A genetic mixed bag

One of the subtlest features of the evolutionary model, and one often misunderstood even by people who understand and accept natural selection, is what we mean by "selective advantage."

On the surface, it's simple enough; any inheritable feature that confers longer, healthier life or more (and more vigorous) offspring.  The problem is, there are two twists on phenotype that make this a bit more complicated than it seems at first.

The first is that physical expression of genes is seldom unequivocally either good or bad for the organism.  The "unequivocally bad" ones are often discussed in introductory biology classes because they are simple; Tay-Sachs disease, for example, caused by inheriting a particular recessive allele from both parents, kills the brain cells and usually causes death by age four.  But most traits have good features and bad, so the question becomes, "Is this good for the organism on balance?"  One instance is our upright posture and bipedal gait.  It confers some advantages -- two of the more commonly-cited ones are leaving our hands free to manipulate tools, and giving us greater sight-distance for spotting predators.  (Nota bene: no one's sure which of those advantages led to our ancestors walking upright, or if it was something else entirely; saying "these are some of the advantages" is not the same as saying "these were the advantages that drove selection for this trait.")  The downside of upright posture, though -- given that we still have the basic spine shape as our knuckle-walking forebears -- is that humans have some of the worst lower back problems to be found in the animal world, with the only ones having it worse being Bassett hounds and dachsunds.

And the low-slung backs of Bassetts and wiener dogs are hardly the fault of natural selection.

Another complicating factor is pleiotropy -- which is that many genes have multiple effects, often only loosely related to each other.  The classic example of pleiotropy is the connection between coat and eye color, and inner ear development, in cats.  White, blue-eyed cats are frequently deaf -- the same gene that blocks pigment formation (and causes the white coat and blue eyes) hinders development of the cochlea, resulting in deafness.

What makes it even more complex is that sometimes a gene can have a drastically different set of effects depending on whether you have one copy (are heterozygous) or two (are homozygous).  It was long a puzzle of evolutionary science why some deleterious recessive genes are so common.  If having two copies of a gene kills you, effectively removing two copies of the allele from the gene pool, you'd expect the frequency of the allele to decrease over time.  So why do some really nasty genes stick around?

[Image is in the Public Domain]

Two examples where we've actually figured out the answer are the genes that cause cystic fibrosis (a horrible lung disease which is one of the more common serious genetic disorders in Caucasians) and sickle-cell anemia (an equally-dreadful blood disorder common in sub-Saharan Africans and African Americans).  While having two copies of either of those genes is certainly awful, having only one is beneficial, giving the individual an advantage over both the ones who have two bad copies and the ones who have two good copies of the allele.  In the case of cystic fibrosis, being heterozygous gives infants a significantly lower chance of contracting infantile diarrheal disease, which in cultures with limited access to medical care is a major killer of babies.  In sickle-cell anemia, having one copy of the allele gives you resistance to malaria -- so in malaria-ridden areas, homozygous recessive people die of sickle-cell anemia, and homozygous dominant people die of malaria.  Heterozygous individuals escape both.

Even seemingly unimportant genes can sometimes have unexpected effects.  It was long thought that the blood-type alleles -- nicknamed A, B, and O -- had no effect on anything other than blood transfusion compatibility.  It was recently discovered that the O blood type allele, which is the most common, confers resistance to smallpox.  So in areas that had smallpox epidemics, the individuals who were type A (the most susceptible allele) were much more likely to die, leaving the type Os at a significant selective advantage.  A map of the incidence of smallpox in Europe and a map of the frequency of the O blood type allele line up almost perfectly.

The reason all this comes up is because of a paper last week in the journal Development that looked at a rather horrifying genetic disorder called holoprosencephaly, where something interferes with prenatal forebrain development.  Affected children end up with malformed brains and multiple facial disfigurements -- cleft palate, cleft lip, and eyes that are extremely close together (in fact, sometimes they're fused).  These babies almost always die in utero.

Geneticists at the Max Delbrück Center for Molecular Medicine found two mutations that influenced the development of holoprosencephaly, which are called ULK4 and PTTG1.  Both of these genes regulate expression of the ultra-important sonic hedgehog gene, which is responsible for organ formation, nervous system development, and such fundamental features as symmetrical limb placement.  The researchers found that these two genes prevent holoprosencephaly, which you'd think would be enough of an advantage that it would eventually lead them to becoming fixed (everyone in the population being homozygous) except for rare cases of mutations.

Where it gets more interesting is that the researchers found that ULK4 and PTTG1 have other effects besides stopping holoprosencephaly in its tracks.  ULK4 is associated with schizophrenia and bipolar disorder -- and PTTG1 is linked to cancer.

So like cystic fibrosis and sickle-cell anemia, it's not as simple as saying "this allele is the good one, and this is the bad one."  And because both of the negative effects of ULK4 and PTTG1 affect individuals later in life, very likely after they have made the decision whether to have kids, the positive effect (surviving gestation) far outweighs the negative ones, at least from an evolutionary standpoint.

As I used to tell my AP Biology classes, "evolution doesn't really give a damn what happens to you after you've successfully procreated."  Harsh, but true in its essence.

So genetics and evolution are, like most things, a mixed bag.  They're a lot more complicated than they may seem at first, enough that it's kind of impressive researchers have been able to figure out how they work.  Considering what could potentially go wrong with development, I'm kind of blown away by how often things go right.  When my first wife found out she was pregnant, I spent the next eight or so months worrying, because I knew enough genetics to realize how bad things could be.  When my older son was born -- completely normal, except that he looks exactly like me, which is unfortunate but not fatal -- it was an incredible relief.

It may not be true that "a little knowledge is a dangerous thing," but sometimes it can be a bit stress-inducing.

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London in the nineteenth century was a seriously disgusting place to live, especially for the lower classes.  Sewage was dumped into gutters along the street; it then ran down into the ground -- the same ground from which residents pumped their drinking water.  The smell can only be imagined, but the prevalence of infectious water-borne diseases is a matter of record.

In 1854 there was a horrible epidemic of cholera hit central London, ultimately killing over six hundred people.  Because the most obvious unsanitary thing about the place was the smell, the leading thinkers of the time thought that cholera came from bad air -- the "miasmal model" of contagion.  But a doctor named John Snow thought it was water-borne, and through his tireless work, he was able to trace the entire epidemic to one hand-pumped well.  Finally, after weeks and months of argument, the city planners agreed to remove the handle of the well, and the epidemic ended only a few days afterward.

The work of John Snow led to a complete change in attitude toward sanitation, sewers, and safe drinking water, and in only a few years completely changed the face of the city of London.  Snow, and the epidemic he halted, are the subject of the fantastic book The Ghost Map: The Story of London's Most Terrifying Epidemic -- and How It Changed Cities, Science, and the Modern World, by science historian Steven Johnson.  The detective work Snow undertook, and his tireless efforts to save the London poor from a horrible disease, make for fascinating reading, and shine a vivid light on what cities were like back when life for all but the wealthy was "solitary, poor, nasty, brutish, and short" (to swipe Edmund Burke's trenchant turn of phrase).

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

The stories the bones tell

The field of forensic anthropology has made amazing strides in the past decades.  Fifty years ago, about all we could count on was identification of gender and suspected ethnic origin, and an estimate of age at death.  Now we are able to use data from bones to reconstruct much of the person's life history.

And sometimes, that history is pretty unpleasant.

One of the first cases in which the entire arsenal of sophisticated analytical techniques was used was "Ötzi," the "Ice Man" of the Alps whose body had been hidden underneath the edge of a glacier in the Italian/Austrian Alps for over five thousand years.  What we now know about Ötzi and his origins is kind of mind-blowing.  From pollen grains found in his clothing, we know he died in early summer, but his last meal contains "einkorn" wheat and sloes, both of which are harvested in the fall -- leading to the conclusion that his people knew how to preserve food over the winter.  He had no less than 61 tattoos, all geometrical and presumably symbolic, perhaps representing magical rituals.  (Or maybe, like me, he had ink just because he thought it was cool.)  He had a copper knife and particles of copper residue in his hair, suggesting he or someone he lived very near was involved in copper smelting.  From an isotopic analysis of his tooth enamel, we even know a bit of his life history -- he appears to have spent his childhood near the present town of Feldthurns, Italy, but at some point in his youth went to a valley fifty kilometers farther north.

Things took a grim turn, however, when the forensic anthropologists started looking into how he died.  Initially it was suspected he'd died in a fall down the hillside, as he had cracked ribs and surface bruises -- possibly resulting in his being knocked unconscious and dying of exposure.  But the truth seems a good bit harsher.  Ötzi has an arrowhead lodged in his upper chest, near the upper lobe of his left lung.  This wasn't an old injury; his shirt had a tear at the same place as the entry wound.  The conclusion from the placement and apparent trajectory of the arrow is that it would have severed arteries in his left pectoral muscle, leading to his death from blood loss.

We humans have been doing bad things to each other for a very, very long time.

If you needed further proof of this, consider the paper in Current Biology that came out two days ago, sent to me by a friend and loyal reader of Skeptophilia, and the reason I've gone into this rather morbid subject today.  In "Origin and Health Status of First-Generation Africans from Early Colonial Mexico," by a team led by Rodrigo Barquera of the Department of Archaeogenetics of the Max Planck Institute for the Science of Human History, we hear about three sixteenth-century skeletons recently found in Mexico that tell a horrific tale of abduction, slavery, and abuse.

The three individuals are clearly of African origin, based not only on skeletal morphology but on tooth-filing patterns that are characteristic of the Fang people of Equatorial Guinea, Cameroon, and Gabon.  Not only that, but one of them had a characteristically African strain of hepatitis B, and another had remnants of the bacteria species (Treponema pallidum ssp. pertinue) that causes the horrific tropical disease yaws (if you choose to investigate further into this disease, do not look at the photographs unless you have a strong stomach -- you have been warned), which is most common in west and central Africa.  In fact, the current presence of yaws in Latin America is almost certainly the result of its having been brought in by the African slave trade.

It only gets worse when you read about the evidence of abuse these skeletons show.  The authors write:

Osteological analyses of the three individuals reveal evidence suggesting a life experience of conflict and hardship.  Individual ML8 SL 150 (SJN001) was found with five buck shots and two healing needles (used in traditional medicine) in the thoracic cavity, as well as gunshot wounds.  Both SJN001 and SJN003 (ML8 SLU9B 296) presented porotic hyperostosis and cribra orbitalia, two pathological changes associated with a skeletal response to nutritionally inadequate diets, anemia, parasitic infectious diseases, and blood loss.  Individual ML8 San José 214 (SJN002) displayed several skeletal changes associated with intense labor and heavy manual activity, including enthesopathies on the clavicle and scapulae as well as osteophytic lipping on the joint surfaces with some additional joint contour deformation at the sternoclavicular joint of the clavicle.  Additionally, he suffered from a poorly aligned complete fracture in the right fibula and tibia, resulting in associated joint changes of the knee, including osteochondritis dissecans of the distal femoral surface with joint contour deformation and associated osteophytic lipping of the articular surface margin.  Furthermore, this individual displayed osteoarthrosis of the lumbar vertebrae in addition to signs of deficient oral health and cut marks on the frontal bone.

"All of us involved in the study were highly touched by the whole story about these three persons, everything that they went through," study lead author Barquera said.  "Knowing that they were first-generation enslaved Africans brings a new perspective on the whole subject because you know they were abducted.  You're seeing all these maltreatment signatures on the bones that came with this abduction, what they suffered for the rest of their lives."

And "the rest of their lives" turned out to be short.  All three of the individuals died in their early or mid-twenties.  Whether they died of disease, malnutrition, murder, or the cumulative abuse they'd suffered isn't known, because they show signs consistent with all possible combinations of the above.

All of it brings home once again the accuracy of Thomas Hobbes's words in his book Leviathan, wherein he characterizes the lives of our ancestors as having been "solitary, poor, nasty, brutish, and short."  It's true that a lot of the poorness and nastiness was circumstantial, and due to bad diet and the prevalence of (then-untreatable) diseases.

But a frightening piece of the "nasty, brutish, and short" part was due to the horrible mistreatment of humans by other humans, often for no better reason than territory, power, rivalries, and tribalism.  I wish I could tell you we've grown beyond all that.  I mean, there's been progress; I wouldn't trade my life here in the 21st century for what Ötzi or the owners of the Mexican skeletons endured.  But that insularity, suspicion, and tribalism is deep within our cultural genes, needing little more than a moment's adversity to bring it to the surface.

Bringing to mind another quote, this one from the Latin playwright Plautus -- Homo lupus homini est (man is a wolf to men).

Which, in my opinion, is slanderous toward the wolves.  They may be fierce, but I've yet to see a wolf enslave another wolf.  On the whole, their society seems a great deal more peaceable than ours is.

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This week's Skeptophilia book recommendation is an important read for any of you who, like me, (1) like running, cycling, and weight lifting, and (2) have had repeated injuries.

Christie Aschwanden's new book Good to Go: What the Athlete in All of Us Can Learn from the Strange Science of Recovery goes through all the recommendations -- good and bad, sensible and bizarre -- that world-class athletes have made to help us less-elite types recover from the injuries we incur.  As you might expect, some of them work, and some of them are worse than useless -- and Aschwanden will help you to sort the wheat from the chaff.

The fun part of this is that Aschwanden not only looked at the serious scientific research, she tried some of these "cures" on herself.  You'll find out the results, described in detail brought to life by her lucid writing, and maybe it'll help you find some good ways of handling your own aches and pains -- and avoid the ones that are worthless.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Changing the thermostat

Everyone knows that the human core body temperature is supposed to be around 98.6 F.  At least, that's what we all learned in seventh grade life science, right?

A more curious question is why 98.6 and not some other temperature.  Other mammals need different core body temperatures, but the range is remarkably narrow -- from elephants (97.7 F) to goats (103.4 F), only a 5.7 degree difference overall, and the vast majority of mammal species are in the vicinity of 98-100 F.

In my biology classes, I usually did nothing more than a hand-waving explanation that "our body temperatures are what they are because that's the temperature where our enzymatic and neurochemical reactions work at their optimal rate," but that's a facile analysis at best -- a bit like saying "bake the cake at 350 F because 350 F is the best temperature at which to bake cakes."  It might be true, but it doesn't tell you anything.

Last month we got a better explanation of what's going on than what I used to give (admittedly a low bar).  A paper in Molecular Cell with the daunting title, "A Conserved Kinase-Based Body-Temperature Sensor Globally Controls Alternative Splicing and Gene Expression," by a huge team led by Tom Haltenhof of Freie Universität Berlin's Department of Biochemistry, gives us a window into why we regulate body temperature -- and why things fall apart so quickly when the temperature isn't what it should be.

The team looked at the effects of temperature change not in mammals but in turtles and crocodiles -- which are themselves poikilothermic (known in common parlance as "cold-blooded") but have a temperature-switching mechanism for sex determination.  In crocodiles, incubation of the eggs at a warmer temperature results in males; in turtles, the pattern is the opposite.  (Some lizards have an even odder pattern, where intermediate temperatures result in males, and either low or high temperatures result in females.)

The question was how this was happening.  Something about the temperature must be changing the chemical signaling that guides embryonic development; but how?

Haltenhof's team found that there is a group of enzymes called CDC-like kinases that are extremely temperature-sensitive.  Kinases in general are a hugely important enzyme family that are responsible for phosphorylation, the main way energy is transferred in living organisms.  So if you affect the reaction rate of a kinase, it results in changes in the transfer of energy -- and can have enormous impacts on the organism.

And the CDC-like kinases, Haltenhof et al. found, were acting directly on the DNA, and changing the rate of gene expression.  In crocodiles and turtles, the type of gene expression affected had to do, unsurprisingly, with embryonic development of the reproductive systems.

So far, interesting only to geneticists and herpetologists (and, presumably, to the crocodiles and turtles themselves).  But where it caught my attention was when it was pointed out that the activity of CDC-like kinases is important not only in reptiles, but in humans -- and that overexpression of one of them, cyclin E, is connected with at least one form of cancer.

So this research seems to have implications not only for embryonic development in crocodiles and turtles, but in explaining why our own body temperatures are so tightly regulated.  The authors write: "[CDC-like kinase] activity is likely to also impact on gene expression in pathological conditions such as hypothermia, septic shock, and fever, or in the slightly warmer tumor microenvironment."  And since in general, the core body temperature drops as a person ages, it also made the authors speculate that this could be the key to at least some age-related malfunctions (and perhaps suggest a way to treat them).

[Image licensed under the Creative Commons 24ngagnon, Thermostat science photo, CC BY-SA 4.0]

This also brought to mind another perplexing bit of research that came out in January -- that the average human body temperature is dropping, on the order of 0.03 C per decade.  The standard "98.6 F" was established in 1851 by Carl Reinhold August Wunderlich, who determined this by taking the axillary (armpit) temperature of 25,000 people in Leipzig (and you thought your job was boring).  But a recent study with even more measurements found that currently, the average body temperature is almost a degree cooler than Wunderlich's value.

The speculation in that paper is that the drop in temperature is due to a decrease in the inflammation caused by exposure to infectious agents.  If the 25,000 Leipzig residents were a representative sample from the mid-19th century, 3% would have had an active tuberculosis infection, and that's just one disease.  So the lower average temperature today might have to do with our lower incidence of infections of various kinds.

But it makes me wonder what effect that's having on the CDC-like kinases from the first study.  Because during our evolutionary history, the 1850s condition of harboring infections was much more the norm than our current clean, germ-free-ness.  So while losing our collection of nasty bacteria might be overall a good thing, it might have caused a drop in temperature that could affect other reactions -- ones we're only beginning to understand.

That's yet to be established, of course.  But what it does highlight is how important the body's thermostat is.  Only a four-degree drop in core body temperature is a sufficient level of hypothermia to severely endanger a person's survival; likewise, a six-degree increase would be a life-threatening fever that (if survived) could result in brain damage.  We are only beginning to understand how our temperature is regulated, and why the effects of losing that regulation are so drastic.  But what this new research shows is that our body temperature might have far more ramifications for our health than we ever imagined -- and could be the key to understanding, and perhaps treating, diseases that have up till now defied medical science.

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This week's Skeptophilia book-of-the-week is brand new -- science journalist Lydia Denworth's brilliant and insightful book Friendship: The Evolution, Biology, and Extraordinary Power of Life's Fundamental Bond.

Denworth looks at the evolutionary basis of our ability to form bonds of friendship -- comparing our capacity to that of other social primates, such as a group of monkeys in a sanctuary in Puerto Rico and a tribe of baboons in Kenya.  Our need for social bonds other than those of mating and pair-bonding is deep in our brains and in our genes, and the evidence is compelling that the strongest correlate to depression is social isolation.

Friendship examines social bonding not only from the standpoint of observational psychology, but from the perspective of neuroscience.  We have neurochemical systems in place -- mediated predominantly by oxytocin, dopamine, and endorphin -- that are specifically devoted to strengthening those bonds.

Denworth's book is both scientifically fascinating and also reassuringly optimistic -- stressing to the reader that we're built to be cooperative.  Something that we could all do with a reminder of during these fractious times.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Tales of contagion

I have to admit to a morbid fascination with things that can kill you in nasty ways.

Tornadoes, hurricanes, earthquakes, mass extinctions from giant meteorite collisions -- and epidemics.  I remember first reading Daniel Defoe's A Journal of the Plague Year, about an outbreak of the Black Death in London in 1664 and 1665, when I was in college, and being simultaneously horrified and mesmerized at the scale of it.  An estimated 100,000 people died in two years -- a quarter of London's population.

But even that is dwarfed by two other epidemics.  First, there's the infamous outbreak of bubonic plague that started in 1347 and, by some estimates, killed one-third of the human population of the Earth -- something on the order of fifty million people.  The worst, though, was the "Spanish flu" epidemic of 1918 and 1919.  Odd that an event only a hundred years ago, and that killed an estimated 75 million people worldwide -- twice as many as World War I, which was happening at the same time -- is much less known.  Mention the Black Death, and almost everyone has an idea of what it is; mention the Spanish flu, and often all you get is a puzzled look.

Danse Macabre by Michael Wolgemut [image is in the Public Domain]

This all comes up because of a paper by Maria Spyrou et al. that appeared in Nature: Communications last week.  In it, the researchers describe looking for evidence of pathogens in the Bronze-Age burial sites -- and finding evidence that the bubonic plague has been with us for a long, long time.  The authors write:

The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics.  Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000–3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear.  Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia.  We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested.  Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day.

Which is fascinating enough, but it bears mention that there are still a number of epidemics that scientists have no clear explanation for.  Here are three of the most puzzling:

1. "Sweating sickness."  In the late 15th and early 16th centuries, several waves of contagious illness swept through western Europe.  It killed fast -- starting with disorientation, fever, chills, aching joints, and finally progressing to delirium and copious sweating.  Most of the victims died within 36 hours of the onset.  It claimed a number of well-known victims, including Prince Arthur of England -- the son of King Henry VII, and brother of King Henry VIII.  Arthur's death at the age of fifteen put Henry in line for the throne, and set into motion events that would change the world -- such as the English Reformation and the founding of the Anglican Church.  Sweating sickness went as quickly as it started -- the last outbreak was in 1551, and it hasn't been seen since.  Scientists are still mystified as to the cause, but the speculation is it might have been a hantavirus, carried by mice.
2. The Dancing Plague of 1518.  In eastern France and western Germany, people were stricken by a disorder that caused shaking, mania, and... a desperation to dance.  People took to the streets, dancing desperately, many of them until they died of hunger, exposure, heat exhaustion, or stroke.  In Strasbourg alone, at the height of the plague, it was killing fifteen people a day.  It, like the sweating sickness, vanished as soon as it appeared, leaving everyone mystified as to its cause -- although some researchers suspect it might have been caused by ergot, a fungus that grows on wheat and rye and produces lysergic acid diethylamide -- LSD.
3. "Nodding syndrome."  This one is much more recent, having first emerged in the 1960s in Sudan.  It affects children, causing listlessness, stunting of growth (especially of the brain), and a peculiar symptom called a "nodding seizure," often triggered by eating or becoming cold.  The child's head bobs, and (s)he becomes unresponsive, the seizures lasting for up to ten or fifteen minutes.  It's progressive and fatal -- the usual duration being about three years.  To this day no one knows the cause, although some suspect it might be connected to parasitism by the roundworm Onchocercus volvulus, which is endemic in the area and also causes "river blindness."

So this combines my love of horrible things that can kill you with my love of unsolved mysteries.

Anyhow, I realize this is all kind of morbid, and I have no desire to ruin your mood.  After all, we live in an age where most of the worst diseases of antiquity have been vanished; even bubonic plague, if it's caught quickly, can be cured with antibiotics (and yes, there are still cases of it today).  Thankfully, we seem to have gotten rid of sweating sickness and the dancing plague, even if we've replaced them with Ebola fever and chikungunya and West Nile virus.  I'll still take what we've got today over life in the past, which was (accurately) described by Thomas Hobbes as "solitary, nasty, poor, brutish, and short."

Have a nice day.

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This week's recommended read is Wait, What? And Life's Other Essential Questions by James E. Ryan.  Ryan frames the whole of critical thinking in a fascinating way.  He says we can avoid most of the pitfalls in logic by asking five questions: "What?"  "I wonder..." "Couldn't we at least...?" "How can I help?" and "What truly matters?"  Along the way, he considers examples from history, politics, and science, and encourages you to think about the deep issues -- and not to take anything for granted.

Preventing the unknown

Some days it's no great mystery why the general public is dubious about scientists.

I mean, a lot of it is the media, as I've discussed here at Skeptophilia ad nauseam.  But there are times that the scientists themselves put their best foot backward.  As an example, consider the announcement from the World Health Organization this week that their Research & Development Blueprint for priority diseases includes "Disease X."

A disease that is as-yet unidentified.

The blueprint itself says this:

Disease X represents the knowledge that a serious international epidemic could be caused by a pathogen currently unknown to cause human disease, and so the R&D Blueprint explicitly seeks to enable cross-cutting R&D preparedness that is also relevant for an unknown “Disease X” as far as possible.

On the one hand, there's a grain of sense there.  Recognizing the fact that there are "emerging diseases" that are apparently new to humanity, and that could cause epidemics is the first step toward readying ourselves for when that happens.  (Recent examples are Ebola and Lassa fever, Marburg virus, Severe Acute Respiratory Syndrome (SARS), and chikungunya.)

The Ebola virus [image courtesy of the World Health Organization]

But still.  What the WHO is telling the public is that they're putting time and effort into preventing an epidemic from a disease that:

• may not exist
• if it does exist, has unknown symptoms, origins, and mode of transmission
• may or may not be preventable
• may or may not be treatable
• may or may not be highly communicable
• may or may not be carried by other animals
• is of unknown duration and severity

Is it just me, or does this seem like an exercise in futility?

Like I said, an awareness of the unpredictability of disease outbreaks is a start, but this seems like trying to nail jello to the wall.  Each time humanity has been faced with a potential pandemic, we've had to study the disease and how it moves from one host to another, scramble to find treatments for the symptoms while we're searching for an actual cure (or better yet, a vaccine to prevent it), and do damage control in stricken areas.  So I can't see where the "Disease X" approach gets us, except to put everyone on red alert for an epidemic that may never happen.

I think my eyerolling when I read about this comes from two sources.  First, I'm all too aware that life is risky, and although it's certainly laudable to try to reduce the risk as much as you can, the bare fact is that you can't remove it entirely.  After all, none of us here are getting out of this place alive.  And second, there is an unavoidable chaotic element to what happens -- we get blindsided again and again by bizarre occurrences, and the professional prognosticators (not to mention professional psychics) get it wrong at least as often as they get it right.

So there probably will eventually be a new emerging epidemic.  On a long enough time scale, there's probably going to be a true pandemic as well.  I hope that with our advances in medical research, we'll be able to respond in time to prevent what happened during the Black Death, or worse, the Spanish flu epidemic of 1918 to 1919, that killed an estimated 40 million people (over twice the number of deaths as the battlefield casualties of World War I, which was happening at the same time).

In one sense, I take back what I said about not being able to do anything about it ahead of time.  We can give ourselves the best shot at mitigating the effects of an outbreak -- by funding medical research, and encouraging our best and brightest to go into science (i.e., education, a topic I've also rung the changes on more than once).  Other than that, I'm just going to eat right, exercise, and hope for the best.

GMO burrito attack

Many of you have undoubtedly heard about Chipotle's announcement last April that they were switching over to using entirely GMO-free ingredients.  The whole thing had us science types rolling our eyes, because it has been shown repeatedly that GMOs aren't dangerous in general (even though there have been rare specific cases that have had untoward effects, and those have been taken off the market).  Despite the evidence, the health-food cadre applauded Chipotle's move, saying that it was reassuring that at least one restaurant chain was doing the Right Thing.

Which is about all of the good news that Chipotle had in 2015, because beginning in the summer, they have had one problem after another with food-borne illnesses.  First, there was a norovirus outbreak in Seattle in July, followed by another in Simi Valley, California in August, sickening at least 240 people in the process.  August and September saw an outbreak of salmonella in Minnesota that sickened 64.  Another 52 contracted E. coli in October from restaurants in nine different states.  Then norovirus reappeared in Boston in December, causing nausea, vomiting, and diarrhea for 136 patrons.

The whole thing prompted the chain to announce a one-day closure in February 2016 to train staff on food safety, which seems a little after-the-fact but is better than nothing.  And the whole thing would have gone down as another example of dubious handling of a crisis by a corporation, if Mike Adams hadn't gotten involved.

Yes, Mike Adams, the "Health Ranger" and owner of Natural News, who spends much of his time sounding like a raving lunatic.  This time, he says, the bad guys have been caught red-handed.  The series of illnesses contracted by patrons of Chipotle aren't just an example of bad food handling and poor cleanliness standards; no, this is a deliberate attack by "food terrorists" to discredit the restaurant because of their fearless stand on GMOs.

I'm not making this up.  Here's a direct quote:

After observing recent events involving Chipotle and e.coli, here's my analysis of the situation: Chipotle's e.coli outbreaks are not random chance.  They are the result of the biotech industry unleashing bioterrorism attacks against the only fast food company that has publicly denounced GMOs. 

How do we know?  The CDC has already admitted that some of these e.coli outbreaks involve a "rare genetic strain" of e.coli not normally seen in foods.  Furthermore, we also know the track record of the biotech industry engaging in the most criminal, dirty, sleazebag tactics imaginable against any person or company that speaks out against GMOs.

So that's it?  No evidence?  Your "analysis" is based on the E. coli strain being "rare" and that the biotech industry is made up of a bunch of bad guys?  Oh, but wait... he says this same tactic has been used against another victim:

Doctor Oz, for example, was maliciously targeted in a defamation campaign funded by the biotech industry earlier this year.  The onslaught against Oz was initiated because he publicly expressed his support for honest GMO labeling on foods.

No, the investigation (hardly a "defamation campaign") was launched because Oz was giving health advice that was demonstrably false and selling supplements that were ineffective, not because he was against GMOs.  And using Dr. Oz, who still rakes in millions, as an example of a pitiful victim of an "onslaught" leaves me trying to find a word stronger than "disingenuous" and failing completely.

Adams doesn't mince words, however.  He spells it out plainly:

There is absolutely no question that the biotech industry will resort to ANY activity necessary to destroy food companies that oppose GMOs.  And yes, this includes acts of bioterrorism against Chipotle -- something that's ridiculously easy for biotech industry operatives to carry out with simple, low-cost laboratory supplies sold online at places like Amazon.com. 

To be clear, what's really happening at Chipotle is that biotech industry shills are deliberately contaminating Chipotle's food with strains of e.coli in a malicious attempt to destroy both the reputation and finances of the Chipotle food chain...  The idea that exposing the public to e.coli might be harmful to some people doesn't cause them to hesitate for even a moment.  The more people get sick or die from their Chipotle operation, the better for biotech!

What is funniest about all of this is that Chipotle is currently under investigation itself for selling food containing GMOs -- after they declared themselves GMO-free.  "We have always been clear that our soft drinks contained GMO ingredients, and that the animals from which our meat comes consume GMO feed.  But, that does not mean that our meat is GMO, any more than people would be genetically modified if they eat GMO foods," said Chris Arnold, Chipotle’s Communications Director.

So Chipotle is GMO-free in the sense of selling some food that is GMO-free and some that is not, and not being up front with its customers about which is which.  Got it.

And this is the company that the Evil Biotech Terrorists are targeting because they're too green?

[image courtesy of photographer Rosalee Yagihara and the Wikimedia Commons]

Let me reiterate: the vast majority of GMO foods are completely safe to consume.  Certain of them -- Bt corn comes to mind -- actually decrease the quantity of pesticides used by farmers, resulting in a healthier environment.  Others, like the GM papayas that are resistant to ringspot virus, have rescued an entire industry from bankruptcy (and it's to be hoped that the Evil Biotech guys will find a similar way to save bananas from the fungus Tropical Race 4, and oranges from the bacterial disease huanglongbing -- before two of our favorite fruits are a thing of the past).

The problem is, understanding the risks and benefits of genetic modification requires that you learn some science, and for a lot of people, it's easier to listen to people like Mike Adams rant about how the biotech industry is trying to DESTROY THE HUMAN RACE MWA HA HA HA HA HA.  It's not like we haven't had ample evidence that Adams's proclamations are nonsense; but unfortunately, in the media the usual case is that the guy who screams the loudest is the one who gets believed.

For what it's worth, here's my analysis, no screaming needed: there have been hundreds of norovirus, E. coli, and salmonella outbreaks in the past, and there's no need to invent bioterrorists to account for them.  Chipotle could certainly use some improvement in their food-handling standards, however, because five outbreaks in one year is kind of a lot.  Not to mention the fact that before they announce that they're GMO-free, they should make sure they're really GMO-free, for the benefit of people who care about such things.

And last: Mike Adams really needs to shut the hell up.

Sick unto death

New from the Dangerous Nonsense department: there's a new alternative-medicine model out of Germany that claims that viruses and bacteria aren't the cause of infectious diseases.

The website linked above, which was sent to me by a loyal reader of Skeptophilia, had me muttering imprecations under my breath pretty much right from the first line.  The author, Caroline Markolin, starts with a line from the famous 19th century biologist Rudolf Virchow: "If I could live my life over again, I would devote it to proving that germs seek their natural habitat -- diseased tissue -- rather than being the cause of diseased tissue."

Virchow was a brilliant pathologist and cellular biologist, but being good at some things doesn't mean you can't be dead wrong about others.  And the article conveniently fails to mention that Virchow not only disbelieved that pathogens caused diseases, he was also an ardent anti-evolutionist who considered Darwin an "ignoramus."

Be that as it may, we then are treated to quite a confection of nonsense.  Colds and flu, we're told, are actually the same thing, and are both caused by stress, not by viruses:

The common cold is linked to a "stink conflict", which can be experienced in real terms but also figuratively as "This situation stinks!" or "I've had it!". During the conflict-active phase the nasal membrane lining widens through ulceration, which is usually not noticed. In the healing phase, however, when the nasal tissue is being repaired, the nasal membrane swells up. A runny nose (healing always occurs in a fluid environment), headaches, tiredness, an elevated temperature or fever are all typical signs of a vagotonic healing process. If the cold symptoms are more severe, then this is commonly called the "flu". The claim, however, that "influenza" viruses are the culprits, has yet to be proven.

Nor has this claim, of course.  The "germ theory of disease" has over a hundred years of hard data supporting it.  This theory (if I can dignify it by that name) has a few vague generalities, a couple of ten-dollar words like "vagotonic," a photograph of a woman blowing her nose, so q.e.d., apparently.

We then find out that the "Spanish" flu of 1918-1919, that killed between 50 and 100 million people (hard numbers are difficult to come by, since the epidemic occurred during World War I, and many deaths in rural or isolated places went unrecorded), was not caused by a virus, it was caused by "stress."  People were under "territorial fear conflicts" and "death fright conflicts," and sickened from those; the acute, and frequently deadly, symptoms occurred when the body was trying to heal itself and the lung tumors caused by "stress" decomposed.

[image courtesy of the Wikimedia Commons]

Oh, and tuberculosis and AIDS aren't caused by pathogens, either.

And don't take antibiotics.  Ever.  Because they cause cancer.  Lung cancer, Markolin tells us, isn't caused by smoking; to hell with the research, which includes a study that demonstrated that 2/3 of the people who smoke will eventually die from conditions associated with tobacco use.  Cancer is caused by "shock," she says.  In a statement that should be an odds-on favorite for the Circular Logic Award of 2015, she states, "We have to bear in mind that every diagnosis shock can potentially cause... cancer," implying that the diagnosis of cancer is what caused the cancer to appear.

But how was the cancer there to diagnose if the diagnosis caused the cancer, you may ask?  To which I respond: stress vagotonic death fight conflicts.  And fear.  Stop asking questions, because you're going to stress me out and give me a cold.

Oh, and viruses, "if they existed," would "assist in the reconstruction of... tissues."  Because evolution, for some reason.  Microbes are our friends; all disease is caused by emotional conflict.

Makes you wonder, doesn't it, how plants get infectious diseases.  Maybe my tomato plants didn't get late blight last year, maybe they were just feeling lonely and unappreciated.

But I'm certain that Markolin would have some sort of bullshit response to this, too.  Probably that humans with all of their ugly unnatural habits are causing the plants to stress out, and so the tomatoes are picking up on our conflicted quantum vibrational states and becoming sick themselves.

Nothing whatsoever to do with pathogens.  Just like colds, flu, AIDS, tuberculosis, and the bubonic plague.

The difficulty here is that there is a germ of truth (rimshot) to what she's saying.  The mind does have a role in health; stress does cause physical manifestations, probably mediated by the hormone cortisol.  But this is a far cry from saying that all disease is caused by stress, and that pathogens have nothing to do with it.

The problem with all of this is not that a crackpot has a website.  Many crackpots do.  It seems to be a favorite hobby of theirs, in fact.  The problem is that naïve people will fall for this, and fail to seek out proper medical care for curable conditions.  So it's homeopathy all over again; a claim that is entirely unsupported by research and evidence, and only believable if you fall for some hand-waving foolishness that the students in my Introductory Biology classes could debunk without even breaking a sweat.  That hasn't stopped the story, however, from being picked up by Spirit Science, so it's popping up all over woo-woo alt-med websites just in the last few days.  (If you go to the Spirit Science article, don't read the comments.  Really.  I mean it.  It will result in your spending the rest of the day curled up in a corner, whimpering softly.  If you ignore this advice, allow me to say simply that, yes, there are people in the world who are this stupid.  And they vote.)

So the caveat emptor principle applies here, of course.  People should be smart enough not to believe appealing nonsense about preventing the flu by becoming less stressed.  But I still feel some sympathy with the folks who are ignorant, or desperate, enough to fall for something like this, and who will suffer the consequences of that ignorance.

And as far as Markolin and her idiotic theory, I'm about done with it.  The whole thing is stressing me out, and we can't have that.

Chopra on AIDS

At what point does someone cross the line into giving advice so dangerous that the people involved in promoting him are morally culpable if they participate?

Look, it's not that I'm against free speech.  I also believe strongly in the caveat emptor principle -- that people have a responsibility to be well enough informed on matters of science and medicine that charlatans can gain no traction.  But influential people also have a responsibility, and that is to use that influence with care, to consider the harm their words could do, to make certain that what they're saying is scientifically correct (and making amends when they misspeak).

Of course, the most egregious example of how this can go wrong is the current measles outbreak in California, which has sickened 84 people so far and is still accelerating.  The CDC states that the outbreak is "directly attributable to the anti-vaxxer movement," and notes that even with treatment, measles "is a miserable disease" that can cause serious complications and death.  And we can lay the blame for the resurgence of this disease at the feet of such purveyors of unscientific bullshit as Andrew Wakefield and Jenny McCarthy, who despite mountains of verified, reliable research are still claiming that vaccinations are unnecessary at best and dangerous at worst.

But we've talked about the anti-vaxxers before, and they're hardly the only example of this phenomenon.  Just a couple of days ago, for example, we had none other than Deepak Chopra putting his two cents in (although that's vastly overestimating its worth), and he gave his opinion about AIDS...

... and said it wasn't caused by HIV.

The HIV virus [image courtesy of the Wikimedia Commons]

Chopra was being interviewed by Tony Robbins, and the following exchange took place:

Chopra: HIV may be a precipitating agent in a susceptible host. The material agent is never the cause of the disease. It may be the final factor in inducing the full-blown syndrome in somebody who’s already susceptible. 

Robbins: But what made them susceptible? 

Chopra: Their own interpretations of the whole reality they’re participating in. 

Robbins: Could that be translated into their thoughts, their feelings, their beliefs, their lifestyle? 

Chopra: Absolutely.

He goes on to say, "I have a lot of patients with so-called AIDS... that are healthier than most of the people who live in downtown Boston.  They haven't had a cold in ten years...  Someone's told them they have this disease, and they've bought into it.  The label is not the disease, the test is not the disease."

Robbins responds with a comment about a doctor who has stated that HIV is only capable of killing "one helper-T cell out of ten thousand," and Chopra agrees, saying that to get sick from it, we have to "facilitate the process with our own thoughts and beliefs, convictions, ideas, and interpretations."

Then they have the following discussion:

Robbins: There's a test that doesn't even test for the virus, and when they get a positive test, what happens to them? 

Chopra: Then they make it happen. 

Robbins:  Maybe they take something like AZT, a side effect of which is immune suppression...  What keeps us locked into this trap?  What keeps us locked in this trap where we keep promoting a philosophy of fear where we must depend on someone or something outside of ourselves to keep ourselves healthy? 

Chopra:  It's the collective belief system.  It's the hypnosis of social conditioning.  It's cultural, religious, social indoctrination.  

The way out, Chopra says, is realizing that "you are the field of all unbounded possibilities."

Are you mad yet?  I hope so.  Chopra is using his influence -- which is considerable -- to push people away from conventional treatment into accepting vacuous psychobabble, risking their own lives in the process.

You have to wonder how he explains the millions of deaths from AIDS in central and southern Africa.  Many of those people don't have access to medical tests and treatments; a considerable number of them don't have the scientific background to understand what the virus does to the immune system.

You also have to wonder how he'd explain the deaths of young children who contracted HIV from their mothers.  Was their disease due to their parents' lack of acceptance of "the field of unbounded possibilities?"  Or did the children themselves have problems with their "interpretation of the whole reality they were participating in?"

Chopra once was simply a laughable purveyor of woo-woo pseudoscience, of the kind that he evidenced by a statement made earlier in the interview: "You go beyond the molecules, and you find atoms.  You go beyond the atoms, and you find particles.  You go beyond the particles, and you find nothing.  You go beyond the nothing, and you find absolutely nothing."  But now he's crossed the line into endangering people's lives with his claptrap.

I'd much prefer it if people would come to recognizing how dangerous this man is through a greater understanding of science; but the unfortunate truth is that there will always be gullible, credulous, and poorly-educated people out there, and it is immoral to allow people like Chopra to prey on their lack of understanding.  I wish fervently that radio and television stations who are giving this man air time, and book publishers who are promoting his views in print, would say, "I'm sorry, sir, but you are a quack, and you're hurting people, and we're not participating."

But the sad truth is that even if what he's saying is garbage, it's lucrative garbage.  Given the profit motive that drives most of our society, I suspect that Deepak Chopra is going to continue to get richer at the expense of people who are ignorant enough or desperate enough to buy the nonsense he's selling.

Magic eggs and faith healers

It's a question I've asked before: how do "alternative medicine" and "faith healing" therapies that don't work get started, and then continue to sucker people?  You'd think that if you're told that "pressing a quartz crystal to your forehead will cure your headache," the first time you got a headache that didn't go away after the application of a crystal, you'd say, "Okay, this doesn't work," and go take an aspirin (i.e., medicine that is actually effective) instead.

Oh, I know about the placebo effect, and the possibility of spontaneous remission of symptoms.  But still.  That only takes you so far, especially given the crazy, non-scientific basis of some of these so-called remedies.

Take the claim that was just covered in The Daily Mirror -- that in order to cure hemorrhoids, all you have to do is to go to a temple in the Kunagami Shrine, north of Tokyo, and aim your butt at a "holy egg" (actually an egg-shaped rock) while a Shinto priest chants a prayer, and lo!  Your hemorrhoids will be cured.

The article explains how the whole thing works:

Temple priest Osamu Hayakawa explained: "We perform a short service and afterwards individuals have to point their rear ends at the holy egg and say a special prayer. 

"The devout will find the trip to the Kunigami Shrine will have the desired effect." 

Sufferers apparently used to wash in a local river and afterwards ate boiled eggs at the temple to cure themselves of the condition, but the ceremony has been modernised. 

Mr Hayakawa said: "In the modern world, it is not acceptable for people to be showing off their rear ends while bathing in public but we believe that it is fine if the essence of the ritual is still maintained."

Right!  Modernized!  Because that's the word I'd use to describe pointing your ass at a magic egg to cure an unpleasant medical condition.

Of course, we once again bump up against the reluctance people have to criticize silly ideas when they come under the aegis of religion, which this one clearly does.  My reaction predictably, is, "Why not?"  Ideas are just ideas; they either reflect reality, or else they don't.  Just because a particular ridiculous claim is a ridiculous religious claim shouldn't make any difference.

And the magic butt-mending egg is such a counterfactual religious claim.  But before we laugh too hard at the Japanese ritual, keep in mind that it's really no different from Christian claims of faith healing except on the level of details. 

Which, unfortunately leads us into a darker side of this topic.  Just last year, Herbert and Cathleen Schaible of Philadelphia were charged with murder when a second child of theirs died from a treatable illness.  Their seven-month-old son Brandon died of bacterial pneumonia after days of prayer; four years earlier, they'd lost their two-year-old son Kent from a similar illness.  In both cases, they were directed by leaders of their church, the First Century Gospel Church, to use "faith healing" rather than conventional medicine.

"The church believe [sic] that people get sick because they’re not doing the right thing," a church member named John told reporters for NBC Philadelphia.  (He refused to give his last name during the interview.)  "God promised us that if we do his will, that there’s no infection; all these diseases that you name, would not come to you."

And, he added, the arrest of the Schaibles and the criticism of the church leaders amounts to "persecution."

My attitude is: if you want to call it persecution, fine.  The authorities should persecute the hell out of them.  If your faith involves letting a seven-month-old baby die because you think god is punishing him for "not doing the right thing," you have abandoned your right to claim "freedom of religion" for your practice.

But back to my original point; at what point do the adherents to such beliefs look at this sort of thing, and revise their worldview?  How long will it take before people stop, look at all of the examples of diseases left uncured by "the power of prayer," and say, "Okay, this doesn't work?"

Evidently, the answer for some people is, "forever."

I try to be understanding of people, I really do.  But this is one case where I just don't get it.  This is so far off in the realm of the completely irrational that I can't find any point of contact from which I could comprehend them.