Doubt, experiment, and reproducibility

Yesterday I got a response on a post I did a little over a year ago about research that suggested fundamental differences in firing patterns in the brains of liberals and conservatives.   The study, headed by Darren Schreiber of the University of Exeter, used fMRI technology to look at functionality in people of different political leanings, and found that liberals have greater responsiveness in parts of the brain associated with risk-seeking, and conservatives in areas connected with anxiety and risk aversion.

The response, however, was as pointed as it was short.  It said, "I'm surprised you weren't more skeptical of this study," and provided a link to a criticism of Schreiber's work by Dan Kahan over at the Cultural Cognition Project.  Kahan is highly doubtful of the partisan-brain study, and says so in no uncertain terms:

Before 2009, many fMRI researchers engaged in analyses equivalent to what Vul [a researcher who is critical of the method Schreiber used] describes.  That is, they searched around within unconstrained regions of the brain for correlations with their outcome measures, formed tight “fitting” regressions to the observations, and then sold the results as proof of the mind-blowingly high “predictive” power of their models—without ever testing the models to see if they could in fact predict anything. 

Schreiber et al. did this, too.  As explained, they selected observations of activating “voxels” in the amygdala of Republican subjects precisely because those voxels—as opposed to others that Schreiber et al. then ignored in “further analysis”—were “activating” in the manner that they were searching for in a large expanse of the brain.  They then reported the resulting high correlation between these observed voxel activations and Republican party self-identification as a test for “predicting” subjects’ party affiliations—one that “significantly out-performs the longstanding parental model, correctly predicting 82.9% of the observed choices of party.” 

This is bogus.  Unless one “use[s] an independent dataset” to validate the predictive power of “the selected . . .voxels” detected in this way, Kriegeskorte et al. explain in their Nature Neuroscience paper, no valid inferences can be drawn.  None.

So it appears that  Schreiber et al. were guilty of what James Burke calls "designing an experiment to find the kind of data you reckon you're going to find."  It would be hard to recognize that from the original paper itself without being a neuroscientist, of course.  I fell for Schreiber's research largely because I'm a generalist, making me unqualified to spot errors in highly specific, technical fields.

Interestingly, this comment came hard on the heels of a paper by Monya Baker that appeared last week in Nature called "1,500 Scientists Lift the Lid on Reproducibility."  Baker writes:

More than 70% of researchers have tried and failed to reproduce another scientist's experiments, and more than half have failed to reproduce their own experiments.  Those are some of the telling figures that emerged from Nature's survey of 1,576 researchers who took a brief online questionnaire on reproducibility in research... 

Data on how much of the scientific literature is reproducible are rare and generally bleak.  The best-known analyses, from psychology and cancer biology, found rates of around 40% and 10%, respectively.  Our survey respondents were more optimistic: 73% said that they think that at least half of the papers in their field can be trusted, with physicists and chemists generally showing the most confidence. 

The results capture a confusing snapshot of attitudes around these issues, says Arturo Casadevall, a microbiologist at the Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland.  “At the current time there is no consensus on what reproducibility is or should be.”

The causes were many and varied.  According to the respondents, the failure to reproduce results derived from issues such as low statistical power to unavailability of method to poor experimental design; worse still, all too often no one bothers even to try to reproduce results because of the pressure to publish one's own work, not check someone else's.  As as result, slipshod research -- and sometimes, outright fraud -- gets into print.

How dire is this?  Two heartening responses described in Baker's paper include the fact that just about all of the scientists polled want more stringent guidelines for reproducibility, and also that work of high visibility is far more likely to be checked and verified prior to publication.  (Sorry, climate change deniers -- you can't use this paper to support your views.)

[image courtesy of the Wikimedia Commons]

What it means, of course, is that science bloggers who aren't scientists themselves -- including, obviously, myself -- have to be careful about cross-checking and verifying what they write, lest they end up spreading around bogus information.  I'm still not completely convinced that Schreiber et al. were as careless as Kahan claims; at the moment, all we have is Kahan's criticism that they were guilty of the multitude of failings described in his article.  But it does reinforce our need to think critically and question what we read -- even if it's in a scientific journal.

And despite all of this, science is still by far our best tool for understanding.  It's not free from error, nor from the completely human failings of duplicity and carelessness.  But compared to other ways of moving toward the truth, it's pretty much the only game there is.

Drought of the imagination

The observation that politicians tend to lie is so obvious as to hardly need comment.  As far back as 2,400 years ago, Plato observed, "Those who are too smart and honest to engage in politics are punished by being governed by those who are stupid and dishonest."

It's disheartening how little has changed in two millennia.  We are still electing liars and crooks, which means that we ourselves are falling for the lies.  After all, we keep voting for them despite the fact that just about everyone knows full well that most politicians will say and do damn near anything to get elected.

Which brings me once again to Donald Trump.

I had told myself I wouldn't do another post on Trump, that I'd said what I had to say.  Honestly, I hate talking politics anyhow.  I'm pretty non-partisan in the sense that I don't vote any party line, and that I can support a wide range of candidates as long as they approach holding office from the position of respecting facts, being open-minded, and telling the truth.

Unfortunately, this narrows the field pretty severely right from the get-go.

But even from my admittedly cynical standpoint, Donald Trump raises dishonest bullshit to unprecedented heights.  He's not the stupidest person in politics; that dubious honor would go either to Democrat Sheila Jackson Lee of Texas (who asked if the Mars Pathfinder mission had seen the flag that Neil Armstrong had planted yet) or Republican Louie Gohmert, also of Texas (who said that cutting food stamps was a benefit to poor people because it would keep them from becoming obese).

Trump, however, may well be the biggest liar of the bunch.  And I don't think he lies because he's shooting from the hip; I think he lies with complete forethought and understanding of what he's saying and why.  He is a brilliant strategist -- and, I believe, entirely amoral.

Let's consider his statements last week to a rally in Fresno, California.  It's hard to give a political speech in California in the last couple of years without at least addressing the catastrophic drought they've been facing.  It's first and foremost on many people's minds, given the threat to drinking water and agriculture as the rivers run dry and the aquifers disappear.  And what did Trump say?  I'll give you the direct quote, because you won't believe me otherwise:

We’re going to solve your water problem. You have a water problem that is so insane. It is so ridiculous where they’re taking the water and shoving it out to sea.  They [the farmers] don’t understand — nobody understands it.  There is no drought. 

If I win, believe me, we’re going to start opening up the water so that you can have your farmers survive.

I beg your pardon?  There is no drought?  All Trump had to do, all along, is wave his hand and say, "The drought does not exist," and it would just acquiesce and move on to trouble another nation, possibly Mexico, assuming it can cross the wall he's planning to build?

And all we have to do, apparently, is to elect Trump, and he will "open up the water."  Environment be damned.  The water will do what Donald commands.  Otherwise, it will be fired.

To a lot of Trump's naysayers, these are just gaffes, slips of the tongue, speaking without thinking things through first.  I think it's more insidious than that.  Trump knows full well what he's doing, what sort of message plays well with the crowds he's attracting.  He's well-loved among people who distrust science, disbelieve that the climate is changing because of human activities, and think that our leader should be able to bully nature into doing whatever he wants. 

As such, he's wildly popular among the pro-fossil fuel contingent, and his talking points reflect that.  A couple of days ago, he promised that if he is elected, he would "cancel the Paris Climate Plan" that has made some motion toward addressing runaway fossil fuel use and anthropogenic carbon dioxide.   The move was no accident; it was calculated to win support (financial and otherwise) from the fossil fuel industry.  Don't believe me?  Consider his statement to a meeting of oil industry representatives in Bismarck, North Dakota three days ago:

Regulations that shut down hundreds of coal-fired power plants and block the construction of new ones — how stupid is that?... We’re going to deal with real environmental challenges, not the phony ones we’ve been hearing about.

Which reminds me of another quote, this one by George Bernard Shaw: "A government with the policy of robbing Peter to pay Paul can be assured of the support of Paul."

So it's no surprise that the petroleum industry loves the guy.  But what gets me most is the fact that Trump can lie outright to the crowds who attend his rallies, and they continue to cheer.  At least the other candidates are subtle about it; Trump, evidently, has the approach of "go big or go home:"

And you know I should say this, I’ve received many, many environmental rewards. You know, really.  Rewards and awards. I  have done really well environmentally and I’m all for it.  You know we want jobs.  We have to bring jobs back.  And if we can bring this part of the world water, that we have, that we have, but it’s true, I’ve gotten so many of the awards.

Do you know what "environmental rewards and awards" he's received?  I did some digging and I found...

... one.  In 2007, a golf course in Bedminster, New Jersey, owned by Trump, received an award for "environmental stewardship through golf course maintenance, construction, education and research."  And that's it.  One golf course, apparently, constitutes "many, many environmental rewards... so many of the awards."

So Trump keeps bullshitting, and the people keep cheering.  More ironic still, many of the same people loudly complain about the dishonesty of the government -- while this man stands in front of them, uttering outright lies, and none of them bat an eye.

The whole thing is profoundly discouraging, not least because I'm not particularly enamored of the other option I'm likely to be offered in November.  I hate being put in a position of voting not to support a good candidate, but in an attempt to prevent a horrible candidate from winning.  That, however, appears to be what I'm going to have to do.  Unless I can simply wave my hand, unleash my Jedi mind tricks, and say, "These are not the candidates you're looking for," and have the whole lot of them go away.

Cats and quakes

I ran across two stories yesterday that fall squarely into the "You People Do Realize You Have Bigger Problems To Worry About, Right?" department.

In the first, we have a senior Saudi cleric who has issued a fatwa on people taking selfies with cats.  Well, not just with cats.  Also with wolves.  But since cat selfies are way more common than wolf selfies (more's the pity), I can see why he specifically mentioned the cats.

The subject came up because of a question asked at a talk that Sheikh Saleh Bin Fawzan Al-Fawzan was giving, in which someone asked about a "new trend of taking pictures with cats which has been spreading among people who want to be like westerners."  Al-Fazwan was aghast.

"What?" he asked.  "What do you mean, pictures with cats?"

Because that's evidently an ambiguous phrase, or something.  Maybe it has subtleties in Arabic I don't know about.

So the questioner clarified, and after he got over his outrage, Al-Fazwan gave his declaration.  "Taking pictures is prohibited," he said.  "The cats don't matter here."

Which is kind of odd, given that he was being filmed at the time.  But rationality has never been these people's strong suit.

"Taking pictures is prohibited if not for a necessity," Al-Fazwan went on to say.  "Not with cats, not with dogs, not with wolves, not with anything."

Wipe that smirk off your face, young lady.  Allah does not approve of you and Mr. Whiskers.

So alrighty, then.  Now that we've got that settled, let's turn to another thing we had a prominent Muslim cleric worrying about, which was: gay sex.

Of course, gay sex seems to be on these people's minds a lot, and also on the minds of their siblings-under-the-skin the Christian evangelicals.  But this time, the cleric in question, Mallam Abass Mahmud of Ghana, has said that the practice is not only prohibited because it's naughty in Allah's sight (although it certainly is that as well), but because it causes...

... earthquakes.

"Allah gets annoyed when males engage in sexual encounter," Mahmud said in an interview, then went on to add, "Such disgusting encounter causes earthquakes."

As an example, he says that this is why Sodom and Gomorrah were destroyed.  Although as I recall from my reading of Genesis chapter 19, it wasn't an earthquake in that case, but having "fire and brimstone rained down upon them... so that the smoke of the country went up as the smoke of a furnace."  But I guess since gays are apparently the most powerful force of nature known, there's no reason why they couldn't also cause a volcanic eruption or something.

On the other hand, if gays having sex is causing the ground to shake, they must really be enjoying themselves.  I don't know whether to feel scared or jealous.

What crosses my mind with all of this is that there are a few more urgent concerns in the Muslim world than worrying about cat selfies and two guys making love.  Human rights, tribalism, poverty, wealth inequity, corruption, terrorism, radical insurgencies, drought.  To name a few.  You have to wonder if focusing their followers on nonsense is simply a way of keeping the hoi polloi from realizing what a horror much of the Middle East has become under the leadership of people like this.

And given the reactions they got -- which, as far as I can tell, was mostly nodding in agreement -- it appears to be working.  So if you go to Saudi Arabia or Ghana, just remember: no kitty selfies or gay sex.  Or, Allah forfend, you and your gay lover having sex then celebrating by taking a photograph of the two of you with your cat.  That'd probably just cause the Earth to explode or fall into the Sun or something.

A win for sanity

Earlier this year, I did a post lamenting the fact that a woman who is apparently insane was running for a position on the Texas State Board of Education, and (at the time of the post) had the support of 50% of the voters polled.

Her name is Mary Lou Bruner, and she gives every evidence of being a few fries short of a Happy Meal.  She claimed that President Obama was addicted to drugs and financed his college tuition by being a male prostitute.  She blamed the JFK assassination on the Bad Guys "not wanting a conservative president."  She thinks the dinosaurs went extinct because there wasn't enough vegetation for them to eat after the biblical Great Flood.  She said that climate change was dreamed up by Karl Marx.  She thinks that Obamacare is going to mandate forced euthanasia of the unfit.

Last but not least, she said that school shootings are caused by the teaching of evolution.

For the record, I'm not making any of this up, and the actual quotes (should you wish to risk injury from repeated headdesks) are in my original post.  And despite her evidently having a screw loose, she had serious support amongst the voters in Texas.  Unsurprising, given that this is the same state that approved history textbooks that had passages claiming that the Africans brought over in the 17th, 18th, and 19th centuries weren't slaves, they were "guest workers" who had been "brought in to work on agricultural plantations."

So I was feeling pretty pessimistic about the whole thing.  This is why it was with combined surprise and delight that I learned yesterday that Bruner was resoundingly defeated in the runoff election by Keven M. Ellis, the president of the Lufkin School District school board.

"The voters did their homework," Ellis said in his victory speech, which is a phrase I'd definitely like to hear more often.

A spokesperson for the Texas Freedom Network, which has been vociferous in their criticism of Bruner, was less circumspect.  "Texas escaped an education train wreck tonight."

You have to admit, though, she looks mighty good wrapped in an American flag.

What I find interesting is that even Tea Party stalwart Grassroots America, which had backed Bruner initially, withdrew their support the week before the election.  Grassroots America has typically supported candidates who advocate for bringing religion into public schools, mandating the teaching of creationism and/or intelligent design, and excising any mention of climate change from science curricula.  But apparently, Bruner was too loony even for Grassroots America to support, and they quietly pulled their endorsement.  Spokesperson Jo Ann Fleming said that the move was made because of "inaccurate oral and written statements Ms. Bruner made in a meeting with superintendents."

Because evidently calling the president a gay drug-addicted prostitute isn't sufficiently crazy.

Anyhow, the good news is that children in Texas have been issued a reprieve.  I was certain she was going to win, and I've never been so glad to be wrong.

Now, if only the voters will apply the same kind of careful consideration to the elections this November.

Fact-free zone

It's a theme that has cropped up over and over here at Skeptophilia; the fact that people spend a lot more time reacting from emotion than they do from rational thinking.

But the fact of its being familiar doesn't mean it's not maddening.  Which is why I responded to a recent paper that appeared in Perspectives on Psychological Science a couple of days ago with a wince and a facepalm.

Entitled "Evidence for Absolute Moral Opposition to Genetically Modified Food in the United States," and written by Sydney E. Scott and Paul Rozin of the University of Pennsylvania and Yoel Inbar of the University of Toronto, the paper had the following depressing conclusion:

Public opposition to genetic modification (GM) technology in the food domain is widespread (Frewer et al., 2013).  In a survey of U.S. residents representative of the population on gender, age, and income, 64% opposed GM, and 71% of GM opponents (45% of the entire sample) were “absolutely” opposed—that is, they agreed that GM should be prohibited no matter the risks and benefits.  “Absolutist” opponents were more disgust sensitive in general and more disgusted by the consumption of genetically modified food than were non-absolutist opponents or supporters.  Furthermore, disgust predicted support for legal restrictions on genetically modified foods, even after controlling for explicit risk–benefit assessments.  This research suggests that many opponents are evidence insensitive and will not be influenced by arguments about risks and benefits.

Catch that?  45% of the people surveyed think that GMOs should be illegal regardless of the risks or benefits.  In other words, regardless of the evidence.  Apparently, a little under half of the respondents could be presented with persuasive evidence that GMOs are risk-free and have proven benefits, and they still would be against them.

It's a discouraging finding.  There are a great many issues facing us today that drive an urgent need to make smart decisions.  We need to be making those decisions based on facts and logic, not on knee-jerk gut response and inflammatory rhetoric.  Climate change, policy on vaccines, regulation of alternative medicine, even the oversight of public education -- how can we do what's right if we're making decisions irrespective of the facts?

Of course, part of the problem is that even people with access to the facts often don't know the facts.  Witness the study released last week in the Journal of the Federation of American Societies for Experimental Biology that showed that 80% of respondents wanted to have laws mandating labeling identifying all foods that contain DNA.

Yes, you read that right.  Not genetically modified DNA; DNA, period.  To make it even worse, 33% of the respondents thought that non-genetically-modified tomatoes "did not contain genes," and 32% thought that "vegetables do not contain DNA."  As Katherine Mangu-Ward put it over at Reason.com, "When it comes to genetically modified food, people don't know much, they don't know what they don't know, and they sure as heck aren't letting that stop them from having strong opinions."

The problem is, the people who shriek the loudest tend to be the ones with the least comprehension of science.  Senator James Inhofe, who for some baffling reason is the chair of the Committee on Environment and Public Works, thinks that holding up a snowball disproves anthopogenic climate change.  The alt-med/anti-vaccine crowd still believe Andrew Wakefield's discredited study linking vaccinations to autism, despite overwhelming research demonstrating that there is no connection -- and anyone who argues otherwise is said to be "a shill for Big Pharma."  (Makes me wonder when my first Shill Check is going to arrive.  Soon, I hope.  I could use the money.)

Only rarely does anyone look at the evidence and say, "Oh.  Okay.  I guess I was wrong, then."  And the paper by Scott et al. seems to support the contention that if I'm waiting for this to happen, I better not be holding my breath.

Of course, along with resistance to change, another natural human inclination is the whole "Hope Springs Eternal" phenomenon.  So I'm not giving up on blogging, at least not any time soon.  Despite the rather dismal conclusion of the recent research, I'm still hopeful that we can make change, incrementally, by picking away wherever we can.

Thoughts on a drive-by

Note to the guy who roared past me this afternoon as I was out on a run, yelled, "Faggot!  Put a shirt on!", and threw a half-full can of soda at my head:

First, about the epithet.  That's a word that has been hurled at me many times before, starting with the cretins in the locker room in eighth grade, despite their having no information whatsoever about my sexual orientation.  Not that they cared, I suspect.  The mere fact of my being tall and thin, and caring more about playing music and writing stories than I did about football, made me suspect in their eyes.  I was called that, and equivalent words, with clock-like regularity throughout high school and even into college, by people who evidently thought their mission was to make others' lives as powerless and miserable as possible.

I didn't defend myself against the claim then, and I'm not going to do it now.  Back in my public school days, arguing the point would have simply brought more negative attention my way, not to mention being futile.  Now, however, my reasoning is different.  If the gentleman in the jacked-up pickup truck had stopped to discuss the matter with me, I would have just shrugged my shoulders and said, "Why does my sexual orientation make a difference to you?"  I'm not going to defend myself against an accusation that isn't shameful either way.  I'm publicly out as bisexual, but if you want to call me gay, have at it.

Second, I run shirtless when the weather's warm because I like to.  Why that is a problem I have no idea.  One of the simple pleasures of our short summer here in upstate New York is the feel of the sun and wind on my skin, and I'll be damned if I'll forgo that because you think I'm too old, too skinny, or too whatever.  At 55, I finally have reached a point where I'm not ashamed of the body I was gifted by my genetics, and I'm not going to let the snarling of a neanderthal whose IQ matches his hat size shove me back down into self-loathing.  Spent too long there already, and never intend to go back, thanks.

Somehow, I think Mr. Rogers would be on my side in this matter.

The upshot of it all is actually kind of empowering; the startling discovery that you, and people like you, can't hurt me any more.  I have no need of your approval.  I don't care if you think I'm ugly, skinny, gay, or all of the above.  I wish I'd realized all this forty years ago, but we all move at our own pace.

And in the end, all you did is to put a damper on a single afternoon's run.  Tomorrow morning, I'll wake up and I'll be fine.  I'm still going to run, still going to shed the shirt when I feel like it, and still enjoy being outdoors in the sunshine.

You, on the other hand, will wake up tomorrow morning, and still be an asshole.  So on the whole, I believe this means that you lose.

So would David Bowie.

Oh, and finally: your aim sucks.  You missed me with the soda can by about fifteen feet.  I picked up the can, and I'm going to return it to the redemption center and get your five cents' deposit.  Have a nice day.

Signs of the times

I'll be right up front with you.  I have no idea what to do about the problem of immigration, illegal and otherwise.  In my admittedly rather apolitical brain, this whole issue seems so intractably complicated as to admit no reasonable solution at all.

Do I feel sorry for the immigrants, most of whom are coming from corrupt countries with horrific standards of living, with no access to medical care, decent housing, clean food and water, and education for their children?  Of course I do.  In their place, I'd almost certainly be trying to get out, too, whatever the risk or the cost.  However, I also recognize that illegal immigration is... well, illegal.  And if it's against the law, we should either enforce it or else change it.

I also sympathize with the concerns of a birdwatcher/naturalist friend of mine who lives in Sierra Vista, Arizona, only fifteen miles from the Mexican border, who says, "We're being overrun.  This used to be a safe community, but the people trucking the illegals across the border are criminals, pure and simple.  Many of them run drugs and guns along with their human traffic.  I love this place, but not a day goes by that I don't think of getting out, moving further north."

I understand as well the concerns of people who see their culture changing more in a decade than it had in the preceding two hundred years.  This is especially striking in western Europe, where the influx of Muslims has led to some areas coming under something very close to Shari'a law -- people drinking alcohol, women dressed "immodestly," couples displaying affection, anyone showing signs of being homosexual have been harassed, and in some cases, assaulted.

Yes, I know that those incidents aren't as common as the media coverage would lead you to believe, and that for every clash there are thousands of white Europeans and Muslims living side by side in peace.  All I'm saying is that I can see where the fear comes from.

Unfortunately, we humans have a bad tendency, which is to pretend that impossibly complex problems have easy solutions.  "Build a wall."  "Deport 'em all."  "Seal the borders."  And as tempers get high, the rhetoric on both sides becomes increasingly vitriolic -- to the point that desperation sets in, and people are willing to lie to hammer their point home.

The whole thing comes up because of some photographs of street signs in England that have been making the rounds of social media in the last few weeks.  I've seen three so far:

The photos are usually accompanied by a hysterical caption to the effect that them Mooslims are infiltrating everything, to the point that even the street signs have to be captioned in Arabic.  And because the idea here is to engage the emotions and disengage the brain, the response has been uniformly horrifying, condemning the government officials who agreed to the sign change, railing against the immigrants who pushed for its necessity.

The problem is (well, one of the problems is) that the signs are photoshopped.  Put more bluntly, the claim is a bald-faced lie.  How do I know?  Well, a couple of reasons.  First, the Arabic script below the signs doesn't spell out the names of the towns; it's pretty clear that whoever Photoshopped these simply grabbed whatever Arabic text they could find and spliced it in.

In fact, not only does the Arabic below "Harrogate" not say "Harrogate," it says "salaam alaikum."  Which, you have to admit, would be an odd thing to put on a street sign.

Some of the people who have been forwarding the photographs around have further muddied the waters by claiming that the script is Urdu, presumably to stir up sentiment against Pakistanis.  It's not Urdu, it is (as I mentioned earlier) Arabic.  Not that facts seem to matter much, here.

Most damning of all, the photos themselves are simply downloads from Google Street View, and in the originals, the signs have no Arabic subtitles.  Take a look, for example, at the original of the top photograph:

This is clearly the same photograph -- the intrepid Photoshopper simply cropped it and spliced in the Arabic text.  In fact, if you look closely, you'll see that even the clouds are in exactly the same position in the two photographs.

What appalls me most about this is not that some hate-mongering bigot lied.  Hate-mongering bigots tend to do that, after all.  What appalls me most is how easily people fell for it.  We have become so terrified of The Other that when presented with further evidence of a takeover, we don't even stop to consider whether it makes any sense.  We swallow what we're given, and it further bolsters the fear, further squelches the rationality.

It'd be nice if we had answers, if these horrible problems our world is facing did have simple solutions.  The harsh fact, however, is that if they have solutions at all, they will be ones that are costly and require sacrifices.  But one thing I am certain of: your position is never strengthened by lying.  And to the people who are circulating these photographs, just stop.  What you're doing is making an already awful situation worse.