Friday, April 13, 2018

The Sixth Extinction: An Unnatural History

Book Review: The Sixth Extinction: An Unnatural History (Henry Holt & Company, 2014)

This was a fair to good book, mainly a history of mass extinctions and of extinction in general. Kolbert is a writer at The New Yorker and has written about environmental and science topics. I moved this up on my review list since the author just gave a talk about the book at the local university.

She begins with the recent evolutionary success of humans who have managed to vastly increase their population in the past 100 years and vastly affect their environments and planet to the point where we are directly influencing an unprecedented acceleration of the rate of extinction of many species, mainly through habitat loss. Humans began causing extinctions thousands of years ago by hunting animals to extinction, including isolated island species, especially flightless birds, and very likely megafauna as well. When we discovered and developed fossil fuels and subsequent technologies we expanded our population which also expanded human-caused extinctions.

The first chapter is about the Panamanian golden frogs, once extremely populous, now disappearing. She travels to the area to observe efforts to keep the frogs from going extinct. Frog and amphibian extinctions in general have been accelerated recently, even though some have been present on Earth for hundreds of millions of years and several made it through all of the previous mass extinctions. A fungus in the chytrid family, known as Bd for short, is the culprit killing the Panamanian golden frogs.

She talks about what is known as the ‘background extinction rate’ which is the normal rate of extinction for a class of organisms. For example, the current background extinction rate for mammals is 0.25 per million species-years, or roughly one lost mammalian species every 700 years. In contrast, mass extinctions cause substantial biodiversity losses rapidly and globally. They happen close enough in time to be called events, although an event may last hundreds of thousands of years. Mass extinctions often mark the boundaries of geologic periods. The Big Five mass extinctions were: 1) End of Ordovician, 2) End of Devonian, 3) End of Permian, 4) Late Triassic, and 5) End of Cretaceous. According to paleontologist David Raup: the history of life consists of “long periods of boredom interrupted occasionally by panic.” There have been many lesser extinction events as well. Amphibian background extinction rates have not been calculated due to a dearth of amphibian fossils, but it is thought to be less than that for mammals. However, in recent times, most herpetologists have seen several extinctions of amphibian species. In fact, now they are considered the world’s most endangered class of animals, possibly as much as 45,000 times the background extinction rate! Many reef-building corals, fresh-water mollusks, sharks and rays, and mammals are also endangered.

The Bd fungus was thought to have been introduced by importing frogs from other places that were less affected by it. Introduction of invasive species and new diseases is another result of human travel. Humans have managed to globally re-shuffle species, both purposely and accidentally, on an unprecedented scale.

Oddly, humans did not understand that species went extinct until fossils were interpreted by paleontologists. There were theories and ideas about fossils, often referred to the flood of Noah in Genesis. In the late 1700’s the French naturalist Nicolas-Frederic Cuvier interpreted Mastodon fossils from America as remnants from an extinct species. The author visits a paleontology museum in Paris that houses Cuvier’s specimens and sketches. It was Cuvier who established extinction as fact, she notes. He found many fossils in nearby gypsum quarries. The discovery and reconstruction of the bones of the Ohio mastodon by others would cement Cuvier’s idea of extinction. In 1812 Cuvier published a four-volume compendium on animal fossils. Cuvier was also involved in early study and identification of dinosaur fossils. Cuvier’s success (perhaps modest by modern standards) was based on his keen knowledge of anatomy. His senior colleague Jean-Baptiste Lamarck, who asserted that there was a force pushing beings toward complexity (an idea that later merged into Darwin’s evolution) opposed his idea of extinction.

Cuvier believed extinctions were caused by catastrophic events that happened very quickly. Not much later this idea would become known as ‘catastrophism’ and it was the basis of early geological theory in the early-mid 1800’s until Charles Lyell appeared on the scene. Lyell observed rock layers and concluded that geologic processes like sedimentation and erosion were very gradual over long periods of time. He also thought extinction was a gradual process. Darwin read his books as a young college student at 22 as he traveled on his famous voyage to Galapagos Islands and beyond to the South Pacific. He experienced a horrific earthquake while in Chile and measured the local ground uplift with surveying instruments to eight feet. These and other experiences convinced him of the truth of Lyell’s ideas as Lyell also talked about uplift and subsidence, noting that over long periods of time accumulated uplifts could make mountains. Darwin noticed that coral reefs and atolls were a result of the interplay between biology and geology in that sea shelves subsided (dropped) and reefs moved accordingly to waters of shallow depths. He presented the idea to Lyell who was delighted and revised his idea of reefs which erroneously thought underwater volcanoes were the underlying source. Lyell was wrong about other things – ie. catastrophes and destructive events do have a place in geology. Darwin’s key idea of natural selection was also rooted in Lyell’s ‘gradualism’ and followed Lyell’s famous principle that “the present is the key to the past.”

She visits a museum in Iceland that houses the last known specimen of the great auk, an extinct bird, large and flightless, last known from the mid-1800’s. Once numbering in the millions, the bird is one of many species of animals wiped out by humans for food. Darwin also acknowledged human-caused extinction, which in some cases could be directly observed as hunted species became more and more rare.

Next, she considers the ammonites and the work of the Alvarez’s (Luis and his son Walter) in determining their demise was caused by an asteroid impact that defines the end-Cretaceous mass extinction, the stratigraphic boundary being known as the K-T boundary. Paleontologists went around the world looking for the K-T boundary contact in outcrops and successive rock layers before and after, Geochemists got involved looking for evidence of asteroid impact minerals, mainly irridium. Finally, the impact crater was actually found at the Yucatan Peninsula of Mexico. It was not the impact itself that caused the ammonite extinction, wrote the Alvarez’s, but likely the dust which blocked out the sun which killed plants and animals. This is the event that wiped out the dinosaurs. Living things near the impact were simply vaporized. The atmosphere was altered and the ocean chemistry. Species that could live in deeper ocean water had better survival rates. Ammonites can be seen very well in the fossil record to decrease in variety and in amount but in this case the seemingly gradual was really precipitated by a single event. The end-Cretaceous (K-T) mass extinction is thus far the only one (probably “the” only one) confirmed to be from an impact event.

Next, she considers a history of the science of extinction in terms of Thomas Kuhn’s “paradigm shifts” in his historical/psychological study of scientific revolutions. The first paradigm shift was acknowledging extinction which happened with Cuvier and contemporaries in the 1800’s. Lyell’s focus on the gradual was another shift. That idea held up until evidence for asteroid impacts showed that mass extinctions could result from a single catastrophic event. Of course, in reality both gradual and catastrophic processes operate in geology with the catastrophic simply being much rarer than the gradual.  

She goes to Scotland where geologists are looking at graptolite fossils at the end-Ordovician (444 million years ago) boundary defined by the first major mass extinction. Life then was in the sea, having “exploded” in variation in the previous age, the Cambrian. They are looking for the record in the rocks where the sea went from habitable to inhabitable. After verification of the impact explanation for triggering the end-Cretaceous mass extinction, impact was a popular idea for other mass extinctions. However, lack of iridium and other factors favor other explanations. The current theory in favor for the end-Ordovician mass extinction is that of global cooling and glaciation of a previous greenhouse climate. The glaciation dropped global sea levels drastically which ruined sea life habitat and ocean chemistry changed drastically as well. This dropped previously high CO2 levels which cooled the planet further. One idea has it that it was the spread of mosses on the land that decreased CO2 levels and triggered the process. She considers this idea, that it was plants that caused the first major mass extinction. The end-Permian extinction also appears to be a result of changes in climate.  A massive increase in atmospheric CO2 happened then, 252 million years ago. The seas warmed. Reefs collapsed. Some scientists think the CO2 came from volcanos. Some also think that the conditions eventually favored bacteria that produced hydrogen sulfide and that this extended the die-off due to a poisoned atmosphere.

She explores the notion that we have entered a new geologic age informed by humans and the effects of their population growth and technology. Dutch chemist Paul Crutzen termed it the Anthropocene. He noted that humans have transformed between a third and a half of the land surface of the earth, dammed and diverted most of the rivers, added excess nitrogen to the biosphere through fertilization, overfished the oceans, and use half of the world’s freshwater runoff. We have also altered the chemical composition of the atmosphere and the ocean.

Next, she goes to an area in the Tyrrhenian Sea off the coast of Italy where there is an active underwater volcano system that spews CO2 from vents on the ocean floor. Scientists there can study the effects of increased ocean CO2 as one moves closer or further from the source. The extra CO2 produced by humans is partially absorbed by the ocean and this lowers its pH making it more acidic. Scientists there study the effects of more acidic ocean on sea life, particularly life that makes calcium carbonate shells. Some creatures are more adaptable than others, but few can live in the very low PH waters very near the vents. The same is true of a globally acidified ocean – some species will thrive and others suffer. The general prediction is of loss of biodiversity. Ocean acidification was involved in the end-Permian and end-Triassic extinctions and possibly the end-Cretaceous as well as the Toarcian Turnover 183 million years ago in the early Jurassic. Shelled organisms that use calcium carbonate, ie. calcifiers, need to adjust their internal chemistry to the ocean chemistry. Typically, they do that through evolution so the speed at which they can evolve will be a factor. There are no calcifiers near the vents.

Continuing with the effects of ocean acidification on calcifiers she travels to the Great Barrier Reef region in the South Pacific. Corals are a calcifying superorganism. Darwin was right that subsidence is a major factor in reef building. She travels to One Tree island to observe the work of atmospheric scientist Ken Caldeira and others. Caldeira thinks that the coming ocean acidification will surpass that of the last 300 million years. Thus, coral reefs could be the most vulnerable of ecosystems. They are already being affected. She explains pH and calcium carbonate saturation. The sea provides a buffering effect on acidification but the amount of CO2 is increasing the amount of carbonic acid to exceed the buffering effect. In the geologic record limestone-based reefs have come and gone but those reefs consisted of different organisms, many now extinct. Modern coral reefs face other threats too: overfishing that increases algae which compete with the corals for nutrients, agricultural runoff which also spurs algae growth, and siltation resulting from deforestation. Increasing water temperatures cause the corals to lose their colorization mechanisms. This is known as “coral bleaching” and can lead to the death of reefs.

Next, she heads to the Andes in Peru where researchers are studying the effects of climate on the region’s immense biodiversity through observing plots of trees confined to very specific elevations based mainly on temperature. These species are very specific in their requirements. Some species can move upslope faster than others by projecting seeds but others can succumb more easily to rising temperatures. The worry here is that many of the less versatile species will go extinct. The logic is that since there is much greater species variation in the tropics there will much more climate change related extinction there. The trees also host other species of insects, etc. that also have rather exacting condition requirements. One theory simply holds that the tropics have more species precisely because those species are more condition-specific. Another theory notes that it is the age of the tropics in terms of less disruption over time than in temperate and polar zones. They have had more time to diversify. New species are still being discovered in the tropical regions. Species do migrate but if the rate of climate change, mainly increasing temperatures but also differing water conditions, exceeds the rate of migration, some species won’t make it. She explains the species-area relationship graph (S=cAz (z is a superscript – power). What humans change mainly is A or area, changing the availability of certain types of land through development and agriculture. One prediction is that by 2050 9-13% of species will be committed to extinction under the minimum warming scenario and 21-32% by the maximum warming scenario. Others disagree, saying species are better at adaptation and moving. Most do not think that climate change and habitat destruction will cause a major extinction like the big five but may approach some of the minor ones. (Thus, the book’s title may be deceptive. Even the book’s subtitle is questionable since extinction is quite natural as 99.5% of species once in existence have gone extinct. A person asked this question at her talk and she conceded that it may not have been the best subtitle). The tropics have other threats: illegal logging, illegal ranching, and illegal mining. Some have noted that in a warmer world, species’ overall biodiversity will eventually increase rather than decrease as evidenced in the warm Eocene of 50 million years ago. The problem now is that warming is happening much faster than species can keep up.

Next, she moves s over to the Amazon in Brazil to observe some of the “reserves” kept from development – patches or fragments of rainforest. There she visits famed conservationist Tom Lovejoy who convinced the Brazilian government to preserve parts of the area for scientific study. The experiment started in the 1980’s. Here also, new species continue to be discovered. The preserved plots are essentially islands among logged out areas. Like the Andes experiment these areas are megadiverse and species are very specific in actions and in conditions required for thriving. High species diversity also means low population density and so species become isolated by distance. Such populations are much more susceptible to extinction. She notes that while primary forest is declining in the Amazon the amount of secondary forest is growing so this may slow the high species extinction rate predicted somewhat. Timbered forests will regrow if not further developed. There are so many species in the tropics it is hard to count them, let alone count how many have gone extinct.

Next, she considers what has been called the “New Pangaea,” the globalization of species by virtue of human introduction, both deliberate and accidental. Thus, the geographic distribution of some species has advanced hugely. Here she focuses on the loss of bats in Eastern North America due to a fungus that causes what is called “white-nosed syndrome.” This was first observed in 2007 and is killing bats by the millions, especially when they hibernate in caves and mine shafts in the winter. Ballast water of ships, hitching rides on people and cargo in planes, and on people’s stuff and shoes from car travel are some of the ways species expand their distribution. Invasive species have become problematic in many places although some are more problematic than others and some may also be beneficial, ie. introduced species are not always invasive species but often are. Here she explores some of the stories of introduced species. They often become invasive because in new areas their usual predators may not be around. Introduced species can actually hunt other species to extinction as happened with the brown tree snake accidentally introduced from Papua New Guinea to Guam where it extinctified some birds and bats. It merely did what humans do – succeeded at the expense of other species. As in the story of the American chestnut tree succumbing to a fungus that was common to Asian chestnut trees that the fungus evolved with, the fungus killing American bats is not harmful to bats in Europe from where it was likely introduced. The same is true of the chytrid fungus killing the Panamanian frogs. Novelty can kill. She goes through a surprising list of species introduced to North America: dandelions, honeybees, earthworms, queen-Anne’s lace, burdock, plantain, etc. Currently, the emerald ash borer is a problem here in Ohio – I have about 40 or 50 of these trees dying or dead within about 500 ft of my house. Some will fall a limb at a time or maybe from the base. Others nearer will have to be cut down in the next few years. Zebra mussels and Asian carp are aquatic species that have wreaked havoc. Of course, humans have been introducing species from time immemorial as they travelled to new areas. It is just in recent times the process has been vastly accelerated. This has resulted in rises of ‘local diversity.’ While local diversity has been increasing, global diversity has been decreasing.

Next, she visits the Cincinnati zoo which houses (not sure if still there) a Sumatran rhinoceros named Suci. They are the oldest and smallest of the five species of rhinos today but highly endangered. Some housed at zoos are trying to be mated to reproduce. These are known as ‘captive breeding’ programs. The Sumatran rhino, once common from Bhutan to Indonesia, is a victim of habitat destruction and forest fragmentation. There are only a few hundred left in the wild. In their case captive breeding efforts have made the problem worse as many died faster in captivity. A few have been born in captivity so there is some hope. Other rhinos have been overhunted for their horns which are used as an aphrodisiac in Chinese medicine and apparently as a party drug where they are powdered and snorted like cocaine.

While in Cincinnati she also visits the nearby museum at Big Bone Lick where the old mastodon fossils that Cuvier interpreted were found. She considers whether the North American megafauna were driven to extinction by human hunters (the leading theory by far) or by climatic changes or possibly by both. Similar losses of fauna occurred in Australia, New Zealand, Madagascar, and other places. Of course, every loss coincided with the arrival and persistence of humans in those areas. She shows through scientific evidence that pre-historic humans almost certainly caused these extinctions. One issue with some of the big megafauna is that they reproduce sparingly and have one baby at a time so that even a small amount of them killed by humans could have a large effect on their population in a relatively short period of time. Other simulations have shown that the megafauna were very vulnerable to humans, that only a few hundred humans could have wiped them out over a millennium.

Next, she visits Germany to consider the fate of our human deep ancestors, the Neanderthal. The likelihood is that modern humans, homo sapiens, simply killed off and inter-breeded with Neanderthals. Genetic projects are underway to map the Neandertal genome, compare it to the genome of modern humans, and find out where and possibly when they diverged. Apparently, it is a slow process since getting DNA from Neanderthal bones is not easy. We now know that Europeans and Asians share more Neanderthal DNA than Africans. All non-Africans carry between 1% and 4% Neanderthal DNA. Only modern humans, not Neanderthals, used projectiles and made it to Australia, Madagascar and other places (used boats). Paabo, the researcher there in Germany, is a leading DNA-extracting researcher in the realm of humans. He tried and failed to extract DNA from a bone fragment from 17,000 year old homo floresiensis, first discovered in 2004 in Indonesia and identified as a new species. Then in 2010 the first bones of the Denisovans were discovered in a cave in Siberia. Paabo named the species and was able to extract DNA from the finger bone discovered. It was found that modern people from Papua New Guinea share 6% DNA with Denisovans but that modern Siberians and Asians do not. This is likely due to ancient migration patterns. The Neanderthals used tools, buried their dead, and some think they made art and adorned themselves, but after living in Europe for 100, 000 years there is little to show of their “culture.”

Finally, she explores the San Diego zoo, specifically the place there where the DNA of extinct species is preserved. Here there are also very endangered species. One is a rare male alala, or Hawaiian crow named Kinohi. These crows can imitate human speech somewhat like parrots. They are trying to extract his sperm to mate with the few female alalas left. She talked about him in her talk.

Overall, this was a pretty good book and a nice overview of extinction in general. Like I said before, I don’t think the title or the subtitle are ideal since this may not become a “mass” extinction although the rate of extinction has certainly accelerated significantly – and it is not at all unnatural. I think she talked a bit much in her talk about the effects of climate change and the current American political climate as being unhelpful. I would have rather explored more about biology in general.

Saturday, March 31, 2018

Living Downstream: An Ecologist's Personal Investigation of Cancer and the Environment

Book Review: Living Downstream: An Ecologist’s Personal Investigation of Cancer and the Environment – by Sandra Steingraber, Ph.D. (Da Capo Press 1997, 2nd Ed. 2010)

This is an interesting account of the possible relationships between chemicals, particularly synthetic organic chemicals, and incidence of cancer. By nature, it is difficult to discern prime causes of cancer and what might just be influences. The environment a body encounters and imbibes is certainly a factor. She does a good job of stating evidence and trying to tease out relationships in light of both her scientific prowess and her very personal long and thus far successful battle with bladder cancer, diagnosed when she was 20. It is also good as a personal account of the anxieties, hopes and fears, of having cancer, quite touching at times. She is a veteran of over 70 cytoscopic exams where tubes were inserted into her bladder.

In the intro to the 2nd edition she notes that it has been thirty years since she was first diagnosed. When she was diagnosed she was asked by her urologist if she ever worked in a tire factory, the aluminum industry, or with textile dyes. She was asked because bladder cancer is the cancer most thought to be due to exposure to hazardous chemicals. Of all the chemicals used in our society very few have been specifically tested for carcinogenicity – about 2%, although that increases if we extrapolate and categorize by type. Many chemicals known to cause cancer in animals are used in food and consumer products. Genetic factors are extremely important in susceptibility to cancer so that it makes sense that the genetically susceptible are very sensitive to exposure to carcinogens in the environment.

Steingraber’s information sources include the Harvard Medical School library where she did post-doctoral research, right-to-know laws, cancer registries, published studies, and reports about levels of environmental contaminants like pesticides and other chemicals and air pollution. She notes the 1986 federal right-to-know law which requires industrial interests to keep databases of the release of initially some 650 toxic substances into the environment. The database became the Toxics Release Inventory (TRI). This allowed researchers to compare where those releases occurred with local cancer rates and patterns. From 2001 to 2008 the TRI was scaled back and thousands of facilities were no longer required to report.

Steingraber does acknowledge that cancer causation is complex and a recent analysis from Johns Hopkins University notes that most cancers to not have a discernable cause. She notes cancer causation used to be divided among three variables: genes, lifestyle, and environment. Newer analyses indicate that those variables often intermingle in complex ways. Genetic factors may involve epigenetic factors – genetic predisposition to cancer is too simplistic. Substances, natural and synthetic may alter gene expression and change gene behavior. She also mentions endocrine disruption, whereby certain chemicals disrupt our endocrine system which affects hormone production, metabolism, and reproduction. Basically, chemicals can interfere with and mimic hormones. She notes the old toxicology adage – “the dose makes the poison,” but also adds that in endocrine disruption the timing is often very important, particularly exposure early in life. Another complicating factor is chemical mixtures and how they interact with one another and with the body as a whole. Steingraber is an advocate of the Precautionary Principle, which is favored in Europe but has always been a hard sell in the U.S. I don’t agree with her on this – sometimes being overly cautious can cause more harm than good and I think each individual case should be evaluated separately rather than fall under a single regulatory principle. She favors ‘green chemistry’ but there is as of yet much to work out with it. She notes that petroleum and coal are often the sources of carcinogenic synthetic substances and so favors green energy. Of course, petroleum is also the source of many synthetic chemicals that improve health and make our lives safer and more convenient. The bigger part of toxic chemical releases come from coal-burning power plants and emissions from vehicles. She notes that the death rate from cancer has actually fallen and this is due primarily to the success of smoking cessation programs. However, childhood cancer has slowly but steadily increased over the years. She notes that certain industrial chemicals have been proven to cause cancer among those who work with them so that precautions are needed, including outright banning in some cases.

Steingraber recounts her childhood in Central Illinois prairieland/farmland where part of her family farmed. Illinois is 87% farmland. It has been farmed for a long time and pesticide use is abundant, including the use of atrazine. Atrazine in the environment is high during spring planting and lower in winter. It and its byproducts are found in surface water, air, and groundwater as well. A 1992 study found that one quarter of private wells in Central Illinois contained agricultural chemicals, typically in trace amounts. How they get into groundwater and how much varies according to how much used, how much runs off, and the local geology and groundwater configurations are important factors. Even long-banned DDT and PCBs are still found in the environment due to their chemical stability. She notes that:

“Atrazine remains the most frequently detected pesticide [as of publication 2010] in water throughout the United States, found in three of every four American streams and rivers and 40% of all groundwater samples.”

She gives some info/data and anecdotes about DDT, PCBs, and atrazine and introduces Rachel Carson, who succumbed to cancer and whose work led to DDT being banned. Through the book it can be seen that Steingraber venerates Carson and follows in her footsteps. She recounts her visits to the library at Yale University that houses Carson’s papers. She reproduces some of Carson’s notes about her own cancer and impending death and through narrative stories about Steingraber’s friend Jeannie who had an aggressive form of cancer in her thirties and died from it. Carson’s famous 1962 book, Silent Spring, led to the banning or restricted use of several dangerous pesticides, although the chemical industry fought her. In a few isolated cases these pesticides can be useful according to many – such as in very specific applications to prevent malaria which kills many children around the world in tropical countries with abundant mosquitos. Many say DDT could prevent those deaths but there is no access since it is banned internationally. DDT, PCBs, and possibly atrazine (which is not banned in the U.S. but is in Europe) are in some ways associated with cancer although data and conclusions have been inconsistent. Thus, even with these powerful poisons it is difficult to get incontrovertible conclusions. This makes the much less powerful pesticides in use today like glyphosate much more benign by comparison. Steingraber also recounts Carson’s public appearances to fight the chemical/pesticide industry after Silent Spring was published and her struggling cancer patient appearance as she defended her work. Carson argued that pesticides and other chemicals caused cancer before it was generally ceded that that was the case. Steingraber notes Carson’s ode to citizen activists as helping her to speak out and sees herself in the same light – as an activist as well as a scientist – Steingraber has been vocal in recent years in opposition to oil and gas industry activity near Ithaca, NY where she lives – although I think her focus may be misplaced since the fracking revolution likely produces far more benefit than harm and the fears about water contamination are overblown.

She recounts the experience of having cancer throughout the book, the boredom, the anxiety, the fear, the frustration. She also notes cancer trends and trying to tease out trends from the data that is available. She pours through state and federal cancer registries and compares them to TRI data. She looks at cancer incidence rates = number of new cancer cases per 100,000 people per year. Tracking changes in cancer incidence can lead to discoveries that point to sources. Unfortunately, there are often multiple possible sources so that the availability of many of them may correlate with cancer incidence and yet not be related by cause. The adage “correlation does not equal causation” is often relevant to these statistical epidemiological approaches. Teasing out clear relationships from the data can be difficult. She acknowledges these problems.

Incidence rates can change when new detection technologies appear such as mammography for breast cancer. She explores the trends in breast cancer, noting that breast cancer has been dropping irregularly since it peaked in the 1990’s. There are several possible reasons: decline in women taking hormone-replacement drugs, decline in women getting mammograms, disproportional under-reporting, and declining exposure to causative agents. She notes that breast cancer kills 41,000 women in the U.S. yearly. Another reason cancer trends are hard to track is that it is a slow disease and people move to different localities making cancer by region difficult to calculate evenly. She notes that the overall cancer incidence rate is 463 per 100,000. This is more than twice the cancer mortality rate so more people are surviving cancer. Over 11 million people in the U.S. have cancer, are in remission, or are cured. The cancers that are rising are leukemia, non-Hodgkin lymphoma, soft tissue cancers, kidney cancer, and brain and nervous system tumors. Childhood cancers are rising as well, which suggests environmental factors. She notes that children do receive a higher proportion of any poisons in air and water due to body weight and they don’t have lifestyle factors as adults do. She notes that cigarette smoking causes 85-90% of lung cancer with a very high fatality rate and is thus the largest preventable form of cancer.  

Steingraber lauds calls to fund more cancer incidence research as well as research of more potential chemical carcinogens. She notes cancer studies that have grouped people by birth year, by racial/ethnic background, gender, or all of the above. She focuses in on the data about non-Hodgkin lymphomas and notes that people of certain occupations tend to get it such as farm workers and dry cleaning workers. Solvents, PCBs, and certain pesticides (phenoxy herbicides) are suspected sources or triggers. She studies cancer distributions across space and time. One might find cancer clusters and compare them to nearby potential sources of toxins, although one would have to prove that those toxins are there and know something about their toxicological effects. She notes throughout the book that cancer study results are often unclear and inconclusive and can only suggest where and what to study further. She thinks there is a general correlation between industrialization and rising cancer rates. She suggests that increased coal-burning in China and living near a Soviet petrochemical complex in Ajerbaijan correlate well to increasing cancer rates in those places. She implicates coal and petroleum in particular – many synthetic chemicals derive from petroleum. However, it is hard to know how much cancer or cancer influence is derived from petroleum chemicals. We also know that the UV light from the sun causes cancer in those susceptible and that plant substances can be carcinogenic. Lifestyle factors may also stack the deck for or against cancers. Household chemicals, cosmetics, cleaning chemicals, paints, and solvents may be factors. It is hard to know how much with each of these without large, long-lasting, and well-planned studies. More people die of heart disease than cancer (especially now as more and more cancers become treatable) and lifestyle is also a large factor in heart disease. Toxin exposure could be a contributing factor as well. She notes that increasing cancer rates among migrants to a new place certainly suggests an environmental influence.

She calls for a nationwide cancer registry. The National Cancer Institute keeps an atlas of cancer mortality but not incidence (cancer mortality has dropped due to better treatment and sooner detection). She notes a good correlation between cancer mortality and industrial areas. However, she also notes that quality of treatment is a factor and that cancer diagnoses do not seem to correlate as well to industrial activity. She does say that cancer rates seem to match industry more than any other health problems match it. She mentions a study in the UK that correlated leukemia very well to industrial facilities, particularly to those involving chemical solvents at high temperatures. Cancer rates among certain occupations have long been studied: farmers, chemists, dental workers, barbers, hairdressers, firefighters, painters, welders, asbestos workers, miners, printers, fabric and dye workers, certain electronics workers, and plastics manufacturers. Being somehow exposed to dumped chemicals and wastes is also considered, particularly the many Superfund sites. She does also consider methodology and the difficulty of getting from correlation to causation. Here she mentions ecological fallacy as a term meaning to falsely attribute causation to correlation. She complains that uncertainty has been used to delay corrective action for reducing environmental pollution. That can work both ways as those who favor strong regulation of potential toxins often use uncertainty to argue their position – the basis of the Precautionary Principle. It is basically a ‘prove it safe’ vs. a ‘prove it harmful’ debate. I would argue that since many of the toxins are or derive from substances that do much good in the world, including making people healthier and enabling many things – that the burden should be on those to ‘prove it harmful’ for most things – that usefulness to society, cost, and disruption also need to be taken into account.

She goes through a type of epidemiology known as “ecological studies,” which attempt to discern disease trends in large groups. One might study populations where exposure to toxins is likely vs. populations where it is unlikely. Investigation of cancer clusters can be tricky or legitimate requests for such studies can be dismissed by health workers. We are all exposed to various levels of ‘probable carcinogens’ such as metal degreaser trichlorethylene (TCE) as it is in most water supplies. In such cases it is difficult to find a comparison population with no exposure to the toxin. Cancer is more difficult to study because it may take a long time after exposure (to certain toxins) for cancer to develop. People move between exposure and onset. Also, cancer may have numerous causes so that pinpointing it to one cause is not easy. She notes that GIS (geographic information systems) can be very helpful. Environmental epidemiology is wrought with difficulties as well as being amenable to inconclusive results that may suggest causation that is not causation and vice versa.

Steingraber focuses on synthetic organic chemicals as potential sources of cancer although she does not mention that there are natural sources of cancer as well and that some of the synthesized chemicals also do occur in nature, although often in different forms. Crude oil is a natural substance that is toxic if ingested. She notes that:

“Synthetic organic molecules are chemically similar enough to substances naturally found in the bodies of living organisms that, as a group, they tend to be biologically active.”

This is problematic she says. Many organic chemicals are inert in their final forms but active in their intermediate forms during manufacture. If enough of some chemicals get in our systems they may mimic natural body chemicals as is thought to be the way endocrine disruptors act. She also mentions chloroform, considered a probable carcinogen. It is used in many chemical processes and appears in wastewater. It also appears as a byproduct of chlorinated water so removing it may be impossible. Later in the book she does mention favoring alternatives to chlorine use but water companies still prefer chlorine based on cost and feasibility. She laments the ineffectiveness of the 1976 Toxic Substances Control Act (TSCA) which does not require testing for the vast majority of new chemicals on the market. Of course, massive new studies on every new chemical would mean massive animal testing and such tests often involve giving animals massive lethal doses. She notes that barely a handful of chemicals have ever been taken off the market and none for the last nineteen years. Pesticides are regulated differently – Federal Food, Drug, and Cosmetic Act (FFDCA) and Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA). In 1986 the Emergency Planning and Community Right-to-Know Act (EPCRA) passed Congress over massive opposition by industry. It spurred the Toxics Release Inventory (TRI) which requires companies to report the total amount of about 650 toxic chemicals released as waste, by-products, and spills every year. TRI was scaled back in 2008 and 2009 citing homeland security concerns since knowledge of where toxins were stored could be used by those wishing to unleash them for terroristic reasons. However, in order to explore whether environmental toxins are influencing cancer incidence one would need to know what is actual in the environment from day to day or at least on avg.

Toxics and pollutants may be concentrated at places like landfills, particularly at those that accept toxic waste such as heavy metals that have been implicated as carcinogens. Steingraber does her own investigative analysis of industrial toxics released into her childhood area of Tazewell County, Illinois.

She goes back again to endocrine disruptors, mainly those that mimic the hormone estrogen. While this is true of several industrial chemicals just today I read an article about naturally-occurring chemicals in the essential oils used in many soaps, shampoos, and lotions also doing the same thing. The substances in the oils are also known to bioaccumulate rather than fully metabolize. Apparently, there are several ways substances (both synthetic and natural) interfere with hormones. Phthalates used in PVC plastic and added to perfumes and lotions are known disruptors as are a rather toxic chemical group known as organochlorines which includes PCBs, TCE, DDT, dioxin, and several others. Organochlorines tend to persist in the environment. Burning plastic produces dioxin and other organochlorines. She mentions the UN Stockholm Convention on Persistent Organic Pollutants (POPs) as inspiring since it seeks to eliminate the use of the most toxic POPs. Several of the worst organochlorines are on the list.

Steingraber favors so-called green chemistry over petroleum chemistry but it is quite difficult to compete with petroleum (or natural gas liquids and derivatives) as feedstocks. She mentions as one green chemistry success story – the development of a soy-based adhesive that replaces formaldehyde in plywood. She argues that green chemistry should be mandated like smoking cessation and exercise – as health-promoting. However, she doesn’t acknowledge that some of nature’s own chemicals, when concentrated and exposed to creatures can cause health problems too. I think she overly focuses on the synthetics. Too many wood ashes concentrated in one spot can contain carcinogenic heavy metals. Wood smoke is highly toxic. An USDA-organic approved fungicide like copper sulfate can be more toxic than commonly used pesticides as can other highly concentrated natural substances. She does acknowledge that pre-synthetic substances like celluloid and castor oil are also environmentally harmful and so does not advocate for banning all synthetic chemicals, only the most harmful ones. While that may seem reasonable some are difficult to replace. However, her activism to ban fracking and an underground propane storage facility suggest that she does advocate bans.

She goes through some case studies of possible relationships between certain pesticides and breast cancer. She also explains why assays – evaluations of biological or chemical substances – can be expensive, messy, and complex. In assays for potential carcinogens animal studies need to involve large amounts of animals who need to be evaluated for years as cancer often takes a long time to appear. For complete understanding such long complex assays would be needed for each potential chemical carcinogen, ideally. Some researchers have advocated for new chemical screening tools since the time constraints and inconclusiveness of animal assays keep a huge backlog of chemicals for which toxicity is unknown. Better knowledge of the interactions of networks of genes, proteins, and receptors has shown that certain chemicals and classes of chemicals disrupt the pathways of these cell functions.

She discovers that her own cancer, a type of bladder cancer called transitional cell carcinoma, also occurs among beluga whales from the St. Lawrence estuary in Canada. Many workers from a nearby aluminum smelting operation also got that particular type of cancer. PCBs, DDT, chlordane, and other toxins are found in the waters and sediment of the estuary. There is also benzo-[a]-pyrene, product of combustion classed as a polycyclic aromatic hydrocarbon (PAH). Liver cancer in fish has also been linked to toxics.

She laments the change from large numbers of small family farms to less farms but bigger more industrialized ones. Using pesticides reduced the need for crop rotation. She recounts her childhood farm experiences in Illinois. While Illinois corn and soybeans are sold for export, most goes to feed livestock. A significant amount also becomes snacks and corn sugar. She also advocates taxing foods of lower nutritional value, like soda to deal with the obesity epidemic. Obesity and weight gain are risk factors for cancer, probably related to hormones and inflammation. She sees the farm belt as overproducing the two – corn and soy – but they make the best animal feed, snacks, and best grain nutrition for export. Also, larger more industrialized farms are way more efficient and reduce overall land use quite significantly. Corn and soy also account for the largest share of herbicide use. Of course , there is also organic, which uses organically approved pesticides, not synthetic, but which may also have some ill effects. Weeds used to be removed by plowing, hoeing, and disking but these were time and labor intensive. They also released more carbon from soils. Modern no-till methods are better for soil health and retain more carbon. Herbicide-resistant varieties developed through genetic engineering. Though she laments that by 2004 a third of Illinois corn was GMO (probably much more now), this is now widely seen as a good thing since overall pesticide use is down. She does not mention this. She invokes herbicide-resistant weeds which can be problematic but have yet to be a huge problem, especially as herbicides are more targeted in place and time to reduce runoff. She laments the continued use of atrazine, banned in the EU, because of its water solubility and ability to spread all over the environment. She also laments the dead zones caused by nitrogen and phosphorus fertilizer runoff overload. She notes that manure is way less used than it used to be (although she doesn’t mention that manure runoff also contributes significantly to the runoff that creates dead zones). Synthetic nitrogen fertilizers are made from natural gas in fertilizer plants. Although she sees that as a problem it is really the basis for improved yields and preventing more global hunger as well as allowing farmers to make a profit and food to be plentiful and cheap. Fertilizer can also be targeted in place and time to reduce runoff, which also can save farmers money. She goes on to advocate organic farming and agroecology. These are of course good things but in terms of yields and reducing land use for agriculture they are still way behind modern mechanized agriculture utilizing synthetic fertilizer. She seems to think organic farming reduced carbon footprints but more recent analysis suggests it’s the other way around, mainly due to less land required for comparable yields = less deforestation/more reforestation. More modern scientific analysis suggests that organic “methods” combined with efficient and smart use of synthetic fertilizers, and genetic engineering will be the best overall solution. More recently there is CRISPR gene-editing that may make GMOs more versatile. Her call to go back to the old ways of farming on a large scale seems rather anachronistic and naive in light of the massive success of modern methods.

Next, she considers airborne toxins that follow the weather to distribute themselves across the globe, even in remote parts of the world such as the Arctic. She mentions that in 2007 one-third of toxins released into the environment were released into the air. However, much of it probably ends up not heavily concentrated. There are chemical reactions that can combine to make new air contaminants from combusted material like how nitrous oxides and volatile organic compounds (VOCs) contribute to photochemical smog/ground-level ozone. This is a well-known pollutant in many urban areas and is considered to shorten life if one lives in an area of chronic smog. She thinks the increase of lung cancer among non-smokers may be attributed to particulates and smog. Oncologists and pathologists have also suggested that air pollutants like nitrogen dioxide may also help cancer spread from other areas to the lungs where it is difficult to treat.

Next, she considers water pollution, noting that it may be responsible for habitat destruction for many riverine species including water fowl. As in many place, she notes that water quality improved in the Illinois rivers due to the requirements of the 1972 Clean Air Act. The 1974 Safe Drinking Water Act set limits of certain chemicals allowable in drinking water. She notes the concept of “enforceable limits” of a few parts per billion of some substances like benzene and TCE where any amount is considered dangerous but water can only be “cleaned” to those enforceable limits. Most limits are in single-digit parts per billion. She notes that as of 2009 there were only enforceable limits established for 90 contaminants. Any device that heats water (showers, dishwashers, washers) can also release VOCs from the water so that water can also contribute to airborne toxics. Some studies have suggested that showers can be more toxic than drinking toxins in water. Again she considers chlorinated water, noting that chlorine combines with contaminants in water to make toxic by-products, some of which are organo-chlorines. She notes that about 600 of those by-products have been discovered with few tested for carcinogenicity. A few are monitored and regulated – trihalomethanes and haloacetic acids – and chloroform being the most common.  She favors alternative water disinfection strategies although chlorine has proven to be quite effective and removing chlorine has proved deadly in a few cases. She favors activated charcoal and ozonation but it is unclear how they compare to chlorine in effectiveness and cost. Manure from farms (which she laments the loss of) is the most widely implicated source of water contamination – so protection of source water can be key to preventing contamination. She does mention that using activated charcoal, then aeration, then using chlorine as the final (rather than the first) stage can reduce trihalomethanes – although aeration can make them airborne.  She also considers groundwater contamination through time and in different parts of aquifers (groundwater moves slow in some aquifers, faster in others). She notes that contamination in groundwater recharge areas, typically upland is more problematic than in discharge areas, typically lowland. Thus, protection of recharge areas is emphasized. Contaminated groundwater is difficult to remedy.

Next, she considers the effects of garbage incinerators, mainly on airborne contamination. These waste-to-energy plants vary in effect based on how the waste-stream is sorted and how effective are the pollution control systems. In modern times some systems claim 99% of contaminants are removed (although the 1% remaining still worries nearby residents). Places like Sweden use their WTE plants as a source of pride in the use of renewable energy while places in the U.S. may consider them sources of industrial toxicity. Perhaps it depends on how they are marketed and the propaganda. There is a long-standing debate about whether landfilling or WTE plants are better for the environment. Her analysis here is a few decades old so I won’t dwell on it. The bottom line today is how much pollution-control is implemented or in the case of landfills how sophisticated are the leachate collection systems, the groundwater monitoring wells, and the methane collection and pumping systems. Each project should be evaluated separately. Dioxin is one major toxin produced and clearly those who live nearest are the most affected. She documents studies on dioxin and how it may work to lead to cancer but the jury is still out on its effects and what an acceptable level should be. Burning most things produces some dioxins, including burning wood. She favors recycling but that too has costs and it is difficult for recyclers to make money and to get people to do it on a large scale. Zero waste is a nice concept but in reality it is far from achievable without massive changes in social habits.

Next, she considers ‘body burden,’ the sum total of all the effects of ingesting, inhaling, and absorption through skin of contaminants to get an idea of ‘cumulative exposure.’ We can measure the amounts of different contaminants in different parts of the body. The highest amounts of DDT, PCBs, and chlordane were found when those chemicals were most in production and use. Measuring levels of pollutants in people is known as “biomonitoring.” When lead was phased out of gasoline, blood levels of lead in children began to decrease and they ended up decreasing more than the models predicted so we know that changing the levels of some chemicals in the environment can lead to less of them in our bodies in a reasonable amount of time. Biomonitoring has also shown that banning smoking in public places has resulted in less “smoke” in our bodies. In 1999, the CDC began monitoring a group of 5000 people in 15 geographic locations for up to 148 chemicals. One surprise was the amount of flame-retardants we have in our bodies – these are potentially dangerous endocrine-disrupting POPs that we have way more in our bodies than Europeans. She notes that advances in chemistry have made biomonitoring more effective and cheaper. California was the first state to embrace biomonitoring but most states have followed suit.

She knows how cancer works:

“Destroying healthy tissue and clogging vital passageways, metastases are what make cancer deadly”

“… tumors are not just homogenous balls of bad cells. Rather, they are composite tissues, with cancerous and normal cells coexisting in a complex society. But the malignant cells are the ones running the casino.”

“They are Cells Gone Wild. They are defiant, disobedient, unstable, chaotic, and in the view of many cancer biologists, almost purposeful in the ways they disrupt cellular biochemistry.”

She goes through the stages of cancer development in detail, noting the three overlapping stages: initiation, promotion, and progression and how contaminants may affect each stage. More recently two processes: chronic inflammation and abnormal epigenetic regulation have been implicated in transforming cells. Obesity can increase chronic inflammation. Genes affect one’s ability to get cancer and so too does the environment. It is not one or the other but how the two interact. Environmental epigenetics is a new avenue of research investigating how contaminants affect epigenetics, the switches that turn genes off and on or otherwise code them. Oddly, she notes that the Inuit people of Greenland, via their own food chain and the way airborne contaminants have fallen on their region due to weather patterns (called global distillation in terms of contaminant transport) have the highest levels/body burdens of POPs -persistent organic pollutants.

She mentions studies of adoptees and ‘epigenetic drift among twins (the notion that as twins separate geographically that their epigenetic factors change). She is an adoptee and wishes she had access to her genetic history. She thinks the reverse may happen among adoptees – that their epigenetic factors converge with non-adopted siblings due to similar environmental factors. One study among identical twins in Scandinavia suggested that the chance of developing the same cancer as one twin by the other was 11-18%, which shows that genetics is a factor but not as strong a factor as expected, A recent Johns Hopkins study has suggested that cancer is so complex that determining the primary “cause” of most cancers is simply not possible. While cancer may be initiated by accumulations of genetic errors it seems more recently that abnormal regulations of genes by epigenetic factors is the reason. She notes that the Human Genome Study has revealed that we have less genes than thought before the mapping was done but more of those genes are implicated in cancer development than previously thought. She cites the Swedish Family-Cancer Database – the largest dataset of that kind in the world, suggests that family history of cancer plays a modest role in cancer development. She talks about oncogenes and adductors and an enzyme-based chemical detoxification process called acetylation as being factors in the likelihood one would develop cancer – if exposed to carcinogens, particularly early in life. People that are “slow acetylators” are more susceptible and that includes more than half of Europeans and Americans.

She compares a U.S Dept of Health and Human Services brochure to a Genetics textbook regarding the environmental factors of cancer development. The textbook considers environmental factors including smoking, lifestyle habits, and obesity, to be responsible for most (as much as 90%) cancers. Is it mainly a problem of behavior or exposure? We now know that one dietary factor – eating more fruits and vegetables – deceases cancer incidence. She thinks focus on behavioral and lifestyle factors tends to hide the environmental roots of cancer. We do know that occupational exposures, typically more than exposures among the general population to certain contaminants has led to increased cancer rates. She asks whether the obesity factor is also related to greater retention of pollutants, presumably along with greater levels of chronic inflammation. Epidemiologists have cautioned against attributing cancers to single causes and biomonitoring studies and how toxins interact in the body do suggest that complex causes involving many factors could be at play in most cancers.

She calls for green chemistry and the Precautionary Principle but in several cases the Precationary Principle has proven more harmful than beneficial. For instance, in genetic engineering, biotech, and gene editing, the banning of such process in Europe has led to the banning of them in parts of Africa where people could directly benefit from them through less hunger, better nutrition, and more successful and cheaper farming and food. Synthetic chemicals have done a lot of good in the world. Green chemistry is a good idea but may only be marginally applicable. Natural chemicals can also lead to cancer. There are trade-offs and no easy answers. There are extreme costs to re-organizing society on greener principles and there are unknowns. Its easy to say let’s have green energy now but there are toxins associated with these sources as well and tremendous costs and logistical problems. She favors “alternatives assessments” and I can agree – that we should explore alternatives to toxic solutions when possible. She also favors “full-cost accounting” where the health costs of toxic solutions are added in. Apparently, judging from her recent activism, she favors the Precautionary Principle in banning fracking as well. Fracking has resulted in massive decreases of particulate pollution and carbon emissions and better air quality as well as cheaper energy – all due to replacing coal with natural gas in power plants. That would not have occurred if the Precautionary Principle would have reigned as it has in areas where the process is banned. Most things that involve risk also have benefit and these need to be evaluated intently. There is also what is called “risk perception” which among humans has a very strong emotional component due to our evolutionary neurological development. Perception of risk versus real statistical risk can vary considerably. Uncertainty is often exploited by those who favor avoiding risks and those who favor taking risks. Studies have shown, however, that people are more willing to exploit uncertainty and emotionality to promote avoiding risks. Heart disease is bigger problem than cancer and yet people worry more about cancer, seeing it as more of a risk, perhaps because it is thought that we can reverse heart disease with lifestyle changes more than we can reverse cancer the same way.

Overall, this is a very good book: detailed and honestly written. She has worked hard to understand the issue of the environmental factors in the development of cancers. She is no fool. While I disagree with her anti-fracking activism I do understand and agree with her advocacy for better evaluation of chemicals and her call for more studies of environmental factors in cancer as well as getting rid of the most dangerous of chemicals.

Saturday, February 17, 2018

The Yoga of Light: Hatha Yoga Pradipika: The Classic Esoteric Handbook of Kundalini Yoga

Book Review: The Yoga of Light: Hatha Yoga Pradipika: The Classic Esoteric Handbook of Kundalini Yoga – by Hans-Ulrich Rieker, translated by Elsy Becherer (Dawn Horse Press, 1971)

This is the Hatha Yoga Pradipika, by Yoga Swami Svatmarama with commentary by Rieker, who studied intensively for many years with yogis in India. It was translated from Sanskrit to German and here from German to English. The translator sees the Hatha Yoga Pradipika as a “rare and fruitful combination of the two paths: hatha and raja {yogas}.” Rieker says that his translation and commentary here were not written from a desk but from the straw mats of India.

In the introduction Rieker notes that success in yoga can occur but requires devoted self-discipline. He notes the importance of the guru but also says that not every guru is a teacher and yet not every teacher is a guru. He notes that his kundalini guru (presumably Dr. Rammurti S. Mishra) was also quite learned in the shastras (commentaries).

The author notes that the text often reminds that the goal of yoga is to become a siddha, one who has developed powers or accomplishments of a magical or spiritual nature. However, striving for such powers can impede. In the opening stanzas Swami Svatmarama invokes Siva and Parvati, praises the goal of accomplishing raja, or ‘royal’ yoga, then invokes the gurus and siddhas of the lineage, beginning with Goraksha and Matsyendra. I should note that both of these yogis are part of both Hindu and Buddhist yogic lineages – they appear as founders of the Nath Yoga tradition and are also among the eighty-four Indian mahasiddhas of the Tantric Buddhist tradition. The Swami states that some yogis conquered time and roam still.

(10) [Therefore] hatha yoga is a refuge for all those who are scorched by the three fires. To those who practice yoga, hatha yoga is like the tortoise that supports the world.

The three fires refer to the three sufferings that are difficult to avoid: self-created suffering, suffering caused by higher powers, and suffering caused by other beings. Rieker states that sufferings are unfulfilled desires.

The Swami states that hatha yoga should be practiced in secret in a solitary place, preferably a windowless cave laid daily with cow dung! This is of course a cultural notion, but the idea is simply a quiet place free of distractions. Too much food, fasting, labor, company, vow observances, and talking are discouraged. Thus, moderation is encouraged. A cheerful disposition, perseverance, courage, self-knowledge, avoidance of bad company, and faith in the guru’s instructions are said to be the keys to success. Also, there is a passage that relates to the yamas and niyamas from Patanjali: avoiding the causing of harm to the living, avoiding stealing and lying, and to practice moderation – and to practice austerities, cheerfulness, faith, charity, contemplation, modesty, recitation of mantras, observing rules, and reading sacred works.

Before moving on to the next chapter on Asanas, Rieker gives some introductory information about the internal subtle body system of chakras and about the related notions of Ayurveda. Interestingly, he notes that the Tantric Buddhists posit that the yogi must ‘create’ the chakras. Many people seem to view the chakras and subtle body system of winds, channels, and drops sort of literally and fuss over details as if the ideas were scientifically precise. The way I see it, these ideas are props that point us toward drawing our senses inward (pratyahara) and working extensively with these aids or supports allow us to “yoke” our mind to them and reify an imagined perception of them – neurologically, an imagined perception produces similar effects to a “real” perception. The three doshas of Ayurveda, what he calls “the three dominant forces of man,” are explained since the links between yoga and Ayurveda are close. The three doshas are Vata, Pitta, and Kapha. Vata is wind or movement and is associated with the five pranas and their movement throughout the subtle body. Pitta has been translated as “gall” but is often related to temperament. It is the fire of digestion and of asceticism. Kapha has been translated as “life-fluid” or “phlegm” and refers to the liquids of the body and their roles. Kapha is also associated with soma as the divine nectar. The three forces will be in balance for optimum health. As said in the most famous Ayurvedic text, the Charaka Samhita:

“No pain without vata (the stream of life), no inflammation without pitta (the fire of life), and no swellings without kapha (the fluid of life).”

The asanas, or postures, of hatha yoga are said in the text to give the yogi strength, good health, and make the limbs supple. The first few given (with illustrations) are variations of sitting posture – some fairly easy, others difficult. The half lotus posture is called virasana, or hero’s posture. The tortoise posture, kurmasana, is given, where one sits cross-legged pressing the anus with one heel. Here Rieker digresses to note the tortoise symbolism in hatha yoga and Indian mythology – noting the story of Vishnu appearing as a tortoise to dive into the ocean and raise the mountain so the gods and demons (devas and asuras) can successfully churn the ocean milk with the serpent Apesh to produce the nectar. He suggests that this also has yogic symbolism related to raising kundalini. He also notes the line noted previously that “hatha yoga is like the tortoise that supports the world,” which confirms the connection. Thus, it makes the transformation of ocean milk to nectar possible or as Rieker suggests:

“Upon this “axis of the [human] universe” we exert pressure in kurmasana, so that the combined forces of the divine (subconscious) and the earthly (conscious) can accomplish their task.”

Other asanas are given – and most of these are not seen in any modern hatha yoga classes, at least in these forms. They are most often modified to make them easier or in many cases merely possible. A spinal twist posture called matsyendrasana is often modified in several ways to make it do-able. The effect is of churning (think again of the Indian myth of churning the milk ocean) and is sometimes referred to as chalasana (which refers to churning). From the text:

“(27) This matsyendrasana increases the appetite by fanning the gastric fire [pitta], and destroys physical ailments. Kundalini is awakened and the moon is made steady.”

This is said to direct the kundalini or at least the upward-moving prana upward. Rieker notes that variations in asanas and their names have come about from medieval times to now. For example, postures in the much later Gheranda Samhita have changed from those of the Hatha Yoga Pradipika. The kundalini is said to be wound into three and a half coils at the base of the spine just like the snake in the story of the churning of the ocean milk. The “moon” is said to refer to the upper point of the spinal column at the medulla oblongata and is said to be massaged by the matsyendra posture.

The posture called paccimasana is simply a seated forward fold while grasping feet, ideally with head laid between the knees. This is commonly practiced in modern hatha yoga classes and is often said to stimulate the immune system. In HYP it is said to cause “the breath [prana] to flow through the shushumna [central channel.]”

The first product of the ocean milk churning was sheer poison, called halahala. Shiva was said to swallow this poison which turned his throat blue. (Oddly enough there is apparently an Irish myth that is quite similar which suggests that the origin of this story may be of great antiquity since the Celtic and Aryan lines of Indo-European separated possibly several hundred to a few thousand years before the Vedas were thought to be composed). The mayurasana posture of standing on hands close to torso while in a horizontal position is said to neutralize the halahala poison. This is a difficult posture that requires arm/wrist strength and core strength. Rieker and the Swami see the churning of the ocean milk as an allegory for yogic attainment. According to Rieker:

“In the course of yoga training there occurs a transformation of consciousness from the “milk of devotional thinking” through the “poison of imperfect development” to the “nectar of enlightenment.”

Next the very well known posture savasana, or corpse pose, is given. It is simply lying on the back in a resting relaxation mode. However, simple as it is it is also said to be necessary.

The Swami notes that Siva taught 84 asanas. Next, he describes what are said to be the four most important ones. Siddhasana is simply sitting cross-legged with one heel pressing the perineum, the chin to the chest, and eyes focused upward. These positions stimulate the muladhara, swadhisthana, vishuddhi, and ajna chakras. There is another form of siddhasana given where both heels are up without one under. Siddhasana is said to be the most important of the asanas and is said to purify the 72,000 nadis. Nadis are channels throughout the subtle body. The most important nadis, of course, are the three that rise up along the spinal column: ida (left), pingala (right), and shushumna in the center.

The text states that the yogi who meditates on the atman eats moderately and practices siddhasana for twelve years attains siddhis. The atman refers to the soul or self, which the Upanishads first elucidated but which the Buddhists say doesn’t really exist.

Padmasana, or lotus posture is next given. This is like so-called full lotus posture with the arms crossed behind the back and grabbing the opposite feet and with head bowed to chest. Many of us would consider it, like several of the other postures, impossible. Perhaps medieval Indians had more anatomical flexibility or early training in such matters or perhaps approximating the position has a similar effect. Another padmasana is also given which is the basic full lotus posture with eyes focused on nose and tongue at back of upper teeth. The chin is pressed to the chest and the anus is contracted and this is done to slowly raise the air or downward-moving prana (apana vayu). It is said to destroy all diseases. Padmasana is said to straighten the spinal column and thus the shushumna and to draw the “bow of the nadis” as Rieker’s guru stated it. The apana is one of the five pranas. It flows in the lower regions below the diaphragm while prana only moves above the diaphragm. Thus the idea is to tie the two together so that the prana can enter the shushumna at the base of the spine. Apana is raised by frequent contraction of the anus while contracting the throat to force prana down.

Next is simhasana, sitting on the bent legs on the feet with the feet crossed underneath, again impossible for most. Hands are on knees. This is said to “facilitate the three bandhas.”  The bandhas refer to the binds or locks that control the pranas. Another is the simpler position of bhadrasana or gorakshasana, sitting on the feet with hands on thighs/knees. Goraksha was the Buddhist Mahasiddha without legs or arms so that is perhaps a reference to him. This pose is said to control unwanted desires.

The text then mentions concentration on the inner sound (nada), moderation, (with the celibacy of the brahmacharyin leading to fast results) and renouncing the fruits of one’s actions (a theme noted in the Bhagavad Gita). Moderation in diet means “pleasant, sweet food, leaving free one fourth of the stomach.” Sour, pungent, and hot foods are not recommended. Wheat/bread, rice, milk, fats, honey, cucumbers, ginger, water, and rock candy are recommended. In Ayurveda the prescribed foods for yogis are sattvic (light, revealing) referring to the theory of the three gunas (sattva [light, revealing, pure]; tamas [dark, concealing, heavy/inertial, impure]; and rajas [dynamic, passionate]) that are said to be the modes of material nature.

After perfecting the asanas comes pranayama:

“(2) When the breath “wanders” [ie., is irregular] the mind also is unsteady. But when the breath is calmed, the mind too will be still, and the yogi achieves long life. Therefore, one should learn to control the breath.”

The practice of pranayama (controlling the breath) is said to purify the nadis (channels). The yogi is urged to practice “with the mind in a sattvic state.”

Next is given a version of alternate nostril breathing, or nadi shodhana with kumbhaka, or retention of the breath. There are many versions of this about these days from many traditions. I personally have learned it in many different yoga classes, in Tibetan Buddhism, in Tibetan Bon, in Hindu ashrams and centers, and even in occultism – all more or less the same but also with significant variations, mostly surficial. Rieker notes that asanas aim at the spinal column while pranayama in centered in kumbhaka. The prescription in HYP is to practice kumbhaka four times a day. He mentions a commentary that gives the three phases of kumbhaka as holding the breath for 30, 60, and 90 seconds. The text says that the results of the three phases are perspiration, bodily trembling, and prana reaching the center of the head via the central channel (shushumna). Rieker also notes curiously that the yogi when doing asanas should not overly concentrate on the body and bodily position. He then talks about guyhasanas, special asanas given to a student after initiation and describes the process known as kriyavati, whereby the yogi’s body is cold except for the top of the head which is hot (presumably with raised prana) and impossible asanas are able to be performed through the consciousness of the yogi as well as magical feats akin to siddhis.

Milk and ghee are recommended early in a yogi’s practice. Signs of purified nadis are a perceived lightness and brightness of the body. Breath retention improves, the gastric fire is activated, and the inner sound (nada) can be heard. Good health is experienced. Kumbhaka is the key to pranayama and to keeping the breath alive with prana, says Rieker. He notes the stories of yogis living on one breath a day, stories echoed also in the Tibetan tradition. The idea is to keep the breath imbued with prana. Those prone to kapha disorders are prescribed the six techniques of shatkarma. These are also done in Ayurveda. The six techniques are dhauti, vasti, neti, trataka, nauli, and kapalabhati. Dhauti is swallowing a clothing and retrieving it back out from the throat and esophagus. Vasti involves inserting a bamboo pipe into the anus and flushing with water – basically an enema. Neti involves pulling a thread or piece of cloth through the nostrils and out the throat through the sinus cavities. One might also use a neti pot although that is not prescribed in HYP. Trataka is gazing without blinking on a small object such as a candle flame. The text says oddly that trataka should be kept secret. Tantric mahasiddhas also practices “ritual gazes” extensively, including willing things to move via a kind of ‘psychokinesis.” Nauli, said in the text to be the most important of the hatha yoga practices, is described thus:

“33-34 With the head bent forward slowly rotate the innards [intestines and stomach], like a whirlpool in a river, toward the right and the left.”

Nauli is said to remove sluggishness, stimulate the digestive fire, renmove disease, and produce an agreeable feeling. It is also said to train the muscles for dhauti and vasti. It is prescribed for the obese. Often it is given in the form of drawing in the abdomen while leaning forward with hands on knees, then moving it circular. Drawing in and up the abdomen in such a way combined with closing the anal sphincter is also taught in Tibetan meditation as a way to help balance the five pranas.

Kapalabhati, or shining skull breath, refers to quickly inhaling and exhaling like the bellows of a blacksmith, typically through the nose. It is a feature of modern yoga sometimes called ‘fire breath.’

Shatkarma is considered a nadi purification for the lower stages of hatha yoga while pranayama is considered more sattvic and for the higher stages.

The next practice given is closing the anal sphincter while drawing up apana (downward-moving prana) toward the throat and regurgitating what is in the stomach. This is called gajakarani and is said to bring the nadi chakras under control. The apana cannot go to the throat but pushes on the udana current which causes regurgitation. Apparently, this is not much practiced today. The text says that Brahma and the other gods practiced pranayama to remove fear of death and thus we should too. When the nadis are purified the breath will find its way into the central channel and this will bring steadiness of mind called unmani avastha. Kumbhakas are the key to getting there.

Here eight forms of kumbhaka are given along with bandhas, or locks. Jalandhara-bandha after inhalation and uddiyana-bandha after exhalation are given followed by kumbhaka. Jalandhara-bandha involves the ‘moon’ or upper part of spinal column while uddiyana-bandha involves the ‘sun’ or solar plexus. At the same time the throat is contracted and the anus in contracted – this is mula-bandha. Apana is forced upward while prana is forced downward from the throat which is said to lead to youthfulness. This bandha sequence reminds me much of what was called among Indian and Tibetan siddhas – “pot-belly breathing.”

The method for alternate-nostril breathing, or nadi shodhana, is given here in between periods of kumbhaka and also utilizing the ujjayi breath (ocean breath – making an ocean sound with the throat while breathing – this is taught in many modern yoga classes). This is called suryabheda kumbhaka.

Breathing in through the mouth with tongue slightly protruding from the mouth while making a hissing sound is practiced between kumbhakas. This is called sitkari and is said to make one beautiful and strong.

Other pranayamas and kumbhakas are given including bhastrika kumbhaka which is another form of “bellows breath” here prescribed between kumbhakas. Various yoga traditions teach bhastrika in somewhat different ways as I have experienced. Bhastrika kumbhaka is said to cause kundalini to rise and to pierce the three knots in the shushumna. This happens after the prana enters the shushumna and the bandhas bring the solar and lunar currents face to face so they can be knotted together. Bhastrika kumbhaka is a means of testing the learning of previous practices.

The next kumbhaka is rather cryptic – inhale rapidly making the sound of a male bee then exhale making the sound of a female bee. This is called bhramari. Rieker says that only a humming sound is necessary.

Murccha kumbhaka involves slowly exhaling while doing jalandhara-bandha and is said to produce an agreeable stupor.

Then filling the lungs with air the yogi “floats upon the water like a lotus leaf. This is plavini kumbhaka.

The text states there are three types of pranayama: inhalation, exhalation, and breath retention (kumbhaka). Two kinds of kumbhaka are also given: sahita and kevala. The text says one should practice sahita kumbhaka until one is able to practice kevala kumbhaka. Rieker notes that sahita refers to holding the breath without force or exertion and kevala refers to holding the breath when the blood is overoxygenized.   

Arousing kundalini is paramount and can be initiated by the guru and by the practice of certain mudras. Kundalini asleep coiled at the base of the spine closes the gate to the shushumna. Regarding mudras the text states:

“6-9 Mahamudra, mahabandha, mahavedha, khecari, uddiyana bandha, mula bandha, and jalandhara bandha, viparitaka rani, vajroli, and shakticalana; these are the ten mudras which conquer old age and death. – They have been given by Siva and confer the eight siddhis.”

Mahamudra involves pressing the anus with the left heal with right leg extended while practicing jalandhara bandha. This can cause the kundalini to stretch out or uncoil. The prerequisites for mahamudra are purification of the nadis and pranayama. Rieker notes that the goal of mahamudra is to guide the newly unified prana-apana stream into the now opened gate to the shushumna. At this point the two other nadis “die off” and the yogi appears dead and cold like a corpse with only the crown of the head warm. The prana-apana stream is said to carry the kundalini up through the shushumna. Mahavedha involves sitting in full lotus then putting the palms on the ground and lifting up and striking the ground several times with the buttock. It is said to make the prana leave ida and pingala and enter shushumna. Thus, it is the union of the three: sun, moon, and fire.

Next the khecari mudra which can be done by stretching the tongue over a period of months by gradually cutting further into the membrane which connects the tongue to the lower part of the mouth. In such a way it is said that the tongue can be made to reach the eyebrows. The mudra, however, has the tongue curled back into the throat for the yogic purpose of closing “the place where the three paths meet.” This mudra is said to free one from karma presumably due to the suspension of time, according to Rieker. He says the khecari mudra (the word khecari means to ‘move through the empty sky) aids an undisturbable meditative absorption. The mudra is thought to affect some process of endocrine secretion, possibly a glandular secretion that is equivalent to the kapha secretion. This kapha secretion is the soma, or nectar – the same as that hinted in the lore of the churning of the ocean of milk but here in allegorical form. It is said that yogis who perform miraculous feats like being buried for days or eating poisons do so by preparation with khecari mudra so that they will be immune to the dangers. The nectar (of the moon, soma) becomes like a fuel that protects as long as it can be produced. The nectar may cause one to be able to teach all the Vedas and Shastras due to the power of the throat chakra vishuddhi where cognition can be transformed into word. The poison from the churned milk ocean is sequestered in Siva’s throat. The throat where the nectar is secreted represents the “upper part of Mount Meru – that is the shushumna.”

Now he and the text return to the bandhas, first summarizing:

“Mahamudra: the joining of prana and apana.

Mahabandha: preventing prana and apana from reverting their course

Mahavedha: connecting the three nadis by beating the buttocks on the floor

Khecari mudra: bending back the tongue”

Uddiyana bandha – drawing up the intestines toward the navel so that they touch the back and diaphragm. This causes the prana to “fly up” through the shushumna. Mula bandha – pressing scrotum with heel with contacted anus – guides apana upward. Mula bandha awakens the dormant kundalini. “Through mula bandha, prana and apana as well as nada and bindu unite to give perfection to the yogi.” Jalandhara bandha – pressing chin against breast with contracted throat – is said to make the nadis taut and prevent downward flow of nectar from throat. The nectar of the moon is prevented from being swallowed by the sun where it would drop. This is said to stop the aging process. Another practice is mentioned but not elaborated since it can only be learned from a guru. That is the process called viparitakarani, whereby the sun in the solar plexus and the moon in the throat change places. It involves practicing the head stand and is said to be able to reverse aging. I assume the reverse of position changes the relative gravity.

Rieker actually leaves out a section of HYP, slokas 84-103. These describe vajroli mudra, sahajoli mudra, and amaroli mudra. The text says that if one practices the yamas and niyamas one can attain siddhis through the vajroli mudra, even if one maintains a worldly life. I think this is unfortunate. Vajroli mudra is practiced as cutting off the flow of urine in a specific way. It is said that a male can control ejaculation in such a way and females can strengthen vaginal control. I am guessing that perhaps he leaves this section out because he and/or his guru were influenced by the anti-Tantric sentiments among some Hindus, especially toward sexual practices, who were in turn influenced by the morality of Victorian English sentiments. Rieker notes them as “obscure and repugnant practices that are followed by only those yogis who lack the will power to reach their goal otherwise.” That certainly suggests a bias.

Shakti is often defined as the feminine energetic aspect of divinity. Kundalini is also shakti and may be called kundalini-shakti. The text describes the raising of kundalini – shakti calana kriya. She is described as a young widow. Her spouse in sahasrara (crown chakra) is Vishnu. The kundalini serpent should be aroused by grasping it by the tail. Rieker says that prana and apana pull on the head of the serpent. This the allegory continues where the gods (devas) pull the tail and the demons (asuras) pull on the head of the great serpent to churn the milk ocean. Rieker also notes that: “Hatha yoga is composed of jyoti (light) and mantra (sound).” Light and sound are the means to manipulate kundalini through the tail. The kanda where lies the coiled and sleeping kundalini is said to be four inches above the anus. The asanas, pranayama, and mudras purify the nadis and straighten the shushumna so that the kundalini can flow unimpeded.

According to the text, the guru, Siva, is said to be in the form of nada, bindu, and kala. Nada is the lower range of vibration – sound and kala is the higher range of vibration – light. Rieker calls bindu the principle of intelligence. He also calls bindu – sense. Bindu is also “drop, period, zero, seed, the void.” Rieker speaks of three levels of reception of vibrations. The text speaks now of samadhi (meditative absorption) and gives synonyms: “Raja yoga, samadhi, unmani, manomani, immortality, dissolution, emptiness-but-not-emptiness, the highest state, passivity of the intellect, non-dualism, beginninglessness, purity, liberation in this lifetime, the primordial state, and turiya (the Fourth State),…”

It is also the union of mind with atman/Brahman and the union of jivatman and paramatman (individual self and divine self). It is also the union of mind and prana/breath.

“(8-9) He who recognizes the true meaning of raja yoga can by the grace of the guru achieve realization, liberation, inner steadfastness, and the siddhis. Without the grace of the guru and without indifference to worldly things recognition of Truth, [attainment of] samadhi, is impossible.”

The grace of the guru as a requirement and spur to liberation is well attested in Tantra and among the Mahasiddhas.

The text notes that after kundalini is successfully raised then “emptiness [sunya] absorbs prana.” This leads to samadhi and the destruction of karma. Rieker calls samadhi the karma-free state. What he doesn’t say is that samadhi is often considered to be a temporary state with several different forms, at least in other systems such as Buddhism. Samadhi may have different meanings in this regard. Buddhists might say that karma is not created during samadhi but resumes when one comes out of the meditative absorption, unless the state is the irreversible state of enlightenment, which might be considered a sustained samadhi.

“(17) Sun and moon cause day and night. The shushumna [however] swallows time. This is a secret.”

There the sun refers to pingala nadi and the right nostril and the moon refers to ida nadi and the left nostril. Equilibrium between both nostrils and all inner functions is required. The text also notes that mind and prana depend on one another and often change together, where one goes so goes the other.

“(29-30) Dissolution [laya] depends on nada {sound}. Laya produces prana. Prana is the lord of the mind [mano]; mind is the lord of the senses [indriyas]. When mind is absorbed in itself it is called moksha [liberation]. Call it this or that; when mind and prana are absorbed in each other the immeasurable joy of samadhi ensues.”

Laya yoga, the yoga of dissolution, is called passive yoga by Rieker. Dissolution is into the Absolute, into Brahman, and there is no breath (prana) or mind and no longer any subjective experience. The text says that laya is the state of forgetting, forgetting subjectivity in the form of sense objects and impressions (samskaras) on consciousness that become the seeds of karma.

The next topic is shambhavi mudra. Riekers says that: “Dissolution is samadhi; re-creation is shambhavi mudra, work with the sound symbol (mantra) and the image symbol (yantra), the source of inner light.” It involves focusing the eyes outwardly on an external object and the mind inwardly on a chakra. When mind and prana are absorbed by the object(s?) it becomes shambhavi mudra. The word shambhavi refers to Siva as Shambu. Shambhavi mudra and khecari mudra are one in that they both “bring about the state of bliss in the concentrated consciousness of the mind absorbed in atman.” Realization of Truth via shambhavi mudra (as learned from one’s guru) manifests in the form of an inner light. This inner light is said to be the source of all and the highest realization. The lingham, or phallus (of God or Siva), is a symbol of the inner light. Rieker points out that shambhavi mudra is an inner process while khecari mudra is a technical process - blocking the shushumna at the throat with the curled back tongue to stoke the fire. Khecari mudra is the prerequisite for shambhavi mudra. The text also says that through meditation the shakti and mind become one. At this stage the yogi is said to become like an empty pot at the bottom of the sea – simultaneously both empty and full.

The last topic is nada (sound) as described by Gorakshanath. The Swami says that while there are numerous paths to laya, that he thinks nada is the best. The text gives four stages of yoga practice: introduction, transition, attainment, and perfection. In each stage prana pierces one or more of the three knots (granthis) except in the second stage where it also enters the heart chakra – so first the brahma granthi at the heart chakra is pierced which has associated tinkling sounds, then entered into when nada and prana are unified. Then the vishnu granthi at the throat is pierced which is accompanied by a complex sound like that of a big drum, followed by the piercing of the granthi at the agna chakra at the forehead. This initiates the fourth stage which is accompanied by the sound of the flute and the vina (guitar). The Swami states that: I believe that concentration on the space between the eyebrows is the best way to reach samadhi in a short time. For those of small intellect this is the easiest means to attain to raja yoga.” This statement is likely the basis for some of the modern nada yoga cults. The nada is said to progress from ocean-like and drum-like sounds to sounds like flutes and harps experienced from the center of the body. The text speaks of the dissolution of the sensory world into the nada laya so that concentration on the non-conceptual inner sound (nada) after such is developed, effectively replaces any concentration on sense objects and conceptuality. The inner light (kala) and the inner sound (nada) are revealed as indistinguishable. In the Vedas and Upanishads it is said that sound came to be when space (akasha) came to be. “In soundlessness atman and Brahman are one. Whatever is manifested as sound is a power of nature [shakti]. The state of dissolution [laya] of conceptual thought is beyond all form. It is divine [paramesvara]”

The perfected yogi can only be described in contradictory terms: his mind is neither awake nor asleep, he is free from remembering or forgetting, not dead yet not living, seemingly asleep yet awake, etc. He is transcendent yet seemingly immanent.

The Hatha Yoga Pradapika is certainly an enigmatic text. This translation and commentary is fair but informative and with some bias – certainly more has been learned in the 46 years since this one was published. The actual yogic path described in HYP is quite difficult, sometimes seemingly impossible, and often unclear. Embarking on such a path without a guru in a well-defined lineage is likely untenable. However, the principles of the text do give insight and support to a detailed and intricate philosophy of yoga and tantra practiced by both Hindus and Buddhists and possibly Jains. and more recently by a small percentage of Sikhs and modern Western yoga practitioners, at least those who follow Yogi Bhajan’s tradition which is often the main form of “kundalini yoga” presented in the west as such.