Sunday, December 18, 2016

Cats as Carriers of Disease

Peter P. Marra and Chris Santella provide an interesting perspective on our beloved pet cats in their book Cat Wars: The Devastating Consequences of a Cuddly Killer.  They explore the problems that arise because cats are not really domesticated animals; they still can live independently of their human keepers and continue to be effective predators for just about any animal smaller than themselves.  Cats escape from or are abandoned by their owners and become feral.  Given that they breed very rapidly and are prey for few larger animals, they multiply quickly in the wild.  While often providing a useful function in controlling the mice and rat populations near human activities, they are also proficient killers of more valued species such as birds.  The authors are driven mainly by the threat cats present to bird species that are, for a number of reasons, experiencing rapidly falling populations.  The authors conclude that house cats are not a problem if they are kept in the house, but wild cats should be completely eradicated, at least in certain locations.  A review of the authors’ argument can be found here.

As part of their argument for eradication, the authors bring up the topic of disease propagation by feral cats.  Wild cats share the same areas—and feed off of—animals that are reservoirs for serious diseases.  Consequently, they are capable of becoming infected themselves and passing on that infection to humans via bites, scratches, or even by breathing on a human. 

The plague still persists in some regions of the country and transmission to humans via cats does occur, but infrequently.  However, the illness can be fatal if not diagnosed early.

“Cases of plague transmitted from cats to humans are rare in the United States.  From 1977 to 1998 there were twenty-three cases of cat associated human plague in the country.”

A sickness more frequently transmitted is Bartonellosis, more commonly known as cat scratch disease or cat scratch fever.  Infection is likely in cats with estimates of a 40% or greater rate of occurrence.

“….cat scratch fever refers to an infection from a Bartonella bacterium that develops when an infected cat scratches or bites the human skin.  In cats themselves it is usually not a serious problem, and 40% or so of the cats that carry it are asymptomatic.  Humans, similarly, usually are not seriously harmed; a red bump forms, the lymph nodes might swell, and a mild fever may emerge.  However, more serious infections can, and have, occurred, particularly among immune-compromised individuals.”

Rabies is disease that is transmitted by several small to moderate sized mammals that are easily encountered in the wild by cats or dogs.  It is an interesting case of how a virus or bacterium can manipulate a host that has been infected in order to insure its propagation to another specimen.  When infecting an animal the virus travels along nerve fibers as it makes its way to the brain.  Once there it alters the behavior of the host, eventually making it more aggressive.  Meanwhile, the virus is also making its way to the saliva glands so that when the animal bites another animal the virus can be transferred to the next host. 

Dogs have long been the greatest threat to humans when it came to the transmission of the rabies virus.  Prior to the development of vaccines and effective post-exposure treatments, an encounter with the rabies virus was always fatal.  Fear of rabies led to enforced vaccination of pets and the near elimination of wild dogs.  Since there is less awareness of cats as a source of rabies and less popular support for the elimination of wild cats, bites and scratches from cats have become the most serious threat for rabies transmission to humans.

“Since 1988 cats have been the number one domesticated species passing rabies infections to humans.  In 2013, 53 percent of all reported rabid domesticated species were cats, followed by dogs at 19 percent.  The cause of this pattern seems clear—the presence of millions and millions of stray and unvaccinated free-ranging cats on the landscape, many of them sharing feeding stations with wildlife that are susceptible to rabies.”

The animals infected with the disease may not have observable symptoms, and a person infected by the bite or scratch of a rabid animal may go months before symptoms appear.  And once symptoms do appear it is too late and the infected person will die.  Consequently, any such interaction with an unknown or undocumented animal requires anti-rabies treatment.  Since cats can appear to be cuddly animals, especially to children, they can be particularly dangerous.

“….the vast majority of the 38,000 post-exposure rabies treatments conducted annually are the result of people interacting with a suspected rabid cat.  Each of these post-exposure prophylaxis treatments cost public health departments and U.S. taxpayers somewhere in the neighborhood of $5,000 to $8,000, amounting to at least $190 million across the United States each year.”

Cats are also the unique source of a parasite called Toxoplasma gondii.  The life cycle of this parasite requires an infected cat to spread the disease to other animals via cysts (oocysts) that are excreted into the environment where other animals can ingest them and allow the cysts to transform into tachyzoites which then multiply rapidly, and ultimately into something called bradyzoites.  These secondary hosts are then eaten by cats and the infectious cycle begins again.

Unfortunately, humans and other valued species can be infected by these cysts that infected cats distribute.

Toxoplasmosis, the disease caused by Toxoplasma gondii, is one of the most common parasitic infections in humans.  In fact, it is estimated that approximately 30 to 50 percent of the world’s population and up to 22 percent of the U.S. population (more than 60 million Americans) are infected with Toxoplasma gondii….”

The cysts defecated by infected cats are very robust and can last for as long as a year or more in very harsh environments.  Humans can become infected by direct interaction with cat feces or by consuming foods from animals (poorly cooked meat from an infected animal for example) or by eating contaminated vegetables (cats seem to like to defecate in gardens and children’s sand boxes).  Most humans show no symptoms from an infection, but it can generate flu-like symptoms in some individuals.  The consequences of an infection can be quite severe for people with compromised immune systems.

Since so many people are infected by Toxoplasma gondii, and the vast majority of them are asymptomatic, why be concerned?  To begin with, the prime example of a compromised (or nonexistent) immune system exists in the form of a human fetus, and it has long been know that this infection can be transmitted from a pregnant woman to her fetus.

“Pregnant women and their fetuses have been known since the 1920s to be at serious risk.  If infected with toxoplasmosis in the first trimester, one in ten fetuses will be aborted or become malformed—and this is likely an underreported statistic.  Because of this problem, pregnant women have been warned for decades to avoid changing litter boxes and touching cat feces.  Despite these warnings, congenital transfer of Toxoplasma continues to happen across the world.”

Consider what is known about how the disease progresses in infected mice and rats.

“Once in the secondary host, the Toxoplasma oocysts then transform into something called a tachyzoite and multiply asexually rapidly.  Tachyzoites can be as small as one-tenth the size of red blood cells when they invade healthy cells.  There they divide quickly, causing tissue destruction and spreading of the Toxoplasma infection to the new host organism.  Eventually the infection localizes in muscle and nerve tissue—especially in parts of the brain—in the form of cysts called bradyzoites….”

The rabies virus has a strategy for modifying the host’s behavior in order to increase the probability that the host will infect another animal—Toxoplasma gondii does as well.

“Then something odd begins to happen to the newly parasitized host: its normal behavior of fear toward cats turns into attraction.  Specifically, the smell of cat urine—a smell that infected mice and rats were thought to be hardwired to fear and avoid—becomes an attractive aphrodisiac.  This is exactly how the Toxoplasma parasite wants its host to behave, because it turns infected rodents into easy prey.  Once the infected host, along with the parasites infecting its body, is eaten by a new predator, (preferentially a cat or other species of feline), the parasite can begin its sexual reproductive cycle again, infecting a new host, shedding oocysts, and expanding its reach.”

It was generally believed that these bradyzoites were a stable, latent stage that, although it remains in the infected human forever, had little if any effect.  However, if the bradyzoites are capable of altering the brain and changing behavior patterns in rats and mice, why would one assume that they were incapable of doing something similar in humans?

“Then scientists began to look a little deeper and found that the bradyzoites were actually dynamic and replicating.  In fact, one manifestation of toxoplasmosis infection is the development of ocular toxoplasmosis—basically cysts that settle in the eye.  If the cysts burst they can cause a progressive and recurring inflammation of the retina that can result in glaucoma and eventually blindness.  Regrettably, this is not the worst manifestation of toxoplasmosis infection in humans.”

Recent studies have suggested correlations between toxoplasmosis and long-term changes in physical and mental health.  Consider this summary from Wikipedia on the state of knowledge about the long-term effects of toxoplasmosis.

“Some evidence suggests latent infection may subtly influence a range of human behaviors and tendencies, and infection may alter the susceptibility to or intensity of a number of affective, psychiatric, or neurological disorders.   Research has linked toxoplasmosis with schizophrenia.”

“Latent T. gondii infection in humans has been associated with a higher incidence of automobile accidents, potentially due to impaired psychomotor performance or enhanced risk-taking personality profiles.  Moreover, correlations have been found between positive antibody titers [a measure of concentration] to T. gondii and OCD [obsessive-compulsive-disorder], Parkinson's disease, Alzheimer's disease, suicide in people with mood disorders, and bipolar disorder.   Positive antibody titers to T. gondii have been shown to be not correlative with major depression or dysthymia.  Although there is a correlation between T. gondii infection and many psychological disorders, scientists are still trying to find the cause on a cellular level.”

Some researchers are more cautious than others about drawing conclusions from these correlations; some are drawing the direst of conclusions.  The authors describe some of the work and conclusions of Jaroslov Fleger.

“Fleger believes that collectively toxoplasmosis, either through the acute stage of infection or through mental and neurotic illness manifested during the latent phase, has contributed to the deaths of hundreds of thousands of people, if not significantly more, over the last few decades.”

“Jaroslov Fleger….believes that malaria, now considered to be the most devastating protozoan killer of humans, will be ‘dethroned’ by toxoplasmosis.  As long as we continue having outdoor cats, the parasite will spread.”

More on Fleger and related research can be found in an article by Kathleen McAuliffe in The Atlantic: How Your Cat Is Making You Crazy.

For those of you who are not concerned that cats might be killing too many birds, perhaps you might wish to consider the human health consequences detailed for toxoplasmosis.  You can still have cats; you just have to keep them inside.

The interested reader might find this article informative:


Thursday, December 15, 2016

Cats as Predators: The Damage They Do

Of all the cultural conflicts that tear our nation apart, perhaps the one that receives the least attention is that between bird lovers and cat lovers.  That is a pity because there are significant issues involved that affect all of us.  Peter P. Marra and Chris Santella inform us that there are things that require more of our attention.  They bring us up to date with their book Cat Wars: The Devastating Consequences of a Cuddly Killer.

The authors believe that the domestic cat species that have become popular as pets evolved from species of the wild cat appropriately named Wildcat. 

“Recent genetic studies corroborate the notion that today’s domestic cats evolved from several subspecies of wildcats and suggest that, of the five, the Near Eastern Wildcat is likely the domestic cat’s nearest relative.  This also confirms the hypothesis that domestication of the cat occurred somewhere in the Fertile Crescent.”

It is assumed that just as wolves and humans discovered a mutually beneficial coexistence leading to the domesticated dog, wildcats and humans did as well, resulting in the domesticated cat.  Whereas wolves and humans could share the same food, the wildcat probably learned that mice and rats and other small mammals started hanging around human food stores looking for an easy meal.  Since mice and rats are preferred meals for wildcats, it is easy to see humans concluding that letting wildcats hang around was a good idea. In this relationship, natural selection would enhance the survivability of wildcats that were less hostile to humans and would eventually give rise to versions of the domestic cat.

The attractiveness to humans of the domestic cat and its utility as a mouse and rat eliminator encouraged humans to begin carrying them wherever they travelled.  This meant that cats were introduced into environments in which they were not naturally occurring and would become an “invasive species.”  That term implies the animals would multiply beyond any natural controls and cause damage to the local ecology.  The authors begin their narrative with the experience of David Lyall who took up a position as a lighthouse keeper on Stephens Island off the coast of New Zealand and brought with him a pet cat named Tibbles who would soon deposit a litter of newborns in its new home.  Like many islands that had long been isolated, Stephens had developed unique flora and fauna—and had never experienced anything as voracious as the domestic cat.

“Cats make the perfect pet for an isolated island inhabitant, in part because they can obtain most of their own food from their surroundings.  Lizards, birds, or small mammals provide a sufficient diet.  Cats are carnivores and need to consume primarily protein and some fat to stay healthy.  They are ambush predators, sitting for long periods, motionless and quiet, waiting for the right time to pounce.  They are quick and efficient and excel at what they do—otherwise they die.  Cats have retractable, razor sharp claws that extend from their strong paws to pin down prey.  Once the prey is immobilized, cats inflict the kill bite with two sharp canines, usually to the neck, and quickly begin tearing into scales, fur, or feathers.  Cats can kill animals as large as rabbits and squirrels, but their primary prey consists of smaller rodents like mice and voles as well as birds the size of (and including) sparrows and wrens.”

“Cats do not always kill out of hunger.  They seem to be stimulated by the chase and if not hungry will still kill; cat owners who allow their cat to roam freely may have received a ‘present’ of a bird or mouse, a testament to their pet’s predatory competence.”

Cats reproduce at an astonishing rate, and in an environment where they have no significant threat from predators, their population will grow until limited by lack of food or by disease.

“Cats average three litters a year; the average number of kittens in each litter is four to six.  Kittens can come into estrus as early as four months after being born, so the numbers of cats can multiply very quickly!”

A single pregnant cat, as in the case of Stephens Island, is all that it takes.

“A female cat can produce a litter of as many as eight kittens, sometimes more, and if a male is around, she can be impregnated again within days after giving birth.  If an unrelated adult male is not around, siblings will eventually mate with one another, or offspring will mate with their mother.”

On Stephens Island, David Lyall, a naturalist at heart, had the unique experience of discovering a new species of bird on the island only to realize that within a year the proliferation of cats that he had initiated had rendered the bird extinct.  It would take 26 years of cat killing to rid the island of the predators.

Cats are an invasive species in the United States as well.  The problem with domestic cats is that most of them are feral and must live off the land by eating birds and other small mammals.

“The Loss et al. paper positioned the domestic cat as one of the single greatest human-linked and direct threats to wildlife in the United States, and emphasized that more birds and mammals die at the mouths of cats than from wind turbines, automobile strikes, pesticides and poisons, collisions with skyscrapers and windows, and other so-called direct anthropogenic causes combined.”

The numbers of predator cats and their victims are staggering.  Counting feral cats is not a simple task.

“Rough estimates do exist and include between 20 and 120 million unowned outdoor cats, with 60 to 100 million cats the most frequently cited range.”

But feral cats are not the only problem.  The estimated number of owned cats is about 84 million.  These are cats that are treated as pets and, presumably, fed and vaccinated against disease by their owner.  Unfortunately, many of these owners allow their cats to wander outside where they can hunt and contribute to the killing even though they have no need for food.

“Based on eight different studies, between 40 percent and 70 percent of owned cats were allowed outside; three additional studies suggested that between 50 percent and 80 percent of these animals actually hunted.”

The unowned, full-time hunters were the most prolific killers.

“Loss et al. estimated that each individual unowned cat annually kills 1.9 to 4.7 amphibians, 4.2 to 12.4 reptiles, 30.0 to 47.6 birds, and 177.3 to 299.5 mammals per year.”

Combining the estimates from both owned and unowned cats one arrives at the death toll.

“The final mortality numbers showed that cats killed between 1.3 and 4 billion (median 2.4 billion) birds per year, with unowned cats causing the majority of the mortality (69 percent)….The final estimates for mammal mortality were also alarming; 6.3 to 22.3 billion (median 12.3 billion) mammals were killed every year by outdoor cats.”

Since there are few organizations defending the rights of mice and rats, the focus will be on birds. 

The authors provide data indicating that numerous bird species studied have shown significant declines in number over recent decades.  Cats are not the only contributor to these declines; they compete with environmental disruption caused by the growing human population.  However, the cat problem is the one least justifiable in terms of benefits for humans—or for cats. 

The killing of billions of birds is not the only negative result.  Cats prowling around outside and interacting with animals that are susceptible to plague and rabies can acquire those maladies and infect humans.  Control of wild dogs has been effective, but uncontrolled cats are now the greatest threat for rabies transfer. 

Cats are also the unique source of a parasite called Toxoplasma gondii.  The life cycle of this parasite requires an infected cat to spread the disease to other animals via cysts (oocysts) that are excreted into the environment where other animals can ingest them and allow the cysts to transform into tachyzoites which then multiply rapidly.  These secondary hosts are then eaten by cats and the infectious cycle begins again.

Unfortunately, humans and other valued species can be infected by these cysts that cats distribute.

Toxoplasmosis, the disease caused by Toxoplasma gondii, is one of the most common parasitic infections in humans.  In fact, it is estimated that approximately 30 to 50 percent of the world’s population and up to 22 percent of the U.S. population (more than 60 million Americans) are infected with Toxoplasma gondii….”

The infection will sometimes produce only mild flu-like symptoms in healthy individuals, but the invasive parasite does not go away; it lodges itself—hopefully in a dormant state— in tissue and will remain there as long as the individual is alive.  This latent stage was long thought to be benign, but recent studies have suggested correlations between infection and long-term changes in physical and mental health.

Infection in a person with a compromised immune system can be dangerous and even fatal.  The unborn fetus has no active immune system making infection via the mother a serious concern.

“Pregnant women and their fetuses have been known since the 1920s to be at serious risk.  If infected with toxoplasmosis in the first trimester, one in ten fetuses will be aborted or become malformed—and this is likely an underreported statistic.  Because of this problem, pregnant women have been warned for decades to avoid changing litter boxes and touching cat feces.  Despite these warnings, congenital transfer of Toxoplasma continues to happen across the world.”

Ardent bird lovers and cat lovers can both agree that there are too many unsupervised cats in the environment, feral cats spread disease, and that life for a cat in the wild is short and brutish.  Cat owners often assume that cats are quite capable of living on their own outdoors, making it easy to abandon them when it becomes convenient.  They may live outdoors, but few of them will thrive, and none will die of old age.

“Unowned cats without veterinary care are prone to disease (including feline leukemia, renal failure, feline panleukopenia, plague, rabies, and toxoplasmosis….).  They are vulnerable to predation by other animals, especially Coyotes and, to a lesser extent, eagles, owls, foxes, and Raccoons.  And they are frequently hit by cars—the most common cause of demise in outside cats.  Such are the hazards if they survive to adulthood, but estimates suggest that 50 to 75 percent of kittens born outdoors do not, dying from exposure, parasites and disease.  If they do reach adulthood, the life expectancy of an outdoor cat without caregivers providing regular feeding, water, and sometimes makeshift shelter is two years.  Outside cats that receive such care have a much longer life span, averaging 10 years.  The average life span of an inside cat is thirteen to seventeen years, depending on the breed.”

It would seem that a cat owner has a moral responsibility to keep her beloved pet inside and safe from harm.

So if everyone can agree that there are too many cats running around outside, what does one do about it?  The place to start is to keep from adding more cats to the environment.  Cat abandonment should be a crime.  There are leash laws for dogs, why not leash laws for cats.  Allowing an owned cat to run free could become a crime at some level.  But what to do with cats already running wild?

The main response from those concerned with protecting cats from harm is to foster trap-neuter-return (TNR) programs.  The assumption was that if a wild cat was trapped, taken to a facility and neutered, and then allowed to return into the environment, this would lead to a decrease in the population of feral cats.  Unfortunately, the data does not support this hypothesis.  Studies of wild cat colonies suggest that one would need to neuter 70-90 percent of the population before the numbers would begin to decline.  This level of TNR efficiency would be extremely difficult to reach.

The authors conclude that there is no alternative to the total elimination of the wild cats.  It can be done—at least locally.  As an example, they describe a program put in place on Ascension Island, a British territory.  Combined poison baiting and trapping (plus euthanasia) efforts began in 2002 as a means of ridding the island of cats.  By 2006 all the cars were gone.  The total cost of the effort was $1.3 million.

“Whether you consider $1.3 million an outrageous sum to pay to save a few birds or a wise investment in biodiversity will depend on your philosophical stance.  But from a purely financial perspective, there is little question that eradication—at least on a local level—will trump endangered species remediation every time.  A breakdown of per species dollars invested in conservation efforts for endangered species from 2004 to 2007 shows that $60.5 million was spent to resuscitate populations of the Southwestern Willow Flycatcher, $67.4 million to protect Red-cockaded Woodpeckers, and nearly $83 million to protect Bald Eagles.”

Thursday, December 8, 2016

Brains, Energy, and Humanity’s Most Important Achievement: Learning to Cook

Suzana Herculano-Houzel created a revolution in our knowledge of the mammalian brain and its evolution when she discovered a simple technique that would, for the first time, allow measurement of the numbers of various cells that make up brain material.  She presented results from studies using this technique in her book The Human Advantage: A New Understanding of How Our Brain Became Remarkable.  A brief summary of her findings can be found here.

Not surprisingly, the most interesting results from her studies centered on what could be determined about the human brain.  Humans are primates and are considered to be one of what are often referred to as the great apes.  When Herculano-Houzel evaluated her data on the neuron cell count in the brains of various classes of mammals, she discovered what she referred to as “the primate advantage.”  Taking the number of neurons in a brain as a proxy for the cognitive capacity of the brain, the primate advantage consisted in the fact that primates had evolved the means to control neuron cell size so that for a given brain size, a primate brain would contain more neurons than the brains of other classes of mammals, whose neurons gained size as brain mass increased.  Primates then had greater cognitive capacity per unit of brain mass, but not necessarily greater cognitive capability.  Capacity becomes capability when the neurons are used to learn things that provide an advantage to the possessor of the brain. 

An example was provided to demonstrate the size of this “primate advantage.”

“Once we knew the neuronal scaling rules for rodent brains, in 2006, we could already do some rough calculations.  With the equations relating the number of neurons in a rodent brain to the mass of the brain and of the body, we could estimate that a rodent brain that had anything in the order of 100 billion neurons, as the human brain was supposed to have, would weigh more than thirty kilograms [66 pounds] and belong in a body that weighed more than 80 tons.  In other words: if we were rodents, we would look like a blue whale, have to live in water, and carry an impossibly large brain, one that would likely collapse under its own weight.”

Herculano-Houzel eventually determined that the human brain contained about 86 billion neurons.

She was always puzzled by the assumption that humans were somehow exceptional to an extent that seemed inconsistent with the notion that humans evolved in the same manner as other animals.  The fact that humans were primates closely related to gorillas and chimpanzees (the great apes) that were comparable in size but only had about a third the brain mass of a human supported this notion of human exceptionality.  Once she had data on primate species similar to that for rodents she could apply scaling rules to the number of neurons versus brain size, and brain size versus body size.

“According to the neuronal scaling rules that apply to primates, we would expect a generic primate brain with a total of 86 billion neurons to weigh about 1,240 grams (2.75 pounds) in a body weighing about 66 kilograms (145 pounds).  These numbers are just about right for us humans, with our, on average, 1,500 gram (3.3 pound) brains and 70 kilogram (155 pound) bodies.  The conclusion should come as no surprise to a biologist: we are that generic primate with 86 billion neurons in its brain.  Our brain is made in the image of other primate brains.”

If that explanation is correct, then the other great apes must be the exceptions because they have much smaller brains than the scaling rules suggest.  Therein resides an interesting tale of how humans, in fact, became exceptional.  It was not the brain we were born with that makes us exceptional, it is what we did and what we continue to do with that brain that made us unique.

It is necessary then to explain why the other great apes ended up with smaller brains in order to understand why we ended up different.  Consider that the amount of energy required to keep a neuron functioning is believed to be about constant and independent of neuron cell size, although it is a function of the brain region.

“What our findings indicate, however, is that within each of these neuronal types, cerebellar or cortical, variations in cell size across species are accompanied by neither an increased nor a decreased energy cost: neurons of the same type still cost the same across species, regardless of their size, with a fixed average energy budget per neuron across species.”

Nonprimate species have brains that increase with body size, but their neurons also become larger as brain size increases. Consequently they end up with many fewer neurons for a given brain size than primates and avoid creating an excessive energy demand to support their brains.

On the other hand, primate brains, with their large number of neurons in a relatively small size, consume a large amount of energy.  A human requiring a 2000 calorie diet to maintain its body weight would be devoting 500 of those calories to keeping its brain functioning.  A large brain with a lot of neutrons produces a large energy requirement that must be satisfied.  Herculano-Houzel provides an argument to support the hypothesis that given the environment in which the great apes evolved, their available food sources, and their physical capabilities, it is not possible for gorillas and other great apes to greatly exceed their current caloric intake and thus could not support a much larger brain.

Field studies of apes in the wild tally the amount of time they spend foraging for food.  Since apes tend to be on the lean side and generally do not gain excess weight, one can assume that they forage until they attain their needed nutrition.  What was discovered was that the bigger the ape, the more food that could be gathered and consumed in a given time period.  However, as body weight increased, the energy demand of the body increased faster with weight than the ability to consume more calories.  That meant that there was, in principle, a maximum mass that an ape could attain.  It also means that there was no extra energy available to support larger brains.  These apes could have evolved to a smaller size and, perhaps, could have acquired a larger brain as compensation, but natural selection seems to have decided against that strategy for those apes in their particular environments. 

“….the lineages that remained on all fours (and gave rise to modern apes) seemed to have invested any additional kilocalories [what we refer to as calories are technically kilocalories] amassed per day from longer times foraging and feeding into growing larger bodies.  For knuckle-walking species that are, for anatomical reasons, not very mobile, becoming as large as they could afford must have been advantageous, earning larger animals higher social status and thus greater access to food, among other privileges.”

Opting for a larger brain can be a risky evolutionary decision.  The brain always gets the energy it needs—and it always needs about the same amount no matter what the animal is doing—or the animal dies.

“Because an individual brain always uses the same amount of energy, no matter whether the rest of the body is starving, having too many neurons is clearly a liability when a species lives close to the limit of its caloric intake possibilities.”

Humans then had to have done something to escape from this brain size dilemma.  The starting point of a new direction was probably becoming bipedal with increased mobility and access to different and more extensive feeding zones, and new classes of survivability issues.

“….for our newly bipedal and suddenly highly mobile australopithecine ancestor, who some 4 million years ago diverged away from the lineage that would give rise to the modern chimpanzee and bonobo, investing the additional kilocalories it amassed per day in a greater number of brain neurons housed in a leaner, lighter body must have proved a much better investment strategy.”

Knowledge of how brain size must have increased over time from archeological evidence suggests that pre-humans adapted physically to the new environment and its challenges by growing slightly larger and increasing brain size as well.  However, the increase in brain size was small until about 1.5 million years ago, when it began to rapidly increase.  The hypothesis is that even though pre-humans learned not only to gather food but also to hunt it, it still faced an energy constraint due to the time required to obtain and consume food.

If one needed a dramatic increase in nourishment one could either figure out a way to acquire much more food, or one could figure out a way to obtain more nourishment from the food supply on hand.  The archeological evidence suggests that around 1.5 million years ago, when brain growth really began to rise rapidly, humans also began to cook their food.  Richard Wrangham’s book Catching Fire: How Cooking Made Us Human took note of this occurrence and formulated a “cooking hypothesis.”

“In a nutshell, the cooking hypothesis proposes that it was the invention of cooking by our direct ancestors and the resulting availability of cooked food that offered the larger caloric intake that allowed the brain of Homo to increase in size so rapidly in evolution.  The circumstantial evidence of the drastic reduction in tooth and cranial bone mass, expected for a species that no longer had to use much effort to chew, was all there, along with the fossil record that put the use of fire with transforming of foods between 1.0 and 1.5 million years ago.  What Wrangham did not have then was an indication that cooking, or some other way to increase caloric input from food, was not simply a bonus, but rather an essential requirement for their brains to become any larger.”

Why was a diet of raw foods so limiting for primates?

“….cooking presupposes the use of heat to denature proteins, break carbohydrate chains, and otherwise modify the macromolecules of food, turning foodstuffs into smaller, softer, more easily chewable and enzymatically digestible versions of their former selves.  Cooking with heat breaks down the collagen fibers that make meat tough and softens the hard walls of plant cells, exposing their stores of starch and fat.  Cooked foods yield 100 percent of their caloric content to the digestive system because they are turned into mush inside the mouth, then digested completely by enzymes in the stomach and small intestine, where, once converted into amino acids, simple sugars, fatty acids, and glycerol, they are quickly absorbed into the blood stream.  In contrast, the same foods may yield as little as 33 percent of the energy in their chemical bonds when eaten raw because these harder foods are swallowed while still in pieces, and thus are broken down and digested only partially.  Only the surface of the raw food crumbs is exposed to digestive enzymes in the stomach and small intestine; most of the unbroken starch finally gets digested in the large intestine by bacteria that keep the energy for themselves.”

Cooking available foods increased the obtained caloric content of those foods by a factor of up to three.  That is clearly a revolutionary occurrence, but the additional energy did not immediately lead to a bigger brain.  First, our ancestors would have to encounter or create situations in which the increased cognitive capacity was needed in order to obtain a survival advantage.  Natural selection would take over at that point.

The human advantage was not so much its bigger brain, but the ways in which our ancestors put that brain to use.  Our brains at birth are rather empty, useless things, but with a lot of potential.  It is the fulfilling of that potential that makes humans unique.

Now that we have learned how critical cooking food has been to human development, it should come as no surprise to learn that returning to eating only raw food has become a bit of a movement in some areas.  The terms crudivore and crudivorisme (for those comfortable with the French language) have arisen.  The English version of wikipedia files it under “raw foodism.”

Herculano-Houzel provides this comment on the topic.

“….despite the amenities of the modern, technological world, obtaining enough kilocalories from raw foods  remains so difficult that the crudivore diet is the ‘tried-and-true” way to lose weight—although not without its drawbacks: the drastic weight loss that ensues, with a constant feeling of hunger, is often accompanied by malnourishment to the point that women on the diet stop menstruating.”

Interestingly, other animals can still be smarter than humans on occasion.  Most animals that have been fed cooked food will gladly trade their raw food for the new stuff.

The interested reader might find these articles informative:

Friday, December 2, 2016

Suzana Herculano-Houzel Explains How Our Brain Became Remarkable

A revolution has occurred in our understanding of how our brain and those of other animals have evolved.  This revolution has produced a profound change in how we should consider ourselves in relation to other species, and, in particular, to how we should compare ourselves to the other great apes.  While areas in science where great amounts of money are involved, in terms of products to be produced or in the quest for research dollars, tend to be argued in the mainstream media, others that aren’t associated with a large revenue stream can rattle around in obscure (to most of us) journals for many years before they are revealed to the general public.  That has been the case with the research started by Suzana Herculano-Houzel and summarized in her fascinating new book The Human Advantage: A New Understanding of How Our Brain Became Remarkable.  Her work began in 2003, was first published in 2005, and after 10 years of additional research is now being presented to the rest of us in her book.

The author, a native of Brazil, had an exemplary academic career with a stint at Case Western Reserve University in Cleveland before obtaining a Ph.D. in neurophysiology at the Max Planck Institute for Brain Research in Frankfurt.  For personal reasons, she returned to Brazil and worked at the Museum of Life in Rio for three years.

“For the first three years back in Rio I designed hands-on activities for the children who visited the museum, created a website, and wrote my first book on Neuroscience for the general public, which landed me a job at her alma mater.”

The year before she initiated her research she was named an associate professor at the Federal University of Rio de Janeiro whose specialty was assumed to be science communication.  However, she was told she could perform research as well if she wished. 

Herculano-Houzel had always been troubled by the quandary that arose when true-believers in evolution reasoned that humans had to be produced by evolution, yet they continually evaluated humans in a manner that placed them beyond the bounds of what could be explained by evolution.  If we are the end point of evolution of the great apes, how could we have evolved to have a brain that was about three times larger in mass?  Why are we so unique?  Her great contribution was to demonstrate that, in terms of evolution, we are not unique.

It was believed that cognitive abilities in a species would be related to the number of neurons contained within the brain.  If that was the case, then how can one discuss the relative brainpower of a given species if this number was not available?  This is the problem Herculano-Houzel wanted to solve.  Prior attempts at measuring neuron numbers utilized a technique known as stereology in which thin slices of a brain would be sampled in depth at a few locations and the results applied to the entire section.  She needed a method both simpler and more powerful for what she intended.

“The highly heterogeneous distribution of neurons across different structures of the brain, however, makes stereology impractical for determining numbers of cells in whole brains.  Neuronal densities vary by factors of up to 1,000 across brainstem structures and the cerebellum.  Even within a single structure, like the cerebellum, different layers have neurons packed in widely varying densities….[Stereology] would be prohibitively expensive even for a well equipped lab.  And it was even more so for myself, with no lab and no funding.”

Her solution to the problem required some trial and error, but no exotic new equipment or materials.  She merely produced what she gleefully refers to as brain soup.  Sections of brain material to be analyzed where sloshed around in a detergent solution that dissolved the cell boundaries but left the cell nuclei intact.  This soup had to be homogenized so that samples of the fluid could be used to visually count the number of nuclei.  This approach was aided by applying chemicals that would attach to the nuclei and produce a blue color.  This provided a total cell count.  To get a separate count of the number of neurons there was a known molecule that would attach itself to neuron nuclei and produce a red color. 

“Counting 500 nuclei (which took around 15 minutes at the microscope) was enough to determine the percentage of neurons with a certainty of 0.2 percent.  Applying the percentage of neurons to the total number of cells in the structure of origin yielded an estimate of the total number of neurons in it.  By subtraction, I had the total number of other cells, presumably mostly glial cells, in the tissue.  Summing the results for the various brain structures—and I started with entire brains subdivided simply into cerebral cortex, cerebellum, and rest of the brain—yielded for the first time, direct estimates of the total number of neurons and other cells in the whole rat brain.  And the entire process took less than a day.”

“Luckily for us, however, there were a few stereological estimates available in the literature for the rat cereberal cortex and cerebellum—and our estimates matched them.”

This picture will help with the nomenclature.

The rather small cerebellum is clearly indicated, as is the brainstem.  The rest of the visible parts make up the cerebral cortex, which is often divided into sections that have more to do with physical structure than function.

 Herculano-Houzel was now off and running.  She had a credible technique.  Now she needed specimen brains—lots of them.  Her studies were restricted to mammalian brains which all have similar structures.  One can postulate that mammals all derive from a single ancestor and the various families of mammals (clades) broke off from that original line and evolved according to its newly determined evolutionary rules.  Determining the manner in which species in a clade added neurons to their brains as the species increased in adult size would be of great interest.

After 10 years of research, Herculano-Houzel and her collaborators had accumulated and published data for six different mammalian families.  What they discovered was that for most species the number of neurons did not scale proportionately with brain size, whether in the cerebral cortex or the cerebellum.  As the family evolved to larger animals with larger brains, the size of the neuron cells increased and thus the number of neurons increased but did not keep up with the gain in brain size.  The primate family was the great exception to that rule.  The small primates studied had somehow developed a mechanism that kept the size of neurons nearly constant as larger species with bigger brains evolved.  Thus a primate brain would pack more neurons per volume than a brain of a different family but of the same size.  This is referred to as “the primate advantage.”

Humans are primates.  The greatest enlightenment provided by these studies was placing the human brain in context.  Previously, it was generally concluded that the human brain was exceptional in size because it was so much larger than those of the other great apes.  However, the scaling rules determined for primates indicated that the human brain is exactly what it should be for a primate of that size.  The other great apes were the outliers.  They possessed brains much smaller than they should have had.  What happened?

Herculano-Houzel attributes the hypothesis that can explain this to Richard Wrangham who presented his thoughts in his book Catching Fire: How Cooking Made Us Human.  Her results corroborate the hypothesis.  It must be recognized that a brain requires an exceptional amount of energy to keep it running.  There appears to be a constant energy requirement per neuron; a bigger brain, or just a rain with more neurons, requires more energy.  For humans, the brain utilizes about 25% of the calories in a normal diet.  For an ape to have developed three times the brain size (as scaling suggested) that ape would have had to have a plentiful supply of calories to support it.  Observational studies of the other apes in the wild suggest that food is not plentiful for them; they work hard foraging for enough food to maintain their weight.  Given such a situation, it seems that natural selection for these apes determined that a larger body and a smaller brain was the more advantageous situation.

How did humans avoid this evolutionary trap?  First of all, they came down from the trees and began to walk on their hind legs.  This made them more mobile and put them in new environments that might change the tradeoff between body size and brain size.  But the issue of energy had to be solved.  Foraging for food might or might not have been more efficient on flat land.  What the historical record suggests is that the brain grew slowly in pre-humans after they became bipeds until about 1.5 million years ago when brain size began to grow dramatically.  This is also about the time that the historical record suggests the pre-humans began to cook their food.

Why is cooking food so important?  The process of cooking makes food much more easily digestible and allows the body to absorb about 100% of the caloric content.  Raw food, on the other hand, provides only about a third of the potential caloric content.  Cooking also saved the time and caloric output required to chew raw food sufficiently that it could be swallowed.

Cooking then could have relieved pre-humans of the energy constraint and allowed them to develop larger brains, assuming that conditions favored a larger brain.

“And once the energy afforded by cooking turns a larger number of neurons from being a liability into being an asset, it becomes easy to envision a rapidly ascending spiral where larger numbers of neurons are selected for, given the cognitive advantage conferred to those individuals who have them and who now also have the time available to use them to hunt in groups, navigate the environment, look for better homing, hunting, and gathering grounds, and care for the wellbeing of their group, protecting it and passing on knowledge about where to find food and shelter.”

The human brain itself is not exceptional in an evolutionary sense—it is basically just another primate brain, albeit a large one.

“Those pieces of science writing which hail the human brain as a wonder often forget to mention that it never, ever starts life as a wonder, but rather as a 300-gram mass that doesn’t do much yet—although it certainly holds great promise.”

The human advantage then is not so much our physical brain as the knowledge that we have accumulated and have learned to impart to our brains.

Many thanks go to Suzana Herculano-Houzel for providing us such interesting insight on a fascinating topic.

The interested reader might find it curious to learn that the human brain has actually begun to decrease in size over recent millennia: Change in Human Brain Size, NaturalSelection, and Evolution

Monday, November 28, 2016

Responding to Trump: Mobilized Women, States’ Rights Advocacy, and Secession

Many liberals awoke the day after the election, assuming they slept at all, feeling that somehow they had been transported to an alien land that had somehow evaded the inevitability of civilization.  It will take some time to deal with this shock and come to grips with a new reality.  There were a few interesting notes on the subject of potential responses that appeared in The New Yorker by Ariel Levy and Jelani Cobb.

Ariel Levy’s piece is available online with the title Can Women Bring Down Trump?  Levy provides the advice and experience of Francesca Comincini who believes that she and other women activists were responsible for finally ending the political career of Silvio Berlusconi.  Berlusconi served several terms as Prime Minister of Italy and had a record of sexism and misogyny that even Trump couldn’t hope to match.

“Comencini pointed out that Trump and Berlusconi have a lot in common. They both amassed fortunes in real estate through questionable business practices. They share a taste for marble, extreme tans, and strongmen: Trump is impressed by Vladimir Putin and Saddam Hussein; Berlusconi was chummy with Muammar Qaddafi.”

“Both have a murky grasp on the concept of consent. (‘We don’t have enough soldiers to stop rape, because our women are so beautiful!’ Berlusconi said in 2009, commenting on new statistics concerning sexual violence. Trump defended himself against one of the many women who have accused him of sexual assault by sneering, ‘She would not be my first choice.’) Much as Trump complained that he ‘wasn’t impressed’ with the view of Hillary Clinton from behind, Berlusconi once dismissed Angela Merkel as ‘unfuckable’.”

Whereas Trump has only been accused of fraud and sexual predation, Berlusconi has actually been convicted on both counts (his conviction for having sex with an underage prostitute was later reversed).

Comencini’s advice for US women is to not despair at this loss, but to let it strengthen resolve.  Act, but act smartly.  She and her sister Cristina organized a series of demonstration in cities and towns across Italy.

“Berlusconi resigned nine months after her group, Se Non Ora, Quando (If Not Now, When), held its demonstrations, which attracted more than a million people.”

“’The rally was friendly, cool—like a rock concert,’ Cristina, a novelist and director, said. Like Trump, Berlusconi was a skilled manipulator of the media, with a keen sense of what messages resonate with his countrymen. The Comencinis strove to battle him with imagery as much as with ideology. They enlisted the Italian actress Angela Finocchiaro to make a video appeal to the nation’s men, asking them to ‘tell the world you don’t want to live in a bad fifties movie.’ They framed sexism and misogyny as not just wrong but lame.”

The Comencinis believes women in this country can also be successful and provide some advice.

“The sisters have a suggestion for their American counterparts as they prepare for the Million Women’s March on Washington, the day after Trump’s inauguration. ‘Do not make something against him, but communicate the idea that women are the nation,’ Cristina said. ‘This is strength—it’s there, it’s something that he has to face’.”

Jelani Cobb provided a note titled Post-Election, Liberals Invoke States’ Rights.  He opens with this lede.

“In response to Trump’s hostility toward immigrants, political leaders in New York and California vow to protect their most vulnerable.”

The fear that the rights of states will be trampled on by an overreaching federal government is usually expressed by conservative Republicans.  With the election of Trump, politicians in both California and New York have expressed the will to defy some of Trumps proclaimed intentions with respect to immigrants.

“On the day after the election, Kevin de León, the pro-tempore president of the California Senate, and Anthony Rendon, the speaker of the California Assembly, released a joint statement whose opening sentence—‘Today, we woke up feeling like strangers in a foreign land’—perfectly summarized the disorientation that millions of Americans were experiencing. More important, the statement pointed out that Trump’s bigotry and misogyny were at odds with California’s values of inclusiveness and tolerance, and, the authors vowed, ‘we will lead the resistance to any effort that would shred our social fabric or our Constitution’.”

“Charlie Beck, the chief of the L.A.P.D., added, ‘We are not going to work in conjunction with Homeland Security on deportation efforts. That is not our job, nor will I make it our job’.”

Andrew Cuomo, the governor of New York issued this statement.

“Whether you are gay or straight, Muslim or Christian, rich or poor, black or white or brown, we respect all people in the state of New York.”

“It’s the very core of what we believe and who we are. But it’s not just what we say, we passed laws that reflect it, and we will continue to do so, no matter what happens nationally. We won’t allow a federal government that attacks immigrants to do so in our state.”

Cobb suggests that these are positions that should be taken seriously.

“Thirty-nine million people live in California—twelve per cent of the population of the United States. The state is home to the economic and cultural axes of Silicon Valley and Hollywood. Last year, its economy became the sixth largest in the world, a spot formerly held by France. Clinton beat Trump by twenty-eight points in California, and by twenty-one points in New York. Now the two states have triggered an uncommon development in a year that has offered us a great number of them: liberals invoking states’ rights.”

Cobb reminds us that we have been here before as a nation.

“In 1798, the passage of the Alien and Sedition Acts increased the residency requirement from five years to fourteen before immigrants could vote, and authorized the executive branch to summarily deport immigrants who were deemed dangerous or who had come from hostile nations. In response, James Madison and Thomas Jefferson, whose Democratic-Republican Party was favored by immigrants, wrote the Virginia and Kentucky resolutions, which held that individual states had the right to nullify unconstitutional laws within their borders. They further stipulated that states had the right to ‘interpose’ themselves against the authority of the federal government.”

“Trump’s hostility toward immigration has taken various iterations, but the common theme is to rid the country of foreign residents deemed dangerous and to prohibit the entry of people from hostile nations. It would appear that, two hundred and eighteen years later, the principles of the Alien and Sedition Acts have sprung, with surprising vigor, from their resting place in history.”

It is not clear where this is going, but California and New York, assuming they are serious, have upped the ante considerably on any moves Trump and the Republicans might choose to make.  Meanwhile, it also provides a thread of hope to those who now live in greater fear for their future.

“The political leaders in New York and California have not yet proposed nullifying federal authority on immigration—they are only resisting it, in the service of the higher principle of democracy and inclusion. That alone can’t forestall the damage that a Trump Administration might do on the issue of immigration. But, for the millions of Americans, immigrants and non-immigrants alike, who also woke up last week feeling like strangers in a foreign land, it is as good a starting place as any.”

The two articles carry a similar message: Don’t despair; fight back.

There is another interesting development that could be worth following.  Consider this recent article: California secession initiative filed with Attorney General.

“Backers are seeking to get what they have dubbed “Calexit: The California Independence Plebiscite of 2019” on the November 2018 ballot.”

“If the initiative is approved by voters, it would force a vote on March 13, 2019, the election date for local, odd-year elections, on whether California should become a ‘free, sovereign and independent country’.”

“Signature gathering cannot begin until the Attorney General’s Office prepares a title and summary for the initiative. Backers expect to begin signature gathering in the spring, according to Louis J. Marinelli, president of the Yes California Independence Campaign.”

“Backers would then have six months to gather valid signatures from 585,407 registered voters — 8 percent of the total votes cast for governor in the 2014 general election — to qualify the measure for the ballot.”

This initiative predates Trump’s election.  One assumed it was going nowhere, but after the election one can only wonder how many Californians will see this as a means to express their emotions, if not their will.

We may be living in interesting times.

Thursday, November 24, 2016

Microbes, Microbial Consortia, Antibiotics, and Our Future

The danger from antibiotic resistant strains of microbes has been well publicized as the occurrence of difficult-to-control infections has grown.  As this resistance is developed it appears to spread quickly to other species of microbes.  The response has been to seek new and more powerful chemicals, but the prospects appear dim.  What is less well publicized is the fact that most of our current antibiotics were obtained by extracting chemicals that are produced by microbes.  One difficulty in finding new antibiotics is that 99% of the world’s microbes seem to refuse to allow themselves to be grown in a laboratory where their products can be assessed and harvested if appropriate.  To obtain an understanding of why this is the case and why microbes can mutate so quickly, we will turn to Paul G. Falkowski and his book Life's Engines: How Microbes Made Earth Habitable

Single celled microbes have been around for billions of years.  Falkowski details the relatively small number of chemical “engines” that evolved to provide the basis of life for these creatures.  He then illustrates how these simple structures could have evolved into more complex multicellular forms and, in so doing, remade the earth into a platform that would support the huge array of large life forms that inhabit the planet today.  Of interest relative to the search for new antibiotics is the symbiotic existence developed by most forms of microbes.

Microbes learned early on that survival is easier if they form cooperative groups.

“Microbes do not live in isolation; most of them are symbionts, that is, they live together and depend on each other for resources.  More specifically, microbes use each other’s waste products for sustenance.  The use of waste products—also known as the recycling of elements—is one of the basic concepts in ecology, and it has strongly influenced the evolution of microbial nanomachines.”

Microbes also have a very flexible and efficient mechanism for evolution.  Rather than evolving via some random genetic variation that is passed on to offspring, microbial evolution is dominated by horizontal (or lateral) transfer of genetic information via mechanisms that are not well understood.  The most direct means is for a microbe to simply absorb genetic material from its environment.  A fraction of the time the material will be incorporated and passed on to subsequent generations.  Genetic material can also be incorporated via interaction with the numerous viruses which inhabit the environment.  Also, similar types of microbes can form a bond together and exchange DNA.

“Horizontal gene transfer is not a biological curiosity; it is a major mode of evolution in microbes.  Simply put, genes that were preadapted by selection in one organism can somehow be transferred to another, completely unrelated organism without sexual recombination.  In effect, this is quantum evolution—an organism that did not have the capability of fixing nitrogen can acquire genes for nitrogen fixation from the environment, and voilà, it instantly can fix nitrogen.”

This method of evolution is important because it can happen so quickly.

“Indeed, the process is frighteningly rapid.  One of the very first examples of horizontal gene transfer was discovered in Japan when it was realized that resistance to antibiotics was acquired by pathogenic bacteria much faster than could be explained by classical vertical inheritance.  When the era of gene sequencing came into its own, it was quickly shown that genes for resistance to many common antibiotics were spread all across the microbial world.”

The collections of interacting microbes that form stable communities are labeled by Falkowski as “consortia.”  Given a large number of members made up of a significant number of species, one arrives at a highly adaptable entity that can respond to dramatic changes in environment.  The microbes of a consortia share their products, and they are also capable of internal communication.

“Microbial communities, or consortia, are microscopic jungles in which tens or even hundreds of species of microbes live in a mutual habitat.  It should be noted that it is often difficult to strictly define what a microbial ‘species’ is.  The traditional definition of the word—that the offspring from sexual recombination is viable—which is testable in animals and plants does not readily apply to microbes….horizontal gene transfer makes defining ‘species’ somewhat specious.”

“On a microscopic scale, the organisms within a consortium are living within very close proximity.  Under such circumstances, the opportunity for successful horizontal gene transfer is greatly enhanced.  Hence, within consortia, gene transfers often allow a distribution of metabolic nanomachines across many groups of microbes, thereby allowing the flows of elements between organisms to be tightly controlled.”

“Controls are imbedded in the chemical signals that are sent from microbe to microbe within the community and that provide information about who is doing what and how many are where.  The system of intercellular signaling, called quorum sensing, resulted from the evolution of specific molecules that are made and used by microbes to assess their own population density, as well as to signal other microbes about who and where they are.  This mode of intercellular communication remains pretty remote to us, although we do know that there are specific molecules sent out be some cells that float around until they attach to specific receptor sites on another microbe’s membrane.”

“Once attached, the molecules work by altering the expression of genes in a cell.  Quorum sensing allows consortia to establish a spatial pattern of microbial metabolism that further increases the efficiency of recycling nutrients.  But it can also alter behavior.”

Given that most of our antibiotics are produced by microbes, Falkowski believes that these forms of molecules are used as a defense mechanism against dangerous microbes.  If true, that would be a rather sophisticated response to a threat by one of these consortia.

Falkowski also reminds us that we carry around our own private consortia of microbes.  We evolved within a microbial bath, and the microbes evolved with us.  We and they are one.  The most important consortia are those that exist within our digestive systems.  They are essential to life, yet we damage them every time we take an antibiotic.  After an individual course of an antibiotic it takes time for the consortia to recover.  Multiple courses taken over a lifetime can result in permanent changes in our individual consortia and produce effects on our health.  Species of microbes can be eliminated entirely if they are not available to be passed on to our offspring.  The medical community is currently struggling to understand how bodily function is dependent on the specifics of our digestive consortia.

It would seem that the reason most microbes refuse to grow in a laboratory is because they are not so much individual species as members of a consortium tuned to and requiring an environment that has not been, and, perhaps, cannot be reproduced in a laboratory.

Raffi Khatchadourian provides a view of the state of antibiotic research with a focus on attempts to gain access to the microbes in the mysterious 99%.  His article appeared in The New Yorker with the title The Unseen.  Khatchadourian uses the efforts of one researcher, Slava Epstein, to access these “unseen” microbes as the theme of his piece.

“Nearly all of microbiology, Epstein eventually learned, was built on the study of a tiny fraction of microbial life, perhaps less than one per cent, because most bacteria could not be grown in a laboratory culture, the primary means of analyzing them. By the time he matured as a scientist, many researchers had given up trying to cultivate new species, writing off the majority as “dark matter”—a term used in astronomy for an inscrutable substance that may make up most of the universe but cannot be seen.”

The available 1% has been tremendously useful to humanity, providing the motivation to access much more of the microbial population.

“The near-universal presence of bacteria in nature—from the deepest layer of the Earth’s crust to the upper atmosphere—is reflected in their protean applications. They can be used to make industrial foods, to engineer perfumes, to produce fuel or to clean it up. More than half the cells in the human body are microbial, and many of them exist as biological dark matter, too; learning how they function could offer countless insights into human longevity. For decades, microbes had been a source of essential pharmaceuticals: chemotherapies, blood thinners, and drugs crucial to organ transplants. From just the one per cent of bacterial life that scientists had been able to cultivate, researchers had derived virtually every antibiotic used in modern medicine.”

The popular notion that microbes produce antibiotics to kill other microbes is dubious, and, in fact, is rather frightening.  One does not wish to envisage a world where microbes are busy producing lethal compounds to kill an enemy.  Humans could one day become the enemy.

“If antibiotics are indeed weapons, then humans are latecomers to an aeons-old arms race, whose rules remain opaque to us. “It is absurd to believe that we could ever claim victory in a war against organisms that outnumber us by a factor of 1022, that outweigh us by a factor of 108, that have existed for a thousand times longer than our species, and that can undergo as many as five hundred thousand generations during one of our generations,” several scientists argued in a recent paper.”

Epstein prefers to assume that what we call antibiotics are used by microbes for cooperative purposes and only become lethal when used at unnaturally high concentrations.

“For one thing, no one has ever measured concentrations of antibiotics in nature which are lethal to bacteria. He is open to the notion that these chemicals might be for signalling, and that they seem like weapons because of how we use them.”

The danger of generating resistant bacteria was apparent as soon as antibiotics were discovered.

“During the Second World War, penicillin was used widely, and it did not take long for resistant bacteria to spread. But many new drugs were being discovered, particularly from easily cultivatable species of actinobacteria. In 1943, there was streptomycin, the first cure for tuberculosis, and on the heels of that came chloramphenicol, chlortetracycline, neomycin, erythromycin. The rush of discovery gave the impression that nature contained an infinitely deep trove of new medicines. In 1962, a Nobel-winning immunologist went so far as to declare “the virtual elimination of the infectious diseases as a significant factor in social life.” Antibiotics became omnipresent. In industrial farming, they were used to hasten animal growth and to shield plants from pests; in medicine they were often overprescribed or incorrectly prescribed. Microbes, meanwhile, kept evolving.”

The 1% could not provide an unending supply of new molecules and progress ground to a near halt.

“As costs rose and results diminished, most of the largest pharmaceutical companies shuttered their antibiotic-discovery programs. The fear now is that the aging war chest will be rendered totally ineffective. Already there are strains of tuberculosis and gonorrhea, among other pathogens, that are resistant to virtually every drug in the medical arsenal. By conservative estimates, there are now seven hundred thousand fatalities from antibiotic-resistant bacteria in the world each year.”

Expressions of unbridled optimism are being replaced with those of despair and of an impending apocalypse.

“In desperation, hospitals have begun to revive old antibiotics that were discarded because they were too toxic. One such drug, colistin, was set aside for decades because its side effects included kidney damage and neurotoxicity. Today, it is a last line of defense against the hardiest of pathogens—though probably not for long. In 2012, the World Health Organization recommended that it be administered under strict regulation, but farmers around the world continued to use the drug liberally, particularly in China, where it was given to livestock by the ton. In 2013, researchers in China discovered colistin-resistant E. coli in the intestine of a pig, and a few weeks ago a similar strain was found in a patient in Pennsylvania—prompting the head of the Centers for Disease Control to declare that ‘the end of the road isn’t very far away for antibiotics’.”

A view of a future with ever-diminishing antibiotic effectiveness is not something one would choose to linger on.

“….a study commissioned by the British government predicts that, if trends continue, annual fatalities from drug-resistant microbes could exceed ten million by 2050, eclipsing those from cancer. Many key advancements in modern medicine could be reversed. As one researcher noted recently, ‘A lot of major surgery would be seriously threatened. I used to show students pictures of people being treated for tuberculosis in London. It was just a row of beds outside a hospital—you lived or you died’.”

Even if people like Epstein are successful at extracting new chemicals from the dark 99%, is that really a solution?  Or does it buy us perhaps another few decades before the ever-adapting microbial armies overwhelm them as well?  Humans like to believe that they rule the earth, but it could be the microbes that are really in charge.

The interested reader might find the following articles informative:

Saturday, November 19, 2016

When Collaboration Kills Creativity

Susan Cain produced a best-selling book on introverts and their place in society: Quiet: The Power of Introverts in a World That Can’t Stop Talking.  She tells us that introversion and extroversion seem to be genetically determined because researchers have been able to correlate responses to stimuli by infants with tendencies toward introversion or extroversion in later life.  Roughly a third to a half of the population falls on the introvert side of the ledger.  There is, of course, a spectrum of tendencies between polar extremes.  Some introverts can perform as extroverts for short periods when necessary.  Some extroverts are also quite capable of quiet introspection when necessary.

These personality differences have also been observed in other animals, suggesting that a blend of the two characteristics within a population is favored by natural selection.  That being the case, Cain is disturbed by trends in education and in workplaces that promote environments suited to the extrovert as the ideals for learning and innovation.  She was moved to produce a chapter titled When Collaboration Kills Creativity.

To understand the issues faced by introverts in an extrovert-oriented world, Cain provides some general characteristics of the two personality types.

“….introverts and extroverts differ in the level of outside stimulation that they need to function well.  Introverts feel ‘just right’ with less stimulation, as when they sip wine with a close friend, solve a crossword puzzle, or read a book.  Extroverts enjoy the extra bang that comes from activities like meeting new people, skiing slippery slopes, and cranking up the stereo.”

In terms of how the two might comport themselves in a work environment:

“Introverts often work more slowly and deliberately.  They like to focus on one task at a time and can have mighty powers of concentration.”

“Extroverts tend to tackle assignments quickly.  They make fast (sometimes rash) decisions, and are comfortable multitasking and risk-taking.”

“[Introverts] listen more than they talk, think before they speak, and often feel as if they express themselves better in writing than in conversation.  They tend to dislike conflict.  Many have a horror of small talk, but enjoy deep discussions.”

“[Extroverts] tend to be assertive, dominant, and in great need of company.  Extroverts think out loud and on their feet; they prefer talking to listening, rarely find themselves at a loss for words, and occasionally blurt out things they never meant to say.  They’re comfortable with conflict, but not with solitude.”

When researchers study the characteristics of people that would be defined as “creative” by society, they arrive at a prototype.

“One of the most interesting findings….was that the more creative people tended to be socially poised introverts.  They were interpersonally skilled but ‘not of an especially sociable or participative temperament.’  They described themselves as independent and individualistic.  As teens, many had been shy and solitary.”

Cain provides a few interesting quotes from creative introverts that describe the mode in which they feel they need to operate in order to be productive.  The first is from Albert Einstein.

“I am a horse for a single harness, not cut out for tandem or team work….Full well do I know that to attain any definite goal, it is imperative that one person should do the thinking and commanding.”

The following quote is by Stephen Wozniak of Apple computer fame.

“Most inventors and engineers I’ve met are like me—they’re shy and they live in their heads.  They’re almost like artists.  In fact, the very best of them are artists.  And artists work best alone where they can control an invention’s design without a lot of other people designing it for marketing or some other committee.  I don’t think anything really revolutionary has been invented by committee.  If you’re that rare engineer who’s an inventor and also an artist, I’m going to give you some advice that might be hard to take.  That advice is: Work aloneYou’re going to be best able to design revolutionary products and features if you’re working on your own.  Not on a committee.  Not on a team.

Corporate executives and educators have marched in the opposite direction by creating environments in which students and workers are never allowed to be alone.  Teamwork and constant communication are supposedly the keys to success.

It was encouraging to note that there are indications that corporations are beginning to take note of the need to accommodate different personality types as part of their mode of operation.  The writer of the Schumpeter page in The Economist produced an article titled Shhhh! which included the following lede.

“Companies would benefit from helping introverts to thrive”

The article references Susan Cain’s book and agrees with her conclusions.

“Most companies worry about discriminating against their employees on the basis of race, gender or sexual preference. But they give little thought to their shabby treatment of introverts.”

“The biggest culprit is the fashion for open-plan offices and so-called “group work”. Companies rightly think that the elixir of growth in a world where computers can do much of the grunt work is innovation. But they wrongly conclude that the best way to encourage creativity is to knock down office walls and to hold incessant meetings. This is ill-judged for a number of reasons. It rests on a trite analogy between intellectual and physical barriers between people. It ignores the fact that noise and interruptions make it harder to concentrate. And companies too often forget that whereas extroverts gain energy from other people, introverts need time on their own to recharge.”

Cain provides us information from studies by psychologists and others of worker and company productivity when open-plan offices are utilized.

“A mountain of recent data on open-plan offices from many different industries corroborates the results….Open-plan offices have been found to reduce productivity and impair memory.  They’re associated with high staff turnover.  They make people sick, hostile, unmotivated, and insecure.  Open-plan workers are more likely to suffer from high blood pressure and elevated stress levels and to get the flu; they argue more with their colleagues; they worry about coworkers eavesdropping on their phone calls and spying on their computer screens.  They have fewer personal and confidential conversations with colleagues.  They are often subject to loud and uncontrollable noise, which raises heart rates; releases cortisol, the body’s flight-or-fight ‘stress’ hormone; and makes people socially distant, quick to anger, aggressive, and slow to help others.”

The Schumpeter article also points out that leadership is not a simple attribute. 

“Many companies unconsciously identify leadership skills with extroversion—that is, a willingness to project the ego, press the flesh and prattle on in public.”

Effective leadership depends on the personalities of the people involved.  Extroverts, with the energy and tendency to dominate that they bring, are effective at managing workers who have well-defined responsibilities, but less so when dealing with those whose task is to think creatively.  In the latter case, introvert managers are more adept at encouraging productivity from that class of employee.

“Many of the most successful founders and chief executives in the technology industry, such as Bill Gates of Microsoft, and Mark Zuckerberg of Facebook, are introverts who might have floundered in the extroverted culture of IBM, with its company songs and strong emphasis on team-bonding. In penalising other people like them, firms are passing over or sidelining potential leaders. At all levels of company hierarchies, that means failing to take full advantage of employees’ abilities.”

Besides backing off on open-plan work areas, companies are encouraged to take into account personality differences in evaluating prospective employees, and to manage time better so that only necessary meetings occur and they are conducted in an efficient manner where all participants are likely to contribute—not just the loudest few.

“Some of the cleverest companies are beginning to look at these problems. Amazon has radically overhauled its meetings to make them more focused. Every meeting begins in silence. Those attending must read a six-page memo on the subject of the meeting before they open their mouths. This shifts the emphasis from people’s behaviour in the meeting to focused discussion of the memo’s contents. Google has downplayed the importance of interviews in recruiting and put more emphasis on candidates’ ability to carry out tasks like the ones that they will have to do at the firm, such as writing code or solving technical problems.”

A few examples of enlightened management are encouraging, but it will take much more to overcome decades of propaganda about the “extrovert ideal.” 

The interested reader might find these articles informative:

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