Archive for the Science Category

Book Review: Polio: An American Story

Posted in Science with tags , , , , , , , , , , , on August 27, 2015 by neandergal

Polio: An American StoryPolio: An American Story by David M. Oshinsky
My rating: 4 of 5 stars

Another must read for anyone entering the biological sciences..! A great medical history book that really gives an insight into the human fight against the Poliovirus that left children permanently disabled, and sometimes in an iron-lung. This book brings home the torment suffered by children and parents alike during the desperate search for a prevention throughout the decades of the last century.

View all my reviews

Ask a Scientist : “So What’s a Parasite Anyway?” Lecture Jim McKerrow Cont.

Posted in Science with tags , , , , , , , , , , , on April 20, 2013 by neandergal


Parasites, parasites of the intestinal walls! Which is the most gross of them all? The most gross parasite title has to go to the most common of helminths, Ascaris lumbricoides.

According to the World Health Organization, Ascaris Lumbricoides infects approximately 30% of the world’s population. Infections for the most part, are in the rural areas of developing countries that use untreated human waste for fertilizer and irrigation. Without access to clean water and expensive fertilizer, farmers are left with little else to use, but human waste to grow their produce. A 2008 report in National Graphic news on the use of Human Waste cites that 200 million farmers world wide use human waste for fertilizer. The eggs from human feces used as fertilizer end up in the soil where they can stay fertilized for up to 10 years.

The eggs find their way into the human food chain via contaminated unwashed hands during food preparation, unwashed fruit and, or undercooked vegetables or fruit. When fertilized eggs are ingested, the eggs hatch in the upper intestinal tract where the larvae then penetrate the wall and move into the portal and systemic circulatory system. Once in the circulatory system, the larvae enter the lungs. In the lungs, the larvae penetrate aveoli walls and make their way up the bronchial tree to the throat. The larvae is swallowed by the host and ingested. In the lower intestines, the larvae attaches to the mucosa of the wall and feeds off the host’s partly digested food and grows to an adult. Adult Ascaris lays up to 200,000 eggs per day. The eggs are then excreted in feces. The infected feces returns to the land as fertilizer and the life-cycle of A lumbricoides repeats.

The Ascaris worm grows to approximately 30cm and about 2-4mm in diameter. The females are a little thicker and longer with their vulva making up a third of the length of the body. Gulp!

Introduction to Microbiology, 9th Edition, Tortora, Gerard.J, Funke, Berdall R., Christine L. Case. Publisher: Pearson Benjamin Cummings. 2007 print.
Center for Disease Control – Ascariasis page
National Geographic 2008 report on use of human waste as fertilizer.
Ask a Scientist website
Dr. J. McKerrow UCSF page.

Ask a Scientist : “So What’s a Parasite Anyway?”

Posted in Science with tags , , , , , , , , , , , on April 4, 2013 by neandergal

rhodnius_prolixus“So What’s a Parasite?” was one of a lecture series called, “Ask a Scientist”. The lectures are for “curious humans” and I for one am curious about parasites and other nasties.

I attended the lecture by Dr. Jim McKerrow from the University California San Francisco’s Department of Pathology and Laboratory Medicine on parasites that took place in a toasty warm tent heated by gas lamps at the SF StrEAT Park in the Mission, San Francisco.

Anyway, I just want to share some gross pictures and remind you how the Lord God made all these creatures great and small; very, very small. Some of these creatures are so small that they live in the guts of bugs and some organisms are so small that they burrow into the skin infecting various organs reining havoc on their host by making them extremely sick and sometimes even killing them.

As the audience drank beer and tucked into their Mexican food from the various food trucks in the StrEAT park, Jim started by introducing the dining audience to the parasite responsible for Chagas’ disease. Chagas’ disease is a protozoan that damages the cardiovascular system.The protozoa Trypanosoma cruzi grows in the gut of the bug and is transmitted by the triatomine bug via its feces. The bug bites the skin of its victim and defecates in or near the wound which subsequently irritates the person or animal who then scratches the wound rubbing the feces into the wound even more. T. cruzi makes its way into the bloodstream and hides in the muscular wall of the heart and intestines causing damage.

Parasite - Trypanosoma cruzi

The parasite can be transmitted across the placenta from the infected mother to her baby. All blood for blood transfusion in the USA is tested for the T. cruzi parasite since many of them remain in the blood stream.

According to the World Health Organization, 7 to 8 million people worldwide are infected with Chagas’ Disease — many of whom are in Latin America.

More bugs to follow… Stay tuned and don’t scratch!

Additional Sources:

WHO Media centre Factsheets
Ask a Scientist website
Dr. Jim McKerrow page at UCSF

Big Pharma Conspiracy and Kooks, Oh My!

Posted in Science with tags , , , , , , , on October 22, 2011 by neandergal

       The anti-vaccination lobby are convinced of big-pharma conspiracies; the wicked witch of FDA is corrupt, etc, etc. That is their single line of defense along with the isolated study that confirms their belief that vaccines harm. Anti-vaxxer kooks refuse to acknowledge hundreds of studies across developed nations showing that vaccinations do not cause harm and that vaccines do not, or ever have caused autism.

       In kook-land, the lack of critical thinking is astonishing. Which is more probably? Doctors, pharmaceutical companies, governments from all over the world are in cahoots with each other to harm children in the name of profit, or that as nations, and as human beings, we really just simply want to stop the spread of disease and ultimately eliminate it?

       Let’s stop for a moment to think about what if there really was a conspiracy between all the doctors, nurses, clinicians, every single person that worked for a pharmaceutical company, every government agency, educator and anyone else involved in healthcare from ALL OVER THE WORLD were all in cahoots to make a PROFIT by deliberately harming children? That is a heck of a lot of people all working together and keeping a secret of monumental proportion.

       Now lets think about if the conspiracy was true.

       If the conspiracy theories were actually true, who exactly would it benefit and to what end? If the big-pharma conspiracy was true, wouldn’t someone, somewhere down the line unveil the truth BACKED UP BY EVIDENCE in the form of DOCUMENTATION?

       In actual fact, if the drug companies, governments, et al really wanted to profit from all of this, then wouldn’t it behoove them to allow children to get sick from so-called “harmless” diseases so they could treat their disabilities from illnesses by discouraging vaccinations?

       Anti-vaxxers are not skeptics, they are deniers. They filter out any evidence presented to them that conflicts with their belief that vaccines harm. The process of filtering is refered to as confirmation bias in psychology. Deniers employ the fallacy of confirmation bias repeatedly with their beliefs being constantly reinforced by only surrounding themselves with people that think exactly the same way as they do.

       As proponents of evidence-based medicine, medical researchers examine just that; evidence. IF there was a shred of evidence (and there isn’t), they would examine it and possibly change their minds based on new evidence.

       No evidence exists that suggests vaccines cause autism or other harm that outweighs the benefit of vaccinating. As a matter of fact, subsequent studies confirm over and over again that vaccines are safe and that the very small element of risk does not compare to the overwhelming benefit of vaccinating large proportions of the population.

       A little less emotion and a little bit of critical thinking analysis by pulling back the curtain of reason would reveal the ridiculousness of belief in elaborate conspiracies. Only then can the anti-vaccine kooks draw the conclusion that vaccinations do not harm and that the profit motive behind harming children is utter nonsense.

       Bertrand Russell said that, “The trouble with the world is that the stupid are cocksure and that the intelligent are full of doubt.” Unfortunately, the anti-vaxers will stick close together and continue to march along the yellow brick road to utter stupidity.

Book Review: The Believing Brain

Posted in Atheism, Science with tags , , , , , on June 15, 2011 by neandergal

       Michael Shermer’s recently published book, The Believing Brain: From Ghosts and Gods to Politics and Conspiracies — How we Construct Beliefs and Reinforce Them as Truths, discusses how we believe rather than why we believe. The Believing Brain is not just another book explaining that it’s easier to believe than to question or a rant on religious dogma. The book delves into the neuroscience and psychology of how we believe. The book describes in great detail the types of biases that believers and non-believers can easily fall prey to and commit in their reasoning — including researchers and scientists. The premise of the book is that beliefs come first and the reasons for a particular set of held beliefs come second.

       One of the many mechanisms of belief is what Shermer calls, “patternicity.” “Patternicity” is another word for associated learning. The Human brain is a pattern-recognizing machine. Humans have evolved to connect dots and create links by association. Humans are more sophisticated at patternicity because they have larger and more complex brains than other primates. Recognizing and forming patterns has survival value. Modern humans inherited the genes of their ancestors that were best at pattern recognition because they were more likely to survive and reproduce passing their genes to offspring. However, what humans did not evolve is good “filter systems” that easily detect false patterns. In other words, the brain will see patterns that are either real or unreal. In the face of danger, erring on the side of caution and committing a cognitive Type I error has a greater survival value than committing a Type II error. A type 1 error, or false positive, is a belief that something is true that turns out to be false and a Type II error, or false negative, is a belief that something is false that turns out to be true. The mechanism behind “false patterns” is the same mechanism for detecting real or true patterns. We evolved to see patterns such as face recognition. Our ability to recognize faces at various angles and expressions serve us well from a survival value because we can better detect friend or foe. Our ability to see patterns is the reason why some of the faithful will “see” Jesus or other prophet of their belief system on a piece of burnt toast. On the other hand, patternicity, or associated learning is the reason why humans have progressed scientifically. Associated learning is instrumental to all animal behavior as demonstrated by the behaviorist B. F. Skinner with his experiments with pigeons and rats. Shermer contends that the best tool we have for distinguishing false patterns from true patterns is science. Shermer illustrates the dangers of Type 1 patternicity with a powerful description of the tragic story of 10 year old Candace Newmaker who died in 2000 during an alternative therapy called (attachment therapy) for attachment disorder. Not only do we see patterns, but we also apply purpose or meaning to patterns in what Shermer calls “Agenticity.”

       Shermer suggests that it is our sense of self as to why we ascribe purpose or meaning to events. Agenticity is the cognition that entities outside of ourselves control the universe, what and how we do things and that there is somehow a grand-plan. Agenticity is also responsible for belief in new age nonsense and even in elaborate conspiracy theories. Our sense of self “resides” in the left hemisphere temporal lobe of our brain and can actually be tampered with to induce feeling of spirituality similar to those experienced by people having out of body experiences (OBEs) by using magnetic fields to stimulate “microseizures.” Shermer even plays the role of lab rat to undergo the same type of temporal lobe stimulation by neuroscientist, Michael Persinger. Shermer shares an account of his experience and a fuller neuro-scientific explanation of OBEs and spiritual experiences. Shermer both entertains and dismays us with examples of agenticity including how the CIA and military blew $20 million over a 25 year span on their Stargate psychic spy program. The purpose of Stargate was to hone peoples’ supposed psychic abilities to locate missiles, read minds and even telepathically kill enemy soldiers. Patternicity and agenticity explain the mechanisms behind beliefs, but neurons are the root cause of beliefs.

       The sense of self is why people tend to view the mind and body as separate entities. The mind and body is the same thing. The brain comprises the mind which is a result of neurological connections — lots of them. Shermer blinds us with mind-boggling neurostats that should impress anyone geeky enough to listen at a cocktail party. For example, the brain comprises of approximately a quadrillion neurological connections. A quadrillion is an astronomically large number; 10 to the 15th power (10^15 or 1,000,000,000,000,000). Shermer introduces us to an interesting brief history of neuroscience from Henri Bergson’s élan vital (vital force) to understanding to the physiology of the firing of neurons as a result of a set of action potentials. Dopamine is the neurotransmitter guilty as charged for amplifying the ability to find patterns in randomness through increased firing which results in new neural connections that form long term memory. This sounds like a good thing except that too much dopamine can result in auditory and visual hallucinations. Shermer tells an amusing tale of his close encounter with Nobel Prize winner Kary Mullis (developer of Polymerase Chain Reaction which is a method of replicating sequences of DNA). Mullis reveals his contact with extraterrestrials to Shermer after a few beers… Even brilliant people are also subject to the fallacy of finding patterns in randomness and giving meaning to their false patterns.

        Filtering systems are another mechanism that filters out information that fails to match an idea or set of ideas because we naturally seek out information in the form of patterns that confirm and reinforces the belief or set of ideas; i.e., conformation bias. Shermer contends that the belief in elaborate conspiracy theories such as those of 9/11 truthers or the fans of a losing side of a sporting team are individuals whose “pattern-detection filters are wide open” Conspiracy theorists make patterns from randomness and add an agent such as the government in the case of 911 truthers, or a biased referee in the case of a losing team to add meaning or purpose to their claims. Shermer dismantles the conspiracy theories of holocaust deniers, 911 truthers and the assassination of John F. Kennedy by the CIA by highlighting the fallacious arguments given by conspiracy theorists and provides evidence for how these events unfolded without the agents of government. The list of cognitive biases described in the book read like a basic psychology course, but illustrate where we cognitively fall over in the way we view the world no matter how rational we perceive ourselves.

       Shermer concludes by reiterating that science is a tool that can help control our filtering systems. It is not enough to argue from ignorance and apply an agent to what we don’t know or understand. We must require evidence using science as the tool to find answers to our questions. The burden of proof must lie with the person or group of people making a claim. Science has various mechanisms that help to identify and breakdown biases. Shermer describes how even the scientific method is not perfect, but it is the best tool yet for understanding the natural world.


Shermer, Michael. The Believing Brain: From Ghosts and Gods to Politics and Conspiracies – How we Construct Beliefs and Reinforce Them as Truths. New York: Times Books, 2011. Print.

The way from Utopia to Aipotu? A Proposal

Posted in Atheism, Politics, Religion, Science with tags , , , , , , , , , , on January 4, 2011 by neandergal

        Thomas More’s Utopians assumed that people without a belief in a deity could not possibly have moral values because their ethics stem from religion. Utopians contend that a person cannot be virtuous without a belief in an afterlife or a god because rewards and an eternal life depend on how a person lives in his or her mortal life. Conversely, Aipotutian society recognizes that highly religious societies are more war-like, subjugate women and reduce personal freedom by dictating what people should think and how they should live their lives. Aipotu sees religion as the root cause of many of its societal problems. Aipotu wants to increase public awareness of science and philosophy in the hope that people will discover that faith is not necessary for leading a productive and ethically good life. In order to achieve these goals, Aipotu needs to adopt a secularist agenda that stems the influence of religion in its society. The way to reduce the influence of religion in Aipotu is to limit religious institutions’ power by gradually dismantling them through public policy.

        Since the last major war, Aipotu has witnessed an inverse relationship in the decline of the knowledge and acceptance of science and an increase in religion. Aipotutians increasingly put their lives at the mercy of their faith. They give alternative medicine, astrologers, psychics and religious leaders more credence than scientists and medical doctors. A reduction in the number of scientists and the amount of funding for research is a result of the publics’ distrust of science. The fact that it is financially more lucrative (and intellectually easier) to be a TV evangelist or a quack peddling the latest woo-woo on popular TV shows than becoming a researcher working on a cure for a prevalent disease like cancer or Aids is indicative of how little Aipotutian society values science and reason. The process of increasing Aipotutian’s acceptance of science and reducing their dependency upon religion must begin in childhood, since this is where people learn beliefs. Therefore, the first step is to banish religious indoctrination of children in the schools.

        Although Aipotutian society has no established state religion, the process of religious indoctrination has become increasingly covert. There is a hidden agenda among some educators to teach intelligent design. Intelligent design assumes that because life is so complex, there had to be a designer. Many in the scientific community claim that intelligent design is creationism in disguise. This theory without evidence has found its way into some science textbooks. This method, dubbed the “wedge strategy,” refers to how organizations purporting to promote science push their doctrines into scientific texts. Publishers of biology textbooks omit the theory of evolution to avoid controversy with religious organizations that have a very powerful voice because they represent a growing number of Aipotutian believers. The Aipotutian scientific community blames the omission of evolutionary theory from text books on the country’s appalling lack of understanding of the sciences compared with other nations. Fifty percent of the Aipotutian population believe that the world was created in seven days. According to Aipotutian scientists, evolutionary theory forms the basis of educational curriculum because it is fundamental to understanding the biological sciences and provides the evidence that evolution eliminates the need for a creator. Awareness of the conflict between science and religion can only take place by allowing discussion in school classrooms. This will encourage the development of a healthy skepticism among young minds. A more skeptical mind is more likely to demand explanations for “religious phenomena” and to reject pseudo-science. However, the government recognizes the important of teaching non-denominational religious studies for gaining an understanding of religion’s historical and literary significance rather than for spiritual guidance.

        The teaching of religion is important to maintain an understanding of how people evolve culturally because it provides an insight into how peoples’ attitudes change over time. It is only through the promotion of science and a critical analysis of religion and philosophy that clarifies why the foundation of thought should not rely on faith. Therefore, it is now necessary to ban private faith-based schools in Aipotu.

        Aipotu will purchase private religious schools and turn them into public schools. Teachers previously employed by these schools have the opportunity to continue their teaching careers. The state will rehire these teachers once they become certified by the state to teach in public schools. There is no need to waste human resources. A mandate by the state will forbid the teaching of religious instruction for the purpose of spiritual guidance. Any infringement of this mandate is a case for dismissal from the school. The offending teacher is struck off the state certification register in much the same way a doctor is for gross medical misconduct. It is important for the Aipotutian government to send a clear message that it has zero tolerance for the religious indoctrination of children. The next problem that the Aitoputitian government has is dealing with families that impose their faith on their children.

        The Aipotutian government needs to adopt a firm stance against religious customs, teachings and practices imposed upon children. Aipotutian society considers the religious indoctrination of children by parents tantamount to child abuse. Ancient customs, such as baptism, confirmation and arranged marriages at birth, fall into part of the indoctrination process when imposed upon children. More barbaric customs that involve any kind of bodily mutilation, such as, female genital mutilation, male circumcision (for reasons other than medical), self-flagellation, exorcism rituals, body piercing and tattooing, are punishable by imprisonment of the parents and subsequent removal of the child from its current environment. These types of practices are considered cruel and detrimental to healthy cognitive development because of the physical pain and mental trauma inflicted upon children. The reason is that a child does not have the cognitive development to consent to these practices. Children have a right to a healthy cognitive development and an education that helps them to think freely. The Aipotutian government needs to send the message that children are not chattels. Barbaric religious practices, along with their doctrines, affect not just one country, town or village, but marginalize millions of men, women and children around the world. However, Aipotu is also concerned about not infringing upon personal freedom, despite its long-term agenda in eradicating the imposition of religious doctrine upon others.

        It is imperative to maintain adult individual freedom in Aipotu by not passing legislation that would undermine citizens’ freedoms. There should be no punishment for adults practicing their faith or the bizarre traditions that come with them. If a person makes claims of conversing with some deity or the dead, then their mental health should certainly be called into question. Visual or audible hallucinations are symptoms of mental illness should be treated as such. As in the case of other mental illnesses or delusional concepts, family or individual counseling will have access to mental health services if they want help. It is the hope of Aipotutian society that religious practices will die out with each generation, so there is no need for overly draconian measures for adults. However, Aipotu views conflicts between religious ideologies as a major cause of wars and terrorist activity that eventually lead to the breakdown in the infrastructures of society. The destruction of infrastructures destabilizes whole regions and prolongs conflicts and human suffering. Aipotu can prevent these human catastrophes in their country by dismantling its religious institutions.

        Aipotu needs to seize all religious and sect organizations, and then redistribute the finances between non-governmental agencies and find other functions for the remaining buildings. People previously employed by religious organizations are encouraged to work for non-governmental agencies or other non-church related organizations that work for the common good of society. The religious buildings used by these institutions should become historical artifacts, since they are significant from an anthropological perspective. Churches, cathedrals, synagogues, mosques and temples are not destroyed, but become state properties and are valued for their aesthetic and historical appeal. Some of these beautiful buildings have wonderful acoustics and will become prestigious concert halls. Other buildings will become parts of more sophisticated culture, such as art galleries, theaters or opera houses, and their religious significance will eventually become a thing of the past.

        One day, Aipotutians will view religious thought and rituals as archaic as those buildings. Future generations will view religious practices as bizarre and often inhumane. They will read with dismay about long gone societies that forbade the use of birth control and the termination of unwanted pregnancies, even in the case of rape. They will read with dismay when they learn how women in some societies were forbidden to show their face or expose any part of their body in public and were cruelly punished for doing so. They will read with dismay about the horrifying day when religious fanatics who believed in the promise of an eternal life as a reward for murdering thousands of people by flying two planes containing hundreds of people into buildings containing thousands of people. They will read with dismay how children were taught in those religious relics how an eternal life of damnation would await them upon death for misbehaving. Adults will find it ironic how the faithful viewed sex only for the purpose of procreation. Adults will be amused by the irony of poverty, pollution and overcrowding caused by overpopulation while the poor were told that abortion and the use of contraception was a sin. Most of all, future generations will find it astonishing when they learn how their ancestors believed in almost anything they were told without question. And they will wonder why and how 7th century belief systems existed in a sophisticated 21st century scientific and technological society?

Will Aipotu become a “utopia” if any of these changes ever come to pass?

Taxpayer Dollars to Promote Prayer..? You Better Believe it.

Posted in Atheism, Religion, Science with tags , , , , , , , , , on August 24, 2010 by neandergal

When the emergency technician is about to apply CPR, nobody says: “Wait! Let’s pray first.” exclaims a quote from the Skeptic Dictionary

Well it turns out this may actually be the case in some instances. Biologist and science blogger PZ Myers reports on his blog post how the US government is funding metaphysical methods for promoting health and well being. It is hard to believe that a state department is advocating metaphysical baloney, but the evidence is loudly and clearly displayed on the US Department of Health and Human Services’ website.  

The website content includes an article, Can Hands-on Prayer Help Heal? The article cites a bogus peer-reviewed study published in the September issue of the Southern Medical Journal. The peer reviewed study on “proximal intercessory prayer (PIP)” is the epitome of bad science at its worse. Proximal Intercessory Prayer is a euphemism for “abracadabra” and is a made-up term to describe incantations to the almighty for favors. The study on hearing and sight impaired subjects in Mozambique is bogus because it violated at least three basic scientific method protocols rendering it scientifically flawed. Miraculously, the study passed the peer-review process. 

A scientific experiment requires subjects to be randomized groups that include a control group and measurable variables.  The study was suppose to test the power of prayer on 23 non-randomized sight and, or hearing impaired subjects.  The so called improvements that resulted in prayer were anecdotal rather than empirically based. Anecdotal is testimonial and therefore subjective. 

The article on states, “And while they don’t discount that much of the results may stem from a placebo effect, benefits did seem to occur in some individuals.” The placebo effect is what clinical trials of treatments test for and compares it with the real drug for true effectiveness. Just because the placebo effect may work in some cases, does not make it effective treatment for all or anywhere near most individuals.

In the words of Richard Dawkins, “There are all sorts of things that would be comforting. I expect an injection of morphine would be comforting… But to say that something is comforting is not to say that it’s true.”


PZ Myers: Pharyngula – Our Government at Work

PZ Myers – Pharyngula

Southern Medical Journal