Friday, July 31, 2009

BS-o-meter: Detecting Pseudoscience

A QUANTUM OF SCIENCE

Pseudoscience is no joke.

While some of its claims may be laughable, countless otherwise intelligent people are taken in by claims of better health, extended life, or superior male equipment. Some of these "miracle cures" are harmless (except perhaps to your wallet) but others can be deadly – for instance, "energized water" made by adding the radioactive element radium! As consumers of not just materials but also of information, it is critical for everyone to be able to spot science scams when they come your way.

The single best piece of advice is simply this: Question. Be skeptical. Don’t believe everything you read, or take it at face value. Ask for references. Check the background. Read a book, or talk to an expert. Ask if someone is trying to make a buck – or a convert. And never forget that if it seems too good to be true, it probably is.

Common sense aside, here are some of the hallmarks of pseudoscience:

Use of vague, exaggerated or untestable claims. The language of science is that of objective, measurable quantities or verifiable characteristics. Good science also requires a narrow scope for its claims, and uses negative controls and blind tests to prevent it from reaching unjustified conclusions. Just what type of energy has been added to "energized water" anyway? Any claim that cannot be objectively measured or independently quantified is suggestive of pseudoscience.

Absence of authoritative references or citable sources. Scientists build on the work of those who came before them, and reference those sources extensively to show where their predecessors’ work ends and their own begins. By listing their sources, scientists establish their contribution in the context of previously tested and verified work in the same field, and present it for testing and verification by others. Any theory or claim lacking citations from established scientists in the same field should be viewed with extreme skepticism.

Unrepeatability or lack of openness to testing by other experts. The hallmark of science is reproducibility. If other scientists cannot replicate an experiment using the same conditions and materials described by the claimant, the claim is refuted. Pseudoscience often seeks evade this by making claims that are difficult or impossible to test and thus refute. Pseudoscience will sometimes make claims of "ancient knowledge" or "secret practices" from far-off lands, but these should be recognized as ways to convince the reader to be uncritical and accept the source’s claims without question.

Reductionism. In science, the simplest explanation is usually the correct one. This principle, known as Occam’s Razor, can be applied to any possible pseudoscientific claim as a way of discerning its value. If the explanation seems unduly complicated and unlikely, it is probably untrue.

Absence of progress. Science is constantly growing, learning, self-correcting and progressing. If a field does not constantly add to its body of knowledge, correct imperfections or errors in itself, or add further instances and explain further phenomena, chances are it is pseudoscience. For example, astrology today is almost identical to that of the last two millennia, and phrenology has not changed in the last 150 years since it first gained popularity.

Use of misleading language. Pseudoscience often seeks to cloak itself in the language of science and thus mislead the unsuspecting. This can be difficult for a non-scientist to detect or dispel, but overly-general terms such as "energy/energized" or overly-scientific terms such as "dihydrogen monoxide" (also know as H2O or water) are a sign of obfuscation and an attempt to mislead the reader. "Psi," "aura," "miracle," "natural" and "holistic" are other classic terms frequently misused in pseudoscientific claims.

Personalization of issues. Any theory that attracts extremists, the dogmatic, the charismatic, or that characterizes those who dispute it as enemies, is likely founded on pseudoscience. Often this is true of “scientific theories” propounded by extreme religious groups seeking to support a particular theology with something that sounds like science. Intelligent Design is one of the best examples of this – ultimately, this theory is not testable and thus cannot be the province of science, but rather of faith.

Claims of suppression, or of conspiracy to conceal or refute. Science is an open, peer-reviewed, transparent process – as it must be, in order to be cumulative and build upon itself. Real science is eagerly tested by others in the field, since it is either an innovation to be adopted or a fallacy to be exploded. It is only pseudoscience that shies away from peer review and independent testing. If a theory is supposedly being suppressed by the scientific establishment, it is likely to be in hiding from it instead.

Confirmation rather than refutation. In science, the burden of proof rests on those making a claim, not on the skeptic. Any theory that defies science to disprove it is likely to be pseudoscience.

Self-appointed experts and single-source theories. Successful scientific theories are tested by credentialed scientists and then used in their own work, leading to many examples and instances where it holds true. Often pseudoscience comes from someone lacking appropriate scientific credentials, or someone with unverifiable or obscure degrees from unlikely places. Also, if a theory is held only by a single person or a single group, and especially if that has been the case for an extended period of time, it is strongly suggestive of pseudoscience.

Association with financial gain. The adage ‘if it seems too good to be true, it probably is’ should be applied whenever claims of beneficial discoveries are purported. If a theory or claim is followed by an attempt to sell you a product or service purported to help you, especially in some subjective or non-quantifiable way, it is almost certainly pseudoscience and should be viewed with extreme skepticism.



For more information:

What is Pseudoscience?

H2O dot con: water-related pseudoscience, scams and quackery

Dowsing for Dollars – Fighting High-Tech Promises with Low-Tech Critical Thinking Skills

Crank dot net – a collection of scams and popular falsities on the web


© AQOS / P. Smalley (2009)
Reproduction with attribution is appreciation

Monday, July 27, 2009

Telemedicine: Cell Phone Microscopy

A QUANTUM OF SCIENCE

Can technical innovations bring medical diagnostics anywhere a cell phone can go?

It is increasingly common for medical professionals to use images generated by light microscopy in the rapid evaluation and dissemination of a diagnosis of disease. This practice is so widespread that a medical communication standard has been adopted for using transferring digital images between doctors and institutions. This has resulted in improvements in rapid diagnosis of disease, but rural areas and developing nations lag far behind this due to the prohibitive cost of equipment and training required. Light microscopes and their more exotic cousins (dark-field, fluorescence microscopy, etc) are far from universal medical devices. Worse still for underserved regions, microscopy is an essential tool for diagnosis of diseases endemic to such areas. Tuberculosis, malaria and sickle-cell anemia are just a handful of the afflictions most easily characterized by microscopy, and which are also extremely common in developing nations.

What is strange and in this case fortunate is that rural areas and developing nations are being more quickly served by mobile phone providers, and thanks to this fact researchers in Berkeley, California were able to engineer a device that could interface with a standard cell phone to capture, analyze and transmit high-resolution microscopic images such that positive diagnoses could be made.

Using a Nokia phone equipped with only a 3.2-megapixel CMOS camera, scientists and engineers were able to construct a device consisting of two filters and three lenses that was capable of capturing high-quality microscopic images of blood (allowing positive diagnosis of malaria and sickle-cell anemia) and sputum (allowing positive diagnosis of tuberculosis). The latter required the addition of an LED emitting in the ultraviolet spectrum, permitting fluorescence microscopic images to be captured by the cell phone’s camera. While minimal image modification was required for the light microscopy images, even the fluorescence microscopy images needed only minor processing before they could be analyzed successfully.



The power and utility of this innovation of science and engineering cannot be easily overstated. For a relative pittance, the power of expensive and complex instruments requiring trained technicians to operate is now available to anyone with a cell phone. Soon, underserved rural areas and developing nations will have the possibility of rapid and high-accuracy diagnoses. With this piece of technical know-how the scientists, engineers and medical professionals of Berkeley have pushed back the darkness a little farther and paved the way for a better quality of life for many who suffer only because of where they happen to have been born.

For more information:

Mobile Phone Based Clinical Microscopy for Global Health Applications (Breslauer et al)


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Thursday, July 23, 2009

Biomining: Panning for Gold with Viruses

A QUANTUM OF SCIENCE

How can viruses solve an industrial mining problem?


One of the most abundant forms of life on earth is a humble virus called a bacteriophage. Phage for short, it exists only to infect bacteria; they are harmless to plants and animals. But scientists have long used phage as a way to search for special protein sequences with unique properties – in this case, the ability to selectively bind to specific metal ores.

An emerging technology, gold- and silver-binding phages were known in the literature but only as curiosities until a scientist at the University of British Columbia Institute of Mining Engineering wondered if he could find a phage that bound copper sulfide.

Industrial mining practices typically grind ore into a fine powder to aid in separating the ore of interest from other minerals. Special chemicals called flotation aids are added to this liquid slurry of various minerals and make the copper sulfide particles hydrophobic. These particles then adhere to bubbles in the slurry and float to the top, making a solid layer of the desired ore that can easily be extracted.

The problem comes in when very similar ores are present in the same slurry. To solve this problem, Dr. Scott Dunbar of UBC decided to search for a phage that selectively bound the mineral chalcopyrite (CuFeS2). In collaboration with scientists at the UBC’s Centre for Blood Research and the Department of Biochemistry and Molecular Biology, Dunbar found three unique phages that bound tightly and selectively to chalcopyrite, sphalerite (ZnS), or both. Using these selective phages, researchers were able to enrich ore slurries for the desired mineral ore, even in the presence of the other – in effect, panning for gold among the sand.

From this similarity the term biomining was coined.

Not only the mining industry may benefit from this advance. In addition to the reduction or elimination of flotation reagents from the industrial mining process (a potent source of environmentally unfriendly chemicals), this achievement demonstrates the potential for ore-binding phages as a powerful bioremediation technology. Heavy metals such as lead and cadmium could be more easily removed from contaminated soils using similar phages, and even some nuclear wastes might be amenable to biomining remediation. As an innovative technology, biomining has capabilities that are only just beginning to be imagined, let alone tapped.

For further information:

Virus may lend a hand in copper mining


Biomining with bacteriophage: Selectivity of displayed peptides for naturally occurring sphalerite and chalcopyrite (Curtis et al)


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Tuesday, July 21, 2009

Quantum: Get Stung and Get Paid

A QUANTUM OF SCIENCE

Dr. Duffy wants to give you malaria.

Well, sort of.

Researchers at the Seattle Biomedical Research Institute have developed a weakened version of the malaria bug (Plasmodium falciparum) by deleting from its genome the genetic instructions that allow it to invade the liver and to reproduce. Now SBRI has been approved to conduct human trials using this "neutered" malaria, testing various drugs and vaccines for their effectiveness at blocking the parasite.

And volunteers will get paid somewhere between $2000 and $4000 for their trouble.


For more information:

Seattle Times article "You can get paid to catch malaria"

SBRI press release on the approval to conduct human trials with malaria vaccine

© A Quantum of Science / P. Smalley
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Monday, July 20, 2009

Quantum: Less Antibiotique, merci

A QUANTUM OF SCIENCE

French government program educates about the danger of overuse of antibiotics

From 2002-2007 the French government has operated a program aimed at reducing the use of antibiotics for flu-like symptoms after a report came out showing that France used more antibiotics per capita than any other European nation. Called "Antibiotics are not Automatic" this program targeted overuse of antibiotics for flu-like symptoms, especially among the young. Now a report has been released showing the results of this program. Briefly, overall antibiotic use was down an average of 26% in all regions of the country and for all antibiotic categories (except quinolones). Remarkably, this reduction was even more pronounced among children (35%) and most of all in instances of those complaining of flu-like symptoms (45%). The important thing about this study is that broad health education can work on an entire population and over a reasonable period will result in major adjustment of behavior. Also worth noting is that the information used in the study was obtained through the online electronic database of French medical records, a system not unlike that which is being built by US government funding at present.

For more information:

Significant Reduction of Antibiotic Use in the Community after a Nationwide Campaign in France, 2002–2007 (Sabuncu et al)

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Tuesday, July 14, 2009

Quantum: Obesity fueled by reward-behavior gene

A QUANTUM OF SCIENCE

Obesity risk factor gene found to act in an unlikely place: our minds

Researchers analyzed the DNA of over 30,000 humans in 8 different studies and found three separate localed regions (or "loci") in their DNA where many of those studied had very similar subtle differences ("single-nucleotide polymorphisms"). The presence and number of copies of these genes with subtle differences correlated almost precisely with measurements of waist circumference, body mass index, and obesity. Two of these genes were known from other studies, but the newest gene, NRXN3, has a surprising role in the body. Instead of regulating the growth and proliferation of fat cells, or guiding the metabolic rate up or down, it acts on the central nervous system to modulate so-called "reward behavior," in which the brain receives positive feedback stimulation when a particular behavior is performed.

While these results are enlightening, they are not a genetic test for obesity risk nor even necessarily an indication that science is racing to "cure" obesity. But by understanding the underlying factors better, new strategies to address the expanding epidemic of obesity may be hastened. Moreover, NRXN3, is also associated with susceptibility to addiction and further research may reveal additional therapies to help affected individuals overcome that as well. What is more frightening is the knowledge of how similar those two scourges truly are - obesity as an addiction to food is a chilling idea.

For more information:

NRXN3 Is a Novel Locus for Waist Circumference: A Genome-Wide Association Study from the CHARGE Consortium (Nancy L. Heard-Costa et al)

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Thursday, July 9, 2009

You Give Me Fever

A QUANTUM OF SCIENCE

Emergent viral outbreaks show Ebola is not the only "hot zone" virus worth fearing

Sub-Saharan Africa has long been known as the Hot Zone, a place from which some of the world’s most deadly viruses originated. Among them are the well-known Ebola and Marburg viruses, members of the viral hemorrhagic fever (VHF) family that cause extreme fever, internal and external bleeding and rapid death among a frighteningly high percentage of those infected. Other "Old World" (i.e. African) hemorrhagic viral diseases include dengue and yellow fever. Most VHF viruses are carried by rodents – which seem largely immune – and are spread to humans by liquid contact, though some are capable of aerosol infections. (This latter category includes the Marburg virus, which was weaponized by the former Soviet Union in the 1980’s.) Less well-known cousins in this same family are the so-called New World viruses such as hantavirus, as well as the Argentine, Bolivian, and Venezuelan hemorrhagic fevers.

Late last fall an African travel agent was flown from the city of Lusaka to Johannesburg, South Africa, suffering from high fever and external bleeding. She died a few days later. Within the next several days, the paramedic who received her into the hospital, a nurse who cleaned the room following the travel agent’s death, and a nurse who attended the paramedic after he became ill, all perished from the same virus. Another nurse who treated the paramedic was given an antiviral treatment and survived. This was the beginning and end – for now – of an outbreak of the Lujo Virus, named for the two cities where it was first observed (Lusaka and Johannesburg). A member of the VHF family, it has more in common with the New World branch than it does Ebola or Marburg. Genetic analysis by researchers at Columbia University showed that the Lujo virus was a member of the arenaviridae genus (the name comes from the Latin word for sand, referring to the way viral particles of this genus appear when viewed under a microscope). Strangely, arenaviruses are almost unknown in Africa but have several species native to South America. Comparing the genetic sequence of Lujo to other VHF species from Africa showed significant differences, strongly suggesting that Lujo was not a simple mutant or even a more virulent strain caused by reassortment of viral chromosomes (such as is often the case for the influenza virus). Instead, Lujo appears to be the first high-morbidity, high-mortality VHF virus to emerge from Africa’s hot zone in the last thirty years.

In 2006 a paper was published by Dr. C.J. Peters, a member of the University of Texas Medical Branch, discussing the factors that affect the accelerating rate of emergence of new viruses and increasingly deadly outbreaks. He referenced the Emerging Microbial Threats reports issued by the Institute of Medicine in 1992 and updated in 2002, in which all the data pointed to two major factors at play in the increasing danger of deadly microbial outbreaks: multiple ecologic niches and ever-accelerating human travel and transport. In this paper he describes an arenavirus outbreak in a small village in Bolivia in 1962. The village suffered an outbreak of "black typhus" and out of 600 villager there were 107 cases, of which more than four out of ten perished. This is roughly the same morbidity and mortality rates recorded for the medieval scourge of bubonic plague, better known as the Black Death.

Since the 1960's, large sections of the Amazonian plateau have been deforested, and human activity in those regions has reached levels never before seen. The same is true of sub-Saharan Africa, where the Lujo virus emerged in 2008; had the Lujo virus not been caught before it spread thanks to current medical expertise not available in 1962, the "black typhus" outbreak may well have paled in comparison to the devastation Lujo might have wrought.

The story of ecological niches created through human activity has become hauntingly familiar, and authorities predict that the problem will only worsen as population pressures push humans deeper into the hot zones of viral reservoirs in both the Old World and the New.

For more information:

Viral hemorrhagic fever (overview)

Googleblog article on early news of the Lujo outbreak

News article on Columbia researcher’s efforts to analyze Lujo

Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa (Lipkin et al).

NOVA interview discussing Soviet weaponization of Marburg virus


© A Quantum of Science / P. Smalley
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Quantum: the Cute-Baby Effect

A QUANTUM OF SCIENCE

This just in: women like looking at "attractive" babies more than men do. That's unlikely to make any headlines, but the reverse case is where the surprise comes in: if a baby is "unattractive" through some objective standard, women like looking at it *less* than men do.

Researchers at the Clinical Psychopathology Laboratory or McLean Hospital and Harvard Medical School in Boston report that the length of time that women vs. men spent looking at "normal" babies versus those affected by cleft palate, Down's Syndrome or other congenital birth defects were reversed: women spent longer looking at the "normal" babies than men did, but much less time looking at "unattractive" babies than men did. The authors of the study suggest that this might reflect an evolutionary bias on the part of women to spend less time and attention on the less viable of their offspring, correlating subjective lack of aesthetic appeal with decreased potential for viability.

For more information:

Gender Differences in the Motivational Processing of Babies Are Determined by Their Facial Attractiveness (Yamamoto et al.)


© A Quantum of Science / P. Smalley

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Wednesday, July 8, 2009

Food Safety Overhaul: Chickens and Eggs

A QUANTUM OF SCIENCE

Sweeping and ambitious, administration regulations would enact mandatory oversight and tracking of critical foods

Today the Obama administration announced a major overhaul of the US food safety system. Overseen almost entirely by the FDA, some 150,000 individual commercial food producers would be subject to sweeping new regulations that would require traceability for all food and food additives sold in the US. This is a significant increase in the level of government oversight of the food industry and is a response to several high-profile outbreaks of food poisoning in the last several years. These include recent E. coli and Salmonella outbreaks leading to the recall of tremendous amounts of food throughout the US. Notably, Salmonella in peanut products and E. coli in ground beef both originated in US commercial food manufacturers as a result of poor hygiene and lack of mandatory safety regulations. Worse still, it took unconscionably long for the FDA to track down exactly where the problem started, leading to a much larger outbreak than necessary.

To prevent this from happening again, the new legislation calls for a Reportable Food Registry to be established and overseen by the FDA. This registry would ensure that any outbreak of food poisoning or adulterated food would be instantly reported to the FDA, which would then be able to use the registry to track down where the adulterated food came from, what other foods it might have come in contact with or been used in, and what distributors to alert. Not only would this increase the response time of the FDA, it would also allow traceability for the agency such that random testing of large numbers of those 150,000 individual commercial food manufacturers would not be required. If a tomato in Denver turned up positive for Salmonella, FDA scientists could quickly determine that it came from a wholesaler in Texas who purchased it from a grower in Louisiana. From there, all tomatoes that came from that grower or that passed through that wholesaler would be identified and the distributors notified to pull the tomatoes off their shelves.

This is a massive undertaking but a significant benefit to the food safety network in the US. Previously it might have taken FDA scientists weeks to trace a single infected tomato back to that grower in Louisiana, and in that time panicked distributors might destroy untold volumes of perfectly safe tomatoes, costing the food industry huge amounts of money. With the Registry, that process might take less than 48 hours, and the cost savings to distributors and wholesalers is the reason that the food industry generally supports this legislation.

One particular area of concern for the Obama administration is eggs – specifically, chickens, eggs, and Salmonella. It has been known for twenty years that infected chicks produce Salmonella-laden eggs that cannot be detected easily by the current food safety inspection systems in place. The new legislation mandates that egg growers take steps to eliminate rodents (a prime source of Salmonella contamination) and only purchase chicks from growers who also take steps to monitor Salmonella among their stock. Additional regulations require refrigeration during more of the lifespan of an egg, something that about half of all egg producers already do voluntarily and which would reduce the potential for Salmonella growth. As mentioned above, egg growers are generally in favor of these regulations – even though it will cost them some money for testing and prevention, they believe the increase in public confidence will more than make up for the estimated one-cent per dozen increase in the cost of eggs.

They’re almost certainly right. In this case, it doesn’t matter whether the chicken or the egg came first, so long as both of them come before the Salmonella.

For more information:

FDA Reportable Food Registry

Article from The Washington Post on the new legislation

New York Times article focusing on egg safety regulations


© A Quantum of Science / P. Smalley
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Monday, July 6, 2009

Newest Alzheimer's Drug: Coffee?

A QUANTUM OF SCIENCE

New research suggests caffeine may not only protect but can also reverse Alzheimer's Disease symptoms

Today's issue of the Journal of Alzheimer's Disease contains two reports involving the effects of caffeine on mice bred to mimic the biochemical degeneration of cognition found in human Alzheimer's disease. Briefly, the major source of this neural degeneration is the accumulation of a protein called Amyloid-β (or Aβ). A natural protein, Aβ can sometimes mis-fold and in that state becomes impervious to the normal cellular processes that break down aging proteins for recycling. Because it cannot be broken down, mis-folded Aβ accumulates and eventually causes cell death in the tissues surrounding it. Alzheimer's disease results when this takes place in brain tissue.

Researchers are interested in the process by which Aβ mis-folds, accumulates and - just possibly - might be eradicated. In the studies published today in the Journal of Alzheimer's Disease, researchers found that caffeine can not only protect Alzheimer's-prone mice from the accumulation of Aβ, but can even reduce Aβ levels in the brains and blood of mice who already have advanced Alzheimer's conditions. This is not the first report of caffeine's effects, but the two studies are back-to-back illustrations of the growing body of evidence linking caffeine to treatment for Alzheimer's even after the condition is diagnosed. Additionally, the levels of caffeine used in this study are relevant - the equivalent of about five cups of coffee per day for a human. This is exciting as it suggests that caffeine treatment might be possible without resorting to levels so high as to cause dangerous side-effects to humans.

For more information:

Caffeine Reverses Cognitive Impairment and Decreases Brain Amyloid-β Levels in Aged Alzheimer’s Disease Mice (Arendash et al)

Caffeine Suppresses Amyloid-β Levels in Plasma and Brain of Alzheimer’s Disease Transgenic Mice (Chuanhai et al)

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Thursday, July 2, 2009

Music Gene

A Genetic Basis for Music?
A QUANTUM OF SCIENCE

Musical legacy found in a gene associated with social interaction traits – including love

Researchers in Finland recently reported a study in which 19 Finnish familes (343 individuals) with many professional or active amateur musicians among them were studied for genetic similarities. The study found that a single gene, AVPR1A (for arginine vasopressin receptor 1A), held a strong statistical correlation to creative musical abilities such as pitch, tempo and composition, especially when members of multiple generations all shared musical ability. So what is arginine vasopressin?

Peptide hormones, of which the vasopressins are a subfamily, are composed of short cyclic chains of amino acids (nine, in this case) and regulate a number of physiological functions. Arginine vasopression (abbreviated AVP) controls hydration through kidney function, including the stimulation of urine dilution and concentration in balance with the body’s need for extra water. For this activity it is secreted into the bloodstream, but some AVP is also found in the brain, where it binds to a specialized receptor – the one encoded by the gene AVPR1A. Binding of AVP to AVPR1A stimulates the brain to release neurotransmitters that play into "social behavior" responses, including the mate bonding behavior found in voles and, to a greater or lesser extent, in humans. Some studies have even suggested that these same neurotransmitters play a role in feelings of altruism, or love.

Is there a single gene that determines who is musical and who is not? These findings are preliminary and far from exhaustive, but they point to a biological function encouraging the spread and preservation of the AVPR1A gene. If, as suggested, the AVP/AVPR1A peptide hormone receptor plays a role in social behavior and other emotional attachment activities in higher mammals, it could easily be linked to the development of early human societies via the universal language: music.

For more information:

Original PLOS article


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