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.

Wednesday, October 17, 2018

Reunion recap

Robert Burns famously said:
O, would some power the giftie gi'e us
To see ourselves as others see us.
It would frae many a blunder free us,
An' foolish notion.
I got a lesson in that general principle this past weekend, when I went to my 40th high school reunion.  Which was a little surreal from another aspect, which is that I can't really believe that much time has passed.  I don't feel like I'm a week or so shy of 58 years old, but I had confirmed for me several times at the party that yes, actually we are that old.

Maybe the reason I don't feel old is because my personality, and especially my sense of humor, kind of plateaued some time around tenth grade.  I mean, I still laugh at fart jokes.  I suppose that's why I ended up teaching adolescents, I'm right on their emotional level.

But there was another eye-opening thing about the reunion, which was how many people remembered me with apparent fondness.  I didn't think I was disliked in school so much as I felt invisible, kind of a nonentity.  Because of my shyness and anxiety my social life was zilch, and I figured most of my classmates had their attention focused on the popular kids -- the confident ones, the star athletes, the party animals, the class clowns.

Me, I read a lot, ran a lot, listened to music, and tried to figure out how to do the bare minimum homework it took to get by in classes I didn't like.  Other than that, I pretty much just tried to keep my head down and fly under the radar.  I did have a bit of a reputation for being a smartass (something that got me in trouble more than once), but overall, I felt like someone no one much would have a reason to notice.

I was bowled over by the warmth with which I was greeted on Saturday night.  I received dozens of hugs and handshakes, and was told over and over how well people remembered me.  I thought that some of it might be Facebook -- since I post links to my novels and to Skeptophilia there, I knew that the dozen or so of my former classmates who are Facebook friends would know a bit about me.

But it's more than that, because I received the same kind of welcome from people who aren't connected to me on social media, and most of whom I literally have not seen since we graduated in June of 1978.  I left that evening feeling a mixture of elation and sadness -- elation because I was evidently much better liked than I ever dreamed, and sad because I hadn't realized it at the time, and had spent the intervening years thinking of myself as having been the amiable, bookish nobody, the kid who everyone looked past, who never got into the yearbook, whom no one really knew.

What this all points up is how completely inaccurate our own self-assessments are.  I wish I'd known sooner.  I might have been less afraid, less worried about what others thought, less concerned that everyone else seemed more popular than me.  I might have had the courage to join clubs, go to dances, ask out the cute girl I had a life-threatening crush on.  To put it succinctly, I might have had a hell of a lot more fun.

Me having fun, of all things

But as my grandma always said, if wishes were horses, then beggars would ride.  You can't change the past; all you can do is recognize it for what it is, realize you were doing the best you could with what you knew then.  Forgive yourself for what you didn't know, what you misunderstood, for your missteps and fumbles and awkward moments.  We've all had them, and they apparently matter far, far less than we usually think at the time.

So the party was great, and being that this is southern Louisiana, there was enough food to feed the French army, a well-stocked bar, and music and dancing and socializing until the wee hours.  I arrived home Monday night, exhausted and still feeling a little disembodied.  And the oddest thing of all is that I -- as neurotic and anxious as I am -- fell asleep with the thought, "Hey, they said there'll be a 45th reunion in five years.  I'm already looking forward to it."

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

This week's Skeptophilia book recommendation is something everyone should read.  Jonathan Haidt is an ethicist who has been studying the connections between morality and politics for twenty-five years, and whose contribution to our understanding of our own motives is second to none.  In The Righteous Mind: Why Good People are Divided by Politics, he looks at what motivates liberals and conservatives -- and how good, moral people can look at the same issues and come to opposite conclusions.

His extraordinarily deft touch for asking us to reconsider our own ethical foundations, without either being overtly partisan or accepting truly immoral stances and behaviors, is a needed breath of fresh air in these fractious times.  He is somehow able to walk that line of evaluating our own behavior clearly and dispassionately, and holding a mirror up to some of our most deep-seated drives.

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




Tuesday, October 16, 2018

Apocalypse not

Can I explain something, for what I devoutly hope is the last time?

The Yellowstone Supervolcano is not about to erupt.

This claim has been going around for some time, in various guises.  Once it was because a tourist saw some bison acting oddly and from that jumped to "all the wildlife are leaving the park" and from there to "so it's about to blow sky-high."

Well, this was four years ago, and if the Supervolcano had erupted, I think we would have noticed.  So it's a big "nope" on that one.  Bison may be cool animals, but as geologists, they suck.

Then it got picked up by the conspiracy theorists, who conjectured that NASA or DARPA or FEMA or some other evil government acronym had found out that eruption was imminent, and was conspiring to cover it up so as not to cause mass panic, except some people with websites who really ought to be sedated found out, and were letting us know so we could get the hell out.  All of which was well-meant, I suppose, but it became a moot point when the eruption once again failed to materialize.

[Image licensed under the Creative Commons Clément Bardot, Grand Prismatic Spring, CC BY-SA 3.0]

The latest iteration, which I have now seen posted as a serious claim at least a half-dozen times on social media, is that (1) Yellowstone is going to erupt, and (2) there's a secret NASA program to drill into it and bleed off the heat so they can prevent it.  At least NASA gets cast as one of the good guys, here; I'm sure the scientists are sick unto death of being portrayed as rubbing their hands together and cackling while plotting to destroy the world.

This comes from the apocalyptic site Breaking Israel News, and includes stuff like the following:
After initially denying that the unusual amount of seismic activity witnessed last year was an indication of imminent danger, NASA scientists are proposing a solution that could save half the world while admitting that their intervention could initiate the explosion it was intended to prevent. 
Last year, increased seismic activity at Yellowstone generated a great deal of concern.  More than 2,300 tremors were recorded between June and September, one of the largest earthquake swarms ever recorded at the site.  Though geologists assured the public that the activity was normal for the site, another series of quakes and unusual eruptions beginning in February, increased fears that the supervolcano was waking up.  An investigation revealed magma filling up in the underneath chamber of the supervolcano.  In July, a massive, 100 ft.-wide fissure opened up in the Grand Teton National Park near Yellowstone, further increasing fears. 
To look only at the most egregious errors in that passage:
  1. The solution to "save half the world" was proposed in a theoretical sense only by Brian Wilcox of NASA/JPL.  It involves pumping water down a drill shaft into the rock surrounding the volcano, then pumping the resulting steam back to the surface (and using it for electricity production).  This would "bleed off" the heat from the volcano, which would freeze and no longer be a threat.  The problem with this is twofold: first, it would cost 3.46 billion dollars, and second, the bleed-off of heat would be so slow (and the volcano is so large) that it would take hundreds, possibly thousands, of years to cool it enough to stop an eruption.  Which Wilcox says, right there in his paper.
  2. The 2,300 tremors between June and September are completely ordinary.  The Yellowstone area gets shaken multiple times on a daily basis, and most of them are too small to feel.  It's a seismically active area.  Recall what "seismically active" means.
  3. The fissure in the Grand Tetons had zilch to do with the Supervolcano.  It happened because mountains have landslides sometimes.  Saying it indicates an imminent volcanic eruption is no more sensible than connecting eruptions to bisons acting weird.
So you don't need to cancel your vacation plans to Wyoming yet.  Scientists assure us that there will be plenty of warning if the volcano shows signs of an eruption.

Anyhow, the woo-woos need to give this one a rest, because we're all safe, from that threat, at least.  You'd think the more imminent threat would be climate change and the fact that Trump and his followers seem to be trying to create Nazi Germany 2.0.  Compared to that, I'll accept the risk of Yellowstone erupting without a second thought.

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

This week's Skeptophilia book recommendation is something everyone should read.  Jonathan Haidt is an ethicist who has been studying the connections between morality and politics for twenty-five years, and whose contribution to our understanding of our own motives is second to none.  In The Righteous Mind: Why Good People are Divided by Politics, he looks at what motivates liberals and conservatives -- and how good, moral people can look at the same issues and come to opposite conclusions.

His extraordinarily deft touch for asking us to reconsider our own ethical foundations, without either being overtly partisan or accepting truly immoral stances and behaviors, is a needed breath of fresh air in these fractious times.  He is somehow able to walk that line of evaluating our own behavior clearly and dispassionately, and holding a mirror up to some of our most deep-seated drives.

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




Monday, October 15, 2018

The right to bigotry

New from the "What The Hell Did You Think Was Going To Happen?" department, we have: states that have passed "Religious Freedom Restoration Acts" -- which allow doctors and other professionals to refuse services to LGBTQ people on the basis of "freedom of religion" -- have markedly poorer health outcomes for sexual minorities than ones that have not.

An analysis done in Indiana by medical researchers at the Pittsburgh Graduate School of Public Health analyzed the number of "unhealthy days" -- days on which the individual reported poor physical or mental health -- before and after the passage of an RFRA law, as a function of whether the subjects were heterosexual or LGBTQ.  The results couldn't be clearer.  Before and after the passage of the RFRA, the number of unhealthy days climbed for LGBTQ individuals, but remained constant for heterosexuals; and the same statistic in states that did not have RFRAs showed no change for either demographic in the same time period.

"Although we can’t say for certain what caused this significant increase in unhealthy days for sexual minority people in Indiana, the change coincided with intense public debate over enactment of the RFRA law," said lead author John R. Blosnich, assistant professor at the Pitt School of Medicine.  "If some other general, statewide factor was at work, we would expect to see the same increase in unhealthy days for heterosexual people in Indiana, and we didn’t see that."

"The Indiana case suggests that the character of the RFRA law might be an important factor in its broader impacts on public health,” said study co-author Erin Cassese of the University of Delaware.  "Some RFRAs are stronger than others, and Indiana’s RFRA law ‘has teeth’ in the sense that it can be used in private litigation, including cases where businesses wish to deny services to sexual minorities. It also permits courts to grant compensatory damages against whomever brings the suit – making a court challenge to a service denial a much riskier proposition...  This project adds to a growing body of research demonstrating that experiences of discrimination are associated with poor health outcomes in a range of minority populations.  While debate over RFRA laws doesn’t typically engage with questions of public health, this project suggests negative health outcomes might be a consequence of this type of policy, and thus warrant some consideration by policymakers."

[Image licensed under the Creative Commons Benson Kua, Rainbow flag breeze, CC BY-SA 2.0]

I find it absolutely infuriating when mainstream Christians portray themselves as a persecuted group whose religious views have to be enshrined in law even if those views allow them to discriminate against others.  And here I thought one of the main teachings of Jesus was "love thy neighbor as thyself."  I guess what Jesus meant to say was "love thy neighbor as thyself, unless thy neighbor is the wrong color, wrong religion, or likes to do things with his or her naughty bits that make you feel squinky."

Oh, and then there's the part about "First, cast out the beam from thine own eye; and then shalt thou see clearly to remove the mote from thy brother's eye."  Also kind of inconvenient, that.

And lest you think this is only a problem in the United States, Australia's Prime Minister Scott Morrison has been staunchly defending a law currently on the books in every state but Queensland and Tasmania that allows schools to expel kids if they come out as LGBTQ.

"That is the existing law," Morrison said.  "We are not proposing to change that law to take away the existing arrangement that exists."

Which is about as articulate as Donald Trump's comment that Hurricane Florence "was one of the wettest we've ever had from the standpoint of water." 

As an aside, where the hell are we finding these politicians, anyhow?  Back in the day, it seemed like at least they could put together a grammatical sentence, even if what that sentence contained wasn't necessarily something I agreed with.

Oh, but I'd forgotten about Dan "Mr. Potatoe" Quayle, who once said that we should be optimistic, because "things are more like they are now than they ever have been."

Never mind.

What I honestly don't get about this is how often discrimination rests on religious views, when you hear "mercy" and "charity" and "love" as being some of the cardinal virtues in pretty much any religion you look into.  It's kind of appalling when the people who sing "What A Friend We Have in Jesus" and "The King of Love My Shepherd Is" in church on Sunday are the same ones who are telling gay people to roast in hell the other six days of the week.

So that's today's exercise in anger induction.  You'd think we'd have gotten past all this bigotry as a species by now.  I guess we've come a way -- when I was a kid, hardly anyone would even admit to being LGBTQ, much less make a stink about it if they were discriminated against.  But what this makes clear is that the bigots aren't ready to give up their narrow-mindedness without a fight... and that we still have a long way to go.

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

This week's Skeptophilia book recommendation is something everyone should read.  Jonathan Haidt is an ethicist who has been studying the connections between morality and politics for twenty-five years, and whose contribution to our understanding of our own motives is second to none.  In The Righteous Mind: Why Good People are Divided by Politics, he looks at what motivates liberals and conservatives -- and how good, moral people can look at the same issues and come to opposite conclusions.

His extraordinarily deft touch for asking us to reconsider our own ethical foundations, without either being overtly partisan or accepting truly immoral stances and behaviors, is a needed breath of fresh air in these fractious times.  He is somehow able to walk that line of evaluating our own behavior clearly and dispassionately, and holding a mirror up to some of our most deep-seated drives.

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




Saturday, October 13, 2018

The danger of myside bias

Fighting bad thinking is an uphill battle some days.

I'm very much including myself in this assessment.  I have biases and preconceived notions and places where I stumble just like everyone else.  Fixing these errors would be nice -- can you imagine the world if all of us were able to think clearly and make our decisions based on evidence?

A pipe dream, I know, and all the more so after I read a new paper in Journal of Cognitive Psychology called "My Point is Valid, Yours is Not: Myside Bias in Reasoning About Abortion," by Vladimíra Čavojová, Jakub Šrol, and Magdalena Adamus of the Institute of Experimental Psychology at the Slovak Academy of Sciences in Bratislava, Slovakia.

In an elegant piece of research, Čavojová et al. gave a series of logic puzzles to volunteers who had been asked in a prior questionnaire what their attitudes toward abortion were, and whether they had prior experience with formal logic.  They were then asked to determine whether various syllogisms were valid or not.  Some were neutral:
All mastiffs are dogs.
Some mastiffs are black.
Therefore, some of the things that are black are dogs. 
(Valid)
Some had to do with abortion:
All fetuses are human beings
Some human beings should be protected.
Therefore, some of those who should be protected are fetuses. 
(Invalid)
To solve each of the syllogisms, it should be irrelevant what your opinion on abortion is; the rules are that if the premises (the first two statements) are true, and the argument is valid, then the conclusion is true.  The participants were told from the outset to treat the premises as true regardless of their views.

Gregor Reisch, Logic Presents Its Main Themes (ca. 1505) [Image is in the Public Domain]

What is fascinating is that both people who were pro-choice and pro-life had a hard time rejecting invalid syllogisms that gave them a conclusion they agreed with, and accepting valid syllogisms that gave them a conclusion they disagreed with.  This pattern held equally with people who had training in formal logic and those who did not.  It's as if once we're considering a strongly-held opinion, our ability to use logic goes out the window.

The authors write:
The study explores whether people are more inclined to accept a conclusion that confirms their prior beliefs and reject one they personally object to even when both follow the same logic.  Most of the prior research in this area has relied on the informal reasoning paradigm; in this study, however, we applied a formal reasoning paradigm to distinguish between cognitive and motivational mechanisms leading to myside bias in reasoning on value-laden topics (in this case abortions).  Slovak and Polish (N = 387) participants indicated their attitudes toward abortion and then evaluated logical syllogisms with neutral, pro-choice, or pro-life content.  We analysed whether participants’ prior attitudes influenced their ability to solve these logically identical reasoning tasks and found that prior attitudes were the strongest predictor of myside bias in evaluating both valid and invalid syllogisms, even after controlling for logical validity (the ability to solve neutral syllogisms) and previous experience of logic.

Which reinforces my not very optimistic notion that however good our brains are, humans remain primarily emotional creatures.  When something elicits a strong emotional response, we're perfectly willing to abandon reasoning -- and sometimes aren't even aware we're doing it.

All of which bodes nothing good from any attempt to correct these errors.  As we've discussed before, even trying to combat bad thinking initiates the backfire effect, wherein people tend to double down on beliefs if they're challenged, and even if they're given concrete evidence that they're wrong.

Makes you wonder what I think I'm accomplishing by writing this blog, doesn't it?

It's not futile, however; however this emotional bent is impossible to eradicate, you can adjust for it as long as you know it's there.  So I suppose this research should give us hope that even if we can't think with perfect clarity all the time, we can at least move in the right direction.
 **************************************

This week's Skeptophilia book recommendation is from the brilliant essayist and polymath John McPhee, frequent contributor to the New Yorker.  I swear, he can make anything interesting; he did a book on citrus growers in Florida that's absolutely fascinating.  But even by his standards, his book The Control of Nature is fantastic.  He looks at times that humans have attempted to hold back the forces of nature -- the attempts to keep the Mississippi River from changing its path to what is now the Atchafalaya River, efforts in California to stop wildfires and mudslides, and a crazy -- and ultimately successful -- plan to save a harbor in Iceland from a volcanic eruption using ice-cold seawater to freeze the lava.

Anyone who has interest in the natural world should read this book -- but it's not just about the events themselves, it's about the people who participated in them.  McPhee is phenomenal at presenting the human side of his investigations, and their stories will stick with you a long time after you close the last page.

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




Friday, October 12, 2018

Last week's episode

One of the enduring mysteries of neuropsychology is how memory is encoded.

As I tell my introductory neuroscience students, think of the simplest thing you can.  Your middle name.  What 2 + 3 is.  What three colors are in the American flag.  Now, where was that information before I asked you?  And how did you retrieve it?  And where does it go when you no longer are thinking about it?

We have some ideas about where memory is stored, given recent studies with fMRI machines.  Scientists can see what parts of the brain are active when you recall different types of information, and we now know that different types and durations of memory are stored in different places.  But the other two pieces -- how memory is stored and how it is retrieved -- we honestly have no idea about.

We got another piece of the puzzle last week with some new research by Gabriel Radvansky of Notre Dame University and Aya Ben-Yakov and Rik Henson of the University of Cambridge.  What they were interested in is episodic memory, our brain's ability to slice what it recalls up into discrete chunks, rather like the chapters in a story.  They looked at what happens at the boundaries -- what we perceive as the end of one episode and the beginning of another.

"So much research is done with these little bits and pieces — words, pictures, things like that,” Radvansky says.  "But those dry tidbits aren’t what the human brain usually handles.  The mind is built to deal with complex events... Research like this helps us identify ‘What is an event, from the point of view of the brain?’"

[Image is in the Public Domain]

They had participants watching one of two movies, Forrest Gump and Bang! You're Dead!, and using fMRI watched what happened when obvious boundaries were reached -- a scene fade-to-black, a jump to a new location or new characters, and so on.  But what is interesting is that the brain perceives other moments as boundaries as well.  At any of those moments, activity in the hippocampus increases dramatically, suggesting that this is the structure that helps us divide what we remember into distinct episodes.

Laura Sanders, writing about the research in Science News, explains further.  "These transitions didn’t always involve jumps to new places or times in the story. One such boundary came near the beginning of Forrest Gump as Forrest sits quietly on a bench.  Suddenly, he blurts out his famous greeting: 'Hello. My name’s Forrest. Forrest Gump.'  The hippocampus may have helped slice that continuous bench scene into two events: before talking and after talking.  Such divisions may help package information into discrete pieces that can then be stored as memories."

In real life, of course, there are seldom such definitive boundaries.  A few artificial ones exist -- when it's quitting time at work, when the bell rings in a school, when your alarm clock goes off.  Most of the rest of life proceeds along fairly smoothly, but what this research suggests is that you don't store or recall memories that way.

Which is another nail in the coffin of the idea of our memories being accurate.  Research has been chipping away for years at the notion that we have any kind of a decent record of the past, but the results have shown the reality is very much the opposite.  Here, we find that our brains are slicing up what we've experienced into chunks with more-or-less arbitrary boundaries, leaving us with the sense of life being a series of disjointed episodes rather than any kind of continuous record of events.  

I'm also interested in what we remember of the boundaries themselves.  In movies, when a scene shifts, it usually doesn't occur to us to ask what's happening during the gap, and we don't form any kind of strong memory of the jump itself (at least, I don't).  What the Radvansky et al. research suggests is that when discrete edges don't exist, we superimpose them on what we remember.  So do we have the same kind of foggy sense of recall during these brain-created boundaries as we do when we're watching movies?

In any case, this is an interesting new piece of the puzzle of our memory, and how we create a picture of past events.  Now, I wish they'd get to work on two of the most intriguing memory-related events -- déjà vu and the "tip of the tongue" phenomenon.  Since we finally seem to be closing in on how we store memories, I have no doubt that scientists will one day be able to account for these, as well.

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

This week's Skeptophilia book recommendation is from the brilliant essayist and polymath John McPhee, frequent contributor to the New Yorker.  I swear, he can make anything interesting; he did a book on citrus growers in Florida that's absolutely fascinating.  But even by his standards, his book The Control of Nature is fantastic.  He looks at times that humans have attempted to hold back the forces of nature -- the attempts to keep the Mississippi River from changing its path to what is now the Atchafalaya River, efforts in California to stop wildfires and mudslides, and a crazy -- and ultimately successful -- plan to save a harbor in Iceland from a volcanic eruption using ice-cold seawater to freeze the lava.

Anyone who has interest in the natural world should read this book -- but it's not just about the events themselves, it's about the people who participated in them.  McPhee is phenomenal at presenting the human side of his investigations, and their stories will stick with you a long time after you close the last page.

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




Thursday, October 11, 2018

Trompe l'oeil

I have a fascination for optical illusions.

Not only are they cool, they often point out some profound information about how we process sensory input.  Take the famous two-and-a-half pronged fork:


The problem here is that we're trying to interpret a two-dimensional drawing as if it were a three-dimensional object, and the two parts of the drawing aren't compatible under that interpretation.  Worse, when you try to force your brain to make sense of it -- following the drawing from the bottom left to the top right, and trying to figure out when the object goes from three prongs to two -- you fail utterly.

Neil deGrasse Tyson used optical illusions as an example of why we should be slow to accept eyewitness testimony.  "We all love optical illusions," he said.  "But that's not what they should call them.  They should call them 'brain failures.'  Because that's what they are.  A clever drawing, and your brain can't handle it."

(If you have some time, check out this cool compendium of optical illusions collected by Michael Bach, which is even more awesome because he took the time to explain why each one happens, at least where an explanation is known.)

It's even more disorienting when an illusion occurs because of two senses conflicting.  Which was the subject of a recent paper out of Caltech, "What You Saw Is What You Will Hear: Two New Illusions With Audiovisual Postdictive Effects," by Noelle R. B. Stiles, Monica Li, Carmel A. Levitan, Yukiyasu Kamitani, and Shinsuke Shimojo.  What they did is an elegant experiment to show two things -- how sound can interfere with visual processing, and how a stimulus can influence our perception of an event, even if the stimulus occurs after the event did!

Sounds like the future affecting the past, doesn't it?  It turns out the answer is both simpler and more humbling; it's another example of a brain failure.

Here's how they did the experiment.

In the first trial, they played a beep three times, 58 milliseconds apart.  The first and third beeps were accompanied by a flash of light.  Most people thought there were three flashes -- a middle one coincident with the second beep.

The second setup was, in a way, opposite to the first.  They showed three flashes of light, on the right, middle, and left of the computer screen.  Only the first and third were accompanied by a beep.  Almost everyone didn't see -- or, more accurately, didn't register -- the middle flash, and thought there were only two lights.

Sorry, I couldn't resist.

"The significance of this study is twofold," said study co-author Shinsuke Shimojo.  "First, it generalizes postdiction as a key process in perceptual processing for both a single sense and multiple senses.  Postdiction may sound mysterious, but it is not—one must consider how long it takes the brain to process earlier visual stimuli, during which time subsequent stimuli from a different sense can affect or modulate the first.  The second significance is that these illusions are among the very rare cases where sound affects vision, not vice versa, indicating dynamic aspects of neural processing that occur across space and time.  These new illusions will enable researchers to identify optimal parameters for multisensory integration, which is necessary for both the design of ideal sensory aids and optimal training for low-vision individuals."

All cool stuff, and more information about how the mysterious organ in our skull works.  Of course, this makes me wonder what we imagine we see because our brain anticipates that it will there, or perhaps miss because it anticipates that something out of of place shouldn't be there.  To end with another quote from Tyson: "Our brains are unreliable as signal-processing devices.  We're confident about what we see, hear, and remember, when in fact we should not be."

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

This week's Skeptophilia book recommendation is from the brilliant essayist and polymath John McPhee, frequent contributor to the New Yorker.  I swear, he can make anything interesting; he did a book on citrus growers in Florida that's absolutely fascinating.  But even by his standards, his book The Control of Nature is fantastic.  He looks at times that humans have attempted to hold back the forces of nature -- the attempts to keep the Mississippi River from changing its path to what is now the Atchafalaya River, efforts in California to stop wildfires and mudslides, and a crazy -- and ultimately successful -- plan to save a harbor in Iceland from a volcanic eruption using ice-cold seawater to freeze the lava.

Anyone who has interest in the natural world should read this book -- but it's not just about the events themselves, it's about the people who participated in them.  McPhee is phenomenal at presenting the human side of his investigations, and their stories will stick with you a long time after you close the last page.

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




Wednesday, October 10, 2018

Neanderthal family reunion

Last year, I did a 23 and Me DNA test.

Besides the not-particularly-earthshattering conclusion that I'm mostly French, Scottish, German, and Dutch, I was amused to find that the test showed I have 284 Neanderthal markers.  This puts me in the 60th percentile as compared to the population overall, which probably explains why I like my steaks rare and run around half naked when the weather is warm.

What's fascinating is that some research released last week, a paper in Cell by David Enard of the University of Arizona and Dmitri A. Petrov of Stanford University called, "Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans," has shown that some of these genes didn't get passed along the usual way, but by a process called transduction -- when viruses transmitted from one host to another carry novel genes with them.

The authors write:
After their divergence 500,000 to 800,000 years ago, modern humans and Neanderthals interbred at least twice: the first time ∼100,000 years ago and the second ∼50,000 years ago.  The first interbreeding episode left introgressed segments (IS) of modern human ancestry within Neanderthal genomes, as revealed by the analysis of ancient DNA from a single Altai Neanderthal individual sequenced by Prüfer et al. (2014).  This first interbreeding event appears not to have left any detectable segments of Neanderthal ancestry in extant modern human genomes.  In contrast, the second interbreeding episode left detectable IS of Neanderthal ancestry within the genomes of non-African modern humans. 
Recent advances in the detection of introgression have led to the discovery that the majority of genomic segments initially introgressed from Neanderthals to modern humans were rapidly removed by purifying selection.  Harris and Nielsen (2016) estimated that the proportion of Neanderthal ancestry in modern human genomes rapidly fell from ∼10% to the current levels of 2%–3% in modern Asians and Europeans.
This history of interbreeding and purifying selection against IS raises several important questions. First, among the introgressed sequences that were ultimately retained, can we detect which sequences persisted by chance because they were not as deleterious or not deleterious at all to the recipient species, and which persisted not despite natural selection but because of it—that is, which IS increased in frequency due to positive selection?  If any of the introgressed sequences were indeed driven into the recipient species due to positive selection, can we determine which pressures in the environment drove this adaptation? 
Recently we found that proteins that interact with viruses (virus-interacting proteins [VIPs]) evolve under both stronger purifying selection and tend to adapt at much higher rates compared to similar proteins that do not interact with viruses.  We estimated that interactions with viruses accounted for ∼30% of protein adaptation in the human lineage.   Because viruses appear to have driven so much adaptation in the human lineage, and because it is plausible that when Neanderthals and modern humans interbred they also exchanged viruses either directly by contact or via their shared environment, we hypothesized that some introgressed sequences might have provided a measure of protection against the exchanged viruses and were driven into the recipient species by positive directional selection.  Consistent with this model, several cases of likely adaptive introgression from Neanderthals to modern humans involve immune genes that are specialized to deal with pathogens including viruses.
Which is amazingly cool.  Viruses are parasites, and as such usually wreak havoc with our systems, but here we have viruses acting as carriers not only for genes that generate diversity, but that protect our cells from the damage viruses can cause.

Great-great grandpa Ugg [Image licensed under the Creative Commons Stefan Scheer, Neandertaler reconst, CC BY-SA 3.0]

"It's not a stretch to imagine that when modern humans met up with Neanderthals, they infected each other with pathogens that came from their respective environments," lead author David Enard said.  "By interbreeding with each other, they also passed along genetic adaptations to cope with some of those pathogens."

"Many Neanderthal sequences have been lost in modern humans, but some stayed and appear to have quickly increased to high frequencies at the time of contact, suggestive of their selective benefits at that time," Petrov said.  "Our research aims to understand why that was the case.  We believe that resistance to specific RNA viruses provided by these Neanderthal sequences was likely a big part of the reason for their selective benefits."

"One of the things that population geneticists have wondered about is why we have maintained these stretches of Neanderthal DNA in our own genomes," Enard added.  "This study suggests that one of the roles of those genes was to provide us with some protection against pathogens as we moved into new environments."

So having Neanderthal DNA isn't something to be ashamed of.  All of this highlights how incredibly cool the evolutionary model is, and the depth of its explanatory power.  Now, y'all'll have to excuse me.  I'm going to go get a snack.  I wonder if I have any roast mammoth left in the fridge?  Probably not.  I guess grilled cheese will have to do.

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This week's Skeptophilia book recommendation is from the brilliant essayist and polymath John McPhee, frequent contributor to the New Yorker.  I swear, he can make anything interesting; he did a book on citrus growers in Florida that's absolutely fascinating.  But even by his standards, his book The Control of Nature is fantastic.  He looks at times that humans have attempted to hold back the forces of nature -- the attempts to keep the Mississippi River from changing its path to what is now the Atchafalaya River, efforts in California to stop wildfires and mudslides, and a crazy -- and ultimately successful -- plan to save a harbor in Iceland from a volcanic eruption using ice-cold seawater to freeze the lava.

Anyone who has interest in the natural world should read this book -- but it's not just about the events themselves, it's about the people who participated in them.  McPhee is phenomenal at presenting the human side of his investigations, and their stories will stick with you a long time after you close the last page.

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