Curse to cure

The always-hilarious Gary Larson, whose ability to create absurd combinations of cultural references is unparalleled, had a Far Side comic strip showing a typical office waiting room.  Sitting in one of the chairs, cross-legged and reading a magazine, is a mummy.  The secretary -- with the trademark Larson bouffant hairdo and cat's-eye glasses -- is on the phone to her boss, saying, "Mr. Bailey?  There's a gentleman here who claims an ancestor of yours once defiled his crypt, and now you're the last remaining Bailey, and... oh, something about a curse.  Shall I send him in?"

The whole "Mummy's Curse" thing usually brings to mind the "Boy King" Tutankhamen, and the claim that twenty members of the expedition that opened the tomb died not long afterward.  There are three caveats to this, however: the deaths happened over a decade, suggesting that Tut wasn't in a great hurry to get his vengeance; a statistical study showed that the average age at death of the people who did succumb to "King Tut's Revenge" was no lower than that of the background population; and there is a plausible case to be made that at least two of the deaths (Howard Carter's personal secretary, Richard Bethell, and Bethell's father Lord Westbury, both of whom were murdered) were killed by, or on the orders of, none other than Aleister Crowley.

Whether this last bit is true or not remains very much to be seen; in my opinion, the case relies on highly circumstantial evidence, and after a hundred years it's doubtful we'll ever know for certain.  What I'm pretty sure of is that a scattered bunch of deaths, over ten years or so, of men who were mostly upper middle-aged is not really that much of a mystery, and the curse is nothing more than an attempt to give an added frisson to an archaeological find that honestly is interesting enough without all the supernatural trappings.

On the other hand, consider the opening of the tomb of Casimir IV Jagiellon, King of Poland and Grand Duke of Lithuania.  Casimir is considered one of the most able Polish kings, and consolidated his territory, won many military victories, and generally was a force to be reckoned with.  He died in 1492, and was interred with much pomp and circumstance in Wawel Cathedral in Kraków.

Casimir IV Jagiellon of Poland [Image is in the Public Domain]

In 1973, a team of twelve historians and archaeologists opened his tomb.

Within weeks, ten of the twelve were dead.

So do we have a real-life example of tomb desecration?  Oh, and something about a curse?

It turns out that (unsurprisingly) there's nothing supernatural involved here, either.  No need to invoke ancient Polish witchcraft.  The unfortunate researchers succumbed to infections of Aspergillus flavus, a pathogenic fungus that secretes an especially nasty group of organic compounds called aflatoxins.  Fungal infections are notoriously hard to treat -- fungal cells are similar enough to animal cells that chemicals which will kill a fungus often don't do our own tissues any good at all.  Fungal spores are also incredibly tough and long-lived; the Aspergillus spores that killed the research team members had likely been there since the tomb was sealed, over 530 years ago.

But Aspergillus isn't all bad.  A team at the University of Pennsylvania just published a paper in Nature Chemical Biology looking at a different set of compounds the fungus produces -- and found they target and disrupt cancer cells, especially those in leukemia.

The chemicals are called ribosomally synthesized and post-translationally modified peptides.  The biochemists call them RiPPs, even though the actual acronym would be RSaPTMPs, which I have to admit would be a little hard to pronounce, so RiPPs it is.  And the scientists found that the RiPPs produced by Aspergillus flavus had as much potency against leukemia cells as cytarabine and daunorubicin, two of the go-to drugs used to treat the disease for decades.

"Nature has given us this incredible pharmacy," said Sherry Gao, senior author of the study.  "It's up to us to uncover its secrets.  As engineers, we're excited to keep exploring, learning from nature and using that knowledge to design better solutions."

Which I think you will all agree is a better approach than superstition about opening graves.

Still, it's probably best to be cautious in any tomb-raiding you're planning on doing.  Curses not withstanding, aspergillosis is nothing to mess around with.  Even if the fungus turns out to have some beneficial features, remember to wear your respirators the next time you investigate the burial sites of fifteenth-century Polish kings.

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The broken branch

When I first became interested in paleontology, I think what came as the biggest surprise was how many lineages had become completely extinct.

I knew about the dinosaurs, of course; everyone knew about the dinosaurs.  But I remember one of my books on prehistoric animals showing a family tree of mammals, and branching off way near the bottom was a line marked multituberculates, that suddenly just... ended.  What on earth were those?

Turns out they're a group of small, superficially rodent-like mammals with strange knobbly teeth, that thrived for 130 million years -- coexisting with the dinosaurs for much of it -- before suddenly and inexplicably vanishing during the Miocene Epoch.  But they were hardly the only broken branch on the tree.  There were also the massive, hulking brontotheres, including the famously slingshot-horned Brontops, that lived during the Paleocene and Eocene, dying out around 34 million years ago.  And around the same time there were the mesonychids, scary-ass carnivorous mammals that looked like a cross between a bear and a wolf but were actually more closely related to horses.

All three groups gone forever, leaving no descendants.

Far from being the common picture of a slow, gradual progression, from something like a worm to a fish to an amphibian to a reptile to a primitive mammal to primates to *trumpet fanfare* Homo sapiens, sitting of course on top of the evolutionary tree as befits the Pinnacle of Creation, the family tree of life is more like an unruly and tangled shrub with thousands of splits and bifurcations -- and just as many snapped-off branches.  Whole groups of organisms have turned into dead ends; I wrote a couple of years ago about the bizarre Ediacaran Assemblage, a group of Precambrian species that are so different than the familiar life forms we see around us today that paleontologists have been unable to determine where exactly they fit in the overall taxonomic scheme, or if perhaps they, too, left no descendants.

But they are hardly the only species that are, as the researchers put it, "of uncertain affinities."  In fact, the whole topic comes up because of a paper by Corentin Loron of the University of Edinburgh et al., that looked at a peculiar life form that was one of the first really huge terrestrial organisms, an eight-meter-tall... um... something called Prototaxites.

From their cell wall structure, they pretty clearly weren't plants.  The hypothesis was that Prototaxites was some kind of enormous fungus; a mushroom the size of a small tree, more or less.  But now... well, here's what Loron et al. found:

Prototaxites was the first giant organism to live on the terrestrial surface, reaching sizes of 8 metres in the Early Devonian.  However, its taxonomic assignment has been debated for over 165 years.  Tentative assignments to groups of multicellular algae or land plants have been repeatedly ruled out based on anatomy and chemistry, resulting in two major alternatives: Prototaxites was either a fungus or a now entirely extinct lineage.  Recent studies have converged on a fungal affinity...  Here we test this by contrasting the anatomy and molecular composition of Prototaxites with contemporary fungi from the 407-million-year-old Rhynie chert.  We report that Prototaxites taiti was the largest organism in the Rhynie ecosystem and its anatomy was fundamentally distinct from all known extant or extinct fungi.  Furthermore, our molecular composition analysis indicates that cell walls of P. taiti include aliphatic, aromatic, and phenolic components most similar to fossilisation products of lignin, but no fossilisation products characteristic of chitin or chitosan, which are diagnostic of all groups of extant and extinct fungi, including those preserved in the Rhynie chert.  We therefore conclude that Prototaxites was not a fungus, and instead propose it is best assigned to a now entirely extinct terrestrial lineage.

After reading this, my brain (being basically like the neural equivalent of a giant, out-of-control pinball game) immediately bounced from there to thinking about the "Abominable Mi-Go" from the Lovecraft mythos, which were giant race of creatures that lived in Antarctica when it was warm and habitable hundreds of millions of years ago, and were "fungoid, more vegetable than animal, but truly allied to neither."  Of course, in Lovecraft's universe, the Mi-Go also had wings and kidnapped people and stored their consciousness in what amounted to big metal test tubes, and I don't think Loron et al. think Prototaxites could do all that.

In any case, the current study is fascinating from a couple of standpoints.  First, that the world in the early Devonian would have looked drastically different than it does today -- no trees, and in fact barely any plants larger than club mosses and (very) early ferns.  And second, that there were these towering things sticking up in the landscape, like giant accusing fingers, bearing only a distant (and as-yet uncertain) connection to any other living organism.

Recent advances in paleontology have shown that the nineteenth-century conception of the Great Chain of Being was missing out on some of the most interesting parts -- organisms so different from today's nine-million-odd species that we can't even figure out quite where to pigeonhole them.  And as we uncover more fossil evidence, we're sure to find others, and add further branches to the snarled and twisted family tree of life on Earth.

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Analysis of a partnership

You probably recall from biology class the word symbiosis -- when two organisms share living space.  This sort of relationship can result in a fused life form where even so, the two participants retain a discernible separateness.  (Remember the Trill from Star Trek?)  The melding can go deeper, though; lichens, commonly seen growing on rocks and tree trunks in damp areas, are an example of such a composite, in this case between one or more types of fungus and photosynthetic cyanobacteria.  Deeper still are mitochondria -- the organelles in all eukaryotic cells that conduct cellular respiration and provide the majority of the energy required by the organism -- which are the descendants of single-celled aerobic bacteria that billions of years ago formed a partnership with their host cells so mutually beneficial that now, neither can live without the other.

Symbiosis is usually broken down into three broad classes.  The distinction is how the participating organisms fare.  That one of them benefits in some way is a given; if both were harmed, the relationship would be strongly selected against and probably wouldn't persist very long.  It's what happens to the other that determines what kind of symbiosis it is:

• parasitism -- one organism benefits, the other is harmed (an example is disease-causing bacteria)
• commensalism  -- one organism benefits, the other breaks even (such as the bacteria passively riding on our skin)
• mutualism -- both organisms benefit (such as a good many of the bacteria in our gut, which have increasingly been found to be absolutely essential for health)

The trouble is, nothing in biology is clear-cut.  Our commensal skin bacteria occupy niches that, if they were eradicated, might be taken over by pathogenic species.  (Thus the adjuration by doctors not to overuse topical antibiotics and hand sanitizers.)  So are they actually mutualistic?  Then there are the species that help in some ways and harm in others -- or, perhaps, help one species and harm another.

This, in fact, is why the whole topic comes up today.  Scientists in New Zealand have been working to preserve endangered species on the islands.  There are quite a few, owing to the country's geological (and thus biological) isolation -- it's developed a singular group of endemic species that are uniquely vulnerable to loss of habitat from agriculture and from the introduction of exotic species like cats, pigs, and the ubiquitous sheep.  One such species is the rare Cooper's black orchid (Gastrodia cooperae), which is nearly invisible for most of the year -- the only above-ground part is a long, creeping stem -- and puts on a flower stalk once during the growing season.

[Image licensed under the Creative Commons Kathy Warburton/INaturalist (CC BY 4.0)]

Orchids are notorious for being difficult to grow from seed.  The seeds are minute, and most orchid species are extreme specialists, able to survive only in a very narrow range of conditions.  The result is that conservation efforts are fraught with difficulty.  Trying to germinate the seeds in the lab requires knowing exactly what that particular species needs, which can mean a lot of trial-and-error, and the potential loss of batches of seeds when the efforts fail.

The Cooper's black orchid is no exception.  It's so rare it was only identified in 2016, and is known to live in only three sites in New Zealand.  Fortunately for this species, there is a related orchid species, Gastrodia sesamoides, that is quite common and appears to need many of the same conditions that the Cooper's black does, so scientists have been trying to identify what those conditions are so they can be replicated in the lab.

And it turns out that one of the conditions is the presence of a symbiotic fungus -- Resinicium bicolor.  The fungus infiltrates the roots of the orchid, creating a greater surface area for nutrient and water uptake, much like the mycorrhizae familiar to organic gardeners that can increase crop yields without the addition of inorganic fertilizers.

Where it gets interesting is that Resinicium bicolor was already known to botanists -- as a plant pathogen.  It's a deadly parasite on Douglas firs, an introduced tree in New Zealand that is much used for lumber, causing "white-rot disease."

So is Resinicium a mutualist or a parasite?  The question is, "with respect to what?"  It's lethal to Douglas firs, but essential to the Cooper's black orchid (and, presumably, other native orchid species).

Biology, as I mentioned before, isn't simple.

That, of course, is why it's so endlessly fascinating.  The more we look into the complexity of the natural world, the more it brings home the truth of the quote from Albert Einstein: "Life is a great tapestry.  The individual is only an insignificant thread in an immense and miraculous pattern."

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Tooth and claw

Aficionados of The X Files will no doubt recall "Field Trip," which ranks amongst the creepiest, twistiest, most atmospheric episodes they ever did.  Fox Mulder and Dana Scully are charged with investigating the disappearance of a young couple while on a hiking trip -- and after that, their mantra "Trust nothing and no one" becomes literally true.

What had happened (obviously, *spoiler alert*) is that first the couple, and then Mulder and Scully, had been attacked by an underground fungus that works in a particularly insidious way.  Inhaling the spores, which are released whenever you take a step on the ground, induces hallucinations intended to make you hold still while the fungus slowly digests you.  It stimulates your brain with images while dissolving away your body.  Every time the real reality -- the tendrils of slime mold creeping across your skin -- intrudes, the hallucinations become more intense, more engaging, more real.

Until there's nothing left of you to fight back.

While the details of the episode are fiction, nature itself has plenty of examples that are just as horrifying.  The pathogen Toxoplasma gondii, common not only in humans but in domestic cats, wild mice, and rats, alters the brains of the hosts, but each in its own way.  Rats and mice become unafraid of predators, and in fact become attracted to the scent of cat urine; cats and humans become more affectionate -- and neurotic.  Each of those alterations in behavior is engineered by the parasite to maximize its chances of jumping to another host.  Lancet worms (Dicrocoelium dendriticum) parasitize ground-dwelling ants, and induce them to climb blades of grass and simply wait there, because the worm has a second stage of its life cycle in which it has to pass through the digestive tract of a ruminant, like a deer or a cow.  So it basically triggers the ant to commit suicide so it can make the jump.  Worse of all -- and most like the fungus in "Field Trip" -- there are the baculoviruses, which infect caterpillars.  Once parasitized, the caterpillars become attracted to sunlight, so they climb to the very tops of tree branches, where they die.  And then explode, showering their comrades lower down in the tree with viral particles.

Another way that "Field Trip" got it right, though, was some of the nasty stuff pulled by members of kingdom Fungi.  You have to wonder how we ever figured out that any of them were edible:

Not only are some of them amongst the most toxic living things known (the closely-related death cap [Amanita phalloides] and destroying angel [Amanita bisporigera] mushrooms, for example), they have a lot of other insidious strategies.  Most fungi are decomposers, but like the fungus in "Field Trip," a few of them have developed methods for hastening their unfortunate prey into decomposition.

This, in fact, is why the topic comes up; a new study of oyster mushrooms (Pleurotus ostreatus) found that the underground mycelium (network of root-like tubes) of the species actually hunts and kills nematodes (roundworms) using something one of researchers described as "a lollipop filled with nerve gas."  The toxocysts, as the lollipops are called, are consumed by the nematodes, and when they burst, it releases a chemical called 3-octanone, which triggers calcium to flow into the muscles of the worm.  This paralyzes it -- and the fungus has dinner.

Oyster mushrooms aren't the only species that goes after nematodes.  It makes sense to choose them as prey; nematodes are one of most numerous animals in the world.  I still recall my invertebrate zoology professor grossing us all out (something he specialized in) by telling us that if you made all organic matter disappear except for nematodes, you could still see where all the other life forms were by the haze of parasitic nematodes they'd been carrying, outlining where they'd been like some kind of ghostly remnant of their bodies.

But the fungi still maintain the upper hand.  There are fungi which have evolved harpoons for skewering nematodes.  Others create what amount to glue traps.  One species produces something like a spiked collar -- with the spikes pointing inward.  The weirdest one is the fungus Arthrobotrys oligospora, which creates a noose.  When a nematode crawls through the noose, the loop suddenly inflates, strangling the hapless worm, which is then digested.

Nature is red in tooth and claw, man.  And it's not just the animals.  Remember the first line of Stephen King's wonderful novel The Girl Who Loved Tom Gordon: "The world had teeth, and could bite you with them any time it wanted."

Truer words never spoken.

Anyhow, I've probably skeeved you out sufficiently for one day.  Just think about all this next time you see innocent-looking little mushrooms popping up in your lawn. 

You never know what's going on beneath the surface.

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Mushrooms on Mars

So far loyal readers of Skeptophilia have sent me four different links to the same underlying story, along with a message along the lines of "Whaddya think of this?"  The links all take various angles on a paper by Rhawn Gabriel Joseph and Xinli Wei in Advances in Microbiology claiming that photos taken by the Mars rover Curiosity show the presence of live fungi.

Without further ado, here are the photos, which are real enough:

[Photos are in the Public Domain courtesy of NASA/JPL]

When I saw the top photo, my immediate thought was that if you think the only way to explain wiping away stuff and having it reappear is if the stuff is a living organism, you need to come take a look at how long furniture in my house remains clean after being dusted.  I'll admit that I'm kind of housework-impaired, and chances are one day I'll go missing and when people come to investigate they'll find me trapped inside an enormous dust bunny, but still, the fact remains that "dirt blows around" seems to be a universal tendency.  Second, the lower photo looks like a fungus or at least fungus spores, but saying "it looks like X, so it is X" is not how science is done.

The claim has generated a lot of hype and also a lot of backlash from actual science types, such as this scathing piece by Tristan Greene over at TheNextWeb, wherein Joseph and Wei basically get their asses handed to them for leaping to an entirely unwarranted conclusion based on a handful of photographs that can be explained by any number of other, more likely hypotheses.  There are lots of microscopic round things besides fungal spores, so without any sort of biochemical analysis there's no way these can conclusively be labeled as alive, much less as terrestrial-type fungi.

Rhawn Gabriel Joseph, however, is not a man to take this sort of criticism lying down.  Saying Joseph is "combative" is a little like saying Stalin had "anger management issues."  He has sued NASA for ignoring his previous claims about life on Mars, sued Springer (the academic publishing company that publishes the journals Nature and Scientific American) for retracting one of his papers, and on his website defiantly proclaims that he has "published major scientific studies in the fields of neuroscience, development, embryology, evolution, quantum physics, consciousness, genetics, and astrobiology."

Funny, if he's an expert in basically everything, how just about every reference to him in actual scientific journals describe him as a "crank," a "kook," and "a self-aggrandizing spotlight seeker."

Then there's the issue of the journal the paper is published in -- Advances in Microbiology.  AiM is one of the journals owned by SCIRP -- Scientific Research Publishing -- a China-based company long associated with predatory, pay-to-play practices:

[T]here may be some strong and honest articles published in SCIRP journals. However, these articles are devalued and stigmatized by association with all the junk science that SCIRP publishes.  The authors of the good articles are being victimized by the publisher’s policy of publishing pseudoscientific articles like “Basic Principles Underlying Human Physiology.”  SCIRP only rarely retracts articles, preferring instead to protect the interests of its customers, the paying authors.

Oh, and apropos of not much, here's the photo of himself he has on his website:

No, I'm not joking.

The issue here goes back to the ECREE Principle; Extraordinary Claims Require Extraordinary Evidence.  Okay, maybe those are Martian fungal spores.  But before you can conclude that, you'd better have some damn good evidence supporting your claim, something more than "we see stuff moving around":

Hundreds of dimpled donut-shaped "mushroom-like" formations approximately 1mm in size are adjacent or attached to these mycelium-like complexes.  Additional sequences document that white amorphous masses beneath rock-shelters increase in mass, number, or disappear and that similar white-fungus-like specimens appeared inside an open rover compartment.  Comparative statistical analysis of a sample of 9 spherical specimens believed to be fungal "puffballs" photographed on Sol 1145 and 12 specimens that emerged from beneath the soil on Sol 1148 confirmed the nine grew significantly closer together as their diameters expanded and some showed evidence of movement.

Look, no one would be more excited than me if the rovers did discover Martian life.  Honestly, it's not that I think microbial life on Mars is all that unlikely.  It's just that you don't support your claims in science by pointing and yelling, "Hey, lookit that!" over and over.  If these are fungal spores, then there are a lot of them, so it's only a matter of time before they'll be detected by the actual rigorous biochemical analysis the rovers are equipped to do.

And I can guarantee that the results will be published in a reputable science journal, not an open-access affair like Advances in Microbiology, and almost certainly the lead author won't be some Disco-Era refugee who claims to be the intellectual equivalent of Stephen Hawking, David Eagleman, Charles Darwin, Carl Sagan, and Gregor Mendel put together.

So, sad to say, that's where the issue stands.  If I'm wrong, I will happily eat crow and publish an update and/or retraction.  I'd like to think the firestorm Joseph has ignited will cause him to retreat in disarray, but his motto seems to be "Death Before Backing Down," so I'm guessing this isn't the last we'll hear from him on the topic.  Stay tuned.

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I have often been amazed and appalled at how the same evidence, the same occurrences, or the same situation can lead two equally-intelligent people to entirely different conclusions.  How often have you heard about people committing similar crimes and getting wildly different sentences, or identical symptoms in two different patients resulting in completely different diagnoses or treatments?

In Noise: A Flaw in Human Judgment, authors Daniel Kahneman (whose wonderful book Thinking, Fast and Slow was a previous Skeptophilia book-of-the-week), Olivier Sibony, and Cass Sunstein analyze the cause of this "noise" in human decision-making, and -- more importantly -- discuss how we can avoid its pitfalls.  Anything we can to to detect and expunge biases is a step in the right direction; even if the majority of us aren't judges or doctors, most of us are voters, and our decisions can make an enormous difference.  Those choices are critical, and it's incumbent upon us all to make them in the most clear-headed, evidence-based fashion we can manage.

Kahneman, Sibony, and Sunstein have written a book that should be required reading for anyone entering a voting booth -- and should also be a part of every high school curriculum in the world.  Read it.  It'll open your eyes to the obstacles we have to logical clarity, and show you the path to avoiding them.

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