The U.S. Preventive Services Task Force has published new guidelines for prostate cancer screening.  The report in the Annals of Internal Medicine points out that the benefits of the Prostate Specific Antigen (PSA) test are uncertain or minimal, whereas the risks are large and dramatic.  The PSA test itself is just a simple blood test; it is what happens after an elevated PSA result is obtained that causes the harm.

The level of PSA which indicates cancer is not the same for every man.  Therefore, it is necessary to do surgical biopsies to determine if there is cancer.  A positive PSA test causes anxiety and may lead to unnecessary surgical biopsies which can be painful and cause serious complications.  Several studies have shown that men age 65 and older who were not treated for prostate cancer were equally likely to survive as those who were treated.  Many of the ones who were treated ended with impotence, incontinence or other undesirable side effects.  The new recommendation basically concludes that if the therapy is not providing substantial benefit, the screening is not beneficial either.

In the US, prostate cancer is diagnosed in about 186,000 men each year, and about 29,000 die from it.  There is some evidence that the phytonutrients and polyphenols in pomegranate fruit juice and green tea can reduce PSA levels and prevent prostate cancer.[1,2]

[1] Arshi Malik, Farrukh Afaq, Sami Sarfaraz, Vaqar M. Adhami, Deeba N. Syed, and Hasan Mukhtar, Pomegranate fruit juice for chemoprevention and chemotherapy of prostate cancer, Proc Natl Acad Sci U S A. 2005 October 11; 102(41): 14813–14818.

[2] Gupta S, Ahmad N, Mukhtar H., Prostate cancer chemoprevention by green tea, Semin Urol Oncol. 1999 May;17(2):70-6. PMID: 10332919

The northern hemisphere of Mars has a giant basin, called the Borealis Basin, that covers about 40 percent of the surface of Mars.  The basin is 8,500 km across and 10,600 km long, and it is larger than the combined area of Asia, Europe and Australia.  The northern-hemisphere basin is one of the smoothest surfaces found in the solar system, whereas, the southern hemisphere is high, rough, heavily-cratered terrain, which is 4 to 8 km higher in elevation than the basin floor.

The Mars Reconnaissance Orbiter project from NASA has provided some interesting information about the topography and gravity of Mars that has shed some light on the mystery of why the two halves of Mars are so different.  MIT scientists have used the data to deduce that the basin was formed by the impact of a colossal asteroid[1,2].  The scientists also created models to calculate the kind of impact that would have been required to create the basin.

It is estimated that the impact on Mars ocurred around 3,900 million years ago.  This is the time when the Earth and the Moon were subjected to a cataclysmic meteorite bombardment, also called the Late Heavy Bombardment.  It is possible that the debris of the great cosmic collision in Mars was the cause of the devastation of the Earth and the Moon during their early development.

[1] Jeffrey C. Andrews-Hanna, Maria T. Zuber, W. Bruce Banerdt, The Borealis basin and the origin of the martian crustal dichotomy, Nature 453, 1212 - 1215 (26 Jun 2008), doi: 10.1038/nature07011, Letters to Editor

[2]  David Chandler, Solar system’s biggest impact scar discovered, MIT News Office
June 25, 2008

Aubrey de Grey

For thousands of years, preachers have been promising us eternal life, in heaven or hell, depending on what we believe. Now, Aubrey de Grey, a British biomedical gerontologist, thinks that we can achieve eternal life right here on Earth by rejuvenating the human body. The idea of immortality seems preposterous given that, thus far, no multicellular organisms have been found to live forever.

Aubrey de Grey cannot be easily dismissed. His ideas about Strategies for Engineered Negligible Senescence (SENS) are based on sound scientific principles and modern discoveries in genetics. De Gray would like to identify all the components that cause human tissue to age and design remedies for each of them to forestall disease and eventually push back death.

Immortal life may be nothing more than a pipe dream, but there are enough serious scientists studying the process of aging that in a few decades there may be significant advances in the science of life extension. The Methuselah Foundation is a non-profit organization that promotes interest in scientific anti-aging research. The foundation awards prizes to researchers who break records in the extension of the lifespan of experimental animals.

Automation has been wonderful for humanity.  Many of the things on which we depend are produced by machines at a fraction of what they would cost if they were produced manually.  Cheap watches, cheap cars, cheap clothing, cheap computers, everything is cheap, cheap, cheap because it is mass produced using assembly lines with many different types of machines.

In the past, people worried that machines would replace them.  Labor unions fought against the adoption of automation that would result in job losses.  Eventually, the proponents of automation won because the prices for products could be lowered while production could be increased thus saving the jobs.  Our machines are powered by cheap coal and petroleum which originated from the decay of prehistoric plants and animals, but burning coal and petroleum increases the levels of carbon dioxide in the atmosphere.  Carbon dioxide is a “greenhouse gas” that is associated with global warming.

Times have changed.  Petroleum is not so cheap anymore.  Greater costs provide an incentive to search for new forms of energy.  The idea of burning biofuels, i.e, fuels derived from contemporary plant matter rather than from ancient organisms, has a lot of appeal because it provides an alternative to expensive petroleum and limits the increase of greenhouse gases.  The carbon dioxide generated when a biofuel is burned, is the same gas that was sequestered from the atmosphere by the plant as it grew.  Thus, there is no net increase in carbon dioxide.  The use of ethanol from corn has been promoted as a fuel on the basis of this thinking.

However, there is one BIG problem.  The World Bank estimates that the grain required to fill a 25-gallon sport-utility vehicle tank with ethanol could feed one person for a year.  The United States uses approximately 375 million gallons of fuel per day.  It is not possible to quench this tremendous thirst for fuel with all the corn fields of Iowa and Kansas.

In the past, machines used coal and petroleum products that were not suitable for human or animal consumption. Now, humans and farm animals will have to compete with machines for food.  The use of human food to power machines seems inhuman, immoral, and short-sighted.

In the late 1860s Thomas Huxley suggested that birds descended from dinosaurs. In 1911, Othenius Abel proposed that birds came first and that dinosaurs are descendants from birds. Skeletons of “transitional” bird forms found in the 1990s strengthened the argument that birds descended from dinosaurs. Recent discovery of well-preserved protein from a Tyrannosaurus rex bone has made it possible to analyze the fragments of collagen proteins and determine that Tyrannosaurus rex was definitely related to birds.[1] A chart presented by the scientists shows Tyrannosaurus and Gallus next to each other, which means that Tyrannosaurus and chickens are related.

There are skeptics who doubt that protein from dinosaurs would have remained unaltered for 65 million years, but the analysis of molecular data from long-extinct organisms may have the potential for resolving relationships in the vertebrate evolutionary tree that have been impossible to determine with current phylogenetic techniques.

Not too many years ago, Michael Crichton wrote the science fiction story “Jurassic Park“, where extinct creatures were brought back to life by replicating DNA from fossils.  Although Crichton’s idea is far-fetched, the idea of cloning a woolly mammoth using DNA from a frozen specimen found in Siberia has received more serious consideration.

Learn about the Timeline of the Earth

[1] Molecular Phylogenetics of Mastodon and Tyrannosaurus rex, Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, and John M. Asara, Science 25 April 2008: 499

Human protein requirements vary significantly

A recent study showed that lower protein diets extended the life of fruit flies.[1] Proponents of low protein diets feel that this study provides justification for lower protein in human diets. Unfortunately, this is not a valid conclusion because different species have different nutritional requirements. Nutrition is not an ideology. Nutrition is a science and any conclusions about what is good and what is bad should be based on scientific evidence.

The study on fruit flies, conducted at the University of Sydney, showed that the highest longevity was achieved by a protein-to-carbohydrate (P:C) ratio of 1:16, whereas the egg-laying rate was maximized at a P:C ratio of 1:2. The maximum lifetime egg production, which corresponds to the optimum nutrition for fruit flies, was attained with a P:C ratio of 1:4.

Human protein requirements depend on many factors, including the degree of physical activity. The chart above shows this variability. The Institute of Medicine, the scientific body which establishes national nutritional policies, recommends a minimum of 0.8 grams of protein per day per kilogram of body weight.[2] This corresponds to 54 grams of protein for a person weighing 150 pounds (68 kg). So how does this compare with the fruit fly diet?

The Zone diet promoted by Dr. Sears has a a proportion of 30% Protein, 40% carbohydrate, and 30% fat. The Zone diet P:C ratio is 1:1.3 which is considerably higher in protein than any of the fruit fly diets. However, the standard USDA diet recommends a proportion of 15% Protein, 55% Carbohydrate, and 30% fat. The P:C ratio of the USDA diet is 1:3.7 which is very close to the optimal 1:4 ratio for the fruit fly. Maybe we are not that different from fruit flies after all.

[1] Lee KP, Simpson SJ, Clissold FJ, Brooks R, Ballard JW, Taylor PW, Soran N, Raubenheimer D., Lifespan and reproduction in Drosophila: New insights from nutritional geometry. Proc Natl Acad Sci USA. 2008 Feb 11; PMID: 18268352

[2] Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids (Macronutrients).

Making bread is relatively easy. Mix some flour, yeast, some sugar, a pinch of salt, water, and voilà all you have to do is bake the dough after it rises.

Sourdough bread is different. Sourdough doesn’t use ordinary yeast. It uses a “sourdough starter” which is a brew of wild yeasts and acid-producing bacteria. These yeasts and bacteria are very particular. You have to coax them to come out of hiding by providing the right conditions for them to multiply and to prevent competing bacteria from gaining a foothold.

I had failed several times at making a sourdough starter by mixing flour and water. I typically ended with containers of stinking gruel which had to be discarded. Recently, through an e-mail exchange about carbohydrate chemistry, I found out that Debbie Wink had systematically studied the conditions best suited for creating a sourdough starter. It turns out that acidifying the initial culture suppresses undesirable bacteria and gives the good yeasts a chance to get started. Debbie’s solution was simple and elegant: use unsweetened pinapple juice instead of water for the first three days of incubation. The pineapple juice provides the right amount of acidity for the sourdough yeasts and bacteria to thrive.

Recently, I made my first loaf of sourdough bread. It is the accomplishment of an elusive goal.

Cancer kills over half a million people per year in the U.S. and is the second most common cause of death. Many of these deaths could be prevented by not smoking. The popular concept that cancer is one disease is inaccurate. Cancer is the result of uncontrolled cellular replication caused by damage to the DNA of the cells. Toxic chemicals, such as those found in tobacco, can cause changes in the chemical structure of the cells. The body gets rid of damaged cells by a process called apoptosis which is a series of biochemical events that lead to disintegration of the cell and disposal of the cellular debris. Tumors develop when damaged cells are not destroyed and they continue to reproduce.

German biochemist Otto Warburg (winner of the 1931 Nobel prize in physiology or medicine) proposed that abnormal energy metabolism caused cancer. He showed that tumors have an acidic extracellular environment, and proposed that a switch from oxidative respiration to glycolysis, which produces lactic acid, starts the cell transformation toward cancer. Warburg’s work stimulated interest in the possibility that there was some kind of link between pH and cancer, but it has taken seventy years to show this.

Recent research has identified cellular signaling pathways that become active under alkaline conditions. Dr. Rui Zhao and her colleagues have found that artificially increasing the intracellular pH removes amide functional groups from key cellular proteins (Bcl-xL) and result in apoptosis. This research raises hope that inducing alkalinization may prove an effective strategy to treat a range of cancers.[1]

[1] Gross L (2007) Manipulating Cellular pH Suggests Novel Anticancer Therapy. PLoS Biol 5(1): e10

Bonobo - the gentle ape

I recently watched a re-run of a PBS NOVA special about bonobos.[1] For some time, scientists have known that chimpanzees and bonobos share about 98% of their DNA with humans. Current research has shown that bonobos can use and understand language.[2] Analysis of the behavior of the two apes indicates that chimpanzees are bullies, fighters, and murderers who dominate by force, whereas bonobos are peace-loving, social, and sometimes join peacefully with non-related groups of bonobos. Researchers think that unity between the high-ranking bonobo females and year-round social sexual encounters between all members of the bonobo group help to reduce conflicts.

Humans have aggressive traits as well as social traits. The NOVA program tried to imply that the personality of humans may be closer to bonobos than to chimpanzees because we aggregate into social groups, we are very sexual, and we have some altruistic traits. However, as a background to the story, the program mentioned the regional war that spread through the Congo which is the native habitat of bonobos. The researchers studying the bonobo were detained as spies and were lucky to survive the ordeal. The war brought great misery to the area when food became scarce and thousands of people lost their lives through aggression, starvation, or disease.

There is great irony in trying to find good qualities in mankind when there are so many conflicts around us. The lessons of the great world wars have been largely forgotten. Words like Korea, Viet Nam, Iraq, Gaza, Sudan, and Abu Ghraib evoke images of chaos, destruction, famine, and new forms of torture like “waterboarding”. We may be closer to chimpanzees than we would like to admit.

[1] Nova Special on the Bonobo

[2] Linguistic Capabilities of the Bonobo

The formulation of valid logical arguments is one of the pillars of the Scientific Method.  An argument consists of one or more premises and one conclusion.  A premise is a statement that is offered in support of the conclusion. Premises and conclusions are statements that may be true or false. A valid logical argument presents true premises that logically lead to a true conclusion.  Arguments may be either deductive or inductive.  The premises in deductive arguments provide complete support for the conclusion, whereas for inductive arguments they provide some degree of support, but not complete support.  Fallacies are arguments that are defective because the premises do not provide the proper support for the conclusion.  These are the most common fallacies:

An Ad Hominem fallacy is an argument which is used to discredit what a person said by attacking the person rather than by disproving the statement.  An Ad Hominem fallacy is invalid logic because the character, circumstances, or actions of a person are not relevant to the truth or falsity of the claim being made.   For example, in the argument “President Bush is a bad president because he goofed off in college”, the conclusion that President Bush is a bad president may be true, but the statement that he goofed off in college which may also be true does not provide enough support for the conclusion.

An Appeal to Authority is an argument where the premise references an authority to support the argument.  Appeals to authority may be wrong when the authority is not a reliable reference for a particular subject, for example:  “President Bush said that our mission in Iraq was accomplished therefore it must be true”.

Appeal to Ridicule is a fallacy in which ridicule or mockery is used in the premise as a justification for the conclusion.  For example, “Copernicus said that the Earth goes around the sun.  He is crazy!”  Ridiculing Copernicus does not disprove that the Earth goes around the sun.