Microcosm by Carl Zimmer

Microcosm: E. coli and the New Science of Life by Carl Zimmer

Escherichia coli bacteria was discovered by the German-Austrian pediatrician Theodor Escherich. He found it in baby diapers.

Beneficial Bacteria
E. coli inhabit the human colon and most strains of E. coli are beneficial, not pathogens. In fact, most of the bacteria in your colon are non-pathogenic. When you take antibiotics to kill pathogenic bacteria, the antibiotics often also kill friendly bacteria, resulting in diarrhea.

E. coli bacteria in the intestines neutralize acid by producing an alkaline, foul-smelling substance called cadaverine.

E. coli makes proteins called siderophores that grab iron atoms in the environment and move it inside the E. coli bacterium, where it is held by an iron storage protein until it is needed by the cell.

Biofilm is an extracellular matrix, largely made up of polysaccharide mucus, that helps the E. coli bacteria to cooperate to promote their group survival. It protects the bacteria from antibiotics, predators, and dehydration.

Evolutionary Cooperation
The author discusses recent theories of evolution that assert that natural selection favors not just traits that help an individual organism survive, but also traits that help the survival of their close genetic relatives, from its immediate family to its species. An E. coli bacterium will often perform acts that harm itself, but help neighboring E. coli bacteria survive, by improving their shared environment.

The E. coli bacteria in the gut are called facultative anaerobes, which means that they can live in either the presence or the absence of oxygen. The E. coli bacteria scavenge oxygen in the gut to maintain the colon in an anaerobic state. This makes the colon hospitable for anaerobic microbes.

Regulation of Heat-Shock Proteins
E. coli produces proteins called heat-shock proteins that help the bacterium to handle proteins that have been partially denatured (unfolded) by heat. There are two kinds of such helpers: (a) ones that help repair (refold) the damaged proteins, and (b) ones that help destroy the proteins which cannot be repaired. The level of production of these heat-shock proteins is regulated in an interesting way. The messenger RNA for the sigma 32 regulatory protein assumes a functional shape for transcription on the ribosome only when bacterium is hot. After the sigma 32 protein is synthesized, it turns on the transcription of the genes for the heat-shock proteins. There is also a feedback loop where excessive amounts of heat-shock protein will shut down their production.

E. coli produce toxic proteins called colicins that kill neighboring bacteria of other species. The colicins have three mechanisms of action. Some colicins form pores in the membranes of the enemy bacteria, some prevent protein synthesis, and some attack DNA. E. coli also produce other proteins, called immunity proteins, that protect them from harm by their own colicins.

Type III Secretion System
This is a needle-like structure on the outside membrane of E. coli cells that allows them to inject toxins into the host cell.


E. coli have complex structures on their outer membranes called flagella that help them move. Flagella evolved from the more primitive structure described above, the Type III secretion system.

A virus that attacks (eats) bacteria is called a bacteriophage (or just phage, for short). If the DNA of the virus integrates into the host chromosome, that DNA segment is called a prophage. It can be passed down to the descendants of the bacterium, and sometimes can cause a viral infection in the descendent bacteria. Many prophages develop mutations that prevent them from ever escaping the host chromosome back into a virus capsid. They are called defective prophages.

This form of diarrhea was discovered by Kiyoshi Shiga. Only recently was it discovered that the shigella bacterium is actually a group of strains of E. coli that have developed the ability to move around inside eukaryotic cells. The Shigella bacterium spreads from host cell to cell by loosening the tri-cellular tight junction of intestinal epithelial cells. The Shiga toxin attacks the RNA part of the bacterial ribosomes, halting protein synthesis. Shiga toxin is encoded by a gene in a lambdoid prophage integrated into the bacterial chromosome. These shigella strains also differ from normal E. coli in that they do not have flagella and do not produce cadaverine.

E. coli Strain O157:H7
The pathogenic O157:H7 strain of E. coli occasionally found in undercooked, contaminated ground beef produces a shiga-like protein toxin that is coded for by a defective prophage gene.

Riboswitch Sensors
Recently, it has been discovered that the synthesis of vitamin B12 (cobalamin) by E. coli is regulated in a novel way. This regulatory mechanism involves the messenger RNAs that code for coenzyme B12 biosynthesis and transport proteins. When vitamin B12 binds to a nucleotide sequence of such a messenger RNA, the mRNA changes its shape. In this new conformation, the mRNA will no longer bind to the ribosome and so will not be translated into a biosynthesis or transport protein for vitamin B12. Ron Breaker of Yale University gave the name riboswitch to the nucleotide sequence of the mRNA that binds the vitamin molecule.

RNA World
Starting in 1968, a number of scientists have speculated that the earliest life on earth consisted not of DNA and proteins, but rather of RNA only. These RNA molecules acted as both holders of genetic information (like DNA) and as performers of chemical reactions (like proteins). In the 1980s there were discoveries supporting this theory. It was discovered that there are RNA molecules that act as enzymes, that is, they catalyze chemical reactions. They are called ribozymes. More recently, French virologist Patrick Forterre has proposed the theory that the switchover from RNA-based life to DNA-based life happened independently for each of the three domains: archaea, bacteria, and eukaryote. He has further proposed that the DNA of cells was first introduced by DNA viruses.

Genetically Modified Organisms (GMO)
The author is an advocate of genetic engineering, which started with E. coli, but which has now spread to higher forms of life. He goes into some detail on a particular plant GMO called “Golden Rice”. Golden Rice was developed by Ingo Potrykos of the Swiss Federal Institute of Technology and Peter Beyer of the University of Freiburg. This rice GMO makes vitamin A, which is needed for vision. Millions of poor children go blind every year, because do not eat enough vitamin A.


Dancing in the Glory of Monsters by Jason Stearns

Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa by Jason Stearns

Background from Wikipedia
The original people in Rwanda and the Congo were the ancient hunter-gatherers of Africa. They were the ancestors of both the Mbuti people of the Ituri rainforest, and the Twa of the African Great Lakes region. The Hutus arrived from West Africa, as part of the Bantu expansion. Lastly came the Tutsi, a Nilotic herding and warrior people, who became the rulers of the Hutu. Due to mixed marriages with the Bantus, the Twa have become somewhat taller than their Mbuti brethren. The Twa do not own land or cattle, but instead support themselves as game hunters, guards and potters. Thirty percent of the Twa were killed during the 1994 genocide.

The First and Second Congo wars, which took place in the Democratic Republic of the Congo during late 1990s and early 2000s, is the subject of this book. The Democratic Republic of the Congo has also been known as Zaire and the Belgian Congo. The Congo wars have killed five million people. Most of the deaths were civilians, not soldiers. Most of the civilians deaths were caused by displacement from farms, food requisitions by the army, malnutrition, poor sanitation and disease. There were also 200,000 rapes. The United Nations did not make a military intervention to stop either the Rwandan genocide or the Congo wars, but instead provided only humanitarian aid. The book begins with the Rwandan genocide, because that was the trigger for the Congo wars.

Hutus and Tutsi
A social stratification, with the Tutsi herders above and the Hutu farmers below, existed in Rwanda before the arrival of the Europeans. However, this stratification was fluid, and a Hutu could become a Tutsi by making enough money to buy cattle. When the European colonists arrived in the 19th century, they introduced identity cards, which were labeled with the person’s ethnicity: Tutsi, Hutu, or Twa. The Europeans favored the Tutsi with jobs in the colonial administration. Even after colonization, marriages between Hutus and Tutsis were still commonplace. The Kiga (the mountain people) of Uganda and Rwanda were classified as Hutus by the Europeans, but they saw themselves as Kiga not Hutu. There are also many ethnic Tutsi, called Banyamulenge, living in the Congo, near Lake Kivu.

Rwandan Genocide
Juvénal Habyarimana was president of Rwanda from 1973 to 1994. The French shipped weapons to the Hutus in the civil war between the Hutu Rwandan Armed Forces (FAR) and the Tutsi Rwandan Patriotic Front (RPF). The cease-fire in the civil war ended when Juvénal Habyarimana’s plane was shot down on April 6, 1994. The genocide was organized by the Hutu government in Kigali. Much of the genocide was performed by the Interahamwe and Impuzamugambi Hutu youth militias. There were about two hundred thousand killers. The Rwandan Patriotic Front, lead by Paul Kagame, invaded from Uganda and captured the Rwandan capital of Kigali in July, 1994. The Hutu soldiers then fled to the African Great Lakes region of the Democratic Republic of the Congo (DRC).

Hutu Refugees
One of the main problems in the refugee camps near Lake Kivu, was that the Hutu refugees from Rwanda included both the machete killers and innocent Hutus who fled for fear of being killed simply because they were Hutus. They were mixed together in refugee camps. The international aid brigades could not differentiate between soldiers and civilians, so they gave food and medical aid to all. Cholera was a major problem in the camps. The Rwandan Patriotic Front raided refugee camps, killing FAR militiamen, and forcing the repatriations of Rwandans. Half a million Rwandans eventually returned home. There was much more foreign aid given to refugee camps in the Congo, than to the orphans and widows in Rwanda.

Mobutu Sese Seko
Mobutu Sese Seko (Joseph Mobutu), ruler of the DRC since the 1960s, was supported by the West because he opposed the socialist countries Angola, the French Republic of the Congo, and Tanzania. There was lots of mineral wealth in the Congo: turquoise, copper, cobalt, zinc, tin, tungsten, and diamonds. But the mineral revenues went mostly to the rulers, and not to building, or even maintaining, the country’s infrastructure. Mobutu Sese Seko had supported the Hutu-dominated FAR in the Rwandan civil war. Mobutu also provided a haven in the DRC for Agathe Habyarimana, the widow of Juvénal.

First Congo War (1996-1997)
In 1996 a regional coalition formed to overthrow Mobutu: Angola, Uganda, Rwanda and Burundi. Yoweri Museveni, president of Uganda, and Paul Kagame, president of Rwanda, sought out Laurent Kabila in Dar es Salaam in Tanzania, to be the head of the new Congo government, replacing Mobutu. In October 1996 the Rwandan army invaded the Congo, starting at the African Great Lakes region. The overthrow of Mobutu Sese Seko happened in May 1997. Mobutu fled across the Congo river to the Republic of the Congo.

Regime of Laurent Kabila
Laurent Kabila was sworn in on May 29, 1997 in Kamanyola stadium. Congolese who had fled abroad during the reign of Mobutu Sese Seko returned to take up government appointments. Laurent Kabila ruled the Congo from May 1997 to August 1998. During this time, Kabila did nothing to help the people, but only consolidated his power. On the plus side, he was not as bad as Mobutu.

Second Congo War (1998-2003)
The Congolese Rally for Democracy (RCD) was formed in 1998 to remove Laurent Kabila from power in the Congo. It was made up of leaders from Rwanda, Uganda and Burundi. Once they crossed the border into the Congo, the RCD soldiers received insufficient supplies from Rwanda, so they had to pillage the countryside, making enemies of the villagers. Many Bantu Congolese saw the Banyamulenge Tutsi as foreigners, who were not loyal to the Democratic Republic of the Congo. Local (Mai-Mai) militias fought the RCD, because they saw that army as a proxy for Rwanda. Laurent Kabila armed these Mai-Mai militias, and said that any Tutsi with a weapon, whether soldier or civilian, should be shot. Zimbabwe, Angola, Namibia and Chad supported the Kabila regime. In particular, Robert Mugabe, dictator of Zimbabwe, supported Kabila, because Kabila owed him money and so should stay in power long enough to pay Mugabe back. Also, Mugabe made money by selling arms to Kabila.

Movement for the Liberation of the Congo (MLC)
Part of the second Congo war was a rebellion in the northern Congo by the Movement for the Liberation of the Congo (MLC), lead by Jean-Pierre Bemba. Bemba was a businessman, involved with coffee, air transport and mobile phones. The MLC was more homegrown than the RCD, but it did receive some backing from Uganda. The MLC gained control of the northwestern province of Equateur, then moved eastward to the northeastern province of Orientale. In the Ituri region of the Orientale province, the MLC got bogged down in the local ethnic conflict between the Hema herders and the Lendu farmers, so it retreated back to Equateur.

End of Second Congo War
Kabila was assassinated in January 16, 2001. Laurent’s son Joseph Kabila took over the reigns later that month. An agreement signed in April 2002 at the Inter-Congolese Dialog in Sun City, South Africa, made Joseph Kabila president and Jean-Pierre Bemba premier. A second agreement was reached at the Inter-Congolese Dialog in December 2002. The transitional government specified by this treaty started governing in July 2003.

In Sheep’s Clothing by George K. Simon, Jr.

In Sheep’s Clothing: Understanding and Dealing with Manipulative People by George K. Simon, Jr. 

About the Author

The author, George K. Simon, Jr., has a Ph.D. in clinical psychology from Texas Tech University.

The Covert-Aggressive Personality

The book is mainly about a character disorder called covert-aggressive personality. These are people who are self-aggrandizing, but hide their aggression under a façade of charm and good manners. The author calls these people manipulators.

Tactics of the Covert-Aggressive Personality

  • Evasion: vague answers to direct questions
  • Changing the subject
  • Veiled threats
  • Making the victim feel guilty or ashamed

Protecting Yourself

Those who believe that all human beings are basically the same inside are vulnerable to manipulators. You need to be able to assess the character of others. Be aware of your vulnerabilities. Recognize the tactics employed by manipulators.

Manipulators vs. Neurotics

Manipulators don’t care if they do something wrong. Neurotics are their opposite; neurotics worry excessively about the possibility of making a mistake. Many neurotics, those with a perfectionist bent, carry an extra burden in our society, making up for the manipulators by contributing more than their fair share.

Distinction from Passive-Aggressive

The covert-aggressive personality is distinct from the passive-aggressive personality:

  • Covert-Aggressive: Veiled Offense
  • Passive-Aggressive: Veiled Defense

The covert-aggressive personality tries to control others, without being openly hostile. The passive-aggressive personality resists being controlled, without being openly defiant. For example, instead of refusing to obey his boss’s request to come in to work on the weekend, he agrees to come into work on the weekend, but at the last minute he calls and makes the excuse that his child is sick.


Manipulators often cloak their self-serving behavior and ambition by pretending to be devoted to a noble cause. They don’t genuinely care about those who suffer. Many of those in religious and charitable endeavors have a hidden agenda to advance their careers by appearing to be humanitarians.

The Second Brain: A Groundbreaking New Understanding of Nervous Disorders of the Stomach and Intestine by Michael D. Gershon

The Author
The author is not a gastroenterologist, but a neurobiologist, whose interest in the serotonin neurotransmitter took him down into the bowels of medicine. This book is a history of the development of the understanding of the intestinal nervous system, a history in which the author played a major role.

How Science is Actually Done
The author describes numerous experiments he and other conducted to figure out the intestinal nervous system. There is a great deal of information and the writing gets rather technical at times. This would be a good book for a college undergraduate science major to read.

Autonomic Nervous System
The autonomic nervous system is motor not sensory and controls smooth muscles and glands, not skeletal muscles. It has three parts:
• Sympathetic Nervous System
• Parasympathetic Nervous System
• Enteric Nervous System

Sympathetic Nervous System
• The nerve cell bodies are located near the spine
• Its nerves exit the spinal chord near the thoracic and lumbar vertebra
• Controls eye pupil dilation
• Controls male ejaculation
• Its axons release norepinephrine at their synapses

Parasympathetic Nervous System
• Its nerve cell bodies are located near the innervated organ
• Nerves exit the spinal chord near the cranial and sacral vertebra
• The vagus nerve is part of it
• Its axons release acetylcholine at their synapses

Enteric Nervous System
The intestines contain large numbers of interneurons, that is, neurons that connect via synapses only to other neurons, and not to sensory, muscle or gland cells. One of the main neurotransmitters used by these enteric interneurons is serotonin. Serotonin stimulates the peristalsis of the smooth muscles of intestines.

The colon is also known as the large intestine. It probably evolved to help land animals conserve water. The body moves water from inside the lumen of the colon into the bloodstream by removing salt from the lumen of the colon, which causes the water to follow by osmosis. There are lots of benign, symbiotic bacteria in the colon, but there are few bacteria in the small intestines. The purpose of diarrhea is to cleanse colon of pathogenic bacterial.

Development of the Enteric Nervous System
During embryonic development, the neural crest is formed from cells that migrate from the nearby neural tube. These neural crest cells later migrate to the intestines, where they become the enteric nervous system.

Defects of Intestinal Innervation
• Chagas disease (American trypanosomiasis), a tropical parasitic infection common in Latin America, kills enteric ganglia of Auerbach’s myenteric plexus
• Hirschsprung’s Disease (congenital megacolon): babies lack enteric ganglia in the colon, due to a failure in the embryonic development of the enteric nervous system
• Neuronal Intestinal Dysplasia (NID): a congenital disease causing a lack of sympathetic or parasympathetic innervation of the intestines
• From Wikipedia I found that all newborns are kept in the hospital until they have their first bowel movement, in order to identify babies that have intestinal problems, and that in the United Kingdom there is a charity for NID called the Adele Chapman Foundation

Gastric Intrinsic Factor
Gastric glands in the stomach secrete a glycoprotein called gastric intrinsic factor that helps the small intestine absorb vitamin B12.

Liver and Gall Bladder
The liver secretes bile into the duodenum to emulsify fat, which is then digested by the lipase enzyme secreted into the duodenum by the pancreas. Excess bile is stored in the gall bladder. Gall bladder ganglia are part of the enteric nervous system.

Pancreas and the Vagus Nerve
The vagus nerve of the parasympathetic system stimulates the pancreas to increase secretions when eating a meal.

Pancreas and Bicarbonate
• Brunner’s glands of the pancreas produce a bicarbonate alkaline fluid to neutralize the stomach acid in the food that enters the duodenum from the stomach.
• Hormonal regulation: The secretin hormone produced by the duodenal endocrine cells tells the pancreas now much bicarbonate to produce.
• Nerve regulation: The pancreas receives serotonin-releasing neurons from the duodenum which inhibit the release of the bicarbonate.

Pancreas and Digestive Enzymes
• Cholecystokinin is released by endocrine cells in the stomach and travels through the bloodstream to the pancreas, where it stimulates the release of digestive enzymes.
• Gastrin is released by endocrine cells in the duodenum and travels through the bloodstream to the pancreas, where it also stimulates the release of digestive enzymes.

Enterochromaffin Cells
Enterochromaffin cells are found in intestinal lining and were named for the fact that they stain well with chromium dyes, because they have an affinity for chromium. Enterochromaffin cells contain 95% of the body’s serotonin. As was first proposed by the late Edith Bülbring of Oxford University, Fellow of the Royal Society, and pioneer in the study of the physiology of smooth muscle, enterochromaffin cells are sensory receptors that respond to pressure in the intestines by releasing serotonin into the connective tissue of the intestines. The serotonin in the connective tissue then stimulates:
• Secretomotor neurons that in turn stimulate the crypt cells to secrete salt into the lumen, and water then follows the salt into the lumen, due to osmotic pressure
• Enteric nervous system interneurons causing peristalsis
• Neurons that connect to the CNS and cause nausea and vomiting

Serotonin Transporter Protein
Serotonin transporter protein is in the outer membrane of neighbors of the enterochromaffin cells. It removes the serotonin after it has spent enough time stimulating the serotonin receptors.

Interstitial Cells of Cajal
• They are named after are named after the Spaniard Santiago Ramón y Cajal
• They are pacemakers in the enteric nervous system
• They amplify nerve signals
• They originate not in the neural crest, but from mesenchymal precursor cells, from which smooth muscle cells also develop
• Because they are not neurons, the body can produce more of them in adulthood, if some of them become damaged

The Faculty Lounges: and Other Reasons Why You Won’t Get the College Education You Paid For by Naomi Schaefer Riley

History of Academic Freedom
Academic freedom is a solution in search of a problem. There have been few examples of professors who got into trouble for holding unpopular views. Riley mentions two of them. 1894, Wisconsin State Superintendent of Education charged Richard T. Ely of the University of Wisconsin at Madison with teaching and supporting alien and revolutionary doctrines, because he wrote an article in The Nation in favor of organized labor. Ely was acquitted. In 1900, Jane Stanford, the widow of the university’s founder, forced Edward A. Ross of Stanford University to resign, because he supported of socialism.

The Progressive Movement and John Dewey
In 1915, John Dewey and Arthur O. Lovejoy founded the American Association of University Professors. Dewey saw attempts by those outside academia to control the work of professional scholars as being a corruption of the independence of scholars.

Concept of Academic Freedom
Many people have had difficulty coming up with a clear definition of “academic freedom” and stating its limits. Is Holocaust denial an acceptable form of academic freedom? How much does academic freedom prevent administrators from holding faculty accountable for their behavior? Can university benefactors place restrictions on faculty scholarship?

Public Officials and Freedom of Speech
Riley discusses the 2006 U.S. Supreme Court case Garcetti v. Ceballos, which stated that the First Amendment does not allow public officials to keep their jobs, regardless what they say in the performance of their job. It is not clear whether the same principle applies to college professors.

Journalistic Freedom
Journalists are protected from government by the First Amendment. But, unlike college professors, journalists are not protected from being fired by their employer if they publish an article that the owner does not like.

Tenure at the Modern Research University
Stanford University was founded on the German model of a research university, where research was more important than teaching. In most American universities, teaching is regarded as a secondary responsibility of college professors. When research is the main criterion for judging faculty, only professors at other universities who are in the same field can evaluate the performance of professors. Administrators have only limited influence in the granting of tenure.

Adjunct Faculty
Much of the teaching at colleges and universities is performed by graduate students, adjunct faculty, temporary and part-time instructors. Their salaries and benefits are lower than those of full-time, tenure-track faculty. They are often required to share offices. Ph.D.s in the natural sciences can find jobs in private sector, but there is an oversupply of Ph.D. in the humanities, because too many students are admitted to their Ph.D. program. There are also lots of people with masters degrees who can teach, so colleges don’t need to hire humanities doctorates.

Religious Institutions
While it is difficult for administrators to fire tenured faculty at public colleges and universities, at private religious institutions, faculty who violate the religious rules can be fired.

Age Discrimination
In recent years in the United States, the tenure issue has been complicated by the fact that mandatory retirement for tenured faculty has been outlawed by federal age discrimination legislation.

Tenure in the United Kingdom
Maggie Thatcher’s Education Reform Act 1988 abolished tenure for academics appointed on or after November 20, 1987.

Foundation for Individual Rights in Education
The Foundation for Individual Rights in Education (FIRE) defends the academic freedom of college professors, including those who are conservative or libertarian.

Center for College Affordability and Productivity
Richard Vedder of the Center for College Affordability and Productivity lead a survey of school ranking based on outputs rather than inputs. Outputs used included the starting salaries of the graduates, the number of awards that the graduates received, and the amount of debt that the graduates were saddled with. The results were published in Forbes magazine. West Point was ranked #1.

American Council of Trustees and Alumni
This organization rates universities on the breadth of the content of their required courses. A poor rating will be given to schools that allow students to satisfy their breadth requirements with courses that are not rigorous or which are too specialized. Anne Neal is the president of ACTA.

The Author’s Recommendations
The author, Naomi Riley, asserts that you have the right to free speech, but not the right to a job, regardless of what you say. She recommends tenure for researchers only, not for teachers. She comments favorably on “professors of practice”, who receive get multi-year teaching contracts, instead of tenure. Riley says that there is no need for tenure to preserve academic freedom in these 3 situations:
• vocational disciplines: teachers are not doing research
• pre-stipulated political goals (similar to religious strictures)
• schools owned by corporations (e.g., the University of Phoenix)

Bottled Lightning: Superbatteries, Electric Cars, and the New Lithium Economy by Seth Fletcher

Each cell in a battery has a negative electrode (anode) and a positive electrode (cathode) separated by a liquid or solid called the electrolyte. A group of one or more cells connected together is called a battery. Originally, batteries were not rechargeable, but some more recent batteries are rechargeable: the nickel cadmium and nickel-metal-hydride batteries. Two problems with these batteries are: (a) they lose energy capacity when not fully run down prior to charging, and (b) they lose charge when not in use. During the 1990s a new kind of rechargeable battery was developed that did not suffer from these problems. It is called the lithium ion battery, and is the main subject of this book.

Exxon Research and Engineering
While at Exxon Research and Engineering, Michael Stanley Whittingham developed the first rechargeable lithium battery. It had a titanium disulfide cathode and a lithium-aluminum anode. Bob Hamlen figured out how to manufacture it at Exxon’s facility in Branchburg, New Jersey. The battery was first used in digital watches in the 1970s.

Moli Energy
This rechargeable battery was developed by Moli Energy, a Canadian (British Columbia) company named after the elements molybdenum and lithium. They replaced the titanium in Exxon’s battery by molybdenum. Molybdenum disulfide is cheaper and easier to work with than titanium disulfide. Starting in 1988, the batteries were used in NTT mobile phones. One battery in a hundred thousand caught fire. The problem was not caught in testing, because the testers did not think of testing under the five-day discharge, ten-hour-recharge cycle that the phone was subjected to in actual use.

In 1979 John Bannister Goodenough of Oxford University developed a lithium ion battery with a lithium-cobalt-oxide cathode and a lithium anode. Goodenough collaborated with scientists and engineers at the Atomic Energy Research Establishment in Harwell, England. Harwell’s scientists had given him verbal assurances that he would receive a share of the royalties, but when he showed up to sign the paperwork, Harwell’s lawyers were not willing to give him or Oxford University any share of the royalties. But Goodenough signed anyway, because no one else was interested in commercializing his technology.

Compact Power: Lithium Manganese Oxide
Compact Power of Troy, Michigan developed a battery based on the lithium-manganese-oxide research of Michael Thackeray & John Goodenough at Oxford University. Cobalt is toxic, and more expensive than manganese. The batteries have high power and high energy density. CPI is owned by LG Chemical of South Korea. The batteries are used in the Chevy Volt plug-in hybrid car. GM tested battery aging using a pack cycler to artificially accelerate the aging process. GM’s earlier electric car, the EV1, used lead-acid batteries, which were very heavy.

Sony’s Carbon Anode
In the 1990s Sony developed a rechargeable lithium ion battery with a carbon anode, instead of Goodenough’s metallic lithium anode. They called it a lithium ion battery, to distinguish it from a lithium battery, which had the reputation for catching fire. Further development of lithium ion batteries usually keeps Sony’s carbon anode, and instead plays with the chemical composition of the cathode.

Lithium Iron Phosphate
A new type of lithium ion battery was developed in the 1990s, the lithium iron phosphate battery. In this battery, the cathode is made of lithium iron phosphate (also called lithium ferrous phosphate). In 1993, John Goodenough, now at the University of Texas at Austin, and his student Akshaya Padhi, started the development of the lithium iron phosphate battery. They ran into some problems with electrical conductivity. They licensed their technology to Michel Armand of Hydro-Québec, who introduced a carbon coating to improve the electrical conductivity and was able to produced a working lithium iron phosphate battery. Lithium iron phosphate batteries have higher energy density, longer lifetimes and are more safe than lithium cobalt oxide.

Lithium Wars
A123 Systems developed and marketed a similar lithium iron phosphate battery, which they claimed increased electrical conductivity not by using a carbon coating, but by doping the cathode with niobium and zirconium. A patent war started. This is a complicated story. The chemistry itself, on the cause of the electrical conductivity enhancement, is still not clear, so there is no point in describing the legal battles.

Tesla Roadster
Tesla designed their car so that the cells of the battery were separated from one another. So if one cell catches fire, it will not ignite any neighboring cells.

The Last Mughal: The Fall of a Dynasty: Delhi, 1857 by William Dalrymple

Mughal Empire in India

The Mughal empire was founded by Zahir ud-din Muhammad Babur by in 1526. Their culture was more Persian than Mongol. They built the Taj Mahal. In 18th century the Mughal Emperor hired the British East India Company as its tax collector. The British gradually conquered many princely states of India. By the time of the Sepoy Mutiny in 1857, the the Mughal throne ruled only a small part of India, and had no army of its own. The capital of the Mughal Empire was Delhi, a large city on the Yamuna River, which is the largest tributary river of the Ganges.

The Last Mughal

Bahadur Shah II Zafar was the last Mughal ruler of India. He was a Sufi Muslim, whose mother was Hindu. Zafar enjoyed reading poetry by Ghalib and Zauq, and wrote poetry himself. He was 82 years old at the time of the Uprising.


Azimullah Khan Yusufzai: chief advisor to the Nana Sahib

Baniya: merchant or moneylender

Bareilly: a city in Uttar Pradesh east of Delhi

Firangi: Urdu for foreigner

First War of Indian Independence: What many Indians call the Sepoy Mutiny

Ghazal: Sufi Persian love sonnet

Ghazi: Muslim warriors

Gujars: mountain herdsmen of cattle, sheep and goats from northern India

Jama Masjid: India’s largest mosque

Jat: peasant farmers, who suffered from over-taxation by the British

Kanpur: An industrial city in Uttar Pradesh, known for its leather

Maratha Confederacy: Rulers of Delhi, before defeated by the British in 1803

Marwari: moneylenders from Rajasthan

Mewati: people from the Mewat district of Rajasthan

Nana Sahib: a leader of the rebellion, who wished to restore the Maratha Confederacy

Nimach: A city in Madhya Pradesh

Princely States: semi-autonomous nominally sovereign states

Red Fort: the residence of the Mughal Emperors, inside the walled city of Delhi

Sepoys: Persian for soldier, they were in the service of the British East India Company and were overwhelmingly Hindu

Tilanga: soldiers from Telangana in Hyderabad, who spoke Telugu



Emperor Bahadur Shah II Zafar: the Last Mughal,

Zinat Mahal: the Queen of Delhi and senior wife of Zafar


Ghalib (Mirza Asadullah Baig Khan): Urdu and Persian poet, who wrote many ghazals

Sheikh Muhammad Ibrahim Zauq: poet laureate of the Mughal Court in Delhi

Rebel Military:

Bakht Khan: commander of the sepoy and ghazi forces in Delhi

Mirza Mughal: Mirza Sultan Muhammad Zahir ud-din, fifth son of Zafar, nominal commander of the sepoy forces

British Military:

General John Nicholson: Brigadier-General who lead the storming of Delhi

Captain William Hodson: British leader of irregular light cavalry

Going Native versus Christian Evangelism

Many early Britishers in India went native, became fluent in Urdu and Persian, and married Indian women. Delhi was half Hindu and the time of the rebellion, and the Muslims and Hindus got along fine. Things changed during the years just preceding the Sepoy Mutiny, when many evangelical Protestant missionaries tried to convert the Indians to Christianity.


The British were out of touch with the feelings of the sepoys. They demanded that the Hindus sepoys serve abroad, which would violate their religious prohibition against crossing the black water. To load the new Lee-Enfield rifle, a soldier had to first bite off the end of the cartridge. The cartridges were, in fact, greased with beeswax and linseed oil, but a rumor spread that the cartridges were greased with beef and pork. The Hindus and Muslim sepoys saw this as a British attack on their religions.

Sepoy Mutiny in Meerut Cantonment

The rebellion started among the sepoys of the Bengal Army, who were mostly upper-caste Hindus from Uttar Pradesh and Bihar. The sepoys of the 3rd Light Cavalry at the Meerut Cantonment of the Bengal Army mutinied on 11 May 1857.

Kanpur Massacre

The massacre at Kanpur became a rallying cry by the British when committing atrocities against Indian women and children. But it is unclear exactly what happened. From reading Dalrymple’s book and consulting Wikipedia, this appears to be the sequence of events:

  1. General Wheeler’s army surrendered to Nana Sahib at Kanpur.
  2. Nana Sahib then held about 200 British women and children hostage in the Bibighar house when bargaining with Colonel James Neill,
  3. Nana Sahib ordered a female official (Begum) named Hussaini Khanum, to supervise the hostages,
  4. When approaching Kanpur to rescue the British hostages, Colonel James Neill burned Indian villages, killing many women and children,
  5. The rebels at Kanpur may have heard of Colonel Neill’s atrocities,
  6. An unknown person ordered that the hostages be killed, but the sepoy soldiers refused to kill the hostages,
  7. Begum Hussaini Khanum ordered Azimullah Khan, chief advisor to the Nana Sahib, to kill the women and children,
  8. Azimullah Khan then hired butchers to murder the British women and children with meat cleavers,
  9. Their bodies were then thrown down a dry well by sweepers.

Sepoy Rebels Arrive to See the Mughal

The sepoys from Meerut travelled to Delhi to see the Mughal. They were joined by Indian convicts released from prison, sepoy regiments from Nimach, Muslims from Rajasthan, sepoys from Tilanga, Jat peasant farmers lead by Shah Mal Jat, and sepoys from Nimach, under the command of General Sudhari Singh. The Mughal Zafar became the prisoner of the rebels and had no choice but to join the mutineers. Zafar had no treasury to pay the rebel troops. All he could give them was his blessing. The British fled Delhi. Delhi residents who remained became afraid of the sepoys. There was widespread looting by the lower classes, untouchables, and sweepers. The targets of the looting and killing were the British, Christians, Marwaris, Jain moneylenders, jewelers, cloth merchants, confectioners. Gujar bandits and Mewati tribesmen surrounded the walled city and robbed those who were leaving or entering. Bakht Khan arrived from Bareilly with sepoy troops and four thousand Muslim ghazi civilians. The arrival of the ghazis created a conflict over Muslims slaughtering cows. Zafar objected to jihad against the Hindus; he said that they were fighting the British, only.

British Siege of Delhi

There was a 3-month siege of Delhi. The British bombarded Delhi with artillery from a ridge overlooking the walled city. The British received a great deal of intelligence from their many spies, from the Hindu loyalists supported the British. William Hodson was Chief of Intelligence and Rajab Ali was his principal assistant. But the rebels received very little intelligence about the British forces. There were many more rebel troops than British troops, and the rebels could have defeated the British on the ridge, who were greatly outnumbered before British reinforcements arrived. The sepoys were not trained in strategy and Mirza Mughal, while nominally their leader, had no military experience.  Mirza Mughal pressured the baniyas (moneylenders and merchants) to contribute money to the cause, but they refused. The Queen, Zinat Mahal, tried to negotiate an agreement with WIlliam Hodson that would preserve the Mughal dynasty, but they were unable to come to terms.

British Received Reinforcements from the North

British troops near Delhi were short of transportation (e.g., camels, bullocks), so it took them awhile to assemble a force capable of retaking Delhi. They received support from the north:

  • Sikh mercenaries,
  • Punjabi Muslims,
  • Gurkhas from Nepal,
  • Pathans (Afghan) mercenaries,
  • John Nicholson and his Moveable Column

British Retake Delhi

John Nicholson and his Moveable Column, which arrived at Delhi Ridge on Friday 14 August, 1857. The British assaulted on the walled city: at four of its gates. They used explosives to break down the gates. They used swords and guns to kill all men of fighting age. Being an Indian loyal to the British did not protect you. One of the main battles was with jihadi warriors from the Jama Masjid mosque, which was taken by Sikh mercenaries fighting for the British. Many Delhi residents fled the city when it became clear that the British would win. The Red Fort and Palace were taken last. The British destroyed Mughal libraries. British Prize Agents looked for hidden wealth. There were mass rapes of Indian women by British soldiers.


Members of the royal family were hunted down and executed. William Hodson captured and executed Mirza Mughal and two other princes. Hodson accepted the surrender of Bahadur Shah II, promising to spare his life. It was actually the British who had rebelled against the Mughals to whom they had sworn allegiance as tax collectors. Therefore, it would be illegal to try the Mughal Emperor Zafar for rebellion. Zafar, his wife Zinat Mahal, two sons and others were sent by the British to house arrest in Rangoon. Zafar died in 1862 in Rangoon. The army of the East India Company became part of the British Army. The East India Company was eventually dissolved.The British blamed the Muslims, not the Hindus, for the uprising. even though the sepoy soldiers were almost all Hindu, with only a small minority of Muslims, and even though the Mughal Emperor Zafar was a victim of the uprising, not its instigator. After the Uprising, Indian Muslims fell into disrespect.