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.

Monday, December 31, 2018

Holy genes

I get together with my buddy Dave every Saturday morning for a workout at the gym, followed by coffee at our local café.  Dave's a polymath, a writer, and a thinker, so our conversations tend to lead into some deep waters.

And sometimes into profoundly depressing ones, like the one this past Saturday, wherein we discussed the likelihood of humanity eradicating itself either through greed, a deliberate act of self-destruction, accident, or sheer idiocy.  My somewhere-this-side-of-despair opinion is that truly destructive people are few in number, so the old fears of nuclear annihilation or some kind of engineered bioweapon are unlikely to be realized.

Much more likely, I think, are accident and idiocy.  Humanity's track record for saying "hey y'all, watch this!" with regards to solving some kind of environmental issue really sucks -- witness the cane toad in Australia, introduced deliberately to get rid of the sugar cane beetle by scientists who neglected to take into account the fact that beetles can fly and generally toads cannot.  The cane toad population skyrocketed, and it was found that they would eat anything up to and including small mammals, and also secrete a nasty toxin from their skin when attacked -- making them invulnerable to pretty much everything except a shotgun.

Anyhow, if we do engender an eco-catastrophe, I'm guessing it'll be foolishness that's behind it rather than some kind of nefarious plan.  Which is why the article I read over at Coast to Coast last week was so apt.

The story is about a French biohacker who claims to have created DNA whose sequence comes from "holy texts."  Adrian Locatelli came up with some kind of formula for converting the letters in various passages from Book of Genesis and the Qur'an  into a string of A, T, C, and G -- the four nitrogenous bases that make up the alphabet of the DNA molecule -- and proceeded to synthesize strands of DNA with those sequences.

Which he then injected into his own thigh.

[Image is in the Public Domain]

It's not clear what Locatelli was trying to accomplish by doing this.  The speculation is that he was attempting to trigger himself to evolve, Pokémon-like, into some higher form.  Or achieve godlike status.  Or perhaps it was just a publicity stunt.  In any case, it didn't accomplish anything but giving him a sore spot on his thigh, which lasted a few days and then went away.  Fortunately for him, we're pretty good at deconstructing foreign DNA -- after all, every time we eat, we're consuming DNA from the organism our food came from.  Beef, you're ingesting cow DNA.  Broccoli, you're ingesting broccoli DNA.  Slim Jims, you're ingesting... well, DNA from whatever the fuck kind of organism Slim Jims are made of.  I dunno.  But I presume that it was some kind of living thing at some point.

So the Holy DNA Locatelli injected himself with was undoubtedly broken down into ordinary non-holy nitrogenous bases, and any messages he'd encoded from the Book of Genesis and the Qur'an were lost.  Probably a good thing.  When intact material (especially protein) from another organism gets past the breakdown process and ends up in the bloodstream, it can cause serious allergic reactions -- this seems to be what happens with celiac sprue, in which gluten is only partially broken down in the small intestine and triggers a severe immune reaction that is unpleasant at best and life-threatening at worst.

So Locatelli was lucky.  Or maybe it's just because he deliberately avoided passages of text that were "controversial."  But my conversation with Dave came back to me when I read the comment made by biologist Ella Watkins about this "experiment:"  "I know the odds of a nonsense protein being close to anything dangerous in sequence space are relatively low, but this kind of avant-garde attitude and disregard for ethics towards science terrifies me that humanity’s end will be at the hands of an idiot."

To which I can only say: amen.  It's to be hoped that actual researchers are not approaching science with this kind of yee-haw, git-er-done attitude, but the thought that all it takes is one well-meaning moron with access to scientific equipment to unleash a catastrophe is kind of terrifying.  To paraphrase T. S. Eliot -- "This is the way the world shall end, not with a bang, but with a, 'Gee, it seemed like a good idea at the time.'"

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This week's Skeptophilia book recommendation is one of personal significance to me -- Michael Pollan's latest book, How to Change Your Mind.  Pollan's phenomenal writing in tours de force like The Omnivore's Dilemma and The Botany of Desire shines through here, where he takes on a controversial topic -- the use of psychedelic drugs to treat depression and anxiety.

Hallucinogens like DMT, LSD, ketamine, and psilocybin have long been classified as schedule-1 drugs -- chemicals which are off limits even for research except by a rigorous and time-consuming approval process that seldom results in a thumbs-up.  As a result, most researchers in mood disorders haven't even considered them, looking instead at more conventional antidepressants and anxiolytics.  It's only recently that there's been renewed interest, when it was found that one administration of drugs like ketamine, under controlled conditions, was enough to alleviate intractable depression, not just for hours or days but for months.

Pollan looks at the subject from all angles -- the history of psychedelics and why they've been taboo for so long, the psychopharmacology of the substances themselves, and the people whose lives have been changed by them.  It's a fascinating read -- and I hope it generates a sea change in our attitudes toward chemicals that could help literally millions of people deal with disorders that can rob their lives of pleasure, satisfaction, and motivation.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]




Saturday, December 22, 2018

He sees you when you're sleeping

Dear Readers,

I'll be taking next week off to spend some time with family, so there'll be a brief hiatus here at Skeptophilia HQ.  Posts will resume Monday, December 31, but I'll still be happy to receive any suggestions for topics while I'm on break!

So happy holidays to all who celebrate.  See you on New Year's Eve.

cheers,

Gordon

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Ever heard of a tulpa?

I wrote about this (alleged) phenomenon a while back, so long-time readers of Skeptophilia might recall that it is when a bunch of people believe in a fictional character with sufficient fervor that said character becomes real.

Well, in some sense.  Even most true believers don't think they end up as flesh-and-blood, more that they can appear in spirit form (whatever that means when applied to a character that is fictional in the first place).  It all sounds like a lot of wishful thinking to me, although as a fiction writer, I can say with some certainty that I would very much rather the characters in my books not come to life.  There are a few I'd like to have a beer with, sure.  But most of them?

They can stay safely in the realm of the unreal, thank you very much.

Be that as it may, apparently there are now people who think that there's a tulpa who is around mostly at this time of year.  So I'm sure you can predict that who I'm talking about is...

... Santa Claus.

No, I'm not making this up.  In an article over at Mysterious Universe, Brent Swancer tells us about a number of alleged sightings of Jolly Old Saint Nick.  And not to beat the point unto death, these people do not believe that they're seeing someone dressed up as Santa Claus; they think they've actually had a close encounter with the real guy.

The word real, of course, being used advisedly.  I don't want to steal Swancer's thunder, because his article is well worth reading in its entirety, but here's one such account, just so you can get the flavor of it.  A woman named Ana says she saw Santa when she was five years old, and the encounter was not exactly heartwarming:
He must have felt my presence because he turned around and looked at me.  He didn’t look jolly or kind and happy like you would expect Santa Claus to look.  He looked kind of eerie like he was staring into my soul.  Automatically, I ran into my parents’ room and hid under the covers.  I don’t know why I was so scared at the time, but I wrote it off as a dream for a while before I forgot about it completely.  Years later, I remembered it.  I thought it could have been a burglar, but when I asked my parents, nothing was ever missing from that apartment.  The only time we were ever robbed was when we moved later on.  The only explanation I have now is that it was some kind of apparition.
Of course, that's not the only explanation, but you knew I'd say that.

His eyes, how they twinkled!  His dimples, how merry!  [Image licensed under the Creative Commons Jackie, Evil clown Santa Claus, CC BY 2.0]

Loyd Auerbach, a "professor of parapsychology" over at Atlantic University, used the same verbiage to describe the accounts:
I’ve never even heard of people seeing Santa.  The Grim Reaper, yes, but not Santa.  The only possibility of this being real is if it’s an alien or a ghost pretending to be Santa.  We can’t investigate that.  There’s nothing we can do with that.
Um.  We could investigate it if it was the Grim Reaper, but not if it's Santa?  Or if it's not actually Santa, our only options are that it's an alien or a ghost impersonating Santa?

 I think these people need to review the concept of "only possibility."

So anyhow, I think the main issue here is that if it were true, it doesn't exactly paint a reassuring picture of Santa Claus.  In fact, it gives kind of sinister overtones to lines like "He sees you when you're sleeping, he knows when you're awake," not to mention, "I saw Mommy Kissing Santa Claus."  It also gives me pause when I hear the stanza from "Up on the Housetop" that goes:
Next comes the stocking of Little Will
Oh, just see what a glorious fill
Here is a hammer and lots of tacks
Also a ball and a whip that cracks.
Is it just me, or does it sound like Little Will made his Christmas list to fill out the equipment in his My Very Own Li'l Tots S & M Dungeon?

Myself, I find the whole thing vaguely terrifying.  It's a good thing I think it's all a myth.  On the other hand, even if Sinister Santa is a real thing, he's still better than Krampus or the Giant Icelandic Christmas Cat, the Jólakötturinn, who comes out on Christmas Eve and eats bad children.

Which, for the record, I didn't make up.

So a lovely Christmas to all who celebrate, and best of luck avoiding evil Santas or humongous child-eating cats.  Also the Grim Reaper, for what it's worth.

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This week's Skeptophilia book recommendation is Michio Kaku's The Physics of the Impossible.  Kaku takes a look at the science and technology that is usually considered to be in the realm of science fiction -- things like invisibility cloaks, replicators, matter transporters, faster-than-light travel, medical devices like Star Trek's "tricorders" -- and considers whether they're possible given what we know of scientific law, and if so, what it would take to develop them.  In his signature lucid, humorous style, Kaku differentiates between what's merely a matter of figuring out the technology (such as invisibility) and what's probably impossible in a a real and final sense (such as, sadly, faster-than-light travel).  It's a wonderful excursion into the power of the human imagination -- and the power to make at least some of it happen.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]





Friday, December 21, 2018

Mystery disk

I'm always fascinated by a good mystery, and that's definitely the appropriate category for an artifact called the Phaistos Disk.

Found in the Minoan palace of Phaistos, on the island of Crete, in 1908, the Phaistos Disk is fifteen centimeters in diameter, made of fired ceramic clay, and (most interestingly) has an inscription on it.  Here's a photograph:



The Disk is thought to have been made in the second millennium B.C.E., making it approximately contemporaneous with the Linear B script of Crete, which was successfully deciphered in the early 1950s by Alice Kober, Michael Ventris, and John Chadwick.  This accomplishment was the first time that anyone had cracked a script where not only was the sound/letter correspondence unknown, but it wasn't even known what language the script was representing.  (As it turned out, it was an early form of Mycenaean Greek.  Earlier guesses were that it represented Etruscan, a proto-Celtic language, or even Egyptian.  The script itself was mostly syllabic, with one symbol representing a syllable rather than a single sound, and a few ideograms thrown in just to make it more difficult.)

The problem is, the Phaistos Disk is not Linear B.  Nor is it Linear A, an earlier script which remains undeciphered despite linguists' best attempts at decoding it.  The difficulty here is that the Phaistos Disk has only 242 different symbols, which is not enough to facilitate translation.  Once again, we're not sure what the language is, although it's a good guess that it's some form of Greek (other linguists have suggested it might be Hittite or Luwian, both languages spoken in ancient Anatolia (now Turkey), and which had their own alphabet that bears some superficial similarities to the symbols on the Disk).

This lack of information has led to wild speculation.  Various people have claimed it's a prayer, a calendar, a story, a board game, and a geometric theorem, although how the hell you'd know any of that when you can't even begin to read the inscription is beyond me.  But it only gets weirder from there.  Friedhelm Will and Axel Hausmann back in 2002 said that the Disk "comes from the ruins of Atlantis."   Others have suggested it's of extraterrestrial origin.  (Admit it, you knew the aliens were going to show up here somehow.)

Others, more prosaically, think it's a fake.  In 2008 archaeologist Jerome Eisenberg proclaimed the Disk a modern hoax, most likely perpetrated by Luigi Pernier, the Italian archaeologist who claimed to have discovered it.  Eisenberg cites a number of pieces of evidence -- differences in the firing and in how the edges were cut, as compared to other ceramic artifacts from the same period; the fact that it's incredibly well-preserved considering how old it supposedly is; and vague similarities to Linear A and Linear B characters, with various odd ones thrown in (Eisenberg says the symbols were chosen to be "credible but untranslatable" and selected "cleverly... to purposely confuse the scholarly world."

Of course, this didn't settle the controversy.  Archaeologist Pavol Hnila cites four different artifacts, all discovered after the Disk, that have similar characters to the ones on the Disk, and that there is not enough evidence to warrant accusing Pernier and his team of something as serious as a deliberate hoax.

So the mystery endures, as mysteries are wont to do.  I find this fascinating but more than a little frustrating -- to know that there is an answer, but to accept that we may never find out what it is.  That's the way it goes, though.  If you're a true skeptic, you have to be willing to remain in ignorance, indefinitely if need be, if there is insufficient evidence to decide one way or the other.  This leaves the Phaistos Disk in the category of "Wouldn't this be fun to figure out?" -- a designation that is as common in science as it is exasperating.

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This week's Skeptophilia book recommendation is Michio Kaku's The Physics of the Impossible.  Kaku takes a look at the science and technology that is usually considered to be in the realm of science fiction -- things like invisibility cloaks, replicators, matter transporters, faster-than-light travel, medical devices like Star Trek's "tricorders" -- and considers whether they're possible given what we know of scientific law, and if so, what it would take to develop them.  In his signature lucid, humorous style, Kaku differentiates between what's merely a matter of figuring out the technology (such as invisibility) and what's probably impossible in a a real and final sense (such as, sadly, faster-than-light travel).  It's a wonderful excursion into the power of the human imagination -- and the power to make at least some of it happen.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]





Thursday, December 20, 2018

Timey-wimey travel

A lot of us here in the United States would love to have a crystal ball and find out what's going to happen in the next few months.  After all, using logic to predict the direction our government is going is a seriously losing proposition.  As a student of mine put it, "I keep thinking things can't get any weirder.  Then they do."

So allow me to put all your worries to rest.  We now know what's going to happen.

Because a time traveler from the year 2030 has come back to tell us all about it.

His name is "Noah."  Why exactly he decided to come back here is a matter of conjecture, since he claims that we can't change anything he's predicting, as it's in his past.  But there are two things that he says will happen that are a little eyebrow-raising.

First, he says that Donald Trump will win re-election in 2020.  This is a little hard to fathom because I would have thought it'd be a little difficult to run the country from a prison cell.

Second, he says that in 2028, Yolanda Renee King, the granddaughter of Martin Luther King Jr., will be sworn in as president.  This is kind of weird for a completely different reason, which is that she will be only twenty years old at the time.  Currently, you have to be 35 years old to run for president, so this would be a serious change in policy.

On the other hand, the cadre of Old White Men has fucked things up pretty badly, maybe it's time to let the Young People of Color have a chance.

Anyhow, Noah says an amendment to the Constitution will take care of the age issue.  Hard to imagine that getting any kind of traction in Congress, but five years ago, I'd have said the same thing about the likelihood of Congress looking the other way while a sociopathic serial adulterer used the presidency to line his own pockets.  While Billy Graham's son, of all people, called said sociopathic serial adulterer a "Man of God."

So things have to be pretty weird for me to say "no, that couldn't happen" any more.

As for Noah, he says he's not trying to change anyone's mind about anything.  "This is not an opinion, this is a fact from the future that actually happens," Noah said.  "I’m not here to persuade anyone to political opinions."  And apparently, time travel itself isn't all that much fun.  "I have many body implications and things all over myself," he said, "and I step in this giant dome and these things fire up and basically a large electronic weight basically pushes you through time.  It feels like if you got electrocuted."

Which brings up a series of questions, the most important of which is: what the fuck is a "body implication?"  I'm guessing he meant "implant," but who knows?  Eloquence doesn't seem to be emphasized in the schools of the future, if Noah is any indication.

In any case, time travel sounds pretty uncomfortable to me, making me wonder why he did it in the first place.  I mean, if he can't get us to change our ways and avoid the future he's predicting (because we can't change anything that's going to happen), what's his motivation?  From what he's saying, it sounds like pretty much everything is a Dr. Who-style fixed point in time.

So unless time is actually a big ball of wibbly-wobbly timey-wimey stuff, I'm not really seeing the point.


Noah says he has proof, though, and he brings out an x-ray of his hand with a blurry blob on it that he says is an implanted device that is critical for time travel.  Because clearly that wouldn't be easy to fake, or anything.

Anyhow, that's today's dip in the deep end, thanks to a loyal reader of Skeptophilia who alerted me to the claim.  Predictably, I'm unimpressed.  This is hopeful in that it means there's a good likelihood that Trump won't be re-elected.  As far as the rest -- the Constitutional amendment and Yolanda King being elected in 2028 -- I guess we'll have to wait to find out.

Like I said, weirder things have happened.

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This week's Skeptophilia book recommendation is Michio Kaku's The Physics of the Impossible.  Kaku takes a look at the science and technology that is usually considered to be in the realm of science fiction -- things like invisibility cloaks, replicators, matter transporters, faster-than-light travel, medical devices like Star Trek's "tricorders" -- and considers whether they're possible given what we know of scientific law, and if so, what it would take to develop them.  In his signature lucid, humorous style, Kaku differentiates between what's merely a matter of figuring out the technology (such as invisibility) and what's probably impossible in a a real and final sense (such as, sadly, faster-than-light travel).  It's a wonderful excursion into the power of the human imagination -- and the power to make at least some of it happen.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]





Wednesday, December 19, 2018

Deep life, oxygen, and false positives

In the last couple of days we connoisseurs of all things extraterrestrial received some good news and some bad news.

Let's start with the bad news first.

One of the ways astronomers have suggested we might detect life on other planets is the presence of oxygen in the atmosphere, which could be detected spectroscopically.  Oxygen is highly reactive -- it is, unsurprisingly, a strong oxidizer -- meaning that it will tend to react chemically with whatever's around and get bound up into a compound of some sort.  Therefore, the logic went, if there's oxygen in the atmosphere, something must be releasing it faster than it's being removed by ordinary chemical reactions.

Ergo, a living thing (probably doing some variation on photosynthesis).

A piece of research published this week in Earth and Space Chemistry called, "Gas Phase Chemistry of Cool Exoplanet Atmospheres: Insight from Laboratory Simulations," written by a team of scientists from seven different research institutions, came to a startling conclusion -- that atmospheric oxygen might not be a signature of life but a result of photochemistry (chemical reactions triggered by sunlight).

What the researchers did was to expose various mixtures of gases thought to be common components of exoplanet atmospheres to a variety of temperatures (from 25 C to 370 C) and light intensities and spectra, and they found that in many conditions, the energy from the heat and light was sufficient to break down oxidized gases (such as carbon dioxide) and release molecular oxygen.

"People used to suggest that oxygen and organics being present together indicates life, but we produced them abiotically in multiple simulations," said Chao He of Johns Hopkins University's department of Earth and Planetary Science.  "This suggests that even the co-presence of commonly accepted biosignatures could be a false positive for life."

Now, this doesn't mean that if oxygen is found in an exoplanet's atmosphere, it is a false positive; it's just that the He et al. research shows that the finding would not be the slam-dunk astronomers thought it was.  Which is unfortunate.  Given that it's likely that most of the planets hosting life do not have life forms advanced enough to communicate across interstellar space, it'd be nice to have a way to find out they're out there without leaving Earth.  And one of the better possibilities for that has just been shown to be unreliable.

News from the Deep Carbon Observatory, a project that is the collective effort of over a thousand geologists, chemists, and biologists, is more encouraging.  Most of us have the idea that life is only possible on the thin skin of the Earth, and that if you go very deep into the Earth's crust conditions become quickly hot enough and pressurized enough that nothing could live.

Well, that's not true.

The DCO released research last week showing that the amount of life in the "deep biosphere" might amount to as much as twenty billion tons, meaning it would outweigh all of humanity put together by a factor of twenty.  The DCO team drilled three miles deep into the seafloor, and investigated the deepest gold and diamond mines ever created, and everywhere they looked, they found life.

Lots of it.

They found life flourishing at a temperature of 122 C -- twenty-two degrees above the boiling point of water.  They found it in pitch darkness, where there's nothing around to eat except for rocks.  They found it at crushing pressures in the deepest trenches in the ocean.

Sounds like we might have to redefine what we mean by "conditions hospitable for life."

And, germane to the topic of today's post, it will broaden what conditions lie in the "Goldilocks Zone" -- the region surrounding a star where its planets would experience temperatures that are neither too warm nor too cold, but "just right."  Apparently "just right" has a broader range than we ever dreamed, which means that a great many more planets out there might host life than we ever expected.

However, it bears mention that the denizens of the deep biosphere are all simple.  Nothing much more complex than a nematode (roundworm) has been found down there.  So if you were hoping for running across the Morlocks, so far that's a no.


But it's a pretty exciting finding nonetheless, and supports a contention I've had for years -- that life is common in the universe.  Or, as Ellie Arroway put it in Contact, "If not, it'd be an awful waste of space."  Now it's on the chemists and atmospheric scientists to find us a better way to tell that it's there, since the oxygen idea just got shot down.

We'll see what they come up with.  Because I'm certain that it's only a matter of time before we prove beyond any doubt that we're not alone in the universe.

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This week's Skeptophilia book recommendation is Michio Kaku's The Physics of the Impossible.  Kaku takes a look at the science and technology that is usually considered to be in the realm of science fiction -- things like invisibility cloaks, replicators, matter transporters, faster-than-light travel, medical devices like Star Trek's "tricorders" -- and considers whether they're possible given what we know of scientific law, and if so, what it would take to develop them.  In his signature lucid, humorous style, Kaku differentiates between what's merely a matter of figuring out the technology (such as invisibility) and what's probably impossible in a a real and final sense (such as, sadly, faster-than-light travel).  It's a wonderful excursion into the power of the human imagination -- and the power to make at least some of it happen.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]





Tuesday, December 18, 2018

Toddler teleportation

I understand that wild, spooky, improbable explanations are more interesting than prosaic, ordinary ones, but really, people.

Get a grip.

This comes up because of a video that hit YouTube a couple of days ago that alleges to show a toddler teleporting into existence.  With no further ado, here's the clip:


So after watching this, what do you think is more likely?
(1) the editor of the video cut out a piece of the footage, making it look like a kid appeared out of nowhere.
or
(2) Your favorite of the following:
(a) It's a glitch in the Matrix, showing that we're all in an elaborate computer simulation, which works down to the last detail except for occasionally allowing small children to pop into or out of existence.
(b) The child is an alien who did the "energize, Scotty" thing and appeared on a street in Tewkesbury just in time to get caught in a television interview.
(c) The child is from the future.  Why (s)he came back here is a matter of conjecture, but some have suggested that (s)he is here to intervene and save the United Kingdom from Brexit.
(d) Blah blah blah lizard people blah blah Illuminati blah blah New World Order.
Okay, I have to admit to being a little startled the first time I saw it, but "I was a little startled" doesn't mean "I immediately jumped to the most ridiculous, convoluted explanation I can think of, and because I'm a fiction writer, I'm really good at thinking up ridiculous, convoluted explanations, so this is pretty impressive."

My pointing this out is probably a losing battle, however.  The subreddit r/Glitch_in_the_Matrix has, at present, 305,000 subscribers, and it's unwarrantedly optimistic to think that all of them are there just for the shits and giggles.  And there's got to be at least that many subscribers on subreddits and other websites about the Illuminati and New World Order, but I'm not going to go to said websites and find out, because They Are Always Watching and then They will know I'm checking them out and get suspicious and send the Men in Black to take me out and I'll never be heard from again.

You know how it is.


So this is yet another example of grabbing confirmation bias with both hands and running off the cliff with it, and I can say with some certainty that it makes a lousy parachute.  The bottom line is that most everything has a perfectly simple, rational explanation, and there is really no reason to seek out one that demands the existence of Matrices or aliens or time travel or lizard people.

Although Stephen Miller's most recent attempt at simulating a human being by applying paint-on hair does make me wonder about the lizard people.

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This week's Skeptophilia book recommendation is Michio Kaku's The Physics of the Impossible.  Kaku takes a look at the science and technology that is usually considered to be in the realm of science fiction -- things like invisibility cloaks, replicators, matter transporters, faster-than-light travel, medical devices like Star Trek's "tricorders" -- and considers whether they're possible given what we know of scientific law, and if so, what it would take to develop them.  In his signature lucid, humorous style, Kaku differentiates between what's merely a matter of figuring out the technology (such as invisibility) and what's probably impossible in a a real and final sense (such as, sadly, faster-than-light travel).  It's a wonderful excursion into the power of the human imagination -- and the power to make at least some of it happen.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]





Monday, December 17, 2018

Racing against your brain

Being a devoted (if not especially fast) runner, and also ridiculously competitive, I'm always interested in ways to increase my speed and endurance.

It's not, honestly, that I am under any illusion of my becoming a world-class marathoner, or anything.  I'm 58 years old, and don't think there's any way I'd ever have the determination to train intensely enough to be a contender for first place.  But I'd like to see some improvement -- specifically, more improvement than I've seen over the past two years, when I've been stuck averaging around a ten-minute mile while younger and more athletic guys are clocking in with seven-minute miles or better.

Yesterday I found out that some of my problem is probably in my brain, not in my legs.

A study published last week in Nature: Human Behavior called, "Learning One's Genetic Risk Changes Physiology Independent of Actual Genetic Risk," by psychologists Bradley P. Turnwald, J. Parker Goyer, Danielle Z. Boles, Amy Silder, Scott L. Delp, and Alia J. Crum of Stanford University, suggests something astonishing; your performance in a race is more dependent on whether you think you have a variant of a gene that improves stamina than whether you actually have the gene.

The setup was simple.  They tested volunteers to determine which variant of a (real) gene called CREB-1 they had.  One version tends to increase endurance, and the other reduces it, so which variant you have determines how easily you tire.  They then split the entire group four ways; (1) those who have the high-endurance gene and are told they do; (2) those who have the high-endurance gene and are told they have the low-endurance variant; (3) those who have the low-endurance gene and are told they do; and (4) those who have the low-endurance gene and are told they have the high-endurance variant.

The results were unequivocal.  Those who were told they had the low-endurance variant of CREB-1 processed out carbon dioxide less efficiently, tired more quickly, ran more slowly, and gave up sooner than the ones who were told they had the high-endurance variant -- regardless of which variant they had.

Me at the end of a race in Montezuma, New York last year.  It was 95 F and about eight krillion percent humidity, and I definitely was not thinking, "I have excellent endurance and stamina."  My mindset was more, "I hope I can make it across the finish line before I die so at least I won't block the trail for the other runners."


The most amazing thing to me is the carbon dioxide part.  The rest of it I can attribute to attitude -- if I think I'm going to crap out more quickly because of some factor beyond my control, I'm likely to interpret all the stuff runners have to put up with -- the little aches and pains, shortness of breath, sweating, and heart pounding -- as evidence that I'm not going to be competitive no matter what I do.  It's easy to see someone paying unwarranted attention to what happens to all of us when we run, and giving up more quickly, if they figure that it's just their unfortunate genetic makeup causing it.

But the carbon dioxide part is fascinating, because that's not something under any sort of voluntary control.  It's hard to see how you could affect the rate at which carbon dioxide is cleared from the blood by some kind of power-of-positive-thinking phenomenon.  But that seems to be what happened.  "What people haven’t fully appreciated is that that information also puts you into a mindset: 'I’m at high risk or I'm protected,'" study co-author Alia Crum said.  "And that alone can have potent effects on physiology and motivation."

Of course, what I want to know is how.  How could simply thinking that you have good endurance change your physiology drastically enough to result in a measurable increase in speed and stamina?

And more to the point, how can I tap into that?

I've always been pretty dubious about the results of positive self-talk.  I mean, it's probably better than negative self-talk, but I've always thought it was only from the standpoint of making you a generally happier person.  (Not that this is inconsequential, mind you.)  But apparently athleticism has as much to do with mindset as it does with genes, and when elite athletes say that the only way to succeed is to believe you can, there might be something scientific to it after all.

But for me, it falls into the "Now that I know this, what do I do?" department.  I suppose I could try convincing myself that I'm fast and powerful and all the rest, but I have this sneaking suspicion my brain would be saying at the same time, "C'mon, you know that's not true," which would probably spoil the effect.  Or maybe I could have a genetic test for CREB-1 and have my wife lie to me about the results if it turns out I have the low-endurance variant.

Whatever I do, it's probably more important simply to keep training.  But maybe cursing myself when those young bucks zoom past me isn't the best approach -- maybe I should be thinking, "Next time, that'll be me."

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This week's Skeptophilia book recommendation is Michio Kaku's The Physics of the Impossible.  Kaku takes a look at the science and technology that is usually considered to be in the realm of science fiction -- things like invisibility cloaks, replicators, matter transporters, faster-than-light travel, medical devices like Star Trek's "tricorders" -- and considers whether they're possible given what we know of scientific law, and if so, what it would take to develop them.  In his signature lucid, humorous style, Kaku differentiates between what's merely a matter of figuring out the technology (such as invisibility) and what's probably impossible in a a real and final sense (such as, sadly, faster-than-light travel).  It's a wonderful excursion into the power of the human imagination -- and the power to make at least some of it happen.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]





Saturday, December 15, 2018

Viral assassins

In yesterday's post, we looked at viral remnants in our own DNA and their possible role in long-term memory formation.  Today, we'll consider the possibility of using viruses in a different way -- to fight bacterial infections.

As I mentioned yesterday, labeling a virus as "alive" is highly debatable.  They certainly don't seem to respond, at least not in the way a living thing ordinarily does -- moving toward or away from a stimulus.  They're so un-life-like that they can actually be crystallized in a test tube, which makes them more like strange, self-replicating chemicals than they are like organisms.

Which is what makes the research that was published in Cell this week even more astonishing.  In "A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision," by Justin E. Silpe and Bonnie L. Bassler, we learn about a type of bacteriophage (bacteria-killing virus) that seems to be able to sense its prey, and launch an attack when the colony is at its most vulnerable.

Model of a typical bacteriophage [Image is licensed under the Creative Commons Adenosine, PhageExterior, CC BY-SA 3.0]

The prey bacteria is Vibrio cholerae, and it's certainly a deserving target.  It causes cholera, which makes water reabsorption in the intestine run backwards -- the host begins to dump water and blood solutes into the intestine, resulting in diarrhea so severe that an adult can dehydrate and die within twelve hours.  With quick treatment, the survival rate is quite good; without it, over half of infected people die, usually within two days of the onset of symptoms.

The virus that Silpe and Bassler were studying, VP882, can wipe out entire colonies of Vibrio cholerae by detecting a set of molecules responsible for quorum sensing, which is how colonial bacteria are able to respond to their environment differently depending of how many are nearby.  When the number of quorum-sensing molecules is low, the virus and the bacteria coexist peacefully.  When it reaches a certain threshold -- meaning there are lots of bacteria there -- the virus suddenly becomes virulent, attacks the bacteria, and wipes out the entire colony.

Other microbiologists have been quick to see the implications.  If VP882 is capable of killing a colony of cholera bacteria swiftly and efficiently, it could potentially be useful as a therapy.  And if it works for killing Vibrio cholerae, why couldn't it work for attacking other kinds of bacteria?  "If you have a lung infection, you might not be able to diagnose what bacteria [are] responsible in time and choose the right phage," said Mark Mimee of the Massachusetts Institute of Technology.  "To get around that, people use cocktails of different phages.  But manufacturing cocktails and adhering to drug regulations is too expensive...  [But] a single recombinant phage—yeah, that would be really interesting."

In other words, create a single viral assassin that could take out any sort of bacteria you wanted.  Silpe and Bassler were able to get VP882 to respond to signals from other bacterial species, including E. coli and Salmonella, but it remains to be seen if you could engineer one kind of phage that could take on any species of bacteria.

It remains to be seen if this would be a good idea.  In a normal, healthy human body, there are right around the same number of human cells and bacterial cells -- on the order of thirty trillion.  Having a normal intestinal and skin "flora" is critical for good health.  It's been shown that in order to treat intractable cases of ulcerative colitis and infection with Clostridium difficile (another bad guy of the bacterial world), there is a good chance that a fecal transplant will help.

Yes, that's exactly what it sounds like.  I'll leave the details of the procedure to your imagination out of respect for my more delicate readers, but suffice it to say that it results in replacing the sick person's intestinal flora with that of a healthy person -- and has a remarkably high cure rate.

So my question is -- apropos of the viral research by Silpe and Bassler -- if you are given a dose of phage intended to treat (for example) strep throat, what's to stop the phage from wiping out all the other bacteria they come into contact with?  I know the chemical signals differ -- that's how they modulated the kill switch for the virus with the three species of bacteria they worked with -- but it seems like there's a huge possibility for this to go very, very badly.  Yes, the therapy would have to be tested exhaustively and approved by the FDA, but the whole thing is a little worrisome, whatever its promise.

In any case, this highlights how little we understand the unseen microscopic world we're immersed in.  Viruses may not be the unresponsive little blobs we thought they were.  And as for VP882 -- it will be fascinating to see where this goes, and if we might have another weapon in our medical arsenal -- a virus that attacks bacteria.

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One of the best books I've read recently is Alan Weisman's The World Without Us.  I wouldn't say it's cheerful, however.  But what Weisman does is to look at what would happen if the human race was to disappear -- how long it would take for our creations to break down, for nature to reassert itself, for the damage we've done to be healed.

The book is full of eye-openers.  First, his prediction is that within 24 hours of the power going out, the New York Subways would fill with water -- once the pumps go out, they'd become underwater caves.  Not long thereafter, the water would eat away at the underpinnings of the roads, and roads would start caving in, before long returning Manhattan to what it was before the Europeans arrived, a swampy island crisscrossed by rivers.  Farms, including the huge industrial farms of the Midwest, would be equally quick; cultivated varieties of wheat and corn would, Weisman says, last only three or four years before being replaced by hardier species, and the land would gradually return to nature (albeit changed by the introduction of highly competitive exotic species that were introduced by us, accidentally or deliberately).

Other places, however, would not rebound quickly.  Or ever.  Nuclear reactor sites would become uninhabitable for enough time that they might as well be considered a permanent loss.  Sites contaminated by heavy metals and non-biodegradable poisons (like dioxins) also would be, although with these there's the possibility of organisms evolving to tolerate, or even break down, the toxins.  (No such hope with radioactivity, unfortunately.)

But despite the dark parts it's a good read, and puts into perspective the effect we've had on the Earth -- and makes even more urgent the case that we need to put the brakes on environmental damage before something really does take our species out for good.




Friday, December 14, 2018

The memory virus

Nota bene -- Yesterday, I posed a "divergent-thinking" puzzle for my readers, to wit:
A man leaves home, makes three left turns, and as he is arriving back home he sees two masked men waiting for him.  Who are the masked men?
The answer is at the end of this post -- fair warning if you're still working on it!

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It's virus season, which thus far I've been able to avoid participating in, but my students are hacking and snorting and coughing and I figure it's only a matter of time.  Viruses are odd beasts; they're obligate intracellular parasites, doing their evil work by hijacking your cellular machinery and using it to make more viruses.  Furthermore, they lack virtually all of the structures that cells have, including cell membranes, cytoplasm, and organelles.  They really are more like self-replicating chemicals than they are like living things.

Simian Polyoma Virus 40 [Image licensed under the Creative Commons Phoebus87 at English Wikipedia, Symian virus, CC BY-SA 3.0]

What is even stranger about viruses is that while some of the more familiar ones -- colds, flu, measles -- invade the host, make him/her sick, and eventually (with luck) are cleared from the body -- some of them leave behind remnants that can make their presence known later.  This behavior is what makes the herpes family of viruses so insidious -- if you've been infected once, you are infected for life, and the latent viruses hidden in your cells can cause another eruption of symptoms, sometimes decades later.

Even weirder is when those latent viral remnants cause havoc in a completely different way than the original infection did.  There's a piece of a virus left in the DNA of many of us called HERV-W (human endogenous retrovirus W) which, if activated, can trigger multiple sclerosis or schizophrenia.  Another one, Coxsackie virus, has an apparent connection to type-1 diabetes and Sjögren's syndrome.  Thus far, all of the viral infections, whether or not they're latent, are damaging to the host.  So it was quite a shock to me to read a piece of recent research that there's a viral remnant that not only is beneficial, but is critical for intercellular communication -- and individuals without it have trouble forming long-term memories!

In two separate papers published in the journal Cell -- "The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer" and "Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons," each by a large team of neurobiologists and geneticists -- we learn about the proteins Arc and Gag, which were put into our cells by retroviruses (probably) hundreds of millions of years ago, and which generate virus-like particles that transfer from one brain cell to another.  This process seems to mediate memory formation, as mice that have the Arc/Gag gene knocked out are unable to retain long-term memories -- and may even be unable to form them in the first place.

As Sara Reardon explained it, writing in Nature:
Shepherd and Budnik [lead researchers in the two studies] think that the vesicles containing Arc play a part in helping neurons to form and break connections over time as an animal’s nervous system develops or adapts to a new environment or memory.  Although the fly and mouse versions of Arc are similar, they seem to have evolved from two distinct retroviruses that entered the species’ genomes at different times.  "There must be something really fundamental about it," Budnik says, for it to appear in both mice and flies... 
The human genome contains around 100 Gag-like genes that could encode proteins that form capsids.  It’s possible that this new form of communication between cells is more common than we thought, Shepherd says.  "We think it’s just the beginning."
Which is pretty astonishing.  The idea that some viruses might have beneficial effects on the host is weird enough; the idea that they could facilitate something as basic as memory storage is mind-blowing.  As such, they'd be a major driver for evolution -- given that organisms that have strong memory capacity are clearly at an advantage over ones that don't.

So before you curse the viruses this winter, be a little thankful for Arc and Gag and any other genetic parasites we might have that help us to function.  It may be small consolation if you are currently fighting a cold, but keep in mind that without viruses, you might not be keep anything in mind at all.

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The answer to the puzzle: The two masked men are the catcher and the umpire.

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One of the best books I've read recently is Alan Weisman's The World Without Us.  I wouldn't say it's cheerful, however.  But what Weisman does is to look at what would happen if the human race was to disappear -- how long it would take for our creations to break down, for nature to reassert itself, for the damage we've done to be healed.

The book is full of eye-openers.  First, his prediction is that within 24 hours of the power going out, the New York Subways would fill with water -- once the pumps go out, they'd become underwater caves.  Not long thereafter, the water would eat away at the underpinnings of the roads, and roads would start caving in, before long returning Manhattan to what it was before the Europeans arrived, a swampy island crisscrossed by rivers.  Farms, including the huge industrial farms of the Midwest, would be equally quick; cultivated varieties of wheat and corn would, Weisman says, last only three or four years before being replaced by hardier species, and the land would gradually return to nature (albeit changed by the introduction of highly competitive exotic species that were introduced by us, accidentally or deliberately).

Other places, however, would not rebound quickly.  Or ever.  Nuclear reactor sites would become uninhabitable for enough time that they might as well be considered a permanent loss.  Sites contaminated by heavy metals and non-biodegradable poisons (like dioxins) also would be, although with these there's the possibility of organisms evolving to tolerate, or even break down, the toxins.  (No such hope with radioactivity, unfortunately.)

But despite the dark parts it's a good read, and puts into perspective the effect we've had on the Earth -- and makes even more urgent the case that we need to put the brakes on environmental damage before something really does take our species out for good.