing, instead substituting amplification of the individual's propensity for risk-taking and impairing risk assessment! 
    • Activates the integration between the thalamus and amygdala. 
      • Acts differently on the amygdala in comparison to the frontal cortex and hippocampus: Stress strengthens the integration between the Amygdala and the hippocampus, making the hippocampus fearful. 
      • BLA & BNST respond with increased BDNF levels and expanded dendrites persistently increasing anxiety and fear conditioning. 
    • Makes it easier to learn a fear association and to consolidate it into long-term memory.  Sustained stress makes it harder to unlearn fear by making the prefrontal cortex inhibit the BLA from learning to break the fear association and weakening the prefrontal cortex's hold over the amygdala.  And glucocorticoids decrease activation of the medial prefrontal cortex during processing of emotional faces.  Accuracy of assessing emotions from faces suffers.  A terrified rat generating lots of glucocorticoids will cause dendrites in the hippocampus to atrophy but when it generates the same amount from excitement of running on a wheel the dendrites expand.  The activation of the amygdala seems to determine how the hippocampus responds. 
    • Depletes the nucleus accumbens of dopamine biasing rats toward social subordination and biasing humans toward depression. 
    • Disrupts working memory by amplifying norepinephrine signalling in the prefrontal cortex and amygdala to prefrontal cortex signalling until they become destructive.  It also desynchronizes activation in different frontal lobe regions impacting shifting of attention.  
    • Increases the risk of autoimmune disease (Jan 2017) 
  • During depression, stress inhibits dopamine signalling.  
  • Strategies for stress reduction include: Mindfulness. 
, compounding the impact of the illness.  Emma and Charles's father Robert, are also feeling unwell.  Robert dies & Charles and his sister are too overcome to attend the funeral. 

The revolution in Italy in 1848 is followed by: riots in the UK is the United Kingdom of Great Britain and Northern Ireland.   by Chartists still demanding suffrage, and revolution in France with the King abdicating and fleeing to England; a set of shocks which worry the stock market, reducing the value of Charles's investments. 

My Water Doctor
Desmond & Moore explain that Charles had become chronically ill enough to worry his friends: frail and hardly able to walk; and the specialists were all baffled.  His friend, Captain Sulivan recommended the unorthodox but cautious and caring Dr. James Gully who offered a water treatment for chronic disease, at Great Malvern in Worcestershire.  The family accompanied Charles while he was treated for 16 weeks: even new baby Francis who cried all the way to Malvern.  Charles befriended Dr. Gully who acted like his dead father Robert.  His stomach trouble was diagnosed as nervous in origin.  The treatment was complex, changing his diet, dosing with homeopathic medicines, and the water treatments.  Charles improved significantly.  Everyone had a holiday.  

Charles was able to resume his work on the deep and broad study of barnacles are a highly variable group related to crabs and shrimps.  At Hooker's suggestion Darwin studied barnacles for many years to dive deeply and broadly into the origin of species.  Milne-Edwards showed the archetypal crustacean had twenty-one segments.  Darwin believed this primitive shrimp-like creature provided a vision of the common ancestor of crabs, lobsters, and barnacles.  Everything visible externally in barnacles was equivalent to the first three segments of a crab's head, extensively modified and enlarged to fit the rest of the 14 body segments inside.  The feet could protrude to strain food from the water.  Many barnacles are a large female with minute males clinging to their shells.  Desmond & Moore explain Darwin was fascinated by Arthrobalanus where the male was a 'mere bag, lined by a few muscles, enclosing an eye,' antennae, and a gigantic sexual organ, with no vestige of the other fourteen segments of a normal barnacle body.  Their life-cycle includes free-swimming larva with part of the original crustacean's reproductive organs modified to secrete cement, through ducts opening at the tip of the antennae.  The cement glues the larva to a rock where the adult remains inverted. 
.  The more he looked at the animals or their fossils the more he found them infinitely variable.  As he tried to classify them he found it was harder in practice than he had theorized.  He was also concerned about Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
, who he read in the newspaper had been kidnapped.  And Annie, Etty and Elizabeth became ill with scarlet fever.  Fitch's barnacle fossils were exceptional, but many arrived at Down damaged.  Emma had her eighth child, Leonard, with Charles having to assist at the birth. 

Charles also attended some meetings, which made him weary with all the loud and empty argument: his stomach problems returned. 

Our Bitter & Cruel Loss
As Charles and Emma prepare for their ninth baby they observe the deterioration of their oldest surviving daughter Annie's wellbeing indicates the state of an organism is within homeostatic balance.  It is described by Angus Deaton as all the things that are good for a person:
  • Material wellbeing includes income and wealth and its measures: GDP, personal income and consumption.  It can be traded for goods and services which recapture time.  Material wellbeing depends on investments in:
    • Infrastructure
      • Physical
      • Property rights, contracts and dispute resolution
    • People and their education
    • Capturing of basic knowledge via science.  
    • Engineering to turn science into goods and services and then continuously improve them. 
  • Physical and psychological wellbeing are represented by health and happiness; and education and the ability to participate in civil society through democracy and the rule of law.  University of Wisconsin's Ryff focuses on Aristotle's flourishing.  Life expectancy as a measure of population health, highly weights reductions in child mortality. 
.  Her gastric problems and listlessness are similar enough to Charles health issues to be a concern. 

Charles hears that Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
has arrived back from the Himalayan trip safely, but this good news is offset by Annie's deteriorating condition.  Charles accompanies her to Malvern, but even with Gully's support she rapidly becomes worse and dies.  Charles can see no reason that a just god would do this to such a sweet creature.  He finally concludes there is no god.  He returns home to Down to be with Emma and their newborn son Horace.  Neither Charles nor Emma ever fully recovers from the dreadful loss of Annie.  

1851-1860

A Gentleman with Capital
The European revolutions' have passed England by and radical revolt has subsided.  The Darwin family travels up to London to visit the Great Exhibition of 1851 at the Crystal Palace.  Desmond & Moore explain that most people used a railway uses low friction tracks to support an engine and cars which can carry people and goods.  Modern railroads began with the Stockton to Darlington railway built by George Stephenson with a steam powered engine Locomotion No. 1 in 1825.  Electric power, and telegraph network were later leveraged.  Railroads contributed to the colonization of the world, the shift to regimentation with standardized time, maintained the efficiency of the cotton plantation trading network, supported the urbanization of the US, enabled the distribution of Californian lettuce and Midwestern beef with the refrigerated rail car, until government policy drove a shift to road networks, but were dangerous to walk on and supported the distribution of cholera to the US.  The monopsonistic network effects were leveraged by John D. Rockefeller, in building his Standard Oil trust. 
for the first time to see the marvels of empire and industrial might.  And more importantly for Charles, the
This page discusses the effect of the network on the agents participating in a complex adaptive system (CAS).  Small world and scale free networks are considered. 
network effects
centered on London drew liberal, progressive reformers: John Chapman, George Eliot, W. R. Greg, Herbert Spencer, Thomas Henry Huxley, John Stuart Mill, William Carpenter, Robert Chambers published popular periodicals from Edinburgh.  And he wrote Vestiges of the Natural History of Creation, which he marketed brilliantly.  According to Desmond & Moore, he was a golf-playing, overworked, man of the people. 
, Holyoake; who built out a
This page reviews the catalytic impact of infrastructure on the expression of phenotypic effects by an agent.  The infrastructure reduces the cost the agent must pay to perform the selected action.  The catalysis is enhanced by positive returns. 
publishing infrastructure
that promoted ideas such as evolution based on a tree
 
Desmond & Moore review Darwin's financial situation:

Ugly Facts
Desmond & Moore describe the entry and conquest of the naturalist societies: Royal, Linnean; by the liberal progressives.  These people accept Darwin, as a leading geologist and the world's barnacle are a highly variable group related to crabs and shrimps.  At Hooker's suggestion Darwin studied barnacles for many years to dive deeply and broadly into the origin of species.  Milne-Edwards showed the archetypal crustacean had twenty-one segments.  Darwin believed this primitive shrimp-like creature provided a vision of the common ancestor of crabs, lobsters, and barnacles.  Everything visible externally in barnacles was equivalent to the first three segments of a crab's head, extensively modified and enlarged to fit the rest of the 14 body segments inside.  The feet could protrude to strain food from the water.  Many barnacles are a large female with minute males clinging to their shells.  Desmond & Moore explain Darwin was fascinated by Arthrobalanus where the male was a 'mere bag, lined by a few muscles, enclosing an eye,' antennae, and a gigantic sexual organ, with no vestige of the other fourteen segments of a normal barnacle body.  Their life-cycle includes free-swimming larva with part of the original crustacean's reproductive organs modified to secrete cement, through ducts opening at the tip of the antennae.  The cement glues the larva to a rock where the adult remains inverted. 
specialist.  And he accepts them, seeing their interest in science, professionalism and evolution as less threatening to his secretive work on descent than the creationist Anglican hierarchy that is being pushed aside.  He promotes Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
in the Royal Society. 

Charles continued to focus on barnacles until he finally completed and published his studies.  After seven years he hated them but gained a Royal Medal for his trouble.  Charles old mentors struggle with the implications of the details of his work, but he avoids the question of Creation, sticking to species.  Desmond & Moore explain that Darwin sees little threat to his Malthusian, Thomas Robert Malthus was an English cleric, East India Company economist and scholar.  He described the geometrical expansion of populations supported by sufficient resources and the population's subsequent collapse as the land used to grow the resources became fully deployed.  Initially concerned by England's leaders' fears of a French style revolution and disagreeing with William Godwin's visions of utopian progress and the idea of the Noble Savage, he argued for harsh treatment of the unemployed poor, denouncing charity.  Subsequently he softened his position accepting that emigration, education, and celibacy could constrain the impact of exponential population growth.  He socialized with the Wedgwood and Darwin families.  His ideas influenced Charles Darwin. 
, capitalist, competitive mechanism from the rival evolutionary theories of the liberal progressives.  Huxley was a skeptic who Charles hoped would see the value of his ideas.  With barnacles finished, Hooker coming into agreement with his ideas, and a Royal Medal, Charles returns to the study of species. 

Darwin still obsessed about his health.  But after Gully failed to save Annie, he reduced his use of the water regimen.  Trips to London induced the most health issues.  But Hooker's visits to Down also induced illness.  And Darwin enjoyed the spectacle and pomp of Wellesley - Duke of Wellington's funeral. 

Gunships & Grog Shops
Desmond & Moore explain the impact of business and war on Darwin's creative process:
  • The onset of the Crimean War: between France allied with the UK is the United Kingdom of Great Britain and Northern Ireland.   trying to stop Russia gaining control of the trade routes to India & the Near East, required an assault by the British Fleet on the naval base at Sebastopol; leading Charles to think about the struggle in nature: seeds and fruit, frogs and snails establishing a beachhead on alien terrain and ousting the occupiers. 
  • Josiah Wedgwood's potteries, in which Darwin played as a boy, leveraged specialization to gain efficiency and a competitive advantage, which led Charles to realize the same process of 'niche entry' was available to variations within a species to create diversity.  It was not necessary to find a new island to obtain access to niches - specialization was a general mechanism.  
Charles was dismissive of Emma's uncle, the economist Jean Sismondi, who saw the: destruction of the workforce by mechanization, dehumanizing division of labor, unjust division of profits; as scourges.  Struggle and selection were Darwin's guides, but the model generated doubts and questions: mammals, reptiles and fishes were all seen to have similar embryos and converged in appearance.  How could he explain it?  It could be inheritance with the manifestation of variation occurring during development.  Selection must occur later, sustaining or quashing them.  Annie's death pushed Charles to fear his illness was hereditary. 

Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
noted the similarity between plants of Tierra del Fuego and Tasmania and Kerguelen Land.  He proposed this was due to the breakup of a southern super-continent.  Darwin was driven to prove that it could occur through a tidal mechanism.  He setup a series of experiments keeping seeds in salt water and then seeing how effectively they developed.  It was a radical approach which with typical tides was able to explain the spreading of plant species.  But how did the invader become victorious?
 
Charles, having reviewed his notebooks, investigated the embryonic similarity and selection of emerging variants within domestic animal breeding, looking broadly but selecting pigeons as his specialty.  They derived from one ancestral stock.  He talked with the working people who had the expertise in breeding pigeons, visiting their meeting places and joining their clubs.  That enabled him to become an expert, gaining an understanding of how it was done, and breeding his own. 

Horrid Wretches Like Me
Desmond and Moore describe: Darwin's moves to integrate with the liberal progressives, the progressives' marketing of the professional scientific hierarchy in the public's mind; which empowers Huxley, and undermines the Anglican hierarchy's creationist hold on education and researchOwen, loved by politicians and Oxbridge academics, pushed back against Huxley. 

Darwin is convinced Huxley is the key to replacing creation with evolution by natural selection, but Huxley's writing on evolution seems dismissive and confused.  Darwin meets with potential evolutionists: Huxley, Wollaston, Hewett Watson, Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
; to see if Huxley will accept the evidence and become a champion.  Darwin quizzes Huxley so he can at some later date refute each of Huxley's concerns and help him onboard.  At present he decides to keep some distance from the brazen young man.  Instead, Darwin next explored how to present his theory. 

Lyell (2) alerted Darwin to a paper on the 'introduction of species' by Alfred Russel Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
, but it was fashioned obliquely and Darwin dismissed it.  However, Lyell did not, he talked of his concerns with Darwin, who responded by revealing the full details of natural selection.  Lyell urged him to publish, although horrified by the implications: man was only a better sort of Old World ape.  Darwin knew the risks, is an assessment of the likelihood of an independent problem occurring.  It can be assigned an accurate probability since it is independent of other variables in the system.  As such it is different from uncertainty. 
and settled on a tome that could spark a coup among those he aimed to convince. 

A Low & Lewd Nature
Darwin proceeds with writing his tome, driven on by a mission and desperate for recognition:
Charles experiments with seeds have not gone according to plan.  The seeds sink and so he develops new hypothesis, seeds: caught on the foot of a bird, digested by a bird; to explain the transportation mechanism to new geographies.  He is still skeptical of the super-continent explanation, but it gains additional support elsewhere. 

Emma has an unplanned pregnancy, which is successful, but the additional baby boy, Charles Waring, is intellectually challenged.  It increased Charles's fears about inbreeding. 

What Would A Chimpanzee Say?
Richard Owen was vehemently opposed to transmutation, and to Huxley.  Owen obtained early access to a skull of a gorilla from the East India Company and used it to highlight the differences between the apes and man.  To create more barriers he highlighted special structures in man's brain: hippocampus is a part of the medial temporal lobe of the brain involved in the temporary storage or coding of long-term episodic memory.  It includes the dentate gyrus.  Memory formation in the cells of the hippocampus uses the MAP kinase signalling network which is impacted by sleep deprivation.  The hippocampus dependent memory system is directly affected by cholinergic changes throughout the wake-sleep cycle.  Increased acetylcholine during REM sleep promotes information attained during wakefulness to be stored in the hippocampus by suppressing previous excitatory connections while facilitating encoding without interference from previously stored information.  During slow-wave sleep low levels of acetylcholine cause the release of the suppression and allow for spontaneous recovery of hippocampal neurons resulting in memory consolidation.  It was initially associated with memory formation by McGill University's Dr. Brenda Milner, via studies of 'HM' Henry Molaison, whose medial temporal lobes had been surgically destroyed leaving him unable to create new explicit memories.  The size of neurons' dendritic trees expands and contracts over a female rat's ovulatory cycle, with the peak in size and cognitive skills at the estrogen high point.  Adult neurogenesis occurs in the hippocampus (3% of neurons are replaced each month) where the new neurons integrate into preexisting circuits.  It is enhanced by learning, exercise, estrogen, antidepressants, environmental enrichment, and brain injury and inhibited by various stressors explains Sapolsky.  Prolonged stress makes the hippocampus atrophy.  He notes the new neurons are essential for integrating new information into preexisting schemas -- learning that two things you thought were the same are actually different.  Specific cells within the hippocampus and its gateway, the entorhinal cortex, are compromised by Alzheimer's disease.  It directly signals area 25. 
minor, cerebral hemispheres includes the paleocortex a thin sheet of cells that mostly process smell, archicortex and the neocortex.  The cerebral cortex is a pair of large folded sheets of brain tissue, one on either side of the top of the head connected by the corpus callosum.  It includes the occipital, parietal, temporal and frontal lobes. 
completely covering the cerebellum is involved with the efficiency of fine movement. It modulates the force and range of motion and is involved in motor coordination and the learning of motor skills.  Damage to the cerebellum impairs standing, walking, or performance of coordinated movements. A virtuoso pianist or other performing musician depends on their cerebellum.  The cerebellum receives visual, auditory, vestibular, and somatosensory information.  It also receives information about individual muscular movements being directed by the brain.  The cerebellum integrates this information and modifies the motor outflow, exerting a coordinating and smoothing effect on the movements.  However, patients born without a cerebellum have survived reasonably well.  The cerebellum is part of the implicit learning mechanism.  It is required for the rabbit eye-blink to be classically conditioned to respond to a sound, and puff of air (threat to eye).  It integrates the sound and puff and outputs the response to the motor area (blink).  Levitin has shown the cerebellum participates in aspects of emotion and auditory processing.  He found the cerebellum and basal ganglia were active throughout a session listening to music, modeling the beat, rewarding a match between the internal and external rhythm and integrating movement. And he notes the cerebellum providing Williams syndrome sufferers with their capability to play music.   ; and described them all as being God's discrete creations. 

Etty was ill, as was Charles and so he was struggling to produce the further chapters of his tome 'Origin of Species':
To cope with the stress is a multi-faceted condition reflecting high cortisol levels.  Dr. Robert Sapolsky's studies of baboons indicate that stress helps build readiness for fight or flight.  As these actions occur the levels of cortisol return to the baseline rate.  A stressor is anything that disrupts the regular homeostatic balance.  The stress response is the array of neural and endocrine changes that occur to respond effectively to the crisis and reestablish homeostasis. 
  • The short term response to the stressor
    • activates the amygdala which: Stimulates the brain stem resulting in inhibition of the parasympathetic nervous system and activation of the sympathetic nervous system with the hormones epinephrine and norepinephrine deployed around the body, Activates the PVN which generates a cascade resulting in glucocorticoid secretion to: get energy to the muscles with increased blood pressure for a powerful response.  The brain's acuity and cognition are stimulated.  The immune system is stimulated with beta-endorphin and repair activities curtail.  In order for the body to destroy bacteria in wounds, pro-inflammatory cytokines increase blood flow to the area.  The induced inflammation signals the brain to activate the insula and through it the ACC.  But when the stressor is
  • long term: loneliness, debt; and no action is necessary, or possible, long term damage ensues.  Damage from such stress may only occur in specific situations: Nuclear families coping with parents moving in.  Sustained stress provides an evolved amplifier of a position of dominance and status.  It is a strategy in female aggression used to limit reproductive competition.  Sustained stress:
    • Stops the frontal cortex from ensuring we do the harder thing, instead substituting amplification of the individual's propensity for risk-taking and impairing risk assessment! 
    • Activates the integration between the thalamus and amygdala. 
      • Acts differently on the amygdala in comparison to the frontal cortex and hippocampus: Stress strengthens the integration between the Amygdala and the hippocampus, making the hippocampus fearful. 
      • BLA & BNST respond with increased BDNF levels and expanded dendrites persistently increasing anxiety and fear conditioning. 
    • Makes it easier to learn a fear association and to consolidate it into long-term memory.  Sustained stress makes it harder to unlearn fear by making the prefrontal cortex inhibit the BLA from learning to break the fear association and weakening the prefrontal cortex's hold over the amygdala.  And glucocorticoids decrease activation of the medial prefrontal cortex during processing of emotional faces.  Accuracy of assessing emotions from faces suffers.  A terrified rat generating lots of glucocorticoids will cause dendrites in the hippocampus to atrophy but when it generates the same amount from excitement of running on a wheel the dendrites expand.  The activation of the amygdala seems to determine how the hippocampus responds. 
    • Depletes the nucleus accumbens of dopamine biasing rats toward social subordination and biasing humans toward depression. 
    • Disrupts working memory by amplifying norepinephrine signalling in the prefrontal cortex and amygdala to prefrontal cortex signalling until they become destructive.  It also desynchronizes activation in different frontal lobe regions impacting shifting of attention.  
    • Increases the risk of autoimmune disease (Jan 2017) 
  • During depression, stress inhibits dopamine signalling.  
  • Strategies for stress reduction include: Mindfulness. 
of heretical writing Charles began visiting Dr. Edward Lane's Moor Park estate in Farnham for more water treatment.  And he also sent Etty.  They both responded positively.  Charles was enamored with Lane. 

The trends in science and popular culture were moving towards Charles's position and away from Owen.  Huxley and Hooker fully embraced Darwin's ideas as they reviewed drafts of the Origin.  Huxley had realized that evolution could be used as a tool to attack Owen and Creation. 

Charles hoped William would become a barrister.  George was studying engineering.  Horace was learning to read.  But his youngest son Charles Waring, while happy, did not walk or talk.  To allow the Darwin's and Wedgwood's to stay at Down, Charles had the house expanded.  The noise added to his stress. 

Emma supported village life, acting as a nurse and pharmacist.  Charles became a Justice of the Peace and subsequently a magistrate, motivated by the status is a publically accepted, signal that one possesses assets: wealth, beauty, talent, expertise, access & trust of powerful people; to be able to help others. 


Darwin was employing Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
to send over specimens from the Far East.  He encouraged Wallace's theorizing, and noted that his own work was still years away from publishing.  Darwin was shattered when Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
sent a summary of the evolutionary paper he was writing.  While Wallace proposed a different mechanism to Darwin's natural selection, the summary did not show this.  With Darwin's mind full of the Origin he saw the same ideas implied by Wallace's summary.  

Breaking Cover
Darwin found himself in a situation of terrible stress is a multi-faceted condition reflecting high cortisol levels.  Dr. Robert Sapolsky's studies of baboons indicate that stress helps build readiness for fight or flight.  As these actions occur the levels of cortisol return to the baseline rate.  A stressor is anything that disrupts the regular homeostatic balance.  The stress response is the array of neural and endocrine changes that occur to respond effectively to the crisis and reestablish homeostasis. 
  • The short term response to the stressor
    • activates the amygdala which: Stimulates the brain stem resulting in inhibition of the parasympathetic nervous system and activation of the sympathetic nervous system with the hormones epinephrine and norepinephrine deployed around the body, Activates the PVN which generates a cascade resulting in glucocorticoid secretion to: get energy to the muscles with increased blood pressure for a powerful response.  The brain's acuity and cognition are stimulated.  The immune system is stimulated with beta-endorphin and repair activities curtail.  In order for the body to destroy bacteria in wounds, pro-inflammatory cytokines increase blood flow to the area.  The induced inflammation signals the brain to activate the insula and through it the ACC.  But when the stressor is
  • long term: loneliness, debt; and no action is necessary, or possible, long term damage ensues.  Damage from such stress may only occur in specific situations: Nuclear families coping with parents moving in.  Sustained stress provides an evolved amplifier of a position of dominance and status.  It is a strategy in female aggression used to limit reproductive competition.  Sustained stress:
    • Stops the frontal cortex from ensuring we do the harder thing, instead substituting amplification of the individual's propensity for risk-taking and impairing risk assessment! 
    • Activates the integration between the thalamus and amygdala. 
      • Acts differently on the amygdala in comparison to the frontal cortex and hippocampus: Stress strengthens the integration between the Amygdala and the hippocampus, making the hippocampus fearful. 
      • BLA & BNST respond with increased BDNF levels and expanded dendrites persistently increasing anxiety and fear conditioning. 
    • Makes it easier to learn a fear association and to consolidate it into long-term memory.  Sustained stress makes it harder to unlearn fear by making the prefrontal cortex inhibit the BLA from learning to break the fear association and weakening the prefrontal cortex's hold over the amygdala.  And glucocorticoids decrease activation of the medial prefrontal cortex during processing of emotional faces.  Accuracy of assessing emotions from faces suffers.  A terrified rat generating lots of glucocorticoids will cause dendrites in the hippocampus to atrophy but when it generates the same amount from excitement of running on a wheel the dendrites expand.  The activation of the amygdala seems to determine how the hippocampus responds. 
    • Depletes the nucleus accumbens of dopamine biasing rats toward social subordination and biasing humans toward depression. 
    • Disrupts working memory by amplifying norepinephrine signalling in the prefrontal cortex and amygdala to prefrontal cortex signalling until they become destructive.  It also desynchronizes activation in different frontal lobe regions impacting shifting of attention.  
    • Increases the risk of autoimmune disease (Jan 2017) 
  • During depression, stress inhibits dopamine signalling.  
  • Strategies for stress reduction include: Mindfulness. 
:

1860-1871

More Kicks Than Halfpence
Desmond & Moore write twenty years after its inception, Darwin's theory was in print.  It catalyzed, an infrastructure amplifier.   a full war between the professional scientific leadership in London and the Anglican academics and establishment.  But by 1860 the membership of the scientific societies had shifted to professionals: geological survey corps; who observed their environment and concluded it was well represented by Darwin's publications.  While the Anglican hierarchy was able to scotch a proposed knighthood for Darwin, and their reviews of Origin of Species were damming, he was defended by the professionals: Huxley, Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
; in their own reviews. 

The culmination was during the questioning after a debate between Bishop Samuel Wilberforce of Oxford, briefed by Owen on how to attack Darwin, and New York University's Professor John William Draper advocating Spencer's Social Darwinism.  During the questioning, Wilberforce attacked Huxley, quizzing him which of his grand-parents was an ape.  But Huxley responded in kind, and Hooker won the argument in the judgment of the liberals.  The conservatives congratulated Wilberforce.  Darwin recuperating through attending hydrotherapy read Hooker's account with pleasure. 

From the Womb of the Ape
Liberal theologians joined the attacks on the Anglican hierarchy, but they were beaten back, with professors being removed from their positions at the universities.  Huxley maintained his attacks on Owen, delivered through the Natural History Review, and his lectures for working men.  Radical workers had accepted new ideas: French Revolutionary science, materialism, and evolution; early and Darwin's arguments were keenly heard.  The discovery of Archaeopteryx, a bird with teeth, was of popular interest and highlighted the gaps in the fossil record.  Amid the groundswell, Owen proposed expanding the British Museum to provide space for all the examples Darwin used and people hence asked about. 

Charles was busy dissecting, experimenting and writing:
  • Natural Selection - re-reading old manuscripts to leverage the facts,
  • Domestication - deploying some of the facts from the old manuscripts,
  • Orchids - where he highlighted the cross-pollination mechanism; how natural selection explained functional changes. 
Darwin noted that sterile plant hybrids provided a
Barriers are particular types of constraints on flows.  They can enforce separation of a network of agents allowing evolution to build diversity.  Examples of different types of barriers: physical barriers, chemical molecules can form membranes, probability based, cell membranes can include controllable channels, eukaryotes leverage membranes, symbiosis, human emotions, chess, business; and their effects are described. 
barrier
ensure divergence rather than blending together. 

Charles hoped Lyell would give his full support to man being descended from animals, but Lyell's Antiquity of Man was cautious, because he still could not accept the premise. 

Henslow was dying of heart disease is cardiovascular disease which refers to:
  • Conditions where narrowed and blocked blood vessels result in angina, hypertension, CHD and heart attacks and hemorrhagic/ischemic strokes.  Mutations of the gene PCSK9 have been implicated in cardiovascular disease.  Rare families with dominant inheritence of the mutations have an overactive protein, very high levels of blood cholesterol and cardiac disease. Other rare PCSK9 mutations result in an 88% reduced risk from heart disease.  Inflammation is associated with cardiovascular disease (Aug 2017). 
, with Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
standing vigil at his father-in-law's bed side, but Charles was too distraught to visit before the end.  Huxley was devastated when his son Noel died of scarlet fever.  Hooker also lost his six-year-old, second daughter Minnie.  Charles worried that the hereditary weakness that he felt struck Annie, would present in Horace as he reached that age.  Lenny, now eleven, was judged 'slow and backward.'  George was suffering with decaying teeth.  And Etty had been invalided by typhoid is an acute bacterial infection from Salmonella typhimurium.  It is transmitted by the fecal-oral route from contaminated water or food.  It grows in the intestines and blood.  Vaccine exists and is 30 to 70% effective.  It is treated with azithromycin, fluoroquinolones or cephalosporins.  As of 2018 about 21 million people suffer from typhoid infections each year with 161,000 deaths. 


Charles stomach problems, headaches, eczema is atopic dermatitis. 
, and boils, were so bad that Emma insisted he go with her to Malvern to take the waters.  They struggled to find Annie's overgrown grave

A Living Grave
Desmond & Moore describe the alignment of the liberals, progressives and professional scientists with the North in the US civil war, while the Creationists drifted towards the South and its arguments for slavery.  Rising within the Royal Society a clique of Darwinians formed the secretive X Club: Huxley, Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
, Tyndall, Busk, Spencer, Lubbock, Spottiswoode; intent on freeing nature from the reactionary theology, and freeing science from aristocratic privilege, and capturing power themselves.  They altered the election procedures to get allies elected.  They now had enough power to award Darwin the Copley Medal. 

The radical theologians, who had been expelled from their university posts, appealed to the judicial Committee of the Privy Council and won their case.  Tory, Disraeli, satirized Vestiges was the 1844 book, written anonymously by Robert Chambers, which aimed to make scientific progress, advanced anatomy and evolution; broadly accessible, according to Desmond & Moore.  The book was brilliantly written, and highly impressionistic.  Chambers described how Nature self-developed: coalescence of planets, chemico-electrical generation of first life, series of fossil vestiges, emergence of man; in a fascinating way, targeted at ordinary readers.  The book left the impression of an upwardly mobile nature.  It caused a sensation and sold massively.  The scientific evolutionaries: Hooker - noted its egregious blunders, Darwin - considered the geology bad and the zoology worse; to which Chambers responded with corrections in subsequent editions.  The book was attacked by the Anglican elite: Sedgwick. 
in Tancred, and declared he was on the side of man being angels, not apes.  And Pope Pius IX started the shift towards Papal Infallibility, critical of Darwin.  FitzRoy, hating Origins, passed over for Chief Naval Officer in the Marine Department, depressed is a debilitating episodic state of extreme sadness, typically beginning in late teens or early twenties. This is accompanied by a lack of energy and emotion, which is facilitated by genetic predisposition - for example genes coding for relatively low serotonin levels, estrogen sensitive CREB-1 gene which increases women's incidence of depression at puberty; and an accumulation of traumatic events.  There is a significant risk of suicide: depression is involved in 50% of the 43,000 suicides in the US, and 15% of people with depression commit suicide.  Depression is the primary cause of disability with about 20 million Americans impacted by depression at any time.  There is evidence of shifts in the sleep/wake cycle in affected individuals (Dec 2015).  The affected person will experience a pathological sense of loss of control, prolonged sadness with feelings of hopelessness, helplessness & worthlessness, irritability, sleep disturbances, loss of appetite, and inability to experience pleasure.  Michael Pollan concludes depression is fear of the past.  It affects 12% of men and 20% of women.  It appears to be associated with androgen deprivation therapy treatment for prostate cancer (Apr 2016).  Chronic stress depletes the nucleus accumbens of dopamine, biasing humans towards depression.  Depression easily leads to following unhealthy pathways: drinking, overeating; which increase the risk of heart disease.   It has been associated with an aging related B12 deficiency (Sep 2016).  During depression, stress mediates inhibition of dopamine signalling.  Both depression and stress activate the adrenal glands' release of cortisol, which will, over the long term, impact the PFC.  There is an association between depression and additional brain regions: Enlarged & more active amygdala, Hippocampal dendrite and spine number reductions & in longer bouts hippocampal volume reductions and memory problems, Dorsal raphe nucleus linked to loneliness, Defective functioning of the hypothalamus undermining appetite and sex drive, Abnormalities of the ACC.  Mayberg notes ACC area 25: serotonin transporters are particularly active in depressed people and lower the serotonin in area 25 impacting the emotion circuit it hubs, inducing bodily sensations that patients can't place or consciously do anything about; and right anterior insula: which normally generates emotions from internal feelings instead feel dead inside; are critical in depression.  Childhood adversity can increase depression risk by linking recollections of uncontrollable situations to overgeneralizations that life will always be terrible and uncontrollable.  Sufferers of mild autism often develop depression.  Treatments include: CBT which works well for cases with below average activity of the right anterior insula (mild and moderate depression), UMHS depression management, deep-brain stimulation of the anterior insula to slow firing of area 25.  Drug treatments are required for cases with above average activity of the right anterior insula.  As of 2010 drug treatments: SSRIs (Prozac), MAO, monoamine reuptake inhibitors; take weeks to facilitate a response & many patients do not respond to the first drug applied, often prolonging the agony.  By 2018, Kandel notes, Ketamine is being tested as a short term treatment, as it acts much faster, reversing the effect of cortisol in stimulating glutamate signalling, and because it reverses the atrophy induced by chronic stress.   Genomic predictions of which treatment will be effective have not been possible because: Not all clinical depressions are the same, a standard definition of drug response is difficult;, slit his throat. 

Darwin's sister Catherine died in early 1866. 

Darwin was now sensitive to any visit, or criticism, was sick much of the time with symptoms he carefully documented and described to Dr. Chapman, his new doctor:
  • For 25 years extreme spasmodic daily & nightly flatulence
  • Occasional vomiting, on two occasions prolonged during months
  • Vomiting preceded by shivering
  • Hysterical crying, dying sensations or half faint
  • Copious very pallid urine
  • Now vomiting & every passage of flatulence preceded by ringing of ears, treading on air & vision. focus & black dots, Air fatigues, specially risky, brings on the Head symptoms,
  • Nervousness when Emma leaves me ...
Darwin's appearance had changed so greatly, as his body crumbled, that he had to introduce himself to old friends and acquaintances. 

When well enough, Charles was studying:
  • Plants with triple-sexuality
  • Climbers & coiling tendrils written up in The Movements and Habits of Climbing Plants
  • Domestic ducks and geese written up in Variation under Domestication
  • Hypothesis about heredity - Pangenesis, where gemmules came from the whole body and congregated in the reproductive organs.  He only shared it with Huxley, who demurred

Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
tried to heal the split between the ultra-racist, pro slavery Anthropological Society and the abolitionist Ethnological society, delivering a paper that proposed the races had long been separated but had
This page discusses the mechanisms and effects of emergence underpinning any complex adaptive system (CAS).  Physical forces and constraints follow the rules of complexity.  They generate phenomena and support the indirect emergence of epiphenomena.  Flows of epiphenomena interact in events which support the emergence of equilibrium and autonomous entities.  Autonomous entities enable evolution to operate broadening the adjacent possible.  Key research is reviewed. 
emerged
from a single stock just after the ape stage.  He highlighted man's division of labor and stressed that mutual assistance supports the group, which he identified as the unit operated on by natural selection.  He continued that building, fire, clothing, and agriculture had made man master of his environment, the intellect prevailing over selection.  Man's body had stopped evolving while the intellect was improving.  Darwin studied his paper but demurred on the abating of selection.  While Darwin saw war selecting the winners, Wallace asserted in war, the strongest and bravest die first. 

Spencer suggested replacing the term natural selection with survival of the fittest.  Darwin noted this removed the
Rather than oppose the direct thrust of some environmental flow agents can improve their effectiveness with indirect responses.  This page explains how agents are architected to do this and discusses some examples of how it can be done. 
indirect
analogy of nature and breeders both selecting.  But Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
adopted the new terminology and Darwin followed. 

Emerald Beauty
Desmond & Moore explain that by 1866 Charles Darwin's ideas about evolution by selection are becoming accepted nationally: British Association meeting heard from its president W. R. Grove that evolution served the crown's interest with continuity: reason, peace, security; rather than revolution, and internationally: US is the United States of America.  , Russia, Germany - where Ernest Haeckel was training a new generation of university students at Jena in 'Darwinismus.'  But Desmond & Moore note, at the same instant spiritualism, imported from the US, was growing into a serious alternative to science: Robert Chambers published popular periodicals from Edinburgh.  And he wrote Vestiges of the Natural History of Creation, which he marketed brilliantly.  According to Desmond & Moore, he was a golf-playing, overworked, man of the people. 
updated Vestiges was the 1844 book, written anonymously by Robert Chambers, which aimed to make scientific progress, advanced anatomy and evolution; broadly accessible, according to Desmond & Moore.  The book was brilliantly written, and highly impressionistic.  Chambers described how Nature self-developed: coalescence of planets, chemico-electrical generation of first life, series of fossil vestiges, emergence of man; in a fascinating way, targeted at ordinary readers.  The book left the impression of an upwardly mobile nature.  It caused a sensation and sold massively.  The scientific evolutionaries: Hooker - noted its egregious blunders, Darwin - considered the geology bad and the zoology worse; to which Chambers responded with corrections in subsequent editions.  The book was attacked by the Anglican elite: Sedgwick. 
to reflect it, Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
accepted it as important; while the professional scientists: Huxley, Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
; were dismayed. 

Darwin met Haeckel and liked him, but as he struggled to read Haeckel's German language book Generelle Morphologie, it became apparent that Darwin's discoveries and ideas were being used to justify the development of a German Volk and to support a secular Prussian state. 

Charles was also disappointed to discover that his son, William, was a supporter of the white supremacists, who were supporting Governor Eyre of Jamaica in a lawsuit regarding his putting down a peasant revolt with massive force. 

The Duke of Argyll wrote an elegant book illustrating the artistic work of god.  Particularly problematic for natural selection was his discussion of hummingbirds.  Wallace highlighted the weaknesses in the Dukes arguments and Darwin showed that
This page describes the consequences of the asymmetries caused by genotypic traits creating a phenotypic signal in males and selection activity in the female - sexual selection.   
The impact of this asymmetry is to create a powerful alternative to natural selection with sexual selection's leverage of positive returns.  The mechanisms are described. 
sexual selection
would explain the bright coloring of the male birds, and many features of human anatomy. 

Charles was finalizing his book, Variation under Domestication, which was published as The Variation of Animals and Plants Under Domestication, in January 1868, including: pangenesis, problems of interbreeding and arguments to undermine Gray's divine designer.  Additionally Charles published an essay on the impact of selection on man, covering: Ape ancestry,
This page describes the consequences of the asymmetries caused by genotypic traits creating a phenotypic signal in males and selection activity in the female - sexual selection.   
The impact of this asymmetry is to create a powerful alternative to natural selection with sexual selection's leverage of positive returns.  The mechanisms are described. 
Sexual selection
, Human expressions; to halt the criticisms that he had avoided taking a position.  Wallace much preferred natural selection to sexual selection, to Darwin's dismay.  Charles origins arguments were also weakened by physicists concluding: the age of the earth was less than previously assumed, arrival of a variant to a large population would be reabsorbed. 

Sex, Politics & The X
Darwin treated pangenesis as his new baby.  It provided a mechanism to support the plasticity of species detailed in The Variations.  But none of his close scientific friends was convinced, leaving Darwin in despair - his insecurities returned - fear is an emotion which prepares the body for time sensitive action: Blood is sent to the muscles from the gut and skin, Adrenalin is released stimulating: Fuel to be released from the liver, Blood is encouraged to clot, and Face is wide-eyed and fearful.  The short-term high priority goal, experienced as a sense of urgency, is to flee, fight or deflect the danger.  There are both 'innate' - really high priority learning - which are mediated by the central amygdala and learned fears which are mediated by the BLA which learns to fear a stimulus and then signals the central amygdala.  Tara Brach notes we experience fear as a painfully constricted throat, chest and belly, and racing heart.  The mind can build stories of the future which include fearful situations making us anxious about current ideas and actions that we associate with the potential future scenario.  And it can associate traumatic events from early childhood with our being at fault.  Consequent assumptions of our being unworthy can result in shame and fear of losing friendships.  The mechanism for human fear was significantly evolved to protect us in the African savanna.  This does not align perfectly with our needs in current environments: U.S. Grant was unusually un-afraid of the noise or risk of guns and trusted his horses' judgment, which mostly benefited his agency as a modern soldier. 
of: rejection, loss of status is a publically accepted, signal that one possesses assets: wealth, beauty, talent, expertise, access & trust of powerful people; to be able to help others. 
; and hating the book, until it became a popular success, the edition selling out.  And Gray and Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
liked the hypothesis. 

This page describes the consequences of the asymmetries caused by genotypic traits creating a phenotypic signal in males and selection activity in the female - sexual selection.   
The impact of this asymmetry is to create a powerful alternative to natural selection with sexual selection's leverage of positive returns.  The mechanisms are described. 
Sexual selection
was becoming a huge investigation, motivated by the Duke of Argyll's adversarial success.  Charles felt that miniscule changes in looks were important to providing the gorgeous appearance that was being selected.  Charles would send out letters each day to naturalists and breeders across the Empire and then collate responses from: fanciers, farmers, fisheries experts, census statisticians, collectors, and colonists.  He formulated questions to be explored and answered.  Wallace was reviewing natural selections support for advertising features like being poisonous.  But this wasn't applicable to hummingbird throats. 

He answered Argyll eventually by publishing The Descent of Man, and Selection in Relation to Sex, a book that ranged from sexual selection, ape ancestors, to evolution of morality provides rules for identifying right from wrong.  It develops in stages with children using play to work out rules of appropriate behavior.  Kohlberg's 1950s experiments using children led him to conclude moral judgement is a cognitive process that develops in three stages.  Sapolsky raises issues with the framework: Its a model, It does not apply to other cultures, Intuition & emotion are as significant as cognition, Moral reasoning doesn't predict moral actions; and notes the capacity of the frontal cortex to regulate emotions and behavior is far more predictive.  The marshmallow test, performed on three to six year olds, actually predicted their subsequent SAT scores at high school, social success and lack of aggression, and forty years on more PFC activation during a frontal task and a lower BMI!  Jonathan Haidt argues people's moral decisions are rationalizations rather than using reasoning. 
and religion.  Darwin leveraged the ideas of his cousin Francis Dalton and Walter Bagehot. 

His own children were becoming more settled: William was running a bank, Leonard was accepted by the Royal Military Academy, Horace had a place at Cambridge, George had the offer of a fellowship at Trinity College, Cambridge.  And Charles was being showered with awards from Russia and Prussia. 

He was effective at self-promotion, convincing John Murray to publish an English translation of Fritz Muller's Fur Darwin, which Darwin financed, but which sold well. 

Desmond & Moore describe X Club Darwinians taking over the major science posts: Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
was elected president of the British Association, promoting Darwin's ideas in his acceptance speech: Orchids, Tendrils, Origins; while criticizing Natural Theology; Huxley finally adopting a tree of species, convinced by Haeckel, linking birds through ostrich ancestors to dinosaurs; Tyndall firing up the popular imagination with discussions of babies made from chemicals and the thinking capacity of robots. 

The expansion of voting resulted in the Tories being routed. 

Down House became the hub of a correspondence network across the Empire. ...  Mail brought gems to aid his
This page describes the consequences of the asymmetries caused by genotypic traits creating a phenotypic signal in males and selection activity in the female - sexual selection.   
The impact of this asymmetry is to create a powerful alternative to natural selection with sexual selection's leverage of positive returns.  The mechanisms are described. 
sexual selection
[ investigation].  ...  Desmond & Moore conclude Darwin excelled at: collecting and colation, tracking down facts, verifying, extending his old notebook speculations to embrace the globe. 

Disintegrating Speculations
Desmond & Moore write that evolution was becoming generally accepted.  But no one liked Darwin's proposal that natural selection depended on random changes.  Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
, enamored with spiritualism, introduced his paradox is Alfred Russel Wallace's conclusion that the mind is overdesigned for the needs of evolving humans and cannot be explained by natural selection.  Instead Wallace proposed spiritual powers guided human destiny, which horrified Darwin. 
, which horrified Charles.  The mechanism came under intense threat as Thomson's physicists published further results of experiments indicating the age of the earth was far less than random change would need.  Darwin was dubious of the physicists' results, which would undermine all the geology and biology discoveries, and asked George to review the details.  George concluded, it was likely the experiments were P. G. Tait's, who was a bible-toting natural philosophy professor working with Thomson, but he warned Charles of the gravity of the case.  Huxley, the X club's best tactician, attacked the physicists in his lectures, but was criticized for compromising the queen of sciences.  He went on to attack Pope Pius IX and was charged with heresy.  Huxley responded to the attacks by noting that he was agnostic. 

Huxley introduced his disciple, Mivert - who had converted to Catholicism, into the X club, and they supported his becoming a fellow of the Royal Society.  But Huxley's attacks on the Pope turned Mivert into a well-informed traitor.  Mivert published Genesis of Species which included sophisticated attacks on natural selection:
  • Placental dog and marsupial wolf were clearly converged.  How could selection do that?
  • An incipient wing was not functional, which was Darwin's condition for natural selection to act
  • Mivert proposed an inner force to replace Darwin's mechanisms. 
Darwin's strategic response was to update Origin into a sixth edition, which would demonstrate natural selection's answer to Mivert's criticisms. 

Argyll, now Gladstone's Secretary of State for India, attacked Lubbock's Prehistoric Times.  Darwin was pleased when Lubbock was elected to parliament, where the new member tried, but failed, to amend the census questions for Darwin, to assess how many cousins were marrying. 

Darwin was focused on completing Descent of Man, his strategic explanation of
This page describes the consequences of the asymmetries caused by genotypic traits creating a phenotypic signal in males and selection activity in the female - sexual selection.   
The impact of this asymmetry is to create a powerful alternative to natural selection with sexual selection's leverage of positive returns.  The mechanisms are described. 
sexual selection
, while evidence was still flooding in to Down House from colonists and empire builders.  It went on sale as the war between Germany and France was completing with Paris capitulating.  Selling out in three weeks a second edition was printed.  After all the X club's work to drive evolution into the public's consciousness, the new book was treated as everyone's family saga.  At least until Mivert wrote a powerful critique suggesting it was dogma, and arguing:
Darwin arranged to have a US is the United States of America.   critique of Genesis of Species published in the UK is the United Kingdom of Great Britain and Northern Ireland.  .  But it did not sell well.  Darwin's own ideas were under siege. 

1871-1882

Pause, Pause, Pause
Desmond & Moore describe the stress is a multi-faceted condition reflecting high cortisol levels.  Dr. Robert Sapolsky's studies of baboons indicate that stress helps build readiness for fight or flight.  As these actions occur the levels of cortisol return to the baseline rate.  A stressor is anything that disrupts the regular homeostatic balance.  The stress response is the array of neural and endocrine changes that occur to respond effectively to the crisis and reestablish homeostasis. 
  • The short term response to the stressor
    • activates the amygdala which: Stimulates the brain stem resulting in inhibition of the parasympathetic nervous system and activation of the sympathetic nervous system with the hormones epinephrine and norepinephrine deployed around the body, Activates the PVN which generates a cascade resulting in glucocorticoid secretion to: get energy to the muscles with increased blood pressure for a powerful response.  The brain's acuity and cognition are stimulated.  The immune system is stimulated with beta-endorphin and repair activities curtail.  In order for the body to destroy bacteria in wounds, pro-inflammatory cytokines increase blood flow to the area.  The induced inflammation signals the brain to activate the insula and through it the ACC.  But when the stressor is
  • long term: loneliness, debt; and no action is necessary, or possible, long term damage ensues.  Damage from such stress may only occur in specific situations: Nuclear families coping with parents moving in.  Sustained stress provides an evolved amplifier of a position of dominance and status.  It is a strategy in female aggression used to limit reproductive competition.  Sustained stress:
    • Stops the frontal cortex from ensuring we do the harder thing, instead substituting amplification of the individual's propensity for risk-taking and impairing risk assessment! 
    • Activates the integration between the thalamus and amygdala. 
      • Acts differently on the amygdala in comparison to the frontal cortex and hippocampus: Stress strengthens the integration between the Amygdala and the hippocampus, making the hippocampus fearful. 
      • BLA & BNST respond with increased BDNF levels and expanded dendrites persistently increasing anxiety and fear conditioning. 
    • Makes it easier to learn a fear association and to consolidate it into long-term memory.  Sustained stress makes it harder to unlearn fear by making the prefrontal cortex inhibit the BLA from learning to break the fear association and weakening the prefrontal cortex's hold over the amygdala.  And glucocorticoids decrease activation of the medial prefrontal cortex during processing of emotional faces.  Accuracy of assessing emotions from faces suffers.  A terrified rat generating lots of glucocorticoids will cause dendrites in the hippocampus to atrophy but when it generates the same amount from excitement of running on a wheel the dendrites expand.  The activation of the amygdala seems to determine how the hippocampus responds. 
    • Depletes the nucleus accumbens of dopamine biasing rats toward social subordination and biasing humans toward depression. 
    • Disrupts working memory by amplifying norepinephrine signalling in the prefrontal cortex and amygdala to prefrontal cortex signalling until they become destructive.  It also desynchronizes activation in different frontal lobe regions impacting shifting of attention.  
    • Increases the risk of autoimmune disease (Jan 2017) 
  • During depression, stress inhibits dopamine signalling.  
  • Strategies for stress reduction include: Mindfulness. 
on Darwin at the beginning of 1871.  He was now 62 but appeared and felt are subjective models: sad, glad, mad, scared, surprised, and compassionate; of the organism and its proximate environment, including ratings of situations signalled by broadly distributed chemicals and neural circuits.  These feelings become highly salient inputs, evolutionarily associated, to higher level emotions encoded in neural circuits: amygdala, and insula.  Deacon shows James' conception of feeling can build sentience.  Damasio, similarly, asserts feelings reveal to the conscious mind the subjective status of life: good, bad, in between; within a higher organism.  They especially indicate the affective situation within the old interior world of the viscera located in the abdomen, thorax and thick of the skin - so smiling makes one feel happy; but augmented with the reports from the situation of the new interior world of voluntary muscles.  Repeated experiences build intermediate narratives, in the mind, which reduce the salience.  Damasio concludes feelings relate closely and consistently with homeostasis, acting as its mental deputies once organisms developed 'nervous systems' about 600 million years ago, and building on the precursor regulatory devices supplied by evolution to social insects and prokaryotes and leveraging analogous dynamic constraints.  Damasio suggests feelings contribute to the development of culture:
  • As motives for intellectual creation: prompting detection and diagnosis of homeostatic deficiencies, identifying desirable states worthy of creative effort.
  • As monitors of the success and failure of cultural instruments and practices
  • As participants in the negotiation of adjustments required by the cultural process over time 
much older.  His stomach was slowing him down.  While evolution was now accepted widely natural selection was not and Mivert's Genesis was a threat.  Charles responded by:
Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
had become a proponent for Bastian's Beginnings of Life which asserted that germs were still being generated from inorganic chemicals spontaneously.  Darwin and Huxley saw only one life generating event on Earth, at the base of the tree of evolved species and differed with Wallace on this.  Even with Darwin's references, Wallace had not been able to gain employment as a museum director and was struggling financially at this time. 

Huxley had taken on too many jobs, and was also the target of a lawsuit.  It was a terrible stress, so to give him a break the Darwin's had the Huxley's kids come to stay for a while. 

Charles began a book on earthworms, requesting anecdotes from around the world.  And when the new marketing strategy for Origin hugely expanded his popular readership he worked on completing Expression of the Emotions for this audience, to show expressions evolved, that a series of species shared feelings are subjective models: sad, glad, mad, scared, surprised, and compassionate; of the organism and its proximate environment, including ratings of situations signalled by broadly distributed chemicals and neural circuits.  These feelings become highly salient inputs, evolutionarily associated, to higher level emotions encoded in neural circuits: amygdala, and insula.  Deacon shows James' conception of feeling can build sentience.  Damasio, similarly, asserts feelings reveal to the conscious mind the subjective status of life: good, bad, in between; within a higher organism.  They especially indicate the affective situation within the old interior world of the viscera located in the abdomen, thorax and thick of the skin - so smiling makes one feel happy; but augmented with the reports from the situation of the new interior world of voluntary muscles.  Repeated experiences build intermediate narratives, in the mind, which reduce the salience.  Damasio concludes feelings relate closely and consistently with homeostasis, acting as its mental deputies once organisms developed 'nervous systems' about 600 million years ago, and building on the precursor regulatory devices supplied by evolution to social insects and prokaryotes and leveraging analogous dynamic constraints.  Damasio suggests feelings contribute to the development of culture:
  • As motives for intellectual creation: prompting detection and diagnosis of homeostatic deficiencies, identifying desirable states worthy of creative effort.
  • As monitors of the success and failure of cultural instruments and practices
  • As participants in the negotiation of adjustments required by the cultural process over time 
and the means of expressing them.   With this book he aimed to destroy Sir Charles Bell's theological explanation of expressions: Anatomy & Physiology of Expression.  He tried to employ Wallace to develop the book, but Emma pushed him to use George instead.  Charles also experimented on insect eating plants: feeding, poisoning; concluding they were not disguised animals. 

Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
, director of Kew Gardens, came under attack from Gladstone's Commissioner of Works, Acton Smee Ayrton, who was a cost-cutting populist.  It became clear to Darwin that Owen was encouraging the attack hoping to take the gardens under the control of his British Museum.  

A Wretched Bigot
Charles and Emma's friends are aging and die with greater frequency: Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
's wife Fanny, Heslow's daughter, died suddenly leaving him overworked to cope with the children.  Lyell, blind and alone, dies.  Charles contemplates suicide. 

Charles supports the scientists' attempts to block antivivisection laws from being enacted.  He asserts how important dissection is to natural science progress.  The eventual bill on 'cruelty to animals' ignored Darwin's plea. 

Britain is still enthralled by spiritualismEras becomes a convert to the practice, but Charles and Hooker remain suspicious.  They are able to stop a high-level enquiry from providing additional credibility.  The X club has accumulated considerable power.  Reviews now criticize the Darwinians for their revolutionary zeal.  Emma asserts Charles is a bigot. 

Charles restructures Descent, including: an update to hurt Owen, a discussion of cousin Galton's ideas about intelligence as a tool of natural selection, and developing a half-price version - copying Origin - for mass consumption.  Charles rapidly generates a variety of new books that sell well.  Without the children to support, and with a frugal life style and the book revenues, Charles and Emma have huge surplus revenues.  But Charles still worries about becoming destitute.  Galton experiments with pangenesis and concludes it is doubtful.  He suggests the cells of the reproductive organs hold the key to heredity.  Haeckel agrees with Dalton.  Charles hangs on to his idea having received too many anecdotes about parental exercise being associated with children with bigger musculature. 

George, at home recovering from an illness, looks after the proofs of Descent.  He reviews the statistics of first cousin marriages, concluding they happen far more among the wealthy.  He leverages Galton's ideas to propose ways to lower the risk in a article.  Mivert attacks it and Charles.  George publishes a rebuttal which Mivert carefully undermines.  Charles and the X club ostracize Mivert from this point forward. 

Charles performs many experiments on his insectivorous plants, eventually building the conclusions into a further book Cross and Self-Selection, where he shows that cross breeding promotes vigor.  His marriage to a first cousin still plays on his mind. 

Never an Atheist
Charles and Emma were overjoyed at the news they were to be grandparents.  Amy, Frank's wife, was five months pregnant.  The occasion encourages Charles to write a message to be read just by his family, after he is dead.   In it he noted:
It was all complete by 3 August, in time for the birth of his grandchild.  Bernard arrived on 7th September, but Amy developed a fever and she died on the 11th.  Charles and Emma had the house extended so Frank and Bernard could live with them at Down House. 

Charles also wrote a biography of his grandfather, Erasmus, but its details and candor shocked the family who complained it was too: frank, long and boring. 

Fifteen years of experimenting on the sex-lives of plants now resulted in the release of a book: The Different Forms of Flowers on the Same Species.  He was very excited to have shown that triple-sexed flowers were structured so that they were most fertile with
Barriers are particular types of constraints on flows.  They can enforce separation of a network of agents allowing evolution to build diversity.  Examples of different types of barriers: physical barriers, chemical molecules can form membranes, probability based, cell membranes can include controllable channels, eukaryotes leverage membranes, symbiosis, human emotions, chess, business; and their effects are described. 
structures of the same length
- which always came from other flowers.  Since he hated being idle he started work on another book on plant movement.  And Charles was still studying earthworms.  All the work made him sick so he was seeing Dr. Clark about dizziness. 

Huxley's protege Ray Lankester exposed a medium as a fraud.  Charles contributed to the prosecution expenses. 

Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
was awarded the Star of India knighthood, by the Tory government.  Charles enjoyed being back in the establishment.  But he avoided everyone, and especially radicals and Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
.  He was subpoenaed by Charles Bradlaugh, who was defending the publication of a contraception pamphlet.  Charles warned him that he did not approve of contraception, asserting that the decoupling of sex from childbirth would undermine morals provides rules for identifying right from wrong.  It develops in stages with children using play to work out rules of appropriate behavior.  Kohlberg's 1950s experiments using children led him to conclude moral judgement is a cognitive process that develops in three stages.  Sapolsky raises issues with the framework: Its a model, It does not apply to other cultures, Intuition & emotion are as significant as cognition, Moral reasoning doesn't predict moral actions; and notes the capacity of the frontal cortex to regulate emotions and behavior is far more predictive.  The marshmallow test, performed on three to six year olds, actually predicted their subsequent SAT scores at high school, social success and lack of aggression, and forty years on more PFC activation during a frontal task and a lower BMI!  Jonathan Haidt argues people's moral decisions are rationalizations rather than using reasoning. 


The parish was struggling with a farm slump.  Darwin warned the laborers that taking the funds from the friendly society would destroy their long-term financial protection.  It was agreed they would just remove the surplus to assist struggling families.  Charles was now promoting self-help and the self-made man, who he asserted leveraged providence, industry and enterprise to succeed. 

Gladstone visited Down.  Charles supported the Liberal's foreign policy alignment with Russia against the Turks over Christian Bulgaria.  Gladstone asked what evolution indicated regarding America competing with the decaying Eastern civilizations.  Charles agreed that the future belonged to America. 

People still asked Darwin about his views on religion.  He only told his true feelings, agnosticism, to Eras and a few intimates. 

Down Among the Worms
Desmond & Moore explain that Horace had got engaged to Ida Farrer, daughter by the first wife, of 'Theta' Farrer, who was now married to Effie Wedgwood.  Theta had made it clear to Charles and Emma that he was unhappy about Ida's choice.  But the children were determined to marry.  Charles gave Horace 5,000 pounds of railway uses low friction tracks to support an engine and cars which can carry people and goods.  Modern railroads began with the Stockton to Darlington railway built by George Stephenson with a steam powered engine Locomotion No. 1 in 1825.  Electric power, and telegraph network were later leveraged.  Railroads contributed to the colonization of the world, the shift to regimentation with standardized time, maintained the efficiency of the cotton plantation trading network, supported the urbanization of the US, enabled the distribution of Californian lettuce and Midwestern beef with the refrigerated rail car, until government policy drove a shift to road networks, but were dangerous to walk on and supported the distribution of cholera to the US.  The monopsonistic network effects were leveraged by John D. Rockefeller, in building his Standard Oil trust. 
stock to show he would be able to retire comfortably and they married.   When Ida became pregnant, Charles updated his posthumous autobiography

Charles was still sensitive to criticism from Mivert & Samuel Butler, a convert from Darwinism to Genesis of Species, who accused Darwin of plagiarism and duplicity.  Butler was cold shouldered but Mivert's Genesis arguments were undermining Natural Selection - Huxley once again abandoned it.  Charles responded that it was only one of the evolutionary processes he had identified in Variations of Animals which also included: effect of use and disuse of parts, and direct action of external conditions. 

Darwin, always sensitive to Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
's magnanimity over Natural Selection, was worried about Alfred's financial situation and called in favors from the highly placed Darwinians to have them support Wallace getting a Crown pension, which was awarded by Gladstone & Queen Victoria. 

Bradlaugh had been elected to Parliament, but was procedurally blocked from taking up the seat due to being an atheist.  The people were reminded of the power of the church.  Charles still disapproved of Bradlaugh.  And was troubled by being linked to them through the advocacy of Edward Aveling, who had previously been supported by Charles when he published Darwin and His Works. 

Charles was experimenting on earthworms for another book, The Foundation of Vegetable Mould through the Action of Worms.  Earthworms were important in supporting the soil.  And he showed that they dragged leaf fragments to their dens, 'intelligently' selecting the narrow corner to pull in first.  He completed the manuscript before Easter. 

The family was aging badly: Sister Caroline, Fanny Wedgwood, Eras - too much opium left him in constant pain, Emma's sister Elizabeth; and Charles was too.  He left a coded symbol of his love for Emma and Annie as he contemplated his death. 

The Final Experiment
Desmond & Moore catalog Darwin's decline towards death over twelve months from angina on 19th April 1882.   Charles pushed off the proofs of Worms to Frank.  When published it sold phenomenally.  Charles hated inactivity but was too tired to do or think much.  But when he did think his mind was still sharp.  Hooker was a medical officer in the Royal Navy and a botanist, who adored the books Charles Darwin published about his trip to South America, and was, while much younger, befriended by Darwin.  They met while Hooker was walking in Charring Cross with Robert McCormick, the Erebus surgeon & Beagle's surgeon as far as Rio.  Like Charles, Hooker had used the navy to travel to distant parts of the natural world, being part of the Ross Antarctic expedition on HMS Erebus.  With similar interests & experiences, they gravitated to each other.  Hooker followed Darwin's advice and demonstrated total command of his data.  Unlike Darwin: as a boy Hooker had been raised as a puritan, he trained to be a doctor in Glasgow, he did not possess Darwin's wealth; so he had worked his way in the navy as an assistant surgeon.  While he waited for sponsorship for further botanical trips, he helped Darwin with his scientific studies, and became engaged to John Henslow's eldest daughter, Frances, before joining another naval expedition as a botanist sponsored by the Treasury to collect Himalayan plants for Kew gardens.  He collected many new specimens but was also kidnapped, they treated him well, for a time during an excursion to Tibet in a Himalayan pass, adding to Darwin's concerns. 
still used Charles's wealth of detail, and systematic thought process to tighten up his arguments. 

Erasmus became terminally ill.  He died quietly on the 26th of August 1881.  Charles noted he had not been happy, but was always kindhearted, clearheaded and affectionate.  Charles adjusted his will. 

A visit by Dr. Ludwig Buchner, accompanied by Aveling, both of them still under the impression that Darwin was a supporter of atheism, was troubling to Charles, and Emma's religious beliefs.  The family friend and former Down vicar, Brodie Innes, was invited to attend the lunch to send an oblique signal to Buchner and Aveling.  Charles finally diffused the tension at the lunch with a joke: "B[rodie] I[nnes] & I have been fast friends for 30 years.  We never thoroughly agreed on any subject but once and then we looked hard at each other and thought one of us must be very ill."  Over cigarettes Charles asked "Why do you call yourselves atheists?" he preferred agnostic which was less aggressive.  He asserted Free-thought is 'all very well' for the educated, but are ordinary people 'ripe for it?' Aveling and Buchner were not aware of how Charles had kept Origin hidden until Wallace was an evolutionary theorist who wrote Introduction of Species while earning a living catching and shipping species for naturalists in places he visited.  Wallace was a poor lawyer's son, from the Welsh borders.  By fourteen he was apprenticed to a London builder.  He spent his evenings at the socialist 'Hall of Science.'  By the 1840s he was a trainee land-surveyor, paid to redraw property boundaries after the Enclosure Act allowed the wealthy to fence off and claim the commons from the people.  Alfred called it 'a legalized robbery of the poor.'  Having read Humboldt's Narrative and Darwin's Journal, he saved to pay his passage to the tropics to collect specimens and test the ideas in Vestiges.  Wallace travelled to the Amazon in 1848 and the Malay archipelago in 1854.  He shipped beetles, butterflies and bird skins to a London dealer to fund his trip.  He collected specimens from the Far East for Charles Darwin, who corresponded, where Darwin encouraged him to develop his theories.  He had despised Malthus, but reading the sixth edition was sympathetic to the need for birth control.  While in the Moluccan Spice Islands, travelling to New Guinea he caught Malaria, reapplied Malthusian ideas about people to animals and created his evolutionary theory, where he argued the environment eliminated the unfit and aligned with the noble savage where evolutionary forces pushed towards a just society.  He sent a brief summary to Darwin. 
triggered its publication

An Agnostic in the Abbey
Desmond & Moore explain how Charles's family prepared for his internment next to his brother Erasmus in Down churchyard.  But Darwin had built a powerful advocacy group for his science in the X club, and they knew a state burial in Westminster Abbey would seal Evolution's position at the center of science.  They aligned the press, the church, the parliamentary liberals so that the ceremony became a celebration of British excellence.  In death, Charles and evolution were accepted by the 'great and the good' and he would rest with Newton, Lyell, and Herschel


This page introduces the complex adaptive system (CAS) theory frame.  The theory provides an organizing framework that is used by 'life.'  It can be used to evaluate and rank models that claim to describe our perceived reality.  It catalogs the laws and strategies which underpin the operation of systems that are based on the interaction of emergent agents.  It highlights the constraints that shape CAS and so predicts their form.  A proposal that does not conform is wrong. 

John Holland's framework for representing complexity is outlined.  Links to other key aspects of CAS theory discussed at the site are presented. 
CAS
comparative analysis suggests various contributors to Darwin's creation of
This page reviews the implications of selection, variation and heredity in a complex adaptive system (CAS).  The mechanism and its emergence are discussed. 
evolution by natural selection
:
Darwin was in a position to be an innovator is the economic realization of invention and combinatorial exaptation.  It operates across all CAS, being supported by genetic and cultural means.  Creativity provides the mutation and recombination genetic operators for the cultural process.  While highly innovative, monopolies: AT&T, IBM; usually have limited economic reach, constraining productivity.  This explains the use of regulation, or even its threat, that can check their power and drive the creations across the economy. 
as well as being creative.  He was able to leverage his Grandfather Erasmus's status is a publically accepted, signal that one possesses assets: wealth, beauty, talent, expertise, access & trust of powerful people; to be able to help others. 
to gain access to the Edinburgh academics.  And he used these friends and Eras to enter the London scientific institutions.  And his inherited wealth is schematically useful information and its equivalent, schematically useful energy, to paraphrase Beinhocker.  It is useful because an agent has schematic strategies that can utilize the information or energy to extend or leverage control of the cognitive niche.    and government largess allowed him to drive Zoology into the market. Then by leveraging the X club he prepared the way for acceptance of Origin

Desmond & Moore's detailed study highlights the foundations supporting the emergence of Darwin's creations. 




























































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This page looks at schematic structures and their uses.  It discusses a number of examples:
  • Schematic ideas are recombined in creativity. 
  • Similarly designers take ideas and rules about materials and components and combine them. 
  • Schematic Recipes help to standardize operations. 
  • Modular components are combined into strategies for use in business plans and business models. 

As a working example it presents part of the contents and schematic details from the Adaptive Web Framework (AWF)'s operational plan. 

Finally it includes a section presenting our formal representation of schematic goals. 
Each goal has a series of associated complex adaptive system (CAS) strategy strings. 
These goals plus strings are detailed for various chess and business examples. 
Strategy
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This page uses an example to illustrate how:
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  • Business planning activities performed by the whole organization can build awareness, empowerment and coherence. 
  • A program approach can ensure strategic alignment. 
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