Tooth and claw

The earliest living things, way back in the Precambrian Era, were almost certainly either autotrophs (those that could produce their own nutrients from inorganic chemicals) or else scavengers.  One of the reasons for this inference is that these early life forms had few in the way of hard, fossilizable parts, of the kind you might use to protect yourself from predators.  Most of the fossils from that era are casts and impressions, and suggest soft-bodied organisms that, all things considered, had life fairly easy.

But the Cambrian Explosion saw the rather sudden evolution of exoskeletons, scales, spines... and big, nasty, pointy teeth.  There's credible evidence that one of the main reasons behind that rapid diversification was the evolution of carnivory.  Rather than waiting for your neighbor to die before you can have a snack, you hasten the process yourself -- and create strong selection for adaptations involving self-defense and speed.

After that, life became a much dicier business.  I was discussing this just a couple of days ago with the amazing paleontologist and writer Riley Black (you should definitely check out her books at the link provided).  She'd posted on Bluesky about the terrifying Cretaceous mosasaur Tylosaurus proriger, which got to be a mind-blowing twelve meters long (around the length of a school bus).  This species lived in the Western Interior Seaway, which back then covered the entire middle of the North American continent.  I commented to her what a difficult place that must have been even to survive in.  "We always describe the Western Interior Seaway as 'a warm, shallow sea,'" Riley responded.  "Ahh, soothing -- and not like 'holy shit these waters are full of TEETH!'"

What's interesting, though, is that even though we think of predators as mostly being macroscopic carnivores, this practice goes all the way down to the microscopic.  The topic comes up because of a paper this week in Science about some research at ETH Zürich about a species of predatory marine bacteria called Aureispira.  These little things are downright terrifying.  They slither about on the ocean floor looking for prey -- other bacteria, especially those of the genus Vibrio -- and when they encounter one, they throw out structures that look like grappling hooks.  The hooks get tangled in the victim's flagella, and at that point it's game over.  The prey is pulled toward the predator, and when it's close enough, it shoots the prey with a microscopic bolt gun, and then chows down.

Aureispira isn't a one-off.  The soil bacterium Myxococcus xanthus forms what have been called "wolf packs" -- biofilms of millions of bacteria that can be up to several centimeters wide, that glide along soil particles, digesting any other bacteria or fungi they happen to run across. 

A "wolf pack" of Myxococcus xanthus [Image licensed under the Creative Commons Trance Gemini, M. xanthus development, CC BY-SA 3.0]

This one immediately put me in mind of one of the most terrifying episodes of The X Files; "Field Trip."  In this freaky story, people are put into a series of powerful hallucinations after inhaling spores of a microorganism.  The hallucinations keep the victim quiet -- while (s)he is then slowly digested.

Of course, the microbe in "Field Trip" isn't real (thank heaven), but there are plenty of little horrors in the world of the tiny that are just as scary.  Take, for example, the aptly-named Vampirococcus, which is an anaerobic aquatic genus that latches onto other bacterial cells and sucks out their cytoplasm.

But the weirdest one of all is the bizarre Bdellovibrio, which is a free-swimming aquatic bacterium that launches itself at other single-celled organisms, moving at about a hundred times its own body length per second, then uses its flagella to spin at an unimaginable one hundred revolutions per second, turning itself into a living drill.  The prey's cell membrane is punctured in short order, and the Bdellovibrio burrows inside to feast on the innards.

So.  Yeah.  When Alfred, Lord Tennyson said that nature is "red in tooth and claw," I doubt he was thinking of bacteria.  But some of them are as scary as the mosasaurs I was discussing with Riley Black.  The world is a dangerous place -- even on the scale of the very, very small.

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Not magic

I got in a friendly argument online a few days ago with someone who finds my reliance on the scientific method "limited."  (His word.)

He accepts science, he said, but added that if that's your only way of understanding, there's stuff you'll miss.  "There are features of reality that science can't, or won't, study," he said.  "Science deals with what is tangible and quantifiable; there are other ways of knowing that allow you to access what is intangible and unquantifiable.  Without those, you're ignoring half of the universe."

The whole thing put me in mind of biologist Stephen Jay Gould's idea of non-overlapping magisteria -- that there are different domains of inquiry, and science only addresses one of them.  (Gould considered religion to be one of those other magisteria -- and that science and religion could coexist just fine unless one chose to tread on the other's toes.)

The problem with this is that science has been progressively chewing away at the other magisteria, as more and more of the universe is explained scientifically.  Phenomena that were thought to be utterly mysterious are now accounted for by rational scientific models -- heredity and tectonic activity are just two of many examples.  (In some realms -- such as legal documents -- we still have vestiges of this older way of thinking, in calling certain natural occurrences "acts of God.")

Even some religious people are uncomfortable with this approach.  Theologian Dietrich Bonhoeffer referred to it as "the God of the gaps," and pointed out the most obvious problem with it:

How wrong it is to use God as a stop-gap for the incompleteness of our knowledge.  If in fact the frontiers of knowledge are being pushed further and further back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat.  We are to find God in what we know, not in what we don't know.

So accounting for a phenomenon using some not necessarily religious, but non-scientific, explanation is basically nothing more than the argument from ignorance; "we don't yet know how this works, so it must be beyond science to explain."

Emphasis on the word "yet."

Take, for example, the bleeding polenta of Padua.

[Image credit: Exploring the Invisible]

In 1819, there were reports of what some were calling a miracle and others a work of Satan -- the appearance of what seemed to be drops of blood in polenta, bread, and other starchy food.  Whatever it was did look convincingly like blood, as you can see from the above photograph.  Italy in the nineteenth century was a devoutly Roman Catholic country, and the phenomenon was considered a "sign" (of what, depended upon whom you asked; some thought it was a harbinger of the end of the world, unsurprising considering how often this claim still comes up).

But a chemist at the University of Padua, Bartolomeo Bizio, firmly believed that there had to be a natural, rational cause for the spots.  He obtained samples of the red-stained food, and very quickly discovered two things: (1) if he put a drop of the red material on a sterile dish of starch, it rapidly developed red streaks as well; and (2) when he looked at some of it under a microscope, he saw cells -- but not blood cells.  Whatever it was might have the same color as blood, but it wasn't blood.

It was, in fact, a bacteria, which Bizio named Serratia marcescens -- the genus name after Florentine biologist Serafino Serrati, and the species name from a Latin word meaning "decay."  The red color comes from an organic compound called prodiogiosin.  Serratia marcescens has been found to be a more-or-less ubiquitous bacteria in soils and on moist surfaces -- it's responsible for the pinkish color that sometimes shows up in spoiled food and around the edges of unscrubbed sinks and drains.

It's a simple example, but it does show how "it happened because of something supernatural" is not really an explanation at all.  It is, in fact, a way to stop thinking.  Bizio started from the standpoint of "let's assume this has a rational cause," and it was only because that was his baseline assumption that he was able to take the step forward into understanding it.

Now, don't misunderstand me; it's not that I'm sure that science can explain everything, and it's certainly not because I think science has explained everything.  It's more that before we jump to a paranormal answer, we'd better make sure we've ruled out all the scientific ones first.  Because in the past two hundred years, the other magisteria have gradually shrunk as science has explained more and more of the universe.

As the inimitable Tim Minchin put it: "Throughout history, every mystery ever solved has turned out to be -- not magic."

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Microborgs

One of the most terrifying alien species in the Star Trek universe is the Borg, a hive-mind collective of interlinked cyborgs that reproduce by assimilating individuals from other species, not the old-fashioned way (although they may do that, too, judging by how taken the Borg Queen was with Captain Picard in Star Trek: First Contact).  

Turns out the assimilate-your-neighbor approach isn't limited to the world of science fiction.  There are terrestrial species who seem to follow the Borg's mantra of "We will add your biological and technological distinctiveness to our own."  Bacteria are especially good at doing this; they have small, mobile pieces of DNA called plasmids that are capable of being exchanged between cells, allowing gene flow without (strictly speaking) sexual reproduction.  Unfortunately for us, these plasmids frequently contain such human-unfriendly gene constructs as antibiotic resistance sequences and "pathogenicity islands" -- genes that code for a virulent attack on the host, such as the ones in the nasty strains of E. coli that can land you in the hospital.

Recently, however, scientists discovered a species of bacteria that has an assemblage of chunks of assimilated DNA (they actually called these strands "Borgs" after the Star Trek villains) that might prove useful to humans rather than harmful.  A species of Archaea (an odd clade of bacteria relatively unrelated to other, more common species, which includes groups that specialize in living in acidic thermal springs, anaerobic mud, and extremely salty water) called Methanoperedens was discovered in lake mud in western North America, and it was found to consume methane -- and has Borgs that allow it to do so at a spectacular rate.

Methanoperedens is odd even without the superlatives.  Most of the Archaea that metabolize methane don't consume it, they create it.  Methanogens -- Archaea that live primarily in deep ocean sediments -- produce methane as a byproduct of their metabolism, secreting it in the form of methane clathrate (frozen methane hydrate) at such a rate that the abyssal plains are covered with the stuff.  (Some ecologists believe that methanogens are, individual for individual, the commonest organisms on Earth, outnumbering all other species put together.)  

Burning methane clathrate -- "flammable snow" [Image is in the Public Domain courtesy of the United States Geological Service]

Methanoperedens, though, is a different sort of beast.  It lives by breaking down methane.  More interesting still, this ability comes from the fact that it has Borgs almost a third the size of its ordinary complement of DNA, made up of gene fragments assimilated from a dozen different species.

What has sparked interest in this bizarre species is the potential for using it to combat climate change.  Methane is a powerful greenhouse gas -- it has thirty times the heat-trapping capacity that carbon dioxide does -- and there's a significant concern that as the Earth warms, decomposing organic matter in the tundra will trigger a positive feedback loop, releasing more methane and warming the planet further.  If this methane-eating bacteria could consume some of the excess methane, it's possible that it could be turned into a tool for bringing the climate back into equilibrium.

I'm a little dubious, however.  It seems unlikely that any kind of attempt to culture Methanoperedens would be possible on a big enough scale to make a difference.  It'd be nice if we'd just face up to the fact that there is, and always has been, one obvious solution; stop burning so damn much fossil fuel.  We're so desperate to cling to our conspicuous-consumption lifestyle that we can't face the reality of what we're doing to the long-term habitability of the Earth.  (It doesn't help, of course, that a great many of our politicians here in the United States are being funded by the fossil fuel industry.)

Whether or not this bacteria species turns out to have any practical applications, the whole phenomenon of evolution by assimilation of DNA from other species is absolutely fascinating.  We ourselves contain "foreign genes" -- most notably endogenous retroviruses, pieces of viral DNA that have taken up permanent residence in our DNA and which might comprise as much as five percent of our total genome.  (There is good evidence that the activation of certain endogenous retroviruses is connected to the development of multiple sclerosis and some forms of schizophrenia.)

Walt Whitman didn't know how true his words were when he said, "I contain multitudes."

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Primordial soup dwellers

A paper in Nature last week blew my mind from several different perspectives.

Entitled, "Evidence for Early Life in Earth's Oldest Hydrothermal Vent Precipitates," it sounds at first like something that could only possibly interest paleontology and/or geology geeks.  But as soon as you start looking closely, you find that what this paper describes is groundbreaking.

*rimshot*

The group, led by Matthew Dodd of University College London, thin-sliced rock excavated from a piece of the Nuvvuagittuq Supracrustal Belt in Québec, one of the oldest intact rock formations on Earth.  And I do mean thin; the rock slices were, on average, 100 microns thick, or about the thickness of a sheet of printer paper.  And "old" is no exaggeration, either.  The rock is estimated at four billion years old, only three hundred million or so years after the crust solidified from molten magma.

The rock is an iron-rich sedimentary rock that formed at a hydrothermal vent -- a fissure on the deep ocean floor that is spitting out geothermally-heated, mineral-rich water.  We still have these around, mostly in places where the tectonic plates are moving apart, like the Mid-Atlantic Ridge, and even today they host a biome that is unlike any other on Earth.  There are species of shrimp, tube worm, sponges, and bacteria found nowhere else.  Not only that, they are one of only a handful of communities that is disconnected, energetically, from the Sun.  Everything else -- so, almost all life on Earth -- can trace the energy that makes it go back down the food chain and ultimately to a photosynthesizer (usually plants or phytoplankton), which are powered by sunlight.  The hydrothermal vent organisms, on the other hand, are powered by chemical reactions between the seawater and the hot stone of the upper mantle.

And when the scientists looked at the thin slices of the four-billion-year-old rock from Québec, they found...

... fossils.

The formation where the fossil-bearing rock was found [Photograph by Dominic Papineau]

The fossil traces are almost certainly from thermophilic bacteria, but form a colonial structure nearly a centimeter long.  It includes tubes, branching filaments, and spheres that are (the researchers claim) too complex to be explainable by inorganic chemical reactions.  This pushes the earliest life forms back by almost a third of a billion years earlier than the previous estimate, so we're not talking about a small shift, here.

"Using many different lines of evidence, our study strongly suggests a number of different types of bacteria existed on Earth between 3.75 and 4.28 billion years ago," said study co-author Dominic Papineau, in an interview with GeologyIn.  "This means life could have begun as little as 300 million years after Earth formed.  In geological terms, this is quick – about one spin of the Sun around the galaxy."

What this immediately brought to my mind is that it is increasingly looking as if the development of life is much faster and easier than anyone thought, and this bodes well for finding it elsewhere.  Probably lots of elsewheres, considering the billions of extrasolar planets there undoubtedly are in the Milky Way.  Perhaps, too, we might look closer to home; there may even be life in tectonically-active moons in our own Solar System such as Titan and Europa.

I'm not the only one who had this reaction.  "These findings have implications for the possibility of extraterrestrial life," Papineau added.  "If life is relatively quick to emerge, given the right conditions, this increases the chance that life exists on other planets."

Now, bear in mind that still is talking about microscopic life.  Even if the start of life turns out to be common on any sufficiently hospitable planet, that still leaves us with four variables in the Drake equation that are relatively poorly understood -- the fraction of life in the universe that becomes multicellular, the fraction of multicellular life that becomes intelligent/sentient, the fraction of intelligent life that advances in technology enough to send signals into space, and the average length of time such high-tech civilizations last.  So while the current study is encouraging to exobiology aficionados like myself, it may not have a lot of impact on our search for signs of extraterrestrial intelligence.

But no matter how you slice it (*rimshot* again), the Nature paper is amazingly cool.  It's hard to believe that such a short time after the Earth's crust solidified, there were already tiny living things building homes in the oceans.  And it boggles the imagination to think about where else similar life forms might exist -- on some other planet, perhaps, circling one of the stars we see in the night sky.

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Gut feelings

I used to teach a semester-long introduction to neuroscience course.  It was a popular class; let's face it, the human brain and sensory systems are fascinating.  But the problem was, not only is the topic complex, our knowledge of how our minds work is still in its earliest stages.  One of my mentors, Rita Calvo, professor emeritus of human genetics at Cornell University, said to me that if she were a graduate student today trying to figure out what part of biology to study, she'd pick neuroscience in a heartbeat.  "With neuroscience, we're about where we were with genetics a hundred years ago -- we know what structures are involved, we know a little bit about how they work -- but the underlying mechanisms are still largely a mystery."

It's why so often, when a student would ask me a question, my response started out with "Well, it's complicated."  Even simple questions to ask -- for example, "how does our sense of smell work?" -- get into deep water fast.  And in many cases, the answer is simply that we don't have it completely figured out yet.

One realm of neuroscience where this lack of knowledge is particularly troubling is the treating of mental disorders.  The ones I'm most familiar with, because of suffering from them myself -- depression and anxiety -- can be remarkably difficult to treat effectively.  My psychiatric NP, trying to find a medication that would blunt the edge of my depression, said that there's no good way to predict ahead of time which medication will be effective and side-effect-free -- you just have to try them, monitor the situation, mess with the dosage if necessary, and hope for the best.  I had weird side effects from the first three meds I tried -- Celexa killed my sex drive completely; Lamictal gave me the worst acid reflux I've ever experienced; and (worst of all) Zoloft, which is a wonder-drug for some people, made me feel like I was in the middle of a psychological electric storm, with severe agitation, anxiety, sleeplessness, and suicidal ideation.

They got me off Zoloft fast.

We've finally landed on Welbutrin, which is moderately effective -- it evens out the worst days, and doesn't give me any side effects that I've noticed.  So it's better than nothing, but still, far from a miracle cure.

One of the problems with treating depression is that we really don't know what causes it.  It's known to have some tendency to run in families; my mother was chronically depressed, and several other family members have fought varying degrees of mental illness.  This would suggest a genetic component, and that has been supported by research.  Back in 2005, a research review by Douglas Levinson found that there was a small positive correlation between depression and differences in one of the serotonin transporter promoter regions in the DNA, which are involved in the production and transport of one of the most important mood-altering neurotransmitters.  But there are plenty of people in the study who had depressive symptoms and didn't show the gene alteration, and vice versa.

A paper in 2017 by Niamh Mullins and Cathryn Lewis, of Kings College London, was more hopeful; the researchers found several genes that seemed to track fairly well with major depressive disorder within families, but it bears mention that Mullins and Lewis themselves pointed out that genetics can't be the whole picture -- the most recent estimates, from twin studies, are that depression has a heritability of 37%, suggesting that there are multiple genes at work, along with risk factors introduced with what a person went through as a child.

It's complicated.

The latest twist, which was just published last week in Science, is that there may be a contribution to mood disorders from our gut microbiome.  The role of bacteria (beneficial and harmful) in our overall health is often overlooked; but keep in mind that there are more bacterial cells in and on your body than there are human cells, and a great many of them have unknown health effects.  A study in Finland found a significant correlation between development of depression and the presence in the gut of the bacteria Morganella.

Morganella [Image artificially colorized]

Apparently, Morganella is a gram-negative bacterium that has a role in inflammation.  Chronic inflammation has already been implicated in a number of disorders -- not just obvious ones like ulcers and acid reflux, but heart disease, lupus, rheumatoid arthritis, some forms of cancer, and (possibly) Alzheimer's disease.  The inflammation isn't necessarily caused by the same thing in each case, but an increasing body of research suggests that treating the inflammatory response is key to treating the symptoms of some of the most awful diseases humans get.

So, apparently, add depression to the list.  The researchers are up front that this is only a tentative finding; correlation doesn't equal causation, after all.  And even if there was good evidence that Morganella was causing at least some cases of depression, it remains very much to be seen how you'd treat it.  There are (thus far) very few drugs that target only a single pathogen, so the danger is that in trying to eliminate Morganella, you'd simultaneously destroy the healthy part of your gut microbiome -- with highly unpleasant results.

At least this adds another link in the chain.  Diseases as complex as mood disorders are unlikely to succumb to a single treatment strategy.  But as we edge closer to understanding how our own brains work, perhaps we can get a handle on why sometimes they don't -- and perhaps, one day find an approach to treatment that isn't as scattershot and stumble-prone as the one we currently use.

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This week's Skeptophilia book-of-the-week combines cutting-edge astrophysics and cosmology with razor-sharp social commentary, challenging our knowledge of science and the edifice of scientific research itself: Chanda Prescod-Weinsten's The Disordered Cosmos: A Journey into Dark Matter, Spacetime, and Dreams Deferred.

Prescod-Weinsten is a groundbreaker; she's a theoretical cosmologist, and the first Black woman to achieve a tenure-track position in the field (at the University of New Hampshire).  Her book -- indeed, her whole career -- is born from a deep love of the mysteries of the night sky, but along the way she has had to get past roadblocks that were set in front of her based only on her gender and race.  The Disordered Cosmos is both a tribute to the science she loves and a challenge to the establishment to do better -- to face head on the centuries-long horrible waste of talent and energy of anyone not a straight White male.

It's a powerful book, and should be on the to-read list for anyone interested in astronomy or the human side of science, or (hopefully) both.  And watch for Prescod-Weinsten's name in the science news.  Her powerful voice is one we'll be hearing a lot more from.

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

Space germs

I'm fully in support of pure research, which should be obvious to anyone who is a regular reader of Skeptophilia.  But sometimes I run into a paper that leaves me scratching my head.

This happened this past weekend when I stumbled upon a press release from the University of Exeter entitled, "Mammals Could Struggle to Fight Space Germs."  The gist was that a team led by microbiologist Neil Gow did a series of experiments exposing mammalian cells to lab-synthesized peptides containing two amino acids that have been detected in space but not found in terrestrial proteins (isovaline and α-aminoisobutyric acid), and they found that the cell cultures had a "weak immune response."  From this, they concluded that if we're exposed to extraterrestrial microbes, we might really suck at fighting them off.

[Image licensed under the Creative Commons Phoebus87 at English Wikipedia, Symian virus, CC BY-SA 3.0]

This seemed like a rather overblown conclusion, so I went to the original paper (always a good idea; even university press releases are often oversimplifications or miss important points).  In this case, though, the press release was pretty much spot-on.  Here it is, straight from the paper:

The discovery of liquid water at several locations in the solar system raises the possibility that microbial life may have evolved outside Earth and as such could be accidently introduced into the Earth’s ecosystem.  Unusual sugars or amino acids, like non-proteinogenic isovaline and α-aminoisobutyric acid that are vanishingly rare or absent from life forms on Earth, have been found in high abundance on non-terrestrial carbonaceous meteorites.  It is therefore conceivable that exo-microorganisms might contain proteins that include these rare amino acids.  We therefore asked whether the mammalian immune system would be able to recognize and induce appropriate immune responses to putative proteinaceous antigens that include these rare amino acids. To address this, we synthesised peptide antigens based on a backbone of ovalbumin and introduced isovaline and α-aminoisobutyric acid residues and demonstrated that these peptides can promote naïve OT-I cell activation and proliferation, but did so less efficiently than the canonical peptides.  This is relevant to the biosecurity of missions that may retrieve samples from exoplanets and moons that have conditions that may be permissive for life, suggesting that accidental contamination and exposure to exo-microorganisms with such distinct proteomes might pose an immunological challenge.

Okay, I'll admit that this is one possible conclusion you could draw; it certainly has been riffed on often enough in science fiction, starting all the way back in 1969 with The Andromeda Strain.  (You could argue that it goes back further than that, given that at the end of H. G. Wells's 1898 novel The War of the Worlds, the invading Martians are destroyed by terrestrial microbes to which they have no natural immunity.)

The other possibility, however, is that the microbes wouldn't affect us at all.  When pathogens attack our cells, they usually obtain ingress by bonding to receptors on the surface.  Those receptors can be amazingly specific; this is why there are so many strains of flu, some of which only attack birds or pigs... or humans.  The immune species, in this case, lack the surface proteins that can form bonds to the viral proteins, so they don't get in.  The result: no disease.

In fact, it's even more specific than that.  In 2006, an outbreak of H5N1 bird flu generated worries about a pandemic, until it was learned that although highly contagious in birds, it only affects humans if the virus binds deep in the lung tissue -- the receptors in the upper respiratory system aren't able to bind to the virus efficiently (fortunately for us).  The only ones who became ill were poultry workers who were exposed to dust and debris in poultry houses.  No cases of human-to-human transmission were recorded.

So my suspicion is that extraterrestrial microbes probably wouldn't be able to attack us at all.  And given that our tissues would lack the two oddball amino acids the researchers used in their experiments, it seems pretty likely that if the microbes did get in, they'd starve to death.  (Put more scientifically, our proteins would lack two amino acids they need, so we wouldn't be of much use to them as a food source.)

Of course, it's possible that Gow et al. are right, and extraterrestrial microorganisms would consider the Earth an all-you-can-eat buffet.  But given that (1) the number of extraterrestrial microorganisms we've actually studied is zero, and (2) there are equally persuasive arguments to the contrary, it might be a little bit of a premature conclusion.

Now, that doesn't mean we should be bringing outer space debris to Earth, sans quarantine.  Hell, I've read The Colour Out of Space, and last thing I want is to have a gaseous entity from a meteorite cause my limbs to crumble and fall off.  COVID-19 is bad enough, thanks.  We really don't need any more reasons to panic, however.  So for now, let's confine ourselves to dealing with threats that currently exist.

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Being in the middle of a pandemic, we're constantly being urged to wash our hands and/or use hand sanitizer.  It's not a bad idea, of course; multiple studies have shown that communicable diseases spread far less readily if people take the simple precaution of a thirty-second hand-washing with soap.

But as a culture, we're pretty obsessed with cleanliness.  Consider how many commercial products -- soaps, shampoos, body washes, and so on -- are dedicated solely to cleaning our skin.  Then there are all the products intended to return back to our skin and hair what the first set of products removed; the whole range of conditioners, softeners, lotions, and oils.

How much of this is necessary, or even beneficial?  That's the topic of the new book Clean: The New Science of Skin by doctor and journalist James Hamblin, who considers all of this and more -- the role of hyper-cleanliness in allergies, asthma, and eczema, and fascinating and recently-discovered information about our skin microbiome, the bacteria that colonize our skin and which are actually beneficial to our overall health.  Along the way, he questions things a lot of us take for granted... such as whether we should be showering daily.

It's a fascinating read, and looks at the question from a data-based, scientific standpoint.  Hamblin has put together the most recent evidence on how we should treat the surfaces of our own bodies -- and asks questions that are sure to generate a wealth of discussion.

[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.

***************************************

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.

Put down the ducky

Yesterday, we looked at the fact that scientists have actually not admitted that vaccines cause autism.  Today, we consider the fact that your child's rubber duck is not going to kill them, either.

You'd think this would be unnecessary, but in this time of fearmongering and sensationalism, no claim is too outlandish to gain traction as long as it plays on someone's anxiety.  In this case, the whole thing started with a paper in Nature called, "Ugly Ducklings—The Dark Side of Plastic Materials in Contact With Potable Water," by Lisa Neu, Carola Bänziger, Caitlin R. Proctor, Ya Zhang, Wen-Tso Liu, and Frederik Hammes, which found that after several uses, plastic bath toys were covered with bacteria (including fecal coliform bacteria) and various species of fungi.

When I read the paper, my general response was, *yawn*.  Of course bath toys are covered with bacteria.  Everything is.  Add to that the fact that (1) bath water is warm, (2) tubs are generally not spotless to start with, and (3) the bath-taker is immersing his or her naked body into the water with the purpose of washing dirt off, it's no wonder bath water is a soup of various bacteria.

Even fecal coliforms.  Because, I hope, we all periodically wash our butts, too.

But there were people who stumbled on this paper, with its alarming-sounding title (which, as scientific researchers, Neu et al. should have known better than to give it), and immediately interpreted the study as implying that rubber duckies posed a deadly danger to children.  Bacteria!  Oh no!  Must immediately throw away all bath toys!

[image courtesy of the Wikimedia Commons]

Let's just clear up a few things, here.

Even in a healthy human, the number of bacterial cells in or on you exceeds the number of human cells you have.  You read that right; a study way back in 1977 estimated about 39 trillion bacterial cells in or on a typical human, significantly outnumbering the 30 trillion human cells you have (84% of which are red blood cells).  More to the point, the vast majority of these bacteria are either neutral or actively helpful; disturbances in the "intestinal flora" are thought to have roles in such horrible diseases as Crohn's disease, peptic ulcers, CDiff (Clostridium difficile) infection, and ulcerative colitis.  (Which is why there is a promising therapy to treat those using -- I kid you not -- fecal transplants from a healthy individual, to reestablish the right intestinal flora.)

So if your rubber ducky is coated with bacteria, the fact is, so are you.  And most of us are still healthy most of the time.

But that logic evidently wasn't sufficient; there have been various alarming articles on "alternative-medicine" and "natural parenting" sites claiming that not only were bath toys deadly, but there was a systematic coverup of the research, presumably sponsored by Big Ducky.

The whole thing was debunked roundly by Alex Berezow over at the website of the American Council on Science and Health last week.  Berezow went even further with regards to the Neu et al. study; he claimed that they were actively seeking an alarmist reaction for the purposes of publicity:

Amazingly, the authors cite mommy blogs and the sensationalist book Slow Death by Rubber Duck: The Secret Danger of Everyday Things in their paper.  The book is about the dangerous "chemicals" that are poisoning everybody, a chemophobic tactic that we've debunked over and over again. 

Quite honestly, I don't think I've ever seen anything like this in my professional career. Serious scientists don't cite mommy blogs and sensationalist popular science books in peer-reviewed journal papers. 

The authors had a clear strategy in mind: (1) Do a study on a common household object; (2) Produce boring data that doesn't surprise any microbiologist; (3) Write a provocative, fearmongering headline; (4) Market it to a gullible, clickbait-hungry press (like the New York Times), who would repeat their claims without any criticism or critical thinking; and (5) Watch the media interview requests and grant dollars come rolling in. 

Mission accomplished.  The deceitful manipulation of the press for their own professional benefit would be a thing of fascination if it wasn't so utterly disgusting.

And I have to admit he's got a point.

Of course, the craziest thing about the Natural Organic Health people who started running around in circles flailing their arms and making alarmed little squeaking noises after reading the study is that they apparently never thought of the simplest expedient for dealing with the situation if you're worried: wash the fucking toys.  I mean, seriously.  If you think there are nasty bacteria on the rubber duck, scrub it with a little soap and water after your kid's done in the bath.  Or, if you really want to go crazy, wipe it off with some rubbing alcohol.

Voilà.  If not no bacteria -- there nothing that could do that, short of an autoclave, which would turn your bath toys into a puddle of brightly-colored melted plastic -- at least there'll be fewer.

All of this goes to show that if there's nothing to be scared of, people will find something.  Added to the problem that (if Berezow is right about Neu et al. being guilty of deliberate sensationalization) fearmongering sells.  So if you like playing with a rubber ducky in the tub, have at it.  I hear you have to put it down if you want to play the saxophone, but other than that, it's perfectly safe.

Permafrost permayouth

You might have heard about people consuming pills of dried shark cartilage as nutritional supplements.  They're still widely available, in fact.  It's supposed to be anti-carcinogenic.  Why, you might ask, did people get this idea?

Because, the purveyors of shark cartilage pills say, sharks don't get cancer.  So if you grind up shark parts and consume them, you won't get cancer either.

There are just two problems with this practice:

• Sharks actually do get cancer, something that has been known since at least 1908.
• Shark cartilage has been tested and found to have no beneficial therapeutic value whatsoever.  It is, however, kind of critical for the shark itself, and the practice of killing sharks for their cartilage has led to widespread decline in sharks in many parts of the world.

This did not stop two of the most prominent cartilage shark spokespeople, I. William Lane and Linda Comac, from writing a book called Sharks Don't Get Cancer.  When the book was completely trashed by scientists and other reviewers, Lane responded by writing a second book four years later called Sharks Still Don't Get Cancer.

His publisher wisely recommended that Lane eliminate the subtitle he was planning to use, which was So Take That Nyah Nyah Nyah Nyah pfffttptbtbtbtbtb.

As usual, we have people who aren't letting little things like evidence and facts stand in the way of their claim.  You can still buy shark cartilage pills in many pharmacies, including a brand called, I kid you not, "BeneFin."

I bring all this up because yesterday I ran across a story about a woman who is doing something even stupider than consuming shark cartilage to prevent cancer; she is injecting herself with bacteria so she won't age.

It's not just ordinary, garden-variety bacteria, either.  These are bacteria that had been frozen in the permafrost of Siberia for, by some estimates, 3.5 million years, and now have been resuscitated by the thaw.  A Russian professor of geology named Anatoli Brouchkov noticed that the Yakut people who live in the area have a reputation for long lifespans, so he decided that (of course) it had to be because they were drinking melted permafrost water that had the bacteria in it.

Couldn't be genetics, or diet, or anything.

So he treated some plants, fruit flies, and mice with the bacteria, which has been dubbed "Bacillus F."  Brouchkov that they "seemed to have a rejuvenating effect," although gives no details about how he knew.  How do you distinguish between a rejuvenated houseplant and a tired, listless one?  Do non-rejuvenated fruit flies fly about in a dejected fashion?

Be that as it may, Brouchkov is certain enough of his claim that he's drinking water with Bacillus F in it himself.  But an actress who calls herself "Manoush" has gone a step further; she is now injecting herself with the bacteria.

Manoush, best known for such A-list blockbusters as Zombie Reanimation, The Shrieking, Philosophy of a Knife, and The Turnpike Killer, says she started taking the bacteria because like many of us, she's not so fond of the idea of getting old.  "Aging is a disease," she says.  "It is a genetic flaw to me.  Even as a teenager I could never accept the concept of getting older one day.  I don’t care what people think. I will stop at nothing to look and feel younger.  Nothing."

Which, I think we could all agree, would leave us with no option other than injecting 3.5 million-year-old Siberian permafrost bacteria directly into our bodies.

Manoush is absolutely convinced she's now aging backwards.  Me, I'm not sure.  I'm not fond of the gray hair, stiff joints, and crow's feet I've gotten in the past few years, but I don't think the answer is to jump on some loopy idea about anti-aging bacteria.  In fact, injecting bacteria into yourself is kind of a bad idea in general; perfectly normal, ordinary skin bacteria become a serious problem if they get into your bloodstream.  A friend of mine's father, in fact, almost died of a Staphylococcus aureus infection when his thumb got skewered by a rose thorn.

Staphylococcus aureus, I should point out, is a ubiquitous part of our skin flora.  On the surface of your skin, it's harmless.  Inside you, it can result in blood sepsis, which is a quick and spectacularly nasty way to die.

Staphylococcus aureus [image courtesy of the National Institute of Health]

So as much as I'd like perpetual youth, I'm not going to get in line behind Manoush for my bacteria injection.  I'll put up with the gray hair, which I'm told makes me look "distinguished," which isn't as good as "drop-dead sexy," but I guess I'll deal.

I contain multitudes

One of the things that even folks conversant in the evolutionary model sometimes don't know is the extent to which we are composite organisms.

On the gross level (and I mean that in both senses of the word), there is the sheer number of cells in us that are not human.  The adult human body has about 10 trillion human cells, and (depending on who you talk to) between 1 and 3 times more bacterial cells -- intestinal flora, bacteria hitching a ride on our skin, in our mouths, in our respiratory mucosa.  Most of these are commensals at the very worst -- neither harmful nor helpful -- but a significant number are in a mutualistic arrangement with us, which is one of several reasons why the overuse of antibiotics is a bad idea.

Then there are the little invaders we can't live without -- namely the mitochondria, those tiny organelles that every high school biology student knows are the "powerhouses of the cell."  What fewer people know is that they are actually separate organisms, descended from aerobic prokaryotes that colonized our cells 2.5 billion years ago (give or take a day or two).  They have their own DNA, and reproduce inside our cells by binary fission the same way they did when they were free-living proto-bacteria.

Mitochondria [image courtesy of Louisa Howard and the Wikimedia Commons]

But that's not all.  If you're a plant (I'm assuming you're not, but you never know), you have three separate ancestral lines -- your ordinary plant cells, the mitochondria, and the chloroplasts, which are also little single-celled invaders that now plants can't live without.  But even that's not the most extreme example -- the microorganism Mixotricha paradoxa is a composite being made up of five completely separate ancestral genomes that have fused together into one organism.

But back to humans, if you're not already so skeeved out that you've stopped reading.  Because it's even more complicated than what I've already told you -- geneticists Cedric Feschotte , Edward Chuong and Nels Elde of the University of Utah have just published a paper in which we find out that even our nuclear DNA isn't entirely human.  10% of our 30,000-odd genes and three-billion-odd base pairs...

... came from viruses.

We usually think of viruses as pesky little parasites that cause colds, flu, measles, mumps, and so on, but they're more than that.  Some of them -- the retroviruses (HIV being the best-known example) -- are capable of inserting genetic material into the host's DNA, thus altering what the host does.  Certainly, sometimes this is bad; both AIDS and feline leukemia are outcomes of this process.  But now Feschotte, Chuong, and Elde have shown that some of our viral hangers-on have had their genes repurposed to work in our benefit.

These stowaway bits of DNA are called "endogenous retroviruses" (ERVs), and some of them seem to be associated with cancer.  Others have been implicated in multiple sclerosis and schizophrenia.  But what the researchers found is that not all of them are deleterious; the gene that allows us to digest starch, and (even more importantly) the gene that triggers the fusion of the developing embryo to the placenta, seem to have viral origins.

"We think we’ve only scratched the surface here on the regulatory potential of ERVs," Feschotte said.

All of which is pretty amazing.  And it definitely gives one pause when you stop to think of how we define the word "organism."  Am I a single organism?  Well, not really.  Besides my regular human cells, I've got trillions of mitochondria, each with their separate bacterially-derived genome; and 10% of what I think of as "my DNA" came from viruses, at least some of which has then been modified into genes that I depend on to survive.  So humans -- and all living things -- are looking more and more like composite colonies of symbiotic life forms, representing a web of interrelationships that is so complex that it's mind-boggling.

So, to hell with the weird, exotic life forms from Star Trek.  I'm too busy being blown away by how bizarre and cool the life here on Earth turns out to be.

Smoke screen

When evaluating a claim, it's often as important to recognize which questions to ask as it is to understand the science behind the claim itself.  What information did the author leave out -- intentionally or unintentionally?

The reason this comes up is an online article sent to me by a loyal reader of Skeptophilia entitled, "Studies Reveal 'Smudging' Eliminates Dangerous Bacteria in the Air."  The article describes the practice of "smudging," the burning of sweet-scented dried plants, and claims that the smoke is beneficial because it kills bacteria.  (S)he cites an earlier study, published in 2007 in the Journal of Ethnopharmacology, which has the following passage:

We have observed that 1 hour treatment of medicinal smoke emanated by burning wood and a mixture of odoriferous and medicinal herbs (havan sámagri=material used in oblation to fire all over India), on aerial bacterial population caused over 94% reduction of bacterial counts by 60 min and the ability of the smoke to purify or disinfect the air and to make the environment cleaner was maintained up to 24 hour in the closed room.  Absence of pathogenic bacteria Corynebacterium urealyticum, Curtobacterium flaccumfaciens, Enterobacter aerogenes (Klebsiella mobilis), Kocuria rosea, Pseudomonas syringae pv. persicae, Staphylococcus lentus, and Xanthomonas campestris pv. tardicrescens in the open room even after 30 days is indicative of the bactericidal potential of the medicinal smoke treatment.  We have demonstrated that using medicinal smoke it is possible to completely eliminate diverse plant and human pathogenic bacteria of the air within confined space.

So far, so good.  Assuming that the experiment was well-controlled and that there were no obvious design flaws invalidating the results, getting rid of pathogenic bacteria is certainly a good thing.  The author of the first article sums up thusly:

The basic concept is that by burning particular plants parts and resins, the energetic blueprint or spirit/intelligence of that plant is released, producing a medicinal smoke.  The smoke is then utilized to cleanse the energy of individuals, groups, spaces or object.  Herbs like Sage, Palo Santo, Copal, and Sweet-grass are common smudging herbs that are widely used for healing and to remove unwanted energetic and spiritual buildup and also to instill blessings...  Thanks to this amazing study we now know that smudging with sacred herbs is not only soothing to the mind and spirit, it is affecting the health and even safety of the actual environment in which it is done.

Setting aside the whole "energetic blueprint" and plant intelligence nonsense, there are a few questions that come to my mind that neither the author of the original study, nor the author of the post lauding its results, thinks to ask:

1. How many pathogenic bacteria were in the room to start with?  All we're given is the percent reduction (94%), which sounds like a lot -- but 94% of a tiny amount is an even tinier amount, and neither is significant.
2. If there are chemicals in smudging smoke that kill bacteria, could those chemicals be toxic to humans as well?  I'm reminded of all the articles that get passed around saying, "Substance X (usually some naturally-occurring compound) found to kill cancer cells!" -- and it turns out that yes, the substance kills cancer cells, but in vitro.  Whether it kills cancer cells in a human body, and does so without killing the human, remains to be seen.  After all, consider the fact that pissing in the petri dish will probably also kill cancer cells in vitro.
3. Are there other chemicals in the smoke besides the bacteria-killing ones that might be harmful?  In general, it seems like inhaling smoke of any kind is a bad idea.

So let's look at these questions one at a time.

For the first question, there were a lot of hyped-up articles like "There's a Time Bomb Ticking in your Household Dust" that presented a lot of scary stuff (like electron micrographs of dust mites, which look like a cross between a crab and that thing that burst out of the dude's chest in Alien) but little in the way of verifiable detail.  I did find an interesting article by Dr. Harriet Burge, director of aerobiology for EMLab P&K, a New Jersey-based indoor air quality assessment lab, and she had the following to say:

I generally do not recommend bacterial analysis of house dust except in a few unusual situations.  This is because we don't know how to interpret the results.  However, we do receive occasional requests for cultural bacterial analysis of house dust.  These analyses are done by dilution culture and data can be presented as total bacteria, general groupings of bacteria (i.e., Gram negative, Gram positive, Bacillus), sewage screens (total coliforms, Enterococcus, etc.) or species identification for the most abundant colonies.  Sewage screens usually involve presence or absence in house dust.  Otherwise, interpretation is based on the number of colonies present per gram of dust, and/or the relative composition of specific bacterial groups or specific organisms in the dust. 

Given that these requests are not rare, it seems appropriate to develop some interpretation guidelines, at least with respect to average or "usual" populations in house dust.  Unfortunately, few studies have been done documenting concentrations of total culturable bacteria or of any specific organism or group of organisms.  In my experience, these studies are rarely done because the dynamics of exposure to house dust are not clear, and because dust is not considered to contain human pathogens (or at least dust is not considered the primary source for human pathogenic bacteria).

So given that household dust isn't the most common source of transmission for human pathogens, it's unclear whether sterilizing the room would, under most conditions (i.e. we're not talking about an operating room here), lower the incidence of disease.

[image courtesy of photographer Christopher P. Michel and the Wikimedia Commons]

On to the second and third questions, which are related.  On a quick search, the first thing I turned up was a paper from Clinical and Molecular Allergy by Ta-Chang Lin, Guha Krishnaswami, and David S. Chi entitled, "Incense Smoke: Clinical, Structural, and Molecular Effects on Airway Disease" which had the following to say:

Incense smoke (fumes) contains particulate matter (PM), gas products and many organic compounds.  On average, incense burning produces particulates greater than 45 mg/g burned as compared to 10 mg/g burned for cigarettes.  The gas products from burning incense include CO, CO2, NO2, SO2, and others.  Incense burning also produces volatile organic compounds, such as benzene, toluene, and xylenes, as well as aldehydes and polycyclic aromatic hydrocarbons (PAHs).  The air pollution in and around various temples has been documented to have harmful effects on health.  When incense smoke pollutants are inhaled, they cause respiratory system dysfunction.  Incense smoke is a risk factor for elevated cord blood IgE levels and has been indicated to cause allergic contact dermatitis.  Incense smoke also has been associated with neoplasm and extracts of particulate matter from incense smoke are found to be mutagenic in the Ames Salmonella test with TA98 and activation.

So there's that.  I tried to find any studies of white sage (Salvia apiana) and sweetgrass (Hierochloe odorata) -- two of the most common plants in smudge sticks -- to see if either had been studied for toxic effects.  Nothing turned up.  There was lots of stuff about expelling negative vibrations, however.  So this one falls into the "we don't know" category.

On the other hand, it's pretty clear that smoke in general -- even wood smoke -- shouldn't be inhaled.  Incompletely-burned plant material contains polycyclic aromatic hydrocarbons, organic compounds that have been identified as not only carcinogenic and mutagenic, but also directly toxic.

So in the end, we're left with more questions.  On the one hand, incense and smudging smoke smells good and seems to kill nasty bacteria, which is good.  On the other, the bacteria that it kills almost certainly would never have made you sick in the first place, and the smoke is also potentially dangerous for you to inhale, which is bad.  In the final assessment, smudging your house if you have adequate ventilation is probably not going to hurt you, but isn't really going to do much to help you, either, unless you believe in "negative vibrations."

And in the even-more-final assessment, what we really should be doing, even more than burning dead plants in our houses, is asking questions.  Not simply buying whatever you read at face value -- in other words, recognizing that there are questions to be asked -- is the first step.