A (Random) Table of Contents | Common Science Space

Science and Sourdough

Sourdough bread-making depends on two kinds of fermentation, the development of carbon dioxide (and ethanol) by yeast, and the production of lactic acid, and a range of other flavour components, by lactobacilli. Although the organisms are known, their exact makeup varies, and provides for the flavourful variations. There is a recipe.

You Need Creatine

Creatine plays an important role in muscular work and fitness. It is converted to phosphocreatine, which is used to replenish ATP, particularly during anaerobic workouts. Aerobic, long-term athletic activity is not as dependent on phosphocreatine, and is thus not affected by creatine loading.

Three Cancer Myths Revisited

Three stories are often heard with respect to cancer. First, that cancer is at epidemic proportions; it isn’t. Second, that having an abortion increases a woman’s chance of breast cancer later in life. It doesn’t. Third, that vitamin C at high doses helps cancer treatment. That one is still up in the air.

A Brief History of messenger RNA

mRNA vaccines for SARS-CoV-2 (Covid 19) have been engineered and approved for human use. The history of mRNA is one entangled with genetic expression models. The first mention of messenger RNA (mRNA) was in 1960.

Geothermal, a Continuous, Renewable, Energy Source Without Greenhouse Gases or Radioactive Waste

The heat of the earth’s mantle can be used for both heating and electrical power generation. Heat pumps, direct heating from hot wellwater, and power generation from superheated water and steam are available throughout the world. This source of energy is almost entirely free of greenhouse gas production and radioactive waste.

Running Out of Sugar and Hitting the Wall

The use of fat and carbohydrate for energy during the marathon is connected. While muscle glycogen can be used to exhaustion, fat is essentially inexhaustible. But the use of fat by the muscles depends on carbohydrate being available. When carbohydrate is depleted, energy generation from fat goes way down, and the runner hits the wall (bonks). Hitting the wall is due to exhaustion of carbohydrate stores, not hypoglycemia.

Can Biology Save Us From Plastic Pollution?

Plastics currently contaminate the world, including its oceans. There are biological solutions to this pollution. Plastics can be produced from biological materials and disposed of without increasing greenhouse gases. Conventional plastics can also be degraded by certain bacteria to produce the starting material originally derived from petroleum.

Experimenting on Yourself

Do It Yourself treatments for medical conditions have a long history. Sometimes they are clearly useless, other times, they may offer a potential improvement in health. Calorie restriction is one area that is still under contention, at least in humans. But self-treatment with potential vaccines to COVID-19 may be useful in determining the immune response. And self-experimentation made a big difference to our current treatment of stomach ulcers.

GMO

It’s important to evaluate any new and powerful technology for risks as well as benefits, and Genetically Modified Organisms are no exception. However, some stories about damaging effects of GMO are clearly unfounded. In particular, the case of the large scale mass suicide of farmers in India as a result of the introduction of the Bt gene into cotton is demonstrably bogus.

Malaria: No Simple Solutions

When it was first introduced, the insecticide DDT had a near-miraculous effect on the fight against malaria. It was badly overused, particularly in agriculture. Rachel Carson and others began to see evidence for a devastating effect of DDT on bird populations, particiularly raptors, and it was subsequently banned. Malaria made a return, although it is currently checked somewhat by the ancient Chinese drug Artimisinin. There is now a lot of evidence, however, that DDT probably does not have as devastating an effect on birds as originally thought. The issue is not resolved.

Your Travels Are Written in Your Body

Analysis of isotopes by mass spectrometry has been instrumental in many fields. It has helped identify victims of crime, the diets of native Americans 14,000 years ago, and the sources of illegal drugs. The basis for this is, that different parts of the world have different “signatures” of isotopes of common elements, and these serve as identifiers.

Calories In Equals Calories Out?

Most of the calories we consume are consumed by the Basal Metabolic Rate (BMR), which is the energy it takes to drive all of our bodily functions. Additional calories are used for other activities. The idea that we are what we eat (or as much as we eat) is supported by the idea that in the past 50 years Americans have increased their food intake by a large percentage, and correspondingly their Body Mass Indexes.

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The Gila River People, Victims of Modernity

The Gila River people of Arizona have the highest rates of Type 2 diabetes (T2DM), and obesity, in the world. Yet for thousands of years they were successful agrarians, growing foods in the desert while benefitting from the river that sustained them. And they were lean and fit. In the early twentieth century they were deprived of their water and their independence, and subsequently became indigent, obese, and subject to T2DM. Their genetic cousins in Mexico, who are still subsistence farmers, retain the old fit physiotype, and remain relatively free of T2DM. Nature, and nurture, both matter.

The Trouble With Roundup

The much-talked-about chemical herbicide Roundup (glyphosate) is blamed for numerous environmental problems, including the loss of migrating Monarch butterflies. It is thought to cause cancer by many people. However, both of these conclusions may or may not be correct, or may be partially correct. But an existential problem exists for Roundup, and will doom its future: the spontaneous occurrence of weeds resistant to it. Over 125 million acres of farmland in the USA are already infested.

Speed Limits

The speed that a human can run is dictated by various factors, including the source of energy that is being used for the race. Short races are fueled by anaerobic energy sources, and longer ones by oxygen-dependent metabolism. These energy sources are smaller/quicker and larger/slower, respectively. The question of why East Africans are such superb marathoners is considered.

Saving Vision and Lives, One Sweet Potato at a Time

Vitamin A has been found to be essential for overall health, particularly for very young children. A deficiency of vitamin A endangers not only vision, but life itself. The orange vegetables, carrots and orange sweet potatoes, provide a good solution in parts of the world, like Africa, that is at risk for vitamin A deficiency.

A Great New Book

I’ve written a book about Vitamin A, one of the most important, and frequently deficient, micronutrients in the developing world.

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Human Energy Metabolism I: The Body at Rest

The Resting Energy Expenditure of humans is correlated with fat-free mass, with a lot of data scatter. A new method of estimating REE is to use magnetic resonance imaging to estimate organ sizes, and to use estimated energy consumptions per gram of tissue to determine the total REE. This provides a more accurate prediction of REE.

Human Energy Metabolism II: The Body in motion

During exercise, the human body uses between 15 and 25% of the energy of the food it consumes to actually power the exercise. In addition to skeletal muscle, other organs in the body must work much harder during intense exercise. Metabolic efficiency does not vary greatly for a given activity.

The Inefficiency of Humans

Humans, like other animals, use the energy in food for many different things. Doing muscular work such as riding a bicycle can consume a lot of energy, but even highly trained athletes can only convert about 20-25% of the energy of food into such activity. The rest of the calories expended are needed to maintain the body and carry out the myriad functions required for life.

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The Future of Coronavirus

COVID19, and the SARS-Cov-2 virus resonsible for it, will probably be around for some time. Attempts to control the disease now or in the future include case detection and tracing, drugs that specifically target the RNA-dependent RNA polymerase, attachment of the virus to cellular receptors, and mitigation of the cytokine storm that can result from infection.

The Drift of Coronavirus

RNA viruses such as the SARS-CoV-2 virus responsible for COVID-19 mutate at a much higher rate than cellular or viral DNA. This is responsible for the initial jump to humans from bats. It also allows for geographic tracing of the spread of the virus. The different mutation rates of RNA and DNA arise from known principles of their replication.

The Environmental Cost of Beef

Greenhouse gas emissions due to beef production are high, but much lower in the first world than in the developing world because of higher quality animal feed. In the USA, food wastage has a higher greenhouse gas cost than eating beef. Foods like dairy, pork and chicken cause much less environmental damage than beef.

Mice and Men

Laboratory mice have been instrumental in much of biomedical research, including recent efforts to combat cancer with targetted immune cells. The origins of their use, however, are not well known. They arose from the inbred mice raised by “mouse fanciers” over centuries, followed by directed inbreeding in laboratory supply companies. Miss Abbie Lathrop, a retired schoolteacher, was instrumental in bringing the fancy mice to the attention of biomedical scientists.

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Circadian Rhythm I — The Plant World

One of the first observations of circadian rhythm was made with a plant in the early 18th century. Plants undergo circadian rhythm when they raise and lower their leaves during the day. This is not a response to light, it is an intrinsic activity that operates independently of illumination.

Circadian Rhythm II — Us

We humans are well aware of circadian rhythm – every time we take an extended east-west flight we end up a little disoriented at the end. The genetics of human circadian rhythm is being described with an early assist from the humble fruitfly, where genetics studies are relatively easy to do. Some human behaviors are beginning to be understood as arising from genetic alterations in the genes governing circadian rhythm.

You Can Eat Fat, But Don’t Get Fat

Obesity certainly poses a health risk for humans, but the risk is a little more complex than most people imagine. It is possible to be too thin. The lowest risk of dying for adults is actually experienced for body mass index (BMI) in the high-normal or even low-overweight range.

The Big Fat Myth

The idea that dietary fat increases heart disease has been embedded in our culture for a long time, and no amount of evidence that refutes this idea is able to dislodge it from our food guides and thinking. On the other hand, replacing saturated fat with unsaturated fats does appear to have a beneficial effect; replacing fat with carbohydrate does not.

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DNA Profiling I

The discovery that human DNA contained a large number of polymorphic (“having many forms”) sequences was pivotal in developing DNA profiling (fingerprinting). These sequences have different numbers of tandem repeats of short motifs. Unrelated people have numerous differences in these patterns. Such DNA patterns were discovered accidentally, but soon gave rise to a great improvement in forensic science.

DNA Profiling II

The invention of DNA profiling led to immediate application to forensic science. However the initial methods were of limited sensitivity. Invention of the Polymerase Chain Reaction increased the sensitivity enormously, because DNA sequences, such as the fragments containing Variable Numbers of Tandem Repeats, could be amplified thousands, millions, or billions of times. The sequence determination of DNA, its synthesis, and DNA cloning were also instrumental technologies in the development of DNA profiling.

Life Expectancy I: How Far We’ve Come

There was a huge increase in life expectancy in modern world countries during the twentieth century. But there are variations, and the factors which led to an overall increase are more complex than most people think. For example, sanitation was probably more important than antibiotics.

Life Expectancy II: It’s in the Genes

Life expectancy in humans and animals is partially determined by genetics. The nature of the genetic relationship has been illuminated by studies in the roundworm. Energy metabolism is intimately involved.

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The Great Comon Sense of SEWTHA

A physics-based, common-sense approach to our problem with energy usage is provided in a great book by the late Dr. David MacKay. He has shown, with numbers, what we need to do to stop overproducing CO2 and save the world from global warming. The solutions are not easy.

Save the Environment — Don’t Walk, Drive a Car

We waste an huge, and growing, amount of fossil-fuel energy producing food. We also waste a lot of food. There are a number of sensible things we can do to stop wasting so much energy producing food.

The Unexpected Link Between Cheese Consumption and Lung Cancer

We are bombarded with medical stories in which correlations are used as evidence for a link. For example, cheese consumption and the incidence of lung cancer in the USA went up together before 1995, and it could have been used as evidence for a linkage, except that it seems ludicrous. But after 1995, the two trends diverged dramatically. Correlation is not proof.

Single Malt Scotch Whisky 101

Single malt Scotch whisky is made from just 3 ingredients, more or less identical for each distillery. By the time it is bottled, whiskies from different distilleries have widely different compositions and taste. Whisky drinkers know this, and modern analytical studies confirm it. Some components of finished whisky arise during distillation, some are contributed by the charred wood of the barrel, some arise during aging.

How Dinitrophenol (DNP) Kills You

Dinitrophenol (DNP) causes uncontrolled fever and cramping of muscles because it is an uncoupler of mitochondrial energy production. It interferes with the resynthesis of ATP by destroying the proton gradient that drives it.

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Is Air Conditioning Going to Become Futile?

Air conditioning uses a lot of electrical energy. It is particularly significant on hot days in New York City. But it doesn’t contribute significantly to the heat of the city, compared to the effect of sunlight. Putting solar panels on the roofs of buildings would go part way to providing the city’s electrical needs.

The Greatest Innovations and Breakthroughs

A provocative list published in The Atlantic points to the 50 most important innovations and breakthroughs since the wheel.

The Death of Ponte Morandi

The Ponte Morandi in Genoa, Italy, collapsed on August 14, 2018, killing 43 people. The collapse has been blamed directly on corrosion of the reinforced concrete used in its construction. But poor design and management of the structural inspections has also been cited.

Three Cancer Myths Revisited

What Should We Do About Garbage? A Burning Question

Incineration of municipal solid waste to produce electrical energy and heat has been shown to be beneficial to the environment. The latest versions of such incinerators destroy dangerous organic chemicals and remove heavy metals from the effluent.

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We Need to Talk About Methane

Methane contributes to global warming, and its contribution is growing. Levels of atmospheric methane have gone up nearly 70% since 1950. There are many anthropogenic sources of methane, including industrial activities and agriculture, although the eructation and flatulation of cows makes only a modest contribution.

The Art of Scientific Discovery

There are several pathways to biomedical discovery. Some discoveries are the result of a realized intention, some are due to mass screening, some are serendipitous, and some are the product of modern genetics and biological homology. Most are a combination.

The Curious Case of the Friendly Russian Foxes

Wild foxes avoid human contact. However, selection for “friendliness” in a Russia research lab has resulted in foxes that behave like friendly dogs. There is clearly a genetic component of this trait, but also an environmental one. This development is consistent with the Modern Synthesis abouit population genetics, which says that multiple versions of genes already exist in the population, and will emerge rapidly when properly selected for.

Blue-Green Algae: The Good, the Bad, and the Ugly

Blue-green algae, or cyanobacteria, can severely affect bodies of water when they undergo massive blooms. This is currently happening in Florida. But cyanobacteria have been important in other ways: they were probably responsible for creating an oxygen-rich atmosphere on earth, and they undergo a genetically well-understood type of circadian rhythm.

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How Many Calories in Bacon?

Bacon does not contain a massive amount of caloric energy: properly prepared, only about 144 Calories per 100 grams of raw bacon, as determined experimentally. But it is not a health food, and poses other dietary concerns.

The Fading Memory of Water

The conventional scientific world was shocked in 1988 when a respectable and widely-admired French scientist claimed to have proof of a basic tenet of homeopathy. However, his evidence was debunked by further analysis, and he never recovered his reputation as a scientist. There is currently no evidence that he was right.

Using Numbers Instead of Adjectives to Evaluate an Economic Decision

The issue of whether to build a second pipeline to carry crude oil from Alberta to Burnaby, BC, should be considered in terms of whether it will pay off for the governments and the people involved. The argument made here is that it has little economic advantage, while posing serious environmental risk.

The Science of Better Burgers

The effort to cook a better hamburger involves a struggle between safety (insuring that the meat is sterilized by cooking) and taste (avoiding overcooking, which kills the taste). A solution is provided by sous vide cooking at a moderate temperature, for a time long enough to make the burger safe.

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Why There is so Much Talk About Epigenetics

Transgenerational epigenetics is a controversial subject, because if it exists it suggests to some people that Lysenko, the evil Soviet geneticist, and Lamarck, the early French biologist, were right. Well, it may (exist), and they weren’t. Our genetic inheritance is Darwinian, but there may be temporary tweaks due to environmental effects.

Fastball: Movement and Speed

The fastball pitch in baseball is subject to various forces, including the Magnus Force, which works against gravity. The amount, and direction of spin imparted to the four-seam fastball dictates how far it will “fall” on its 450 millisecond trip. Because of the limits of human reaction times, the batter has to make an estimate on where to expect the pitch to be when it crosses the plate. However, the fastball cannot rise. And the knuckleball has a lot in common with round cannonballs.

Chronic Myeloid Leukemia: A Molecular Diagnosis

A surprising observation in the 1950s, that the cells of the cancer Chronic Myeloid Leukemia always bore the same chromosomal abnormality, led to the discovery of the mechanism of this rare, but previously deadly, cancer. The genetic abnormality was due to a chromosomal translocation that activated a particular cellular enzyme, a protein kinase, and this led to uncontrolled growth.

Chronic Myeloid Leukemia: A Molecular Solution

Chronic myeloid leukemia is one of those rare cases where a chance discovery of a molecular inhibitor of a known enzyme can completely stop the disease. The discovery hinged on the fact that CML cells have a characteristic genetic translocation, which was found to activate a potent cellular protein kinase. Chemists found an inhibitor for this kinase, and it turned out to effectively treat the disease. This drug is called Gleevec.