Your Inner Fish by Neil Shubin

Author and Title
Shubin, Neil. Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body

Sir Richard Owen
Sir Richard Owen noticed similarities between the limb bones of various species, before Darwin. The general pattern was one bone in the upper arm, two bones in the lower arm, several small bones in the wrist, then the bones of each of the fingers.

The Fins of Fish
The fish fin does not follow this pattern. Instead of one bone attaching to the shoulder, it has four or more parallel bones attaching to the shoulder. The fin of the lungfish also has several bones, but arranged serially, going away from the shoulder, rather than in parallel. Only one of these bones attaches to the shoulder. The fin of the fossil fish Eusthenopteron has one bone attaching at the shoulder, followed by two bones further out, followed by several more bones even further out.

The Wrist and Hand
Shubin, with his student Ted Daeschler and mentor Farish A. Jenkins, Jr., discovered the first fish with a wrist, the Tiktaalik, in the Canadian Arctic. Next in the course of evolution, after the Tiktaalik, came the amphibian Acanthostega fossil. It has one bone at the shoulder, followed by two bones after the elbow, followed by several digits in parallel.

Genetics of Asymmetry
The author also talks about the genetics of limb development in the embryo. The concentration gradient of the Sonic hedgehog (sic) protein influences the zone of polarizing activity (ZPA). The ZPA is what causes the hand to be asymmetrical, with the pinky and one side and the thumb at the other. The gene for Sonic hedgehog was discovered in 1980 by German scientist Christiane Nüsslein-Volhard and American scientist Eric Wieschaus. The relationship between the Sonic hedgehog protein and the ZPA was discovered by Robert D. Riddle, Cliff Tabin and colleagues at Harvard in the early 1990s.

The fact that invertebrate eyes, such as those of insects, and vertebrate eyes are so different has always posed a problem for theorists of evolution. Invertebrate eyes increase surface area by having many folds in their light-gathering tissue, while vertebrate eyes have bristle-like projections. Detlev Arendt discovered a marine annelid worm called the polychaete that has two kinds of eyes, an invertebrate eye and a vertebrate proto-eye. It has also been discovered that the gene, Pax 6, that controls the differentiation of tissue into eyes is very similar in invertebrates and vertebrates.

Fish have no middle-ear bones. Reptiles and amphibians have one middle-ear bone. Mammals have three ear bones (and a pinna). All of the middle-ear bones evolved from the curved gill arch bones of fish. The stapes (stirrup) evolved from the hyomandibula of the reptile, which connects the jaw to the skull. The hymandibula, in turn, evolved from the second gill arch bone of fish. The malleus (hammer) and incus (anvil) evolved from bones in the back of the reptilian jaw, which in turn evolved from the first gill arch bone.

Three percent of the mammalian genome is devoted to genes that code for receptor proteins that bind odor molecules. In primates with color vision, many of these genes have become non-functional. We have traded smell for vision.

The Hard Parts
For their hard parts, mollusk and crustacean invertebrates, use chitin and calcium carbonate. In vertebrates, hydroxyapatite is the mineral that gives bones and tooth enamel their hardness. Hydroxyapatite first appeared in teeth, not bones, which were then made of cartilage. The upper and lower teeth of mammals fit well together (occlusion), but this is not true of reptiles.

The Snow Lion and the Dragon: China, Tibet, and the Dalai Lama by Melvyn C. Goldstein

Tibet is a sparsely populated region on a high plateau north of the Himalayas. In fact, for thousands of years, many Tibetans have lived in areas that are now provinces of China: Sichuan, Qinghai, Gansu and Yunnan provinces. The Chinese province of Tibet is the largest part of ethnographic Tibet. For the vast majority of its history, Tibet has been an independent country, separate from China. However, because of its peaceful Buddhist nature, Tibet has never had a strong military, and so has not been able to defend itself. At various times in its long history, it has turned to the Mongols, the Manchus and the British to protect it.

The people of Tibet speak a language that is not a dialect of Chinese (the language of the majority Han ethnicity of China). The Tibetan language is similar to Burmese, the Dzongkha language of Bhutan, and various minority languages of Yunnan province. Tibetan has a written script imported from northern India.

Before Buddhism spread to Tibet, they had a shamanistic Bon religion. All Tibet Buddhist sects are part of the Mahayana school of Buddhism. The current “Yellow Hat” Geluk Buddhist sect was introduced into Tibet in around 1400 by an Amdo monk named Tsongkapa. The Yellow Hat form of Buddhism came to dominate Tibet in the years before Tibet came under Manchu rule. The Dalai Lama is the main leader of the Yellow Hat Buddhists, while the Panchen Lama is a secondary leader.

Mongol Empire:
Tibet was conquered by Genghis Khan, paid him tribute, and became part of the Mongol empire. The Chinese interpreted this as Tibet becoming part of China, but the Tibetans saw themselves as parallel to the Chinese, both parts of the Mongol empire. During Mongol rule, the main Buddhist sects were the Red Hat sects, Sakya and Kargyu. When Tibet was allied with the Mongols, Tibet provided the Mongols with religion, and the Mongols provided the Tibetans with military protection.

Ming Dynasty:
During the ethnic Chinese Ming dynasty, Tibet’s relationship with China was one of suzerainty: the Ming dynasty controlled Tibet’s foreign affairs, while Tibet had control of its own internal affairs.

Manchu Dynasty:
The Qing (Manchu) Dynasty ruled China from 1720 to 1911. During the Manchu (Ching) Dynasty, Tibet was under the protection of the Manchus. During the late nineteenth century the British, who were in India, established trade relations with Tibet.

Republic of China (1911):
When Sun Yatsen took power in 1911, he saw Tibet as part of China and wanted to expel the British from Tibet. Britain was not willing to fight for Tibet. Britain did make Bhutan and Sikkim into Indian protectorates. The British made a part of Tibet near Bhutan into the Indian state of Arunachal Pradesh. Mongolia was able to become an independent country after World War II due to the support of Joseph Stalin.

People’s Republic of China (1949):
In 1950 the Chinese People’s Liberation Army invaded Tibet and conquered the Tibetan army at Chamdo. Little blood was shed before Tibet surrendered. Tibet turned to the United Nations for help in preserving its autonomy from China, but the United Nations refused to support Tibet, due to the opposition of Britain and India. Between 1951 and 1959 China left Tibet alone to run its own affairs. In 1959 the C.I.A. supported a rebellion for independence in Tibet, but it failed. The C.I.A. continued to support the Tibetan rebels in their base in Nepal. The Chinese communists claimed that they were trying to liberate Tibet from feudalism and serfdom. They outlawed Buddhism and collectivized agriculture. The Tibetan were allowed to keep their language, however.
During the late 1960s the United States abandoned its support for Tibet, because it wanted to improve relations with the PRC.

Until the twentieth century, no Chinese people lived in Tibet. Many Han Chinese and Hui Muslims have moved to Tibet since 1984 to work in modernizing the Tibet and building infrastructure. There are now many Han Chinese living in Tibet, but they are regarded as being only temporary workers. The Chinese have become more tolerant of Buddhism since Mao passed away. Their religion is no longer outlawed, as it was during the Mao years. The PRC one-child rule is less strictly enforced in Tibet.

Independence Movement:
The Dalai Lama and the exiled Tibetan government live in the Indian state of Himachal Pradesh. In 1989 the Dalai Lama received the Nobel Peace Prize. The rulers of China do not want Tibet, the Uyghur Turkic Muslim people, Taiwan or Hong Kong to be independent. Many Tibetans would settle for what Hong Kong currently has: one country two systems. But the Chinese rulers don’t want them to have that. The United States Congress has made efforts during the past 25 years to give greater recognition to Tibet. The author believes that it is unrealistic to believe that the PRC will ever allow Tibet to become a separate country.

Viruses vs. Superbugs: A Solution to the Antibiotics Crisis? by Thomas Häusler

Antibiotic Resistant Bacteria:
We are in trouble because many common pathogenic bacteria have become resistant to antibiotics. Because of bacterial resistance to antibiotics, many patients end up with chronic infections and limbs that need to be amputated. Boils and carbuncles are caused by staphylococcal bacteria on the skin. Pseudomonas aeruginosa often infects burn wounds. Clostridium difficile causes intestinal infections in hospitals. One bacteria studied was Clostridium, which causes gas gangrene. People lost interest in the phage treatment for typhoid fever when the antibiotic chloramphenicol became available in 1947. In India, many typhoid fever infections have become resistant to chloramphenicol. Antibiotics often fail for bone infections, due to poor circulation. Antibiotics kill beneficial bacteria, also.

Viruses That Eat Bacteria:
A novel solution to this problem is to use bacteriophages. Bacteriophages kill bacteria. Phages kill only bacteria, not plant or animal cells. They are specific. Each strain of phage kills only a particular strain of bacteria. They are more specific than antibiotics. Bacteria mutate or receive plasmids that make them resistant to a particular phage, but that phage can evolve so that it can continue killing that strain of bacteria. Hospital sewage is a good place to look for bacteriophages that attack hospital bacteria. Untreated city sewage are also a good place to look for phages. During World War II, Canadian and American scientists studied using phages to treat typhoid fever, with is caused by Salmonella typhi. Using bacteriophages to treat infection was considered during the early years of molecular biology, but abandoned by most researchers when antibiotics came along, so phages no longer seemed necessary.

Pasteur Institute:
Much of the early science was done by French scientist Félix d’Herelle worked at the Pasteur Institute during World War I
d’Herelle investigated the use of bacteriophage against:
• the Shigella bacteria that cause dysentery (a major problem in the trenches)
• the Salmonella bacteria that infect chickens
• the Vibrio cholerae bacteria that causes cholera (major study in India)

Eliava Institute in Tbilisi Georgia:
Georgiy Georgievitch Eliava studied with d”herelle at the Pasteur Institute in Paris. Later, Eliava brought Félix d’Herelle to Tbilisi. The Institute for Microbiology in Tbilisi was founded in 1923 with Eliava as scientific director. It appears that Eliava may have come to the attention Lavrenti Beria. Eliava disappeared in 1937. Eliava’s stepdaughter Hanna was deported to a camp in Kazakhstan. After the breakup of the Soviet Union, the phage research institute in Georgia has fallen on hard times.

Scientific Rigor:
Early research on the medical use of bacteriophages failed to adhere to the modern standard of scientific rigor. After World War II, Rene Dubos studied the treatment of mouse dysentery with phage in a rigorously scientific way. In order to prove definitively that phages are a good treatment, hundreds of millions of dollars of more research is required. The expense to perform clinic studies to obtain FDA approval for drugs for humans is so great, that much phage research is now being directed towards veterinary products.

In recent years, a number of biotech companies have pursued phage therapeutics:
• Gangagen Biotechnologies of Bangalore (half-bacterial-half-viral hybrid protein to fight staph infections)
• Intralytix (who product ListShield™ is used to kill Listeria monocytogenes on seafood)
• OmniLytics (producer of AgriPhage, a pesticide for bacterial stem canker in tomato plants)
• Viridax (developing phage therapies for staphylococcus aureus respiratory infections)

Soviet Georgia:
The most fascinating item in the book does not concern bacteriophages at all. It is a memoir by a Georgian that states that during Stalin’s reign of terror in the 1930s, members of cinema audiences were afraid to be the first one to stop clapping when Stalin’s photograph was shown, because it might lead to an arrest by the secret police.

Rising Plague by Brad Spellberg

Rising Plague: The Global Threat from Deadly Bacteria and Our Dwindling Arsenal to Fight Them by Brad Spellberg

Infectious Disease in the United States
The three top infectious causes of death in the United states are: sepsis, influenza and pneumonia. Each year, more Americans die of MRSA (Methicillin-resistant Staphylococcus aureus) infections than die of AIDS. MRSA was originally only a hospital-acquired infection, but now it is more often community acquired. Besides MRSA, there are also many other antibiotic-resistant bacteria: Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae.

Hospital Hygiene
Even if hospitals greatly improve their hygiene, and physicians stop over-prescribing antibiotics, there would still be many hospital acquired infections. The reason is that bugs crawl into patients on their catheters, plus their skin is broken during surgery. Also, chemotherapy weakens the immune system and makes patients more susceptible to infection.

Not Much Money in Antibiotics
Pharmaceutical companies are reluctant to spend money on a drug that the patient will take only for a couple weeks. In contrast, blood pressure medications and statins are taken every day for decades.

Don’t Look to Academia for Antibiotics
The author points out that it is not sufficient to fund academic laboratories conducting basic research, because no academic laboratory has ever developed an antibiotic. Only pharmaceutical companies have developed antibiotics. Many foreign drug companies sell their drugs for a ot less than American drug companies, because the foreign drug companies have only manufacturing costs, not research and development costs. Most foreign companies piggy back on American research. After the European Union instituted pharmaceutical price controls, European drug development declined.

Project Bioshield
The author gives details about Project Bioshield, where the government spent a large sum of money developing a new vaccine for smallpox, even though smallpox had already been eradicated from the face of the earth.

Radiation Poisoning
The Hollis-Eden pharmaceutical company was promised a large order for its radiation-poisoning steroid drug Neumune by the U.S. federal government, which reneged on the deal after the drug was developed.

Changing the Rules in the Middle of the Game
The author describes the case of the Oscient biotechnology company and its sinusitis drug gemifloxacin, where the FDA changed its rules for clinical trials in the middle of the game, that is, while the clinical trials are being run.

During the 2001 anthrax scare, the United States government threatened to revoke the German Bayer company’s patent on ciprofloxacin if it did not cut the price in half. Bayer was accused of profiting from people’s suffering. But, to my thinking, Bayer should be criticized only if it created the problem it is attempting to solve. Bayer did not give anyone anthrax.

Irrational Mistrust of Big Pharma
The author is critical of the widespread dislike of pharmaceutical companies for irrational, emotional reasons. Those of us on the political Right are willing to admit that the people running large corporations are motivated more by profits than by compassion. But politicians and government officials are no more moral. They just pretend to be.

Lessons from the Orphan Drug Act
The author suggests that for antibiotic development we pursue something similar to the Orphan Drug Act for rare diseases. For individuals, the author recommends lots of hand washing, avoiding being admitted to the hospital, and, if admitted, keeping your stay short.

In the Land of Invented Languages by Arika Okrent

In the Land of Invented Languages: Esperanto Rock Stars, Klingon Poets, Loglan Lovers, and the Mad Dreamers Who Tried to Build A Perfect Language by Arika Okrent

Artificial Languages
The author of this book is a linguist. The three artificial languages that have gained the most traction are listed in the book’s title: Esperanto, Klingon and Loglan. The vast majority of the hundreds of artificial languages that have been invented have failed to gain many adherents.
Esperanto is special because of its widespread following. It was invented by Ludwik Zamenhof, who was born in Bialystok, Poland. His family spoke Russian and Yiddish, and he also learned several other languages, but he was not a professional linguist. Esperanto was spread by people writing letters to each other in Esperanto. Esperanto replaced its competitor Volapük, which had been invented a bit earlier by a German priest named Johann Schleyer. The symbol of Esperanto is a green five-pointed star. The father of Hungarian financier George Soros was an Esperantist, who changed the family name from Schwartz to the Esperanto word for “will soar”. Interlingua, which was invented during the early twentieth century, is a similar language, and probably a better language than Esperanto, but it has a much smaller following.
A partial success is Blissymbolics, invented by an Central European Jew, Charles Bliss. Bliss became acquainted with Chinese characters while in the Shanghai Ghetto. He later moved to Australia. The pictorial symbols he invented have no associations with sounds. Unlike conventional manual communication boards, Blisssymbolics has a grammar and is able to express more abstract ideas. It was first widely used by Shirley McNaughton at the Ontario Crippled Children’s Centre (now called the Bloorview Kids Rehab) in Toronto in the 1970s. They use it as a bridge to English, by adding letters to the symbol boards.
There are a wide variety of manual sign languages for deaf people. In 1975 Gestuno was invented to be a universal manual language, but it has not received wide acceptance. In wider use is International Sign, which developed spontaneously.
Klingon succeeded because it was tied to the Star Trek cult. It was invented by the linguist Marc Okrand and is owned by Paramount Pictures. Okrand made it as different from human languages as possible, and uses an unusual word order: object-verb-subject. It is an agglutinating language and some of its words are very long.
Suzette Haden Elgin invented a language called Láadan that has extra details for feminine concerns. Láadan has fine distinctions for emotions and intentions. It makes clear whether what you said was said seriously, or in jest. It has linguistic evidentials, which specify the source of information asserted. Elgin is an author of several science fiction novels, and a famous best-seller called The Gentle Art of Verbal Self-Defense.
Loglan (logical language) was invented by a sociologist named James Cooke Brown during the early 1960s. I found Loglan to be the most interesting of the languages discussed, because it succeeded it achieving the goal of avoiding ambiguity. Most languages have lots of ambiguity. For example, if Louise is speaking to Charles about their mutual friend Elizabeth, and uses the pronoun “we”, does “we” mean Louise and Elizabeth, or Louise and Charles? The listener must figure this out from context, which is not always possible. The most famous example of an ambiguous sentence is “Time flies like an arrow”.

The Wisdom of Whores: Bureaucrats, Brothels, and the Business of AIDS by Elizabeth Pisani

The author is a journalist-turned-epidemiologist. She has a master’s degree in Classical Chinese from Oxford University. She also speaks Spanish, French and Bahasa Indonesian. She has a doctorate in Infectious Disease Epidemiology from the London School of Hygiene & Tropical Medicine.
Pisani is very outspoken. She criticizes the political Left for saying that AIDS is a threat to everyone, because it takes the focus away from high-risk groups such as prostitutes and drug addicts. She also criticizes the Left for asserting that poverty is a primary cause of the AIDS epidemic, because it concentrates aid on the poorest people, rather than those at most risk for AIDS. She criticizes the Left for asserting that routine HIV testing stigmatizes homosexuals. She criticized the political Right, for its objections to providing addicts with clean syringes and prostitutes with condoms. She is critical of feminists, for pretending that African women are pure victims of husbands who sleep around, but not admitting that many young African women are also promiscuous. Pisani points out that the main path for the infection of young African women is their association with older men who have more money than young men.
Besides condoms, she also emphasizes the use of sexual lubricants, because they prevent skin tears that can let the AIDS virus in. She also mentions that other STD’s, such as herpes and syphilis, increase the risk for HIV infection, because the skin sores offer a route into the blood stream. Male circumcision substantially reduces transmission of the AIDS virus.
Pisani says that countries, such as Uganda, whose governments speak openly about AIDS, drugs and sex do a better job restraining the epidemic than those that are less candid, such as South Africa.
Pisani is not just a bureaucrat who sits behind a desk. She has spent a great deal of time in Indonesia talking with people in high-risk groups. She is a believer in the idea that the perfect is the enemy of the good. Sure, it would be nice if there were no drug addicts, no prostitutes, and no cheating husbands, but given that no one knows how to change human nature, we should concentrate instead on the prevention of the transmission of the HIV virus among high-risk groups.
Pisani talks about the waria of Indonesia, who are a third sex, people who are physically men, but think of themselves as women. Most of them do not want a sex-change operation, even if they could afford it, because with the loss of the penis would come the loss of the ability to experience orgasms. Waria who are sex workers do not have pimps. I was surprised that Jakarta was such a wild place, since Indonesia is a Muslim country. Pisani mentions that following the lead of the West, homosexuality has become more open in Asia in recent years. Another surprise was the high variability of the frequency of AIDS between different places. For example, there is almost no AIDS in East Timor, especially since the Indonesians have left. 

The Map That Changed the World by Simon Winchester

The Map That Changed the World: William Smith and the Birth of Modern Geology by Simon Winchester


This book is a biography of William Smith, an Englishman who founded the science of geology two hundred years ago. Much of this book is filled with local color and history. People had studied rocks before, but Smith added the dimension of time. The depth at which a rock is found tells us the time in the past when it was created.

Canals and Coal

Canals became important in the late 18th century in England. They greatly reduced the cost of transporting coal, and so fueled the Industrial Revolution. Canals had the advantage over roads that the transit was much smoother and fragile goods were much less likely to break. The best route for a canal depended upon the kinds of rock (hard or soft) that needed to be excavated, and whether the remaining rocks would absorb water.


William Smith was the son of a farmer. He did not seek the profession of scientist. It happened because of his work as a surveyor for the digging of canals in England. While digging, he made some important observations. He noticed that different strata (layers) appeared in the same vertical order at different geographical locations. The thickness of strata varied but not the order. He surmised that each layer (stratum) was not just a local phenomenon, but one that extended throughout much of the country. For example, at one location, the order from top to bottom was: Sandstone, Siltstone, Mudstone, Nonmarine Band, Marine Band, Coal, and Seat Earth. Each strata was layed down at a particular time in the distant past. Smith drew maps of the layers, with a different color for each stratum, showing its geographical extent.

Matching Strata from Different Sites

Most importantly, when deciding whether two strata from different geographical locations were equivalent, Smith considered not only the rock chemistry (grain size, color, reaction to acid), but also the rock biology, what kinds of fossils were in the rock. For example, two strata of limestone were not equivalent, unless they contained the same kinds of fossils (bivalves, ammonites, gastropods, corals).

Gaining Recognition

Much of the book is about the troubles he had getting recognition for his discovery, due to the fact that science was dominated by the upper class, while he was of the lower class. But being of the lower class had the advantage that he worked with his hands, while the upper class sat in their fancy drawing rooms having abstract philosophical discussions unrelated to reality. The author bemoans the fact that Smith had many financial problems. But Smith made a good living surveying for canals and draining swamps. His problem was that he spent too much money, especially for expensive residences in London from which to entertain important guests.