Skeptophilia (skep-to-fil-i-a) (n.) - the love of logical thought, skepticism, and thinking critically. Being an exploration of the applications of skeptical thinking to the world at large, with periodic excursions into linguistics, music, politics, cryptozoology, and why people keep seeing the face of Jesus on grilled cheese sandwiches.

Saturday, April 29, 2023

Pitch perfect

Consider the simple interrogative English sentence, "She gave the package to him today?"

Now, change one at a time which word is stressed:

  • "She gave the package to him today?"
  • "She gave the package to him today?"
  • "She gave the package to him today?"
  • "She gave the package to him today?"
  • "She gave the package to him today?"

English isn't a tonal language -- where patterns of rise and fall of pitch change the meaning of a word -- but stress (usually as marked by pitch and loudness changes) sure can change the connotation of a sentence.  In the above example, the first one communicates incredulity that she was the one who delivered the package (the speaker expected someone else to do it), while the last one clearly indicates that the package should have been handed over some other time than today.

In tonal languages, like Mandarin, Thai, and Vietnamese, pitch shifts within words completely change the word's meaning.  In Mandarin, for example,  (the vowel spoken with a high level tone) means "mother," while  (the vowel spoken with a dip in tone in the middle, followed by a quick rise) means "horse."  While this may sound complex to people -- like myself -- who don't speak a tonal language, if you learn it as a child it simply becomes another marker of meaning, like the stress shifts I gave in my first example.  My guess is that if you're a native English speaker, if you heard any of the above sentences spoken aloud, you wouldn't even have to think about what subtext the speaker was trying to communicate.

What's interesting about all this is that because most of us learn spoken language when we're very little, which language(s) we're exposed to alters the wiring of the language-interpretive structures in our brain.  Exposed to distinctive differences early (like tonality shifts in Mandarin), and our brains adjust to handle those differences and interpret them easily.  It works the other way, too; the Japanese liquid consonant /ɾ/, such as the second consonant in the city name Hiroshima, is usually transcribed into English as an "r" but the sound it represents is often described as halfway between an English /r/ and and English /l/.  Technically, it's an apico-alveolar tap -- similar to the middle consonant in the most common American English pronunciation of bitter and butter.  The fascinating part is that monolingual Japanese children lose the sense of a distinction between /r/ and /l/, and when learning English as a second language, not only often have a hard time pronouncing them as different phonemes, they have a hard time hearing the difference when listening to native English speakers.

All of this is yet another example of the Sapir-Whorf hypothesis -- that the language(s) you speak alter your neurology, and therefore how you perceive the world -- something I've written about here before.

The reason all this comes up is a study in Current Biology this week showing that the language we speak modifies our musical ability -- and that speakers of tonal languages show an enhanced ability to remember melodies, but a decreased ability to mimic rhythms.  Makes sense, of course; if tone carries meaning in the language you speak, it's understandable your brain pays better attention to tonal shifts.

The rhythm thing, though, is interesting.  I've always had a natural rhythmic sense; my bandmate once quipped that if one of us played a wrong note, it was probably me, but if someone screwed up the rhythm, it was definitely her.  Among other styles, I play a lot of Balkan music, which is known for its oddball asymmetrical rhythms -- such wacky time signatures as 7/8, 11/16, 18/16, and (I kid you not) 25/16:

I picked up Balkan rhythms really quickly.  I have no idea where this ability came from.  I grew up in a relatively non-musical family -- neither of my parents played an instrument, and while we had records that were played occasionally, nobody in my extended family has anywhere near the passion for music that I do.  I have a near-photographic memory for melodies, and an innate sense of rhythm -- whatever its source.

In any case, the study is fascinating, and gives us some interesting clues about the link between language and music, and that the language we speak remodels our brain and changes how we hear and understand the music we listen to..  The two are deeply intertwined, there's no doubt about that; singing is a universal phenomenon.  And making music of other sorts goes back to our Neanderthal forebears, on the order of forty thousand years ago, to judge by the Divje Babe bone flute.

I wonder how this might be connected to what music we react emotionally to.  This is something I've wondered about for ages; why certain music (a good example for me is Stravinsky's Firebird) creates a powerful emotional reaction, and other pieces generate nothing more than a shoulder shrug.

Maybe I need to listen to Firebird and ponder the question further.


Friday, April 28, 2023

Sounding off

Noodling around on Wikipedia, sometimes you run into the oddest stuff.

I was looking something up yesterday and saw an associated link to a page called "List of Unexplained Sounds."  Well, I couldn't pass by something like that, so off I went down that rabbit hole.  As advertised, the page is a compendium of odd noises that have been heard (many have been recorded, so we know that those at least aren't someone's overactive imagination).  There are sound clips for a few of them, so I highly recommend going to the page and checking them out.

Here are a few of the ones listed -- with some possible explanations.

Upsweep is the name given to a sound consisting of a repeated series of rising tones that sound to my ears a little like a siren.  The source of the sound has been identified as being somewhere near 54° S latitude, 140° W longitude, placing it a little less than halfway from New Zealand and Cape Horn.  This, to put it mildly, is the middle of abso-fucking-lutely nowhere; in fact, it's not far from Point Nemo, also known as the "oceanic pole of maximum inaccessibility," which at 48°52.6′S 123°23.6′W is the point on Earth that is maximally distant from land.  There's a conjecture that Upsweep might be some kind of sound generated by underwater volcanic activity, but it's not exactly convenient to go out there and check, so that hypothesis is unproven.

The Bloop is a famous noise, once again heard in the Pacific Ocean, that is ultra-low frequency and extremely high amplitude -- meaning it can travel thousands of miles from its source.  The guess here is that the Bloop is a sound made by large icebergs breaking up (or scraping the seafloor), but I've heard an alternate hypothesis that I like better, which is that it's Cthulhu snoring.  Cthulhu, as you probably know, is the octopoid Elder God who was put into a charmèd sleep in his underwater city of Rl'yeh, where he's waiting for his followers to summon him back.  Why anyone would want to do so remains to be seen, because if you've read any H. P. Lovecraft, you know that the ones who try to reawaken him always end up dying in nasty ways, so it seems to me it might be better to leave him blooping peacefully in Rl'yeh.

[Image licensed under the Creative Commons Dominique Signoret (, Cthulhu and R'lyeh, CC BY-SA 3.0]

Some sounds have only been heard once, but are weird enough to bear mention.  These include Julia, which was given its name because it sounds like someone saying the name in a weird, hooting voice.  This is another one that is probably due to icebergs; its origin was pinpointed to somewhere near Cape Adare, Antarctica, but it was loud enough to be recorded by the entire Equatorial Pacific Autonomous Hydrophone Array.

The Ping is much more local; it's only been reported from the Fury and Hecla Strait between Baffin Island and the Melville Peninsula, Nunavut, Canada.  Although it's likely to be from some kind of marine animal, it's strange enough (and has been reported enough times) that "the Canadian military is investigating."

Not all of them are oceanic sounds.  One of the weirdest is the Forest Grove Sound, heard multiple times near Forest Grove, Oregon in February of 2016.  It was variously described as "a mechanical scream," "a giant flute played off pitch," and "akin to a bad one-note violin solo broadcast over a microphone with nonstop feedback."  There was an investigation, and it was never satisfactorily resolved -- and has not been heard since.

Last, there are the Moodus Noises, heard near Moodus, Connecticut, which unlike the Forest Grove Sound, have been heard for centuries (the indigenous people of the area, mostly from the Narragansett Tribe, supposedly have a long tradition of weird noises coming from nearby Cave Hill and Mt. Tom).  The Moodus Noises have a different Lovecraftian connection -- apparently they were the inspiration for the strange noises that came from Sentinel Hill in the spine-chilling story "The Dunwich Horror."  The more prosaic explanation for the Moodus Noises is that they come from microquakes, but -- needless to say -- there are a lot of people who don't buy that, and think the region is haunted.

So there you have it; a sampler of weird and unexplained sounds.  You should definitely check out the page and listen to some of the clips, which are goosebump-inducing.  While I do think they all have perfectly ordinary natural explanations, being a diehard skeptic doesn't mean I'm immune from getting the creeps now and again.


Thursday, April 27, 2023

Fingerprint of a megaflood

The Camarinal Sill is a curious geological feature that lies twenty kilometers to the east of the narrowest point of the Straits of Gibraltar.  It's an underwater rise that at its top is three hundred meters from the surface, with (much) deeper water on either side.

So the tips of the pincers forming the Straits also has a third pincer coming from below.  And to make things ever more interesting, the northern and southern points are on separate tectonic plates -- the Eurasian Plate to the north, the African Plate to the south.  These two plates have different relative motions, which is why around six million years ago, the straits abruptly closed up, and for a time, there was dry land between what are now Spain and Morocco.

The problem is, the region around the Mediterranean Sea is hot and dry (and was back then, too).  With the Atlantic Ocean now cut off, the only inflows of water into the Mediterranean came from all the rivers draining into it.  But the sum total of all that water entering it was still exceeded by the evaporation rate from the parched air passing over it.

So the Mediterranean Sea began to dry up.

Over the next six hundred thousand years, the sea level dropped by several kilometers, leaving behind a desiccated desert and a few widely separated lakes of concentrated brine.  The temperatures in the region rose by an estimated 15 C year-round, creating a climate more like the central Sahara than the pleasant "Mediterranean climate" that places like Italy, Greece, Spain, and southern France now enjoy.  The minerals from the evaporated sea water were left behind, creating layers of salt, gypsum, aragonite, and calcite that can still be seen today. 

Map of western Europe and northern Africa during the "Messinian Salinity Crisis;" the inset is an artist's depiction of the terrain [Image licensed under the Creative Commons Paubahi, Inserciomamifers, CC BY-SA 3.0]

Then, 5.33 million years ago, there was another tectonic shift, and the two sides of the Camarinal Sill pulled apart.

At that point there was a five-kilometer difference in the sea level between the Atlantic and what was left of the Mediterranean Sea; in fact, from the shore of the Atlantic west of Gibraltar to the nearest Mediterranean brine lake was a distance of over three hundred kilometers.

The result was a flood to end all floods.

The "Zanclean Deluge" was so enormous it's hard to visualize.  The waterfall over the newly-created Straits of Gibraltar was so powerful it eroded a nine-hundred-meter-deep gorge in the seabed.  The water level rose by an estimated ten meters a day for a year, ultimately refilling the entire Mediterranean Basin.  

[Nota bene: before any biblical literalists @ me with comments like "Ha-ha, that proves the Great Flood in the Book of Genesis actually happened!", allow me to point out that (1) the Zanclean Deluge had nothing to do with forty days and nights of rain, and (2) 5.33 million years ago our ancestors were small-brained hominins called Ardipithecus that lived in what is now Ethiopia, Tanzania, and Kenya.  There is, I might add, no evidence that Ardipithecus could build giant boats, nor were they capable of going to Australia to fetch a pair of kangaroos so they could be saved from the Flood and bringing them back after God finished smiting the absolute shit out of everyone and the waters receded.  Oh, and (3), don't you people disbelieve in plate tectonics anyhow?] 

Anyhow, the reason this all comes up is that a team of geologists from Utrecht University, the Royal Holloway University in London, and the University of Granada have just found the first unequivocal direct evidence that all this happened -- a deposit of gypsum, sandstone, and marl (lime-rich silt) showing distinct ripple marks from flowing water.  Upon analysis, they showed that the water was traveling really fast (something that can be determined from the wavelength of the ripple marks and the size distribution of the particles), was moving from west to east, and -- the clincher -- the entire formation dated to right around 5.33 million years ago.

Smoking gun, that.

"Now, for the first time, we can directly prove and quantify one of the most catastrophic periods of environmental change on our planet, which until now we had only been able to describe in geophysical models," said Gils Van Dijk, who led the study.  "Moreover, geologists are trained to use contemporary processes on the Earth’s surface to interpret what we observe in rocks.  But here we can’t rely on that knowledge, because we don’t know of any similar phenomena from at least the past one hundred million years."

What's a little sobering is that the tectonic movement that caused the whole thing -- both the closing of the sill and the reopening and subsequent flood -- is still happening.  The African Plate is still inching northward with respect to the Eurasian Plate, so the pattern is going to repeat.  Eventually, Gibraltar will seal up permanently, and the Mediterranean Sea will disappear -- and the coastal regions' pleasant climate will once again become a furnace, like it was 5.5-odd million years ago.

It won't happen within our lifetimes, of course; we're talking geological time scales, here.  But it always bears keeping in mind that the permanence of our landscapes and climates is an illusion, caused by our vision being limited to our short life spans.  On the larger scales, Tennyson was closer to the mark, in his beautiful poem "In Memoriam":
There rolls the wave where grew the tree.
O Earth, what changes hast thou seen?
There where the long road roars has been
The stillness of the central sea.
The hills are shadows, and they flow
From form to form, and nothing stands,
They melt like mists, the solid lands --
Like clouds, they shape themselves, and go.


Wednesday, April 19, 2023

Let's do the time warp

Dear Readers,

I will be taking a short break -- this will be my last post until Thursday, April 27.  Please keep suggesting topics, though!

See you when I return.




I find it fascinating, and frequently a bit dismaying, the range that exists in what people consider "sufficient evidence."

There are us hardcore skeptics, who basically say, "Incontrovertible hard data, right in front of my face, and sometimes not even that."  It then runs the whole spectrum down to people who basically have the attitude, "if my mother's first cousin's sister-in-law's gardener's grandma says she remembers seeing it one time, that's good enough for me, especially if it confirms my preconceived beliefs."

I saw a good example of the latter a while back over at Mysterious Universe in an article by Brett Tingley entitled, "Researcher Discovers Time Warp Near Las Vegas."  Tingley, to his credit, treated the whole thing with a scornful attitude, which (when you hear the story) you'll see was fully warranted.

Turns out "noted paranormal researcher" Joshua Warren, whose name you might know from his television work (some of his finer achievements are Aliens on the Moon: The Truth Exposed!, Weird or What?, Inside the Church of Satan, Possessed Possessions, and -- I shit you not -- Inbred Rednecks), claims to have found a spot north of Vegas where he says that time is running slower than in the surrounding areas.

Okay, let me just state up front that I have a degree in physics.  I certainly wasn't God's gift to the physics department by any stretch, but I did complete my degree.  (I didn't graduate summa cum laude, or anything.  More persona non grata.  But still.)  I bring this up only to say that with all due modesty, I have more knowledge of physics than the average dude off the street.  And because of this, I know that because of Einstein's General Theory of Relativity, there are only two ways to get time to slow down locally; (1) go really really fast; or (2) get close to a powerful gravitational field, such as a black hole.  Even the Earth's gravitational field, huge as it seems to us, causes a time dilation effect so small that it took years simply for physicists to be able to measure it and confirm it exists.  (For reference; your clock here on the surface of the Earth ticks more slowly, compared to a satellite orbiting at 20,000 kilometers, by a factor of 1 in 10,000,000,000.  So being here on Earth is not exactly the answer to lengthening human lifespan.)

[Image licensed under the Creative Commons Kjordand, Treval, CC BY-SA 4.0]

So the whole story is pretty fishy right from the get-go.  But Warren thinks he's proved it.  Here's what he has to say:
At this spot, on June 18 of 2018, I actually measured for the first and only time, time itself slowing down for 20 microseconds.  The weird thing, the real holy grail here, was what we picked up with this brand-new piece of technology.  That signal is always supposed to travel at the same rate of time at any particular place.  The only way that could change is if a black hole approached Earth or something like that, which is never supposed to happen.
You could substitute "never supposed to happen" with "hasn't happened," or "almost certainly never will happen," or "we'd all be fucked sideways if it did happen."  Now, twenty microseconds may not seem like very much, but that kind of discrepancy is not only many orders of magnitude greater than any expected relativistic time dilation effect, it is also well within the range of what would be easily measurable by good scientific equipment.  (Cf. the previous example of the physicists measuring a one-part-in-ten-billion slowdown.)  In other words, if this were real, it not only would be bizarre that it hadn't already been discovered, it would be simple to confirm -- or refute.

But here's the kicker: Warren is basing his amazing, groundbreaking, "holy grail" discovery on...

... one measurement with one piece of equipment.

So my first question is: time ran slower as compared to what?

Of course, even the equipment itself sounds suspicious to me.  It's called a "DT Meter," and no, in this context, "DT" doesn't stand for "delirium tremens," although it might as well.  It's a "differential time meter," and here's how Brett Tingley describes it:
KVVU-TV in Las Vegas reports that Warren made the discovery using a gizmo called a DT Meter, or differential time rate mater.  Warren says the device was created by a Silicon Valley engineer named Ron Heath, who has no discernible presence on the internet.  The device apparently consists of a 100-foot cable with a sensor on one end.  The device sends a signal down the length of the cable and measures the time it takes to reach the other end; theoretically, the device can detect small perturbations or differences in the speed of time itself.
Now, I ask you, which is more likely: that (1) there's a spot in Nevada where time runs slowly, for no apparent reason, or (2) Warren and Heath's gizmo has a glitch?

Of course, that's not slowing down Warren one iota (as it were).  He says that the time warp he discovered is the explanation for all sorts of other things for which he also has no proof:
I think it’s really interesting when you consider that this site where we got this reading, showing this time anomaly, also happens to be one of the most popular UFO hotspots in the area.  The big question at this point is not whether or not we have these anomalies, but what’s causing them?  Is this something natural that gives us a window a gateway into another world or another level of reality?  Or is this the byproduct of some kind of weird technology, be it something secret and man-made or something that’s extraterrestrial?
So the "big question" is not whether the anomaly exists?  I think that's a pretty big question, myself.  But no, we're supposed not only to believe his time warp, but that his time warp explains UFO sightings, and is caused by gateways into another world, etc.

What's baffling is that there are lots of people who apparently find this line of... um... well, I can't call it reasoning... this line of baloney convincing.  Poking about on the interwebz for about ten minutes found lots of places this "discovery" has been posted, mostly by people claiming either that ha-ha, this proves those dumb old physicists are wrong about everything, or that there's clearly a coverup by the government to prevent us from finding out about it, and thank heaven for Joshua Warren bravely posting this online, or even that we should watch this spot closely because it's likely to be where the alien invasion of Earth starts.

All of which left me weeping quietly and smacking my forehead on the keyboard.

Anyhow.  Like I said, I'm glad Tingley scoffed at Warren's claim, because Warren is not even within hailing distance of what anyone with a background in science would find convincing.  It also made me feel marginally better that I'm not the only one scoffing.  But I'd better wrap this up, because for some odd reason I feel like I'm running short on time.


Tuesday, April 18, 2023

The genes of the ancestors

When I had my DNA tested two years ago, I found out I have 330 distinctly Neanderthal markers in my genes.  This, apparently, is well above average for people of western European descent, and may explain why I like to run around half-naked and prefer my steaks medium-rare.

In all seriousness, most people of European descent have Neanderthal ancestry; it's less common in people of African and Asian ancestry, and in the indigenous peoples of Australia and North America.  It makes sense, once you know where they lived.  The Neanderthals were a predominantly European species (or sub-species; the experts differ, and honestly, the definition of species is so mushy anyhow that it's probably splitting hairs to argue about it).  They seem to have split off from the main population of hominins in the region something like five hundred thousand years ago.  The first unambiguously Neanderthal bones are 430,000 years old, and they persisted until 40,000 years ago -- and we still don't know why they died out.

What's certain is that it wasn't a lack of sophistication and intelligence by comparison with contemporaneous Homo sapiens, whatever you might have gleaned from Jean Auel's The Clan of the Cave Bear.  The Neanderthals were plenty smart.  They had culture, made paintings on cave walls, and created jewelry.  To judge by the Divje Babe flute they made music.  They ceremonially anointed their dead, and appear to have had some concept of an afterlife.  They had the same version of the FOX-P2 gene we do, suggesting they had spoken language.  So despite my earlier quip, Neanderthals were far from the slow, sluggish, stupid "cave men" we often picture when we hear the name.

As my own ancestry indicates, there was a good bit of crossbreeding between Neanderthals and "modern" humans.  (I put modern in quotes not only because it's self-congratulatory, but because all organisms on Earth have exactly the same time duration of their ancestral lineages; words like primitive and modern really "less changed since the common ancestor" and "more changed since the common ancestor," but those are clunky.  So I'll continue to use primitive and modern, although with the caveat that they're not value judgments.)

What's interesting, though, is that the genetic input of the Neanderthals was asymmetrical.  Of the Neanderthal markers we carry around, none are on the Y chromosome, indicating that something blocked any contribution of Y-chromosomal genes from our Neanderthal forebears.  It's possible that the answer is simple -- that most inter-species matings were between "modern" human men and Neanderthal women.  But now a new study from The American Journal of Human Genetics, by Fernando Mendez, G. David Poznik, and Carlos Bustamante (of Stanford University), and Sergi Castellano (of the Max Planck Institute for Evolutionary Anthropology) has suggested another reason the Neanderthal Y chromosome didn't survive; mutations that caused male hybrid fetuses to spontaneously miscarry.

The authors write:

Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins.  Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain.  We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup.  We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya)...  This is ∼2.1 times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages.  This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes.  The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct.  We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D.  Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation.  It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

Which is an interesting hypothesis.  It's possible, of course, that there was more than one thing going on, here; there may also have been a skewed distribution of genders in inter-species matings as well as a higher death rate in male children of male Neanderthals and female "modern" humans.   In fact, genetics and culture can sometimes create a feedback loop; the taboo in traditional Basque society against Basque women marrying non-Basque men is thought in part to have come from the high frequency amongst the Basques of the Rh negative blood group allele, resulting in children of Basque women (likely to be Rh negative) and non-Basque men (likely to be Rh positive) having a higher probability of dying of Rh incompatibility syndrome.

So sometimes cultural norms and genetics can intertwine in curious ways.

In any case, that's today's science story, tying together anthropology, genetics, and evolutionary biology, all particular fascinations of mine.  And the fact that it could well be talking about some of my own ancestry adds a nice twist.  Hopefully my forebears will forgive me for my jab about running around naked.  Maybe the most Neanderthal thing about me is that I play the flute.  Kind of turns the "cave man" trope upside down, doesn't it?


Monday, April 17, 2023

An explosion of understanding

One of the reasons I love science is its capacity for inducing wonder.

Albert Einstein said it best: "Joy in looking and comprehending is nature’s most beautiful gift."  Being able to look around you and think, "Okay, now I understand a little bit more of the universe" is nothing short of a thrill.

I recall having that feeling when I first learned about the Cambrian Explosion, a sudden increase in biodiversity that occurred about 540 million years ago, and which produced virtually all the animal phyla we currently have today.  I think it struck me that way because it was so contrary to the picture I'd had, of evolution slowly plodding along, from something like a jellyfish to something like a worm to something like a fish, through amphibians and reptiles and mammals, finally leading to us as (of course) the Pinnacle of Creation.  That view, it seems, is substantially wrong.  While there has been great change on many branches of the family tree of life, all of the basic branches diverged right about the same time.

Fascinating, too, that there were also a variety of branches that left no living descendants, that are so bizarre to our eyes that they look more like something from a science fiction movie.  There's Dickinsonia:

[Image is licensed under the Creative Commons Verisimilus at English Wikipedia, DickinsoniaCostata, CC BY-SA 3.0]

... and Anomalocaris, shown here as a model of what it might have looked like when alive:

[Image is in the Public Domain]

... and the aptly named Hallucigenia, which could be straight out of a fever-dream:

[Image is licensed under the Creative Commons Scorpion451, Hallucigenia Reconstruction Current 2015, CC BY-SA 4.0]

... and my personal favorite, five-eyed, vacuum-cleaner-hose-equipped Opabinia:

[Image is licensed under the Creative Commons Nobu Tamura (, Opabinia BW, CC BY 3.0]

If you'd like to find out more, I encourage you to read Stephen Jay Gould's awesome book Wonderful Life, which will tell you about these four creatures and a great many more besides.

The reason I bring this up is that some research out of Oxford University has elucidated not only the structure of these odd creatures, but the environment in which they lived.  Having fossils from 540 million years ago that were sufficiently intact to determine what they'd looked like while alive is amazing enough; but being able to determine anything about the conditions under which they lived is downright astonishing.  But that's just what Ross Anderson and Nicholas Tosca, of the Department of Sedimentary Geology at Oxford, and their team have done.

Their paper, which appeared in the journal Geology, described microscopic mineralogical analysis of the Burgess Shale of Canada and the Ediacaran Assemblage of Australia, two of the finest deposits of Cambrian Explosion fossils in the world.  And what the geologists found allowed them to make a guess at where the likes of Opabinia and the rest lived: warm, shallow ocean ecosystems that had water rich in iron.

The iron content allowed the formation of the mineral berthierine, which is not only distinctive in its origins, but has an anti-bacterial effect that halted decomposition and prevented decomposition.  This resulted in the phenomenally well-preserved fossils both sites are known for.

"Berthierine is an interesting mineral because it forms in tropical settings when the sediments contain elevated concentrations of iron," Anderson said.  "This means that Burgess Shale-type fossils are likely confined to rocks which were formed at tropical latitudes and which come from locations or time periods that have enhanced iron.  This observation is exciting because it means for the first time we can more accurately interpret the geographic and temporal distribution of these iconic fossils, crucial if we want to understand their biology and ecology."

The whole thing is tremendously exciting.  To not only have an idea of the appearance of these animals, but to be able to picture them in something like their actual habitat, gives us a glimpse of a world five times older than it was during the heyday of the dinosaurs.  It's breathtaking to think about.

I'll end with a quote from another scientist -- Brian Greene, the physicist whose lucid writing about modern physics in his book The Fabric of the Cosmos inspired an equally brilliant NOVA series.  Greene says: "Science is a way of life.  Science is a perspective.  Science is the process that takes us from confusion to understanding in a manner that's precise, predictive and reliable -- a transformation, for those lucky enough to experience it, that is empowering and emotional."


Saturday, April 15, 2023

Egyptian light speed

There's a claim I've now seen three times on social media stating that the ancient Egyptians knew the speed of light.

This is pretty outlandish right from the get-go, as there is no evidence the Egyptians had invented, or even had access to, any kind of advanced technology.  Plus, even with (relatively) modern technology, the first reasonably decent estimate of the speed of light wasn't made until 1676, when Danish astronomer Olaus Roemer used the difference in the timing of the eclipses of the moons of Jupiter when the Earth was moving toward them as compared to when the Earth was moving away from them, and came up with an estimate of 225,300,000 meters per second -- not too shabby given the limited technology of the time (the actual answer is just shy of 300,000,000 meters per second).

But there's something about those ancient Egyptians, isn't there?  There have been "secrets of the Pyramids" claims around for years, mostly of the form that if you take the area of the base of the Pyramid of Khufu in square furlongs and divide it by the height in smoots, and multiply times four, and add King Solomon's shoe size in inches, you get the mass of the Earth in troy ounces.

Okay, I made all that up, because when I read stuff about the "secrets of the Pyramids" it makes me want to take Ockham's razor and slit my wrists with it.  But I was forced to look at the topic at least a little bit when the aforementioned post about the speed of light started popping up on social media, especially when a loyal reader of Skeptophilia said, "You have got to deal with this."

The gist is that the speed of light in meters per second (299,792,458) is the same sequence of numbers as the latitude of the Pyramid of Khufu (29.9792458 degrees north).  Which, if true, is actually a little weird.  But let's look at it a tad closer, shall we?

[Image licensed under the Creative Commons Jerome Bon from Paris, France, Great Pyramid of Giza (2427530661), CC BY 2.0]

29.9792458 degrees of latitude is really specific.  One degree is approximately 111 kilometers, so getting a measurement of location down to seven decimal places is pretty impressive.  That last decimal place -- the ten-millionths place -- corresponds to a distance of 0.0111 meters, or a little over a centimeter.

So are they sure that last digit is an 8?  Measuring the position of the Great Pyramid to the nearest centimeter is a little dicey, given that the Great Pyramid is big (thus the name).  Even if the claim is that they're measuring the position of the top -- which is unclear -- the location of the top has some wiggle room, as it doesn't come to a perfect point.

But if you're just saying "somewhere on the Great Pyramid," there's a lot of wiggle room.  The base of the Pyramid of Khufu is about 230 meters on an edge, so that means that one-centimeter accuracy turns into "somewhere within 23,000 centimeters."

Not so impressive, really.

There's a second problem, however, which is the units used in all the measurements in the claim.  The second wasn't adopted as a unit of time until the invention of the pendulum clock in 1656.  The meter as a unit of length wasn't proposed until 1668, and was not adopted until 1790.  (And some countries still don't use the metric system.  *glares at fellow Americans*)  So why would the ancient Egyptians have expressed the speed of light -- even assuming they could figure it out -- in meters per second, and not cubits per sidereal year, or whatever the fuck crazy units of measurement they used?

Oh, and while we're at it, the first person to slice a circle up into 360 degrees -- the basis, of course, of our system of latitude -- was Hipparchus, who lived in the second century B.C.E.  Which, not to put too fine a point on it, was two-thousand-odd years after the Great Pyramids were built.  So to sum it up: what we're being asked to believe is that the ancient Egyptians sited the Great Pyramid based upon a quantity they didn't know how to measure, expressed in terms of three units that hadn't been invented yet.

Makes perfect sense.

So as expected, this claim is pretty ridiculous, and not even vaguely plausible if you take it apart logically.  Not that there was any doubt of that.  In fact, this is only one of dozens of examples of pseudoscientific metrology, which is the general name for claims that the measurements of ancient structures have some relevance to scientific findings.  The bottom line is that the ancient Egyptians were cool people, and the pyramids they built are really impressive, but they weren't magical or advanced or (heaven help us) being assisted by aliens.

No matter what you may have learned from the historical documentary Stargate.

Oh, and for the record, I didn't invent the unit of "smoot" for length.  A smoot is 1.70 meters, which was the height of Harvard student Oliver R. Smoot, who in 1958 got drunk with his fraternity buddies, and as they were dragging the semi-conscious Smoot home, they decided to measure the length of Harvard Bridge in Smoot-heights.  It turned out to be 364.4 smoots long, plus or minus the length of Oliver R. Smoot's ear.

And considering they were drunk at the time, it's pretty impressive that they thought of including error bars in their measurement.  Better than the damn Egyptian-speed-of-light people, who couldn't even get their measurement to within plus or minus 230 meters.


Friday, April 14, 2023

A strange attractor

We've had a sudden warm, sunny spell -- very unusual for mid-April in upstate New York, where the weather can remain chilly well into May and we've sometimes had snow on Mother's Day.  One thing you have to say for upstaters; we don't waste these opportunities when they come.  There was a steady stream of runners and cyclists on the road past my house, and as for me, I spent the day working in the front yard putting in some new raised-bed gardens.  The result was (1) some landscaping that's going to be gorgeous when it's full of flowers in a couple of months, (2) sunburned back and shoulders (not severe, fortunately, but a little redder than they should be), and (3) sore muscles.

The cloudless skies continued into yesterday evening, which brought me outside once again -- this time to enjoy a glass of wine and watch the stars.  As I sat there, the darkness deepening around me, I was once again astonished by how beautiful a clear night sky is.  It amazes me that anyone can look up into the star-spangled blackness and not be awestruck.  I looked at those hundreds of little pinpoints of light -- each one actually a blazing sun, some of them orders of magnitude bigger than our own -- and wondered, as I have so often before, which of them have planets, and which of those planets might host life.

Then, it struck me how little of the universe I'm actually seeing.  Regular readers of Skeptophilia might recall my posting this image of the Milky Way, but it's worth seeing again:

[Image licensed under the Creative Commons Pablo Carlos Budassi, Milky way map, CC BY-SA 4.0]

I know it's hard to read the text, so I encourage you to go to the site where it comes from, and spend some time zooming in on it.  In particular, find the little circle in the lower center that's labeled "Naked Eye Limit."

Every individual star you have ever seen without a telescope is inside that little circle.

Even our own galaxy is largely a mystery to us.  There's an enormous black hole at its center called Sagittarius A* ticking and purring (I can't help hearing that in Carl Sagan's memorable voice), which we know of by its x-ray and gamma ray signature; much of what else we know was either discovered in the last century using powerful telescopes, or else is inferential.

Amongst the inferential bits is one of the oddest mysteries in astrophysics; the Great Attractor.  The Great Attractor is the apparent center of gravity of the Laniakea Supercluster, a huge assemblage that contains not only the Milky Way and its nearby companions, the Andromeda Galaxy and the Magellanic Clouds, but one hundred thousand other galaxies, each containing something on the order of one hundred billion stars.  (Once again invoking Carl Sagan's voice for emphasis.)

If your mind boggles at this, so does everyone's.  Or should.  But the weirdest thing is that we have no idea what the Great Attractor actually is.  It is "inconveniently placed," as one astronomer put it (well aware that stating it that way is about as ridiculously anthropocentric as you can get).  Between us and it is the center of the Milky Way, so we can't currently see it, and won't be able to for another hundred million years, at which point the Solar System will have orbited around the galactic center and will be pointing toward whatever the Great Attractor is.  It may be a huge collection of galaxies, with enough mass to gravitationally attract everything in the region; it may be something odder.

We simply don't know.

And if that's not enough for you, it was recently discovered that the Great Attractor itself is moving toward something even bigger, the Shapley Supercluster, which is the largest gravitationally-bound structure we know of.

At that point in my musings, my glass of wine was empty, and I felt minuscule enough for one night.  Sitting there, looking up into the vastness of space, left me (as it always does) with a keen awareness of the insignificance of all of our little Earth-bound problems.  It didn't, and doesn't, bother me; being overawed by the grandeur of it all is hardly a bad thing.  It's comforting to know that as we toil through our busy little lives down here, overhead the majestic cosmos still soars, extending in every direction farther than we can see, or even imagine.

I think I'll go outside again this evening.


Thursday, April 13, 2023

The stowaways

Aficionados of the Star Trek universe undoubtedly recall the iconic character Jadzia Dax.  Dax was a Trill -- a fusion of a humanoid host and a strange-looking brain symbiont.  The union of the two blended their personalities, resulting in what was truly a new, composite life form.

Star Trek is amazing in a lot of ways, not least because of their attention to current science and an uncanny prescience about where science is heading.  It turns out that we're all composite life forms.  We carry around something like 39 trillion bacterial cells in and on our own bodies -- the vast majority of which are either commensals (neither helpful nor harmful) or are actually beneficial -- a number that is higher than the number of human cells we have.  Each of our cells also contains mitochondria, which are the descendants of endosymbiotic bacteria that have inhabited the cells of eukaryotes for billions of years, and without which we couldn't release energy from our food molecules.  Plants have not only mitochondria but chloroplasts, yet another species of bacteria that like mitochondria, have their own DNA, took up residence in their hosts billions of years ago, and have been there ever since.

But as we saw in yesterday's post -- about a gene in the retinas of our eyes that we swiped from bacteria -- the rabbit hole goes a hell of a lot deeper than that.  By some estimates, between five and eight percent of our genomes are endogenous retroviruses -- genetic fragments left behind by viruses that spliced their DNA into ours.  Like our bacterial hitchhikers, a good many of these are either neutral or beneficial; for example, the production of bile, estrogen, and several proteins essential for the formation of the placenta are all directly affected by endogenous retroviral genes.  A few do seem to be deleterious, and have roles in certain cancers, autoimmune diseases, and neurological disorders like ALS and schizophrenia.

What brings this topic up is a study this week from the University of Innsbruck that found these stowaways everywhere they looked.  A comprehensive genetic analysis of single-celled organisms found no fewer than thirty thousand viral genes -- ten percent of the microbial genome!

This calls into question what exactly we mean by the word organism.  The canonical definition is "an individual life form of a species."  But is there any such thing?  The ostensibly individual life form called Gordon who is currently writing this post is made of (at least) equal numbers of human cells and cells from different species of bacteria, without many of which I'd be sick as hell, or possibly even dead.  Remove the symbiotic mitochondria from within my cells, and I'd definitely be dead -- within minutes.  Deeper still, at a minimum, one in twenty of the genes in my "human DNA" comes from viruses and bacteria.

Looked at closely, I'm as put together of spare parts as the Junk Man in Lost in Space.  Fortunately, I appear to run a bit more smoothly most days than he did.

In any case, calling me "a single organism" is so far from accurate it's almost laughable.

Honestly, it's kind of cool how interconnected everything is.  Back in the days of the first serious taxonomist, Swedish biologist Carl Linnaeus, scientists had the idea that all living things were categorizable into neat little cubbyholes.  Not only is that incorrect on the species level (something I wrote about in detail a couple of years ago), it's not even true on the individual level or on the level of genomes.  Life on Earth is a huge, tangled skein of threads.  The whole thing puts me in mind of a quote from John Muir: "Tug at a single thing in nature, and you find that it is hitched to everything else in the universe."


Wednesday, April 12, 2023

Stolen glance

Charles Darwin eloquently expressed his own struggle with imagining how the vertebrate eye could have evolved.  If you spend any time reading the writings of creationists or proponents of intelligent design (not recommended unless you have an extraordinary tolerance for pretzel logic), you'll find a quote from The Origin of Species:

To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.

This quote causeth much crowing and fist-bumping amongst the holy, lo unto this very day, usually followed by something like "Even Darwin admitted that evolution by natural selection doesn't work."

It's wryly amusing, given the degree to which anti-evolutionists cherry-pick the scientific evidence they accept and the (much larger amount of) evidence they ignore completely, that this quote is itself cherry-picked, as you'd find out if you went on to read the next two sentences of the book:

When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science.  Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory.

So the argument -- if I can dignify it by that name -- of the anti-evolutionists boils down to our old friend Argument from Incredulity: "I can't imagine how it could have happened, therefore it must be God."

The truth is, we understand the evolution of the eye pretty well.  Lots of animals (for example, flatworms) have light-sensitive spots; and as Richard Dawkins brilliantly explains in his tour-de-force defense of evolution The Blind Watchmaker, once you have any kind of light-sensing ability at all, incremental improvements can result in some amazingly complex structures.  The eye isn't "irreducibly complex" -- the intelligent design cadre's favorite phrase -- at all; simple photosensitive spots led to "cup eyes" which led to eyes like a pinhole camera, and so on.  In fact, the whole process has been repeated more than once.  Complex eyes have evolved independently at least three times, possibly more.

[Image licensed under the Creative Commons Kamil Saitov, Human eye iris 5, CC BY 4.0]

The vertebrate eye is a particularly interesting case.  The transparent proteins in the lens, appropriately named crystallins, were found in 1988 by molecular biologist Joram Piatigorsky to come from the same genes that produce heat-shock proteins, enzymes that protect other proteins against damage from fluctuating temperature.  Take heat-shock proteins and assemble them in layers, you get a lens.  This is an example of exaptation (also called preaptation or preadaptation), where a gene, protein, or structure that evolved in one context develops a function giving it an entirely different use, and that use kind of moves in and takes over.

It's another example of exaptation in the eye that is why the whole topic comes up; in fact, it's not only exaptation, it's exaptation of a gene that was borrowed from another organism entirely.  A paper this week in Proceedings of the National Academy of Sciences looked at a protein in all vertebrate eyes called IRBP (interphotoreceptor retinoid-binding protein), without which our sense of sight wouldn't work.  When light strikes your eye, protein-bound complexes containing retinol (a derivative of vitamin A) absorb the energy, causing them to kink.  This triggers a neuron to fire, sending a signal to your brain.  However, something needs to unkink the complex, thus resetting the switch so it can respond to the next photon to come along.

That's what IRBP does.  Without it, your retinal cells would be able to respond exactly once, then they'd shut down permanently.

This week's paper found something astonishing.  The gene that codes for IRBP doesn't exist in our nearest invertebrate relatives, nor in any other group studied, with one exception -- certain species of bacteria.  What apparently happened is that the common ancestor of all vertebrates swiped a gene from bacteria that coded for a pepsidase -- an enzyme that breaks down and recycles proteins.  This kind of gene-stealing isn't uncommon.  (I did a post a few years ago about a pair of viral genes that seem to be critical for our forming memories, if you want another good example of this phenomenon.)  But like the heat-shock proteins becoming crystallins, the pepsidase made by the gene our ancestors grabbed was useful for something else -- unkinking the protein complexes in our rapidly-evolving eyes.

So our eyes work not only because of proteins gaining additional functions, but because we stole a gene from bacteria.

"Horizontal gene transfer can help to endow organisms with new functions," said Julie Dunning Hotopp, of the University of Maryland School of Medicine’s Institute for Genome Sciences.  "Once these genes take root in a new species, evolution can tinker with them to produce totally new abilities or enhance existing ones.  It is the biological equivalent of upcycling that happens in my Buy Nothing Group."