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.

Friday, July 28, 2017

Silence is golden

A while back my cousin Carla from New Mexico brought to my attention a paranormal phenomenon I had never heard of before.  Carla's husband Dan is a geography professor at New Mexico State University, and the three of us basically have the same approach to the paranormal; namely to discuss it with grave expressions, drawing up maps, passing back and forth grainy, blurred photographs of ghosts, UFOs, and sasquatches ("sasquatchi?" "sasquatchim?" There's got to be a more entertaining plural than "sasquatches"), and examining evidence of Ancient Astronauts Visiting the Earth.  Then we all burst into guffaws because we just can't take it any more.

In any case, Dan (code name: Dr. Monsoon Havoc, B.S., M.S., Ph.D., President, and Director of the Department of Multi-Dimensional Topography) and Carla (code name: Cria Havoc, Vice President, and Director of the Department of Hermetics, Hermeneutics, and Historiography) kindly inducted me two years ago into their organization, ISNOT (Institute for the Study of Non-Objective Theories).   (My code name: Gordon "Whirlwind" McTeague, Director of the Department of Exobiology and Cryptozoology, a.k.a. "The Blond Yeti").  Since then, it's been one adventure after another, as we investigated reports of El Chupacabra, the Connecticut Hill Monster (the upstate New York cousin of Bigfoot), and various sightings of the face of Jesus on grilled cheese sandwiches.  But now... now, we have a serious matter to look into.

Carla/Cria sent me a link with information about a place called the Zone of Silence.  This spot, located about 400 miles from El Paso, Texas, and near the point where the borders of the Mexican states of Coahuila, Chihuahua, and Durango meet, has a lot of the same characteristics as the Bermuda Triangle.  Within this area, "radio and TV signals... are gobbled up," "strange lights or fireballs (maneuver) at night, changing colors, hanging motionless and then taking off at great speed," and there are falls of "small metallic balls... known locally as guíjolas," which are "collected by locals and visitors alike, and treated with great reverence."

My thought on this last part is that if you are the sort of person who might be tempted to treat a small metallic ball with great reverence, you probably should not be allowed to wander about in the desert unaccompanied.

But I digress.

One difference between this place and the Bermuda Triangle is that being dry land (extremely dry, in this case), the Zone of Silence can also host honest-to-Fox-Mulder Close Encounters of the Third Kind.  There have been several reports of meetings with "tall, blond individuals," who spoke flawless Spanish "with a musical ring."  In one case, they were wearing yellow raincoats, and helped some lost travelers whose car was stuck in the mud during one of the area's infrequent, but torrential, downpours.  This is encouraging; most of the other aliens I've heard of seem more interested in evil pastimes, such as infiltrating world governments, dissecting livestock, and placing computer chips in the heads of abducted earthlings, after the obligatory horrifying medical exam on board the spacecraft, about which we will say no more out of respect for the more sensitive members of the studio audience.  Myself, I find reports of helpful aliens distinctly encouraging, and hope you won't think me self-serving if I just mention briefly that if there are any like-minded aliens visiting upstate New York soon, I could sure use a hand cleaning my gutters.

I found this image of a "Nordic Alien" on a website that cautions you against getting into a spaceship piloted by tall blond extraterrestrials, which honestly seems like good advice.  It also says that The Matrix was a coded message warning us about the dangers of being harvested by aliens.  The good news is that if you are approached, all you have to do is say, "I decline your offer to a contract," and they'll have no choice but to retreat in disarray. 

Of course, my more scientific readers will be asking themselves why, exactly, is this spot a "zone of silence?"  Answers vary, as you might expect.  One explanation I've seen proffered is the presence of uranium ore in nearby mountains (because diffuse deposits of radioactive ores clearly attract aliens, cause small metal balls to fall from the sky, and interfere with radio signals).  Another is that this spot represents a "concentration of earth energies."  Whatever the fuck that means.  It is also claimed that there is an "astronomical observatory thousands of years old... a Mexican Stonehenge" in the area.   Well, that's enough for me!  Uranium ore + "concentration of earth energies" + anything that can be compared to Stonehenge = some serious shit!  ISNOT is on it!  Mobilize the troops!

Well, not really.  Sadly, we're not able to mobilize in this direction at the present time.  The disappointing fact is that given the current state of affairs in northern Mexico, it's not all that appealing to go down and visit the place.  I mean, tall blond aliens with yellow rain slickers are one thing; dodging bullets from members of mutually hostile drug cartels is quite another.  I think the field work will have to wait until things calm down a little.

Until then, however, keep your eyes open for any other Non-Objective phenomena that may pop up -- we have three highly trained professionals here at ISNOT who are ready to investigate.  I'll post further research notes here.  You'll be the first to know.

Thursday, July 27, 2017

Zombie cult feud

A Senegalese saying goes, "There are forty different kinds of lunacy, but only one kind of common sense."

I got an object lesson in this principle from a link sent to me by a friend and loyal reader of Skeptophilia a few days ago, wherein I learned that two rival zombie apocalypse cults are currently embroiled in a feud.  The article, by Robyn Pennacchia over at Wonkette, is well worth reading in its entirety.  But my ears perked up instantly when I found out that one of the feuders is one Sherry Shriner.  I knew I'd seen her name before, but where?

A brief search was enough to determine why my memory was jogged.  Back in 2014, I did a post about how the Evil Shadow Government is outfitting us all with microchips in our dental fillings and implanted medical devices, not to mention through vaccination, with the ultimate aim of controlling our behavior in much the same fashion as a ten-year-old uses the remote control to steer his plastic car directly into a wall.

Fortunately, Shriner is one smart cookie, and found out a way to neutralize the chips, something so unexpected and technical and sophisticated there's no way the Evil Scientists would ever have thought of it: magnets. Apparently the chips kind of conk out when they're placed in a magnetic field.  So they turn out to be not such a threat after all, especially if you've ever had an MRI, which must cause the chips to short-circuit so badly that it causes Bad Guy Scientific Laboratories the world over to go up in flames.

But the failure of Shriner's microchip-implant claim apparently didn't discourage her in the least.  She is still around, and has come into the news lately through her alleged connection to a crime you might have heard about -- a woman in Tobyhanna, Pennsylvania shot and killed her boyfriend, supposedly when he asked her to because he'd found out that the leader of the cult they belonged to was a "reptilian alien."

Because that makes total sense.

Anyhow, the leader of the cult, and alleged reptilian alien, is none other than Shriner herself.  Apparently Shriner tried to warn Steven Mineo, the victim of the shooting, that his girlfriend (Barbara Rogers) was a loon.  Not in so many words, of course; what Shriner said was that Rogers was a "Super Soldier."  From Shriner's Facebook page:
They're trying to spin it that I'm responsible for Steve's death?  No, Barb is.  I tried to protect Steve.  I tried to warn him about Barbara Rogers, but he wouldn't listen to me.  He thought I was insulting his 'wife'... when I was just trying to protect him from her!  I knew what she was!  He began to realize that what I said about her was true, and that's why she killed him, to protect her lies and keep her secrets.  They want to call me a cult leader?  No, I am just a humble servant and a Messenger of the Most High.  I spent my life serving HIM, and for that I get beat up by Cain's kids, libtards, Satanists, witches, and haters everywhere.  If you open your eyes it's clear to see she was involved with witchcraft and Satanism.  Steve didn't want to believe it and now he's dead from her hands.  Steve wasn't suicidal, it was her plan all along to destroy him.  So all the lies and garbage against me and others just needs to stop... 
I warned him she was a Super Soldier who would kill him and move on... but I'm the 'False Prophet'...  Perhaps he finally figured her out but it was too late for him.  It wasn't the 'online cult' that killed him, it was Barbara Rogers who they had all warned him about!  They always try to paint me as a cult... nice try libtards.
So yeah, that sounds like the pinnacle of rationality.  The picture becomes even more vivid when you add to that the fact that Pennacchia found out that Shriner also thinks she's Lucifer's sister, and that she's personally interviewed her brother (and in fact wrote a book about it, one review of which begins with the memorable line, "This woman is a delusional loon.").  Oh, and she also sells crystals called "Orgone Blasters," which supposedly will destroy chemtrails, and which are (this is a direct quote from her website) "the only thing that works against Alien-Demonic-Zombie-Vampire beings."

In case those are a problem in your neighborhood.

[image courtesy of photographer Bob Jagendorf and the Wikimedia Commons]

Interestingly, Shriner's "Orgone Blasters" are something I've also addressed here at Skeptophilia.  "Orgone," if you're curious, is a fantastically powerful kind of energy that is the force of "psychosexual release" that happens at orgasm.  How on earth you could use such an energy even if it exists is kind of a mystery, because when most folks have an orgasm they're thinking about other things than how to combat Alien-Demonic-Zombie-Vampire beings.

Or maybe that's just me.  I dunno.

You'd think that'd be enough to think about for today, but in the words of the infomercial: "Wait!  There's more!"  Shriner is currently engaged in a feud with another zombie apocalypse cult, which is called either "Amightywind" or "Almightywind" (even the cult itself seems to be unsure which is correct).  The leaders of this cult, Ezra and Elizabeth Elijah Nikomia, have come up with something even better than Shriner's use of magnets to defeat implanted microchips; they say you can defeat zombies by hitting them with a board:
I tell you this now so when you see these things come to pass you will not fear his army of ZOMBIES that will be slain by the POWER OF THE CROSS of YAHUSHUA ha MASHIACH!  Remember hit them with a board or wood that represents the CROSS.  The dead in YAHUSHUA (Christ) which shall walk and witness to MY Glory will walk as in times of old and testify of Heaven, not to take the MARK of the BEAST!  They shall prove there is life after death.  MY saints you will hear and see in Glorified Bodies that CAN NOT BE KILLED!
So anyhow, Shriner absolutely hates A(l)mightywind, almost as much as she hates "libtards."  Alleged boyfriend-killer Barbara Rogers, Shriner says, was an evil witch affiliated with the Nikomias' group, and there's been a years-long war between their rival cults of an intensity reminiscent of the Hatfields and McCoys:
So all the witches online seem to be rallying their covens and fake Christian ministries to protect fellow witch Barbara Rogers and come against me and paint the lie Steve wanted to die.  Almightywind Witch Cult is run by a woman who was a witch in the Great White Brotherhood of Indiana, broke off from them to begin her own “ministry’ online.  She’s been making hate videos about me for years.  Steve was well aware of them.
And apparently the idea is that the Nikomias talked Barbara into shooting Steve because Steve had allied himself with Sherry Shriner.  From here on it gets kind of confusing, however, so I'll simply direct you to Pennacchia's excellent article if you want more information.

Myself, I'm just glad that Shriner and the Nikomias all live in different states than I do.  I'm sure that New York has its share of wackos, but these three seem like they're in a class by themselves.  And the fact that they're feuding is honestly kind of scary, because when you have people whose grasp on sanity is so tenuous, you never know what they might do.

Or maybe I'm one of the Secret Reptilian Alien Zombie Vampire Libtards.  You can see how that would be just as likely.

Wednesday, July 26, 2017

Brain energy frequency

If there's one thing that gets me really bent out of shape, it's people using scientific words in completely screwy ways.

After all, these days it's not hard to find definitions of words.  If you want to know what a quantum is,  all you have to do is take a thirty-second trip to Wikipedia, wherein you can find not only the scientific definition of the term, but the following wonderful paragraph:
The adjective "quantum" is frequently used in common parlance to mean the opposite of its scientific definition.  A "quantum leap" has been used colloquially since the 1950s to imply a large change, as opposed to the smallest possible change.  It is also used in a range of pseudoscientific beliefs (quantum mysticism), where the adjective is used to imply that a paranormal event is a consequence of quantum physics.
So complete misunderstanding and misuse of scientific terms is nothing more than laziness.  Which is why I read an article over at Qultura called "Energy and the Brain" while making increasingly agitated noises of barely-stifled rage.

[image courtesy of the Wikimedia Commons]

What this article claims is that your brain exists to "process energy."  And I'm not talking about the conventional, physics definition of energy (which once again, a quick trip to Wikipedia would clear up completely); they're talking about some woo-woo bullshit idea about Cosmic Connections To The Universe.  But let me give it to you in their own words:
All information is actually energy in different forms and thinking is the process of reducing energy frequency by processing that information.  Senses are designed to detect, perceive energy in different forms and evaluate the energy frequency.  Sight for example, perceives light energy, working with the right cerebral hemisphere of the brain much in the same way as your hearing perceives audio or sound energy within a certain frequency range.  Senses also differentiate between different energetic states, for example touch differentiates between energy and physical mass and matter (which is actually energy but in a much more inert state).  Even taste and smell can differentiate between different energy states.  Your sense of smell, for example, can tell when the energy within a piece of meat or in milk is of a higher frequency, and either the meat or milk is off, and you should not consume it.  Your senses provide you with sensory input, which all goes to the brain as energy or information to be processed.
Which might win some kind of world record for packing the most scientific inaccuracy into a single paragraph.  Let's look at a concise list of stupid claims in this passage:
  • Thinking does not "reduce energy frequency."  Whatever the fuck that means.
  • Sight does not "work with the right cerebral hemisphere."  The visual cortex is in the occipital lobe of both hemispheres.
  • Touch does not "differentiate between energy and physical mass."  Once again, I'm not even sure what that's supposed to mean.
  • Matter is not "energy in an inert state."  Energy and matter are not the same thing at all -- although Einstein's famous equation shows that you can convert one into the other.
  • Taste and smell are both chemoreceptors -- they work by having receptor proteins that are capable of binding to compounds dissolved in the saliva or floating around in the air (respectively).  They do not "differentiate between different energy states."
  • Spoiled meat does not have a lower frequency than fresh meat.  I'm a bit baffled as to how you could calculate the frequency of meat to start with, as most meat I've seen just tends to lie there.  (On the other hand, if your meat is vibrating, it probably is a bad sign.  And yes, I am aware that this is a double entendre.  And no, I don't care.)
  • High frequencies are not somehow better than low frequencies.  Anyone who thinks so should be required to listen for twenty minutes first to a high note on a piccolo and then to a low note on a cello, and see which they prefer. 
Then they end by stating that your sensory organs provide your brain with input to be processed, which is more or less correct.  So I guess the whole thing about monkeys typing randomly and eventually coming up with the script for Hamlet might have some validity after all.

But even this passage reads like a doctoral dissertation in physics as compared to the last bit.  Here's how the article ends:
[The brain's hemispheres are] what serve to take in energy in different frequencies from the atmosphere around you and process it in a way so as to change or reduce the frequency of the energy and project it back out into the atmosphere.  This is done constantly in different ways and collectively human beings throughout the world are a major influence on energetic frequencies in atmospheric energy.
Right!  Sure!  What?

I mean, tell me if I'm wrong, but what this sounds like is that they're claiming that you can change the weather by thinking about it.  Now, no one would be gladder than me if this were true; heaven knows I'd like to be able to conjure up a warm sunny day in the middle of an upstate New York January snowstorm.  But somehow, atmospheric energy frequencies notwithstanding, I don't think that'd work.

Or maybe I'm just not vibrating at a high enough frequency myself.  I dunno.

You might be thinking that all of this bullshit falls into the "stupid but harmless" category.  And in one sense, you'd be correct.  But as I've said more than once here at Skeptophilia, laziness becomes a habit.  If you simply assume that you know what you're talking about, and blather on without bothering to find out if you're using terms correctly or (in fact) have any idea how science in general works, you are much more likely to fall for pseudoscientific nonsense of more toxic sorts.

Much better to find out what the scientists themselves have to say.  Because, you know, they generally have a pretty good understanding of stuff.  Including "atmospheric energy frequencies."

Tuesday, July 25, 2017

Invasion of the star jelly

Skeptics and rationalists hear the accusation rather frequently that their assumption that everything has a rational explanation is as much a faith as any religion is.  Our conviction that all allegations of paranormal phenomena -- aliens, precognition, ghosts, witchcraft, and so on -- are probably bunk is based on an assumption about how the world works, and because it is an assumption, it is by definition an irrationally-held unprovable assertion.

Take the case of "Star Jelly."  The Lake District, in northern England, just had a bout of Star Jelly a few weeks ago, following a wind and rain storm.  What is it, you might ask?  Not something, I hasten to state, that you'd want to use to accompany your peanut butter sandwich.  Star Jelly is a whitish, gelatinous substance, sometimes found in great globs, out in the woods and hillsides -- usually discovered in the early morning, as if it had appeared suddenly at night. It was first recorded in the 14th century, and has since shown up hundreds of times -- most famously as a two-meter wide disk that showed up near Philadelphia in 1950, inspiring the movie The Blob.

[image courtesy of photographer James Lindsey and the Wikimedia Commons]

What is it, though?  This is where it gets interesting.  Because apparently scientists have not been able to come up with a definitive answer.  The two most common answers -- that it is a mucusy material made by slime molds, or by a species of cyanobacteria called Nostoc -- are unproven.   Analysis of bits of Star Jelly have failed to show any traces of DNA, which you would expect to find if either of the above explanations are true.  Then the woo-woos got involved.  Star Jelly is, they say, one of the following:
  • a substance from outer space that falls to Earth during meteor showers.
  • an extraterrestrial life form.
  • something to do with "chemtrails."
  • the residue left behind when an alien probe self-destructs.
  • ectoplasm.
  • a toxic waste from top-secret government research programs.
  • alien semen.
None of those explanations appeal to me, frankly, especially the last one.  You'd think that if aliens spent all of this time and effort to get to Earth, they'd have better things to do once they got here than to jack off outside during a rainstorm in the Lake District.

I'm the first to admit, however, that the scientific explanations that have been proffered thus far haven't really knocked my socks off.  But nonetheless, I'm still convinced that there has to be a reasonable explanation for the appearance of the mysterious substance.  Why is that?

A study published in 2008 in the neurology journal Cortex made the interesting claim that rationalism and a belief in the paranormal both arose from an underlying brain structure issue -- specifically, that belief in paranormal explanations was correlated with a high degree of cerebral asymmetry.  People who held paranormal beliefs, said lead researcher Günter Schulter, had undergone "perturbations in fetal development" that led to differences in the way the cerebrum was wired.  A study the following year at the University of Toronto showed that the religious and non-religious also showed a difference in brain activity, particularly in the region called the anterior cingulate cortex, a part of the brain adapted for coping with anxiety.

So is rationalism merely a product of brain physiology, and do the critics of skepticism have a point in saying that it is itself a religion?  While our assumption that everything has a rational explanation is just that -- an assumption -- we do have one very powerful argument for our views: Rationalism works.  There are countless examples of phenomena that were once unexplained (or given paranormal explanations) that later were, by the application of basic scientific principles, successfully accounted for with no need for recourse to the paranormal.  To cite one example, which got a lot of airtime with the woo-woos -- remember the orange glop that washed ashore in huge quantities near Kivalina, Alaska a while back, prompting speculation very similar to the aforementioned Star Jelly theories?  (No one, however, seemed inclined to attribute its appearance to masturbating aliens, but otherwise the explanations were much the same.)  Well, the scientists kept saying, "We don't know what it is yet, but it has to be a naturally-occurring substance."  And after study, guess what they found?  It was eggs -- the eggs of a perfectly natural marine invertebrate species.  Rationalism wins again!

Or, to quote the inimitable Tim Minchin: "Throughout history, every mystery ever solved has turned out to be Not Magic."

As far as the Star Jelly -- I'm not troubled by the fact that they haven't figured it out yet.  I'm confident that with study, this will fall to the methods of science just as so many other mysteries have in the past.  So if my skepticism is just a product of my brain's symmetry, or its overactive anterior cingulate cortex, that's okay by me -- because whatever the cause, it has a pretty good track record of leading me to the right answers.

Monday, July 24, 2017

Chemotherapy lies

A musician friend of mine, a flutist of tremendous talent, drive, and skill, was diagnosed with leukemia when she was seventeen years old, only months before her high school graduation.  This was (of course) a devastating blow to a young woman with aspirations to head off to college and pursue a career as a professional musician, but fate often intervenes in the best-laid plans (as Robert Burns said much more eloquently).

She began chemotherapy almost immediately after the diagnosis.  The process was excruciating.  She experienced all of the familiar awful side effects -- hair loss, weakness, nausea, headache.  She lost weight, and felt fatigue so crushing that it was hard for her to do anything other than sleep.  Her family and friends rallied around her, and she called on her own strength of spirit to get her through the pain.

And she made it.  The leukemia went into remission.  She was able to resume normal activities, including playing her beloved flute.  She's been cancer-free for over five years now -- and is soon to release her first album.

[image courtesy of the Wikimedia Commons]

It's stories like this that are why I become apoplectic with rage when I read things like a post that came out at The Mind Unleashed last week.  Entitled, "Chemotherapy Proven to Spread Cancer, Cause Lethal Tumors in Groundbreaking New Study," the writer begins with a bang by saying, "Albert Einstein College of Medicine proves chemotherapy is a cash machine for Big Pharma."  The post goes on to say:
In a groundbreaking new study, they’ve proven that chemotherapy causes cancer cells to spread throughout the body – to replicate themselves, making your cancer worse, not better...  The researchers, George S. Karagiannis, Jessica M. Pastoriza, Yarong Wang, Allison S. Harney, et all, suggest that though chemotherapy may shrink a cancerous tumor, but it simply sends the cancer cells off into other parts of the body to rebuild into yet additional destructive tumors. 
This study makes a massive move in exposing the perpetual fraud of the chemotherapy/cancer industry. In American alone, it’s a $200 billion-dollar industry. It’s part of the reason why our insurance premiums are ridiculously high, and unassuming cancer sufferers, keep suffering.
Of course, the Karagiannis et al. paper, released earlier this month in Science, says nothing of the sort.  Here's the summary of the study the editors of the journal wrote:
Breast cancer is one of the most common tumor types, and metastasis greatly increases the risk of death from this disease.  By studying the process of intravasation or entry of cells into the vasculature, Karagiannis et al. discovered that, in addition to killing tumor cells, chemotherapy treatment can also increase intravasation.  Groups of cells collectively known as tumor microenvironment of metastasis (TMEM) can serve as gateways for tumor cells entering the vasculature, and the authors discovered that several types of chemotherapy can increase the amounts of TMEM complexes and circulating tumor cells in the bloodstream.  The researchers also determined that a drug called rebastinib can interfere with TMEM activity and help overcome the increased risk of cancer cell dissemination.
Two things stand out.  The researchers studied one type of cancer -- breast cancer.  Chemotherapy differs greatly depending on cancer type, so it's highly unlikely that all chemotherapy increases TMEM production.  Second, and most important: did you catch the last line?

They showed that the drug rebastinib acts to prevent metastasis, thus removing any increased risk of TMEM formation resulting from the chemotherapy.

So basically, it's the opposite of what the people over at The Mind Unleashed claimed.  If "Big Pharma" wants us all to stay sick and keep suffering, they're doing a pretty lousy job.  Humans in industrialized countries have the highest overall life span, and (more importantly) the best health, of any society the world has ever seen.  A lot of the credit for this goes to the medical establishment -- especially the development of vaccines and antibiotics.  And the cancer sufferers who owe their lives to chemotherapy far outnumber the ones whose cancer recurred or metastasized due to the drugs they were given.

In other words: the article at The Mind Unleashed is misleading at best, and an outright bald-faced lie at worst.  They took a study whose title seemed to give some vague support to their anti-science stance, and (apparently without reading the actual paper itself) claimed that it proved that "Big Pharma" is engaging in some kind of giant conspiracy to make us all sick.

And this is not just an ordinary lie; it's a downright dangerous one.  Most of us aren't scientists, and a paper like Karagiannis et al. is beyond our ability to comprehend in anything more than a superficial manner.  On the other hand, bullshit alarmism like what I found over at The Mind Unleashed is easy to read -- and easy to swallow whole.  As we've seen more than once here at Skeptophilia, emotional appeals usually work better than intellectual ones.  If you hook into people's fears, you're likely to convince them even if what you're saying makes no rational sense whatsoever.

So what we have here is a claim that could very well make cancer patients -- who are already likely to be in a maelstrom of worry, doubt, and anguish -- decide that what their doctors are recommending is just going to make them worse.  Add to that the fact that even the best chemotherapies cause pretty unpleasant side effects, and you get a toxic combination that could well persuade someone to forgo treatment, or opt for some useless quack "alternative medicine" instead.

The case of Steve Jobs bears remembering -- who, when he was diagnosed with pancreatic cancer, delayed conventional treatment for nine months, opting instead for "alternative medicine" and changes in diet.  Jobs realized his mistake, but too late.  "He wanted to talk about it, how he regretted it," his biographer, Walter Isaacson, said.  "I think he felt he should have been operated on sooner...  I think he felt: if you ignore something you don't want to exist, you can have magical thinking.  It had worked for him in the past.  He did end up regretting it."

In the case of my musician friend, the situation is crystal-clear.  If she had chosen to ignore the advice of her doctors and avoid chemotherapy, she would have died.  Pure and simple.  We are fortunate enough to have a fine person and truly talented flutist still with us, living a healthy and productive life, because of "Big Pharma's chemotherapy/cancer industry."

And the biased, anti-scientific ignorance the people over at The Mind Unleashed are peddling is 100% USDA Grade-A bullshit.

Saturday, July 22, 2017

Reconsidering the junk

Regular readers of Skeptophilia know how much I respect science, and the women and men who have devoted their lives to increasing our understanding of how things work.  The curiosity, drive, intelligence, and creativity of scientists have provided us not only with stunning technological and medical advances, but basic knowledge about everything from the origins of life to the bizarre and counterintuitive behavior of the subatomic particles that make up all the matter in the universe.

Still, scientists are only human.  They make mistakes, misunderstand what the data mean, follow leads in the wrong direction.

Fortunately, science self-corrects.  It still baffles me when people think self-correction in science is a weakness; I call this the "Everything About This Could Be Proven Wrong Tomorrow" argument.  Why anyone would think that a system of knowledge that either couldn't detect errors, or else simply ignored them, would be preferable, is beyond me.

We had a great example of science's capacity to self-correct just this week, in a paper that came out in the journal Cell.  "Sensing Self and Foreign Circular RNAs by Intron Identity," by Y. Grace Chen, Myoungjoo V. Kim, Xingqi Chen, Pedro J. Batista, Saeko Aoyama, Jeremy E. Wilusz, Akiko Iwasaki, and Howard Y. Chang, of Stanford University, the Yale School of Medicine, and the University of Pennsylvania, sounds at first like something that would only be interesting to genetics geeks like myself.  To see why it's much more than this will take a bit of background explanation.

Our traits, and the traits of every living thing on Earth, arise through a pair of processes called transcription and translation.  DNA, as you undoubtedly know, is the master set of instructions for building everything in your body; but somehow, that information has to then direct our cells to produce brown hair or A+ blood type or resistance to malaria or any of a thousand different other features of our bodies.

The way it does that is through synthesizing proteins that then are responsible for guiding everything.  The synthesis of these proteins takes two steps.  The first, transcription, is a little like making a temporary copy (called mRNA) of the instructions from a single page of a cookbook (the DNA).  Then, a structure in the cell called the ribosome reads the copied page (the mRNA), and makes the chocolate cake or honey-glazed spare ribs or eggs Benedict -- whatever the instructions say (those finished dishes represent the proteins).

A diagram showing the process of translation [image courtesy of the Wikimedia Commons]

Our master cookbook -- the DNA in every single cell in our body -- has, according to most estimates, about 30,000 different recipes.  This gives you an idea of how genetic disorders occur -- they happen when one of the recipes has a mistake, produces too much of its final product, or doesn't get read at all.

Anyhow, back in the 1950s and 1960s, when scientists were first figuring out how all of this worked, they assumed that most of the DNA was made up of actual, readable recipes, that produced something essential for the cell.  Otherwise, why would it be there?

So it came as a bit of surprise when it was found that a significant portion of your DNA -- early estimates said it could be as much as 40% -- is "noncoding."  In other words, it's made up of recipes that don't make anything.  This noncoding DNA was derisively labeled "junk DNA" -- although why such a high proportion of our genetic material would have no function whatsoever was a considerable mystery.

I was pretty skeptical about the "junk" epithet right from the get-go.  For one thing, you'd think that stretches of DNA that had no function would eventually get scrambled by random mutations, but at least some of them have patterns (such as the tandem repeat sequences -- regions of DNA that have the same base sequence repeated over and over, and which are remarkably similar even in distantly-related species).  The fact that these patterns get preserved through millions of years of evolutionary distance indicates that changing them causes problems -- i.e., they do have some function, even if we don't know what it is.

Some "junk DNA" probably does deserve the title, of course.  We have old, damaged copies of genes floating around in our DNA, which don't ever get transcribed and simply are hangers-on from our distant ancestors.  We also have odd things called transposons, which are genes that almost act like independent life forms, copying themselves and splicing the copies elsewhere in our genomes.  (Some of those transposons are functional in switching genes on and off, but others are more like intranuclear parasites.)

Anyhow, my point is that I've long suspected that most of the noncoding DNA would turn out not to be useless after all.  And the paper by Chen et al. has just shown us that some of what seemed to be the junkiest of junk DNA -- the introns, pieces of DNA that are transcribed into mRNA but then cut out before the process of translation -- might have a function that is downright critical.

What the paper in Cell suggests is that these introns -- the leftovers bits of RNA after they're spliced out following transcription -- could have a role in the detection of "non-self" -- i.e., the basis of our immune systems.  Chen et al. write:
Circular RNAs (circRNAs) are single-stranded RNAs that are joined head to tail with largely unknown functions.  Here we show that transfection of purified in vitro generated circRNA into mammalian cells led to potent induction of innate immunity genes and confers protection against viral infection...  These results reveal innate immune sensing of circRNA and highlight introns—the predominant output of mammalian transcription—as arbiters of self-nonself identity.
Which I think is astonishing.  These chunks of RNA, which have been compared to the full-page advertisements in a magazine article that you can tear out and throw away without losing any information, might well have a role in protecting us from infection by viruses.  How exactly they do this is beyond the scope of the current study; but just the fact that this is possible will open up huge avenues for research, possibly even leading to treatments for hitherto intractable viral infections.

So what were once derisively considered useless stretches of DNA now appear to be downright critical.  All of which brings me back to my original point; that science is powerful because it has a methodology for sifting out and correcting errors or misunderstandings.  Without that, there would be no progress -- no way, in fact, for us to discern and excise the junk in our knowledge about the universe.

Friday, July 21, 2017

Equatorial travelogue

I just got back yesterday from my expedition to Ecuador with the phenomenal birding tour company Wings, an outfit which I cannot recommend highly enough.  As I mentioned in my previous post, I love Ecuador, but with the planning and leadership of a Wings guide, this was a really special trip.

We spent most of the time near the charming town of Mindo, in a lodge called Séptimo Paraiso (Seventh Heaven).   The name is apt.  The lodge was comfortable, the food was great, and the hikes and birding were stupendous.  In nine days I saw 273 species of birds.  (If you want to get an idea of the phenomenal biodiversity of this tiny country, you should know that 37 of the species I saw were different kinds of tanager, and 43 were hummingbirds.  For comparison purposes, here in upstate New York, we have two tanagers -- one of them quite rare -- and only one kind of hummingbird.)

Of course, the birds aren't the whole reason I love Ecuador.  The scenery is amazing, largely due to the steep-sided ridges and rushing rivers of the Andes.  The weather (where I was, at least) was refreshingly mild -- 80 F during the day, down to maybe 55 F at night.

Rio Mindo [all photographs, unless otherwise marked, were taken by me]

Séptimo Paraiso sits at 0 degrees, 0 minutes, 2 seconds south latitude.  That means the front door was, give or take, 200 feet from the Equator.  We used a GPS on one of our outings to find the exact spot -- within appropriate error bars, of course -- and I took a picture of our entire group straddling it.

The four people on the left are in the Northern Hemisphere, the four on the right in the Southern Hemisphere.

Besides the avifauna, the plant life is fantastic as well.  (And the two are intimately connected; the flora are usually specialized to be pollinated by one particular bird, butterfly, moth, or bat, so high diversity in fauna usually implies high diversity in flora.)  I consider myself a fairly competent field botanist, but I was seldom able to identify plants beyond family, and sometimes not even that.  That, of course, didn't stop me from appreciating them.

"Something in the amaryllis family" is the best I could do with this one.  But it sure is pretty, isn't it?

We did have more than a few truly stunning birds, of course.  Three of them that stand out in my mind are the rare Scarlet-bellied Dacnis, which our guide said we were really amazingly lucky to see:

[image courtesy of the Wikimedia Commons]

The Torrent Duck, which is somehow able to swim upstream in rivers that would easily knock a grown man off his feet:

[image courtesy of the Wikimedia Commons]

And a Crimson-mantled Woodpecker that positively modeled for the camera:

[image courtesy of the Wikimedia Commons]

One of the difficulties of birding as a hobby, however, is that it does not cater to late risers.  I consider myself something of a lark, but after six days of getting up at four in the morning, it was beginning to wear on me a little:

Me in the lounge at Séptimo Paraiso, waiting for some kind soul to bring me a glass of wine and rub my aching feet

The altitude was also a bit tricky.  On day trips into the highlands, all of us became breathless after even brief walks uphill.  The highest we went was 14,400 feet, at Papallacta Pass, but it was foggy and spitting rain (and windy and about 35 F), so I didn't get any pictures.  I did get a few nice shots of Yanacocha, at 13,200 feet:

I'm hoping that all of this hiking around up in the mountains will translate to better endurance for running here at home.  We'll see how that goes.

Anyhow, all in all it was a fantastic trip.  To end this, here are a few things I learned about Ecuador on this trip:
  • The Ecuadorian people are, by and large, some of the nicest, most generous people on Earth.  Despite my toddler-level Spanish (more on that in a moment), I was greeted everywhere by smiles and waves. 
  • That said, if you put your typical Ecuadorian behind the wheel of a car, watch out.  Passing zones, lanes, speed limits, and even stop signs are considered gentle suggestions at best.  Horns are used to communicate a variety of things, such as, "Hi," "Get the hell out of my way," and "My car has a horn."  The last full day of birding, I was with a guide named Jorge, who is a friendly young man who laughs a lot and has an encyclopedic knowledge of South American birds, and who turns into a complete lunatic when he turns the key in the ignition of his truck.  (He crossed himself every time he got into the driver's seat.  I'm not sure if I was supposed to consider this a good sign or a bad sign.)  He was the one who drove us up to the aforementioned Papallacta Pass.  He gave me a big grin as he turned off the highway onto something that barely qualified as a road.  I can say honestly that of the ten scariest things that have happened to me in my life, seven of them happened in the next half-hour.  We drove steadily uphill on narrow dirt roads with potholes the size of lunar craters, large stretches of which had a rock wall on one side and a hundred-foot drop (sans guard rails, of course) on the other.  I think I left permanent finger dents in the door handle of Jorge's truck.
  • If you are going to travel in a country with 250 different species of hummingbirds, don't wear a red shirt.  Hummingbirds consider humans in red shirts to be enormous flowers.  You will spend the entire day dodging small, brightly-colored, feathery projectiles, and trying not to scream like a little girl.
  • Bring enough cash along.  Neither my credit card nor my bank access card worked in the Ecuadorian ATM machines, for reasons I still have yet to figure out.  (I had called and notified my bank about my trip prior to leaving, so it wasn't that they thought my card(s) had been hacked and put a stop on them.)  This put me in the uncomfortable position of having to purchase things only at places that accepted credit cards, which was about 5% of the places we went.
  • The food is amazing.  They have fresh fruits whose names I could barely pronounce, but which are beyond delicious.  I also had ceviche that has my mouth watering just remembering it.
  • My one big regret about this trip is that I didn't put some time into learning more Spanish.  I don't ever want to be That Guy -- the American who goes abroad and expects everyone to speak English and do things the way they're done back home.  The Ecuadorians were remarkably gracious about my pathetic mangling of their language, however; my last day in Quito, I got a grinning thumbs-up from a waiter after ordering a surf & turf, a glass of red wine, and a bottle of mineral water at a restaurant, all in Spanish.  I'm sure he was on some level humoring me, but still, it was nice.  So if you go to another country, spend the six months before you go learning some of the language.  It goes a long way.
Anyhow, there you are -- a brief travelogue of a wonderful country.  I know I'll be back.  You can't do justice to a place like this in just one or two short visits.

I'm thinking a few years would do the trick.