Wednesday, September 30, 2015

Does Mark Watney dream of red potatoes?


Before we get down to business ...

As commander of this blog post, I order you to read The Martian by Andy Weir before you even watch the trailer for the upcoming movie. If you watch the trailer before you read the book you will ruin your life. Plain and simple. I can't even imagine what horrible things will happen to you if you see the whole movie without reading the book first.

Do not deprive yourself of this head trip. There is just no way this film will walk you through this astronaut's brain like the book does. Movies can be wonderful, but this is one of those reading experiences (of which there are infinitely finite) that cannot be matched on screen. 

You'll notice that I'm not linking the movie trailer here. I'm not even pasting a picture of Matt Damon in this post, knowing full well that it will get me more clicks and will beautify this screen, because I don't want anyone looking at any of that until they've read the book. If you're really hearing me, stop reading this blog post and don't come back until you've read the book. Do you read me? Over.

Layers at the base of Mount Sharp (source)
With the movie  The Martian opening this Friday, many people will soon be familiar with Mark Watney and his incredible ordeal. 

This is not a book review. I'm done with those for the time being. The last one I did turned out to be a bit of a disaster.  

I just have a few thoughts about Mark Watney's Martian diet that need to escape through my fingers and out onto your computer screens.

To survive on Mars and to think his way to salvation, he eats a lot of venison, kale, and blueberries.

Psych! He eats a lot of potatoes. You know, the "problem" food that causes disease. The food that so many trademarked diet plans avoid, like the Paleo Diet. 

There was some pre-made, pre-packaged NASA fare for Watney, but no way would it last as long as he needed if he was to try to get off Mars. So he actually grew potatoes. A shitload of them. With a shitload of astronaut shit as fertilizer. 

The whole spirit of the book is one that inspires us to think our way out of problems. To remember that possibility is a state of mind. To be skeptical of our inner skeptics who speak of impossibilities. And it's with that skepticism that I wonder about those potatoes.

Let's forget our questions about soil volume, nutrients, and moisture  (mostly because I don't know how to usefully critique the thorough explanations that Watney provides for his decisions about these things). 

And let's drop the question that drove me crazy until the very end of the book when Watney finally explained that he was microwaving the potatoes and thereby getting more calories from them than he would by eating them raw. Given all the calorie-calculations he ran through while sciencing, the chance that Watney might be eating raw potatoes was slowly killing me (and, potentially, him). 

Now I'm curious about something more fundamental: would potatoes grow the same on Mars as they do on Earth given the gravity's different? Could Watney's Earth botany translate as well as it did on Mars?

His training and thinking might not translate well on Mars if we're talking about making a different kind of tot. I'm fond of this paper hypothesizing how difficult it might be to extend the evolution of our own species, extra-terrestrially. Earth's gravity may matter a whole lot to human reproduction, especially those earliest stages of development. 

link to paper

We're not potatoes, sure, but potatoes aren't yeast. Given that there's less gravity on Mars, can we assume that sciencing all those Earth potatoes in Martian conditions is as straightforward as Watney makes it sound?

I don't think anyone knows the answer to this, however, tons of anyones (like Andy Weir) have more informed guesses than I do. Indeed, it is possible to grow spuds on the space station. So maybe my gravitational question lacks gravitas.  

(That groaner was for you, Mark.)

But one thing is for sure. In The Martian, as in life on Earth, a diet based primarily on potatoes fueled a human for quite some time. Maybe not all humans could handle this, and maybe not all humans could be as extraordinarily brilliant while eating mostly potatoes for so many cold and lonely days. But the potato industry has got to be thrilled. 

Not only is one of humanity's best (fictitious) members existing as one of humanity's best members thanks to potatoes, but the food's public image got a separate but related boost recently. Potatoes, and other similar carbohydrate sources, might have been crucial to our lineage's brain evolution. 

Anthropologists have known for a good while now that "underground storage organs" or USOs, like potatoes past and present and many other species, have probably been a big deal during the last several million years of human evolution. But a recent review paper in the Quarterly Review of Biology argues, based on up-to-the-minute cross-disciplinary findings, that cooked starches were crucial to the evolution of our big glucose-sucking, calorie-burning brains. Here's the paper's abstract:

source (and see Zimmer's write up)

So, Paleo dieters and potato-haters of the world, you have just been publicly flogged by both science fiction and science faction. What do you do now?

Well, if you haven't read The Martian, I'll plug it one last time. 

When you're on about page two you might be cursing me. By then I was cursing the book and everyone who liked it. I nearly gave up at the start for reasons to do with the style of writing (gasp! a blog! Ugh!) and my narrow-minded expectations of astronauts, but I'm so glad I dominated my inner bigot and turned the page. All the pages. To the last page. In solidarity with my new favorite Martian blogger, I'm moved to thank you for reading this gasp! a blog! Thank you. Now get to reading Watney's.

P.S. If you can't access the two articles I reference, email me and I'll send them to you: holly_dunsworth at

Friday, September 25, 2015

On Being Mortal

Ken and I have written a lot about disease causation, prediction and prevention but we haven't written much about the other side, when prediction, prevention and treatment aren't enough, when disease becomes fatal.  We have just read Dr Atul Gawande's book Being Mortal, a beautifully written heartfelt exploration of the end of life.  Dr Gawande is a surgeon at a major teaching hospital, and a professor of health policy, and his job is to save lives, and to teach medical students how to do the same.  He is presumably very good at this.  In the book, though, he writes about the process of learning how to be a doctor when there is no cure and he can't save a patient's life, something he didn't learn in school, and that has taken him decades to learn.  Presumably these are lessons he now teaches to his students, to the great benefit of us all.

Dr Gawande tells his story through many case histories, including that of his father, as he made decisions about how to live, and die, with an untreatable cancer.  He told some of these same stories in the BBC Reith Lectures last fall.  He writes about the tremendous regret he now has about instances in which he just was not able to have the kind of conversation with a dying patient that he now knows he should have had.

We are used to two common medical models, he says, the 'paternalistic' model of the 1960's, when a patient could be treated with a blue pill or a red pill, and the doctor made the choice. "Take the red pill.  It will do you good."  Then, the 'information' model took over -- the doctor supplied information, telling the patient that his/her disease could be treated with a blue pill or a red pill, explaining the pros and cons of each and then asking the patient to choose.  But, we don't face the end of our lives statistically, and weighing the pros and cons of different treatments is not what helps us make decisions about how to proceed, which is what Gawande finally realized after too many painful conversations with his very sick patients.

When terminally ill, a patient is overwhelmed with fears and concerns, and recognizing and acknowledging these is the truly important role a doctor can play when a patient is facing life-threatening illness. After much thought, hundreds of conversations with gerontologists, palliative care physicians, managers of the best assisted living facilities, and with patients, Gawande has come to see that there's another model, the 'interpretive' or 'shared decision making' model.

Gawande now asks his patients, What are your priorities if your time is limited?  What are your goals for treatment?  What are your fears?  And what trade-offs are you willing to accept as a result of your care?  And, he, the patient, and the patient's family choose the course of treatment with the patient's answers in mind.

One patient said that as long as he could watch football and eat chocolate ice-cream he wanted to keep living, so treatment continued for this man longer than it did for, for example, Gawande's father who said that he wanted not to suffer, did not want to be paralyzed, and if he couldn't enjoy seeing friends and family, he wanted no more treatment.  So, he refused further chemotherapy when the trade-offs were no longer acceptable to him.

In modern medicine, it's important to recognize that 'no cure' is not the same as 'no treatment'.  There is almost always something else that can be tried, some heroic measure, some experimental surgery or medicine that can be used to give a patient hope, or even a little more time, even when the illness can't be cured.  Doctors are very good at plugging ahead with all of this, without stopping to ask their patients the kinds of things that Gawande now asks.  The proper goal of the medical system, Gawande now believes, is not to stave off death as long as possible, or even to make a good death, but instead to assist in assuring "a good life to the very end."

According to Dr Gawande, modern medicine is very good at a lot of things, but preventing and treating aging and death are not among them.  Until the 1950's, people in the developed world most often died at home.  Then, increasingly, as it became more and more possible for medicine to intervene in the process, people began to die in hospital -- indeed, at ever increasing expense.  Now, however, people are beginning to choose to die at home again, and the hospice movement is largely responsible for making this work as well as it can.

The primary role of nursing homes (an industry which, according to Gawande, began to grow when the number of hospital beds for the elderly wasn't sufficient once aging and dying were medicalized) is to keep the elderly safe, but at the cost of lost privacy, dignity and control over one's own life. Nursing homes are run for the convenience of the system, not the residents. Fortunately, there are increasingly alternatives that allow people to 'age in place,' in their own homes, or if that's not possible, in an assisted living alternative, with as much or as little aid as they want or need.  

If Gawande's book is an indicator that we are wresting aging and dying back from a system that appropriated it, at great cost in money and suffering, it is reminiscent of the movement to demedicalize pregnancy and childbirth, with the increasing popularity of birthing centers and home births, or of menopause, which once meant hormone replacement therapy for all but no longer does.  There are many things modern medicine does very well, of course.  But there are things it can't and will never do well, including preventing aging and death.  

Still, many people do opt for heroic measures at the end of life.  This is in a sense because of the hope that they can be cured, and perhaps a deeper yearning for immortality.  Is this because medicine has over-promised?  Surely in part.  As Gawande says, patients are usually thinking in terms of 10 or 15 additional years when they hear that yet another treatment can be tried, not weeks or months, but it's more like weeks or months that these heroic measures have to offer.  

But this over-promising is nothing new.  Genetics has been doing it for decades, and the new commitment to precision medicine, genetics and so much more, is more of the same.  Some of this is because of snake oil salesmen, certainly, but not entirely.  Just as we have to blame Trump's popularity not just on Trump, but on the people buying his 'message' as well, it is the age of genetics because the people have bought the message being sold.  This isn't so different from the promise of miraculous cures by some religions (or mountebanks).

Surely there will come a time when we recognize that all that has been promised just can't be done, we won't be able to foretell our medical, academic, economic, or romantic futures from our genomes at birth,  and we'll understand that geneticizing our lives is as much over-promising as is the idea that one more experimental chemotherapy is going to finally cure our incurable disease.    

We put our faith in medicine when we are most vulnerable, hoping against hope that it will save us.  Perhaps it was the miracle drugs of the mid 19th century that encouraged this faith -- antibiotics really did save lives.  And then technology -- kidney dialysis and heart transplants, hip replacements and triple bypass surgeries.  We're very good at technology.  But, we still don't really understand cancer, or mental illnesses, or the cause of so many diseases.  And we won't be able to predict complex disease from our genes (which we've written about many times before on the MT), and we certainly can't prevent aging or death.  Despite the promises.  

Atul Gawande's message is sane and oddly reassuring, but as such it's a radical one as he aims to return control of a patient's present and future back to the patient.  This is a challenge to vested interests, yes, as well as a challenge to the usual way medicine is done in the industrialized world.  But it's a welcome and important one, because it's something we all will face.

Wednesday, September 16, 2015

Lourdes save me!: "Hankering after the lie"

Emile Zola's emotionally powerful book, Lourdes, published in 1894, is a poignantly detailed account of people suffering from severe disease, traveling to Lourdes, France, in the hopes of a miracle cure at the hands of a young maid, Bernadette Soubirous.  It was her visions, years earlier, that started the phenomenon by which the Virgin Mary was supposed to have endowed the local waters with miraculous healing properties.  Zola spent some time at Lourdes, to soak himself in the phenomenon and live up to his idea of 'naturalism', making the novel a kind of fictionalized documentary.

Bernadette Soubirous (source: Wikipedia)
Bernadette's story turned the Grotto at Lourdes into a major pilgrimage destination for those most in agony.  They crowded together in trainloads by the tens of thousands, rumbling across France to Lourdes in the hope of a cure centered around the intervention of God, prayer, priests, or angels. In his sympathetic empathy for people "hankering after the lie" of a miracle just down the track, Zola was understanding, but his explicit, highly angry skepticism was made, one might say, painfully clear.

Zola's tale is full of the wrenching tears, sadness and suffering of people with the most desperate of problems that medicine couldn't cure.  Indeed, this is as most of us will be when our time finally comes.  Most of humanity have died not knowing that their hoped-for miracles never happened. Today there are still desperate or credulous people who seek cures from God or from mountebanks, but at least those who are reasonably educated and have the access mainly trust to empirical medical science; that seems a huge conceptual jump beyond simple, desperate prayers.  Medical science is a huge conceptual jump beyond simple, desperate prayers, and has marvelously transformed our health experience, especially in the developed world. We have to be entirely thankful to the biomedical research and clinical systems for this.  Who would trade our medical (or dental) lives for those of the 19th century?  Still, I'll wonder below whether there's some potential irony in that.

Flooding to miracle waters by the trainload.  Source: Wikipedia
"The need of the Lie, that necessity for credulity, which is characteristic of human nature."
A young woman, Marie, a suffering heroine in Lourdes, had become paralyzed in an accident. She poignantly believes in St Bernadette,  and says glowingly after hours of intense prayers at Lourdes that "At four o'clock I shall be cured!"  And she was--but it was no miracle, as we'll see.

Zola noted in great and angry detail how the simple purity of Bernadette in her (apparent) apparitions and belief in the curative powers of the waters, were quickly shunted aside, and co-opted as a grotesque source of mammon by Church officials, turning Lourdes into a kind of health-tourist Disneyland: "An elaborate organisation had been gradually perfected, donations of considerable amounts were collected in all parts of the world, sufferers were enrolled in every parish...."  Do we not have our equivalent in much of the biomedical system today?  Research clearly is costly, but one must note the similar self-serving and open-ended nature of this enterprise side of things, engaged in by our particular version of the high priests, the academic 'church', and the magical waters it promises in our own time.  This is actually not new, even to medicine, and the various territory-guarding priesthoods of health go back to Hippocrates.

One could perhaps, write a similar novel today.  Patients wouldn't be in crowded trains but in crowded waiting rooms in hospitals, or in the skilled nursing sections of a modern retirement center. The struggle to get 'hospitalisation' care in Zola's time, or tickets on the trains to the curative waters of Lourdes, is today the struggle to get care covered by insurance, or to get a bed or scheduled treatment.  It might seem more orderly, and be administered by bureaucrats rather than nuns and priests, though as Zola clearly documents, the Church was a massive bureaucracy of its own, even when it comes to formal committees--including at Lourdes--to give the imprimatur to claims of miracle (not so unlike today's PR empires trumpeting each daily research miracle?).  The psychological and even material circumstances are quite similar, because the old pathos and wishful thinking are still here, along with the hopes, dreams and judgments, though perhaps they're often harder to see as people sit quietly waiting for the nurse to call their names.

Ironic cautionary notes?
Zola rants at length against a world driven by superstition and false hopes, exploited by religions.  He pleads for a new religion, one based on reason, as he calls it, that is about the realities of finite life and its imperfections, rather than imaginary wishful-thinking.  But there is an irony in his emotional plea, one we might listen to carefully: he notes that this superstition still existed after what, even then, had been a century of science with its touted powers and promises.  The failure of science to cure their diseases was leading people to return to superstition, rejecting science--rejecting reason.

Zola bemoaned that the "thirst for the Divine, which nothing had quenched....seemed to have returned with increased violence at the close of our century of seemed that science alone cold not suffice, and one would be obliged to leave a door open on the Mysterious....what divine falsehood...could be made to germinate in the contemporary world, ravaged as it had been upon all sides, broken up by a century of science?  Ah! unhappy mankind, poor ailing humanity, hungering for illusion, and in the weariness of this waning century distracted and sore from having too greedily acquired science, it fancies itself abandoned by the physicians of both the mind and the body, and, in great danger of succumbing to incurable disease, retraces its steps and asks the miracle of its cure of the mystical Lourdes of a past forever dead!"

We've now had an additional century of science since Zola's book was published.  That we still have unconquered disease is understandable.  Diseases are diverse, and those we still cannot cure or prevent present massive challenges.  Of course, the target is an ever-moving one, with solved problems giving way to the unsolved ones that remain.  For the latter, even highly touted new treatments often only help some patients and it is not at all unusual to see that highly hyped new treatments in reality add but a few months of life, or a partial remission, for but a fraction of those who received them--and it is not necessarily true that those extra months are all that tolerable.  We are aided and abetted in the strong claims by the media, university or commercial spinners, and the interlocked careerist, funding-based mutually reinforcing systems.  So far, in our century, the public is buying it, as ever.

No fault lies in our not having divined (forgive the metaphor!) a cure, and the exaggerated promises of transformative advances are understandable in human terms--but not so different than what was coming from other pulpits in times past.  Is there any danger that the public will again see science, with its opulent cathedrals and assertive promises that often mammonize hope, as an enterprise of false illusions?  The suffering remain, after all, in the realm of fear, not reason.  To what alternative solution--or lie--might their hopes turn?

Of course, our inherent inevitable mortality means even our modern system will ultimately fail every one of us. As sentient organisms we don't want pain, and as knowing organisms we don't want death, and it is all too easy to 'Tsk, tsk' the system when it is others than ourselves suffering from awful diseases, and it's not yet our turn.  Ultimate failure is an open secret that neither the system nor its patients like to acknowledge.  The currently growing hospice movement is facing these realities, unless it too becomes co-opted as a 'system' with its own self-interested self-promotion.  Precedent suggests that may happen, but it's a very good thing at present, as we've noted here before.


Zola visiting Lourdes.  Wikipedia, from the magazine Gil Blas, 1894
Maybe some day we'll have the promised cures, sipping genetics or whatever other magic waters come along.  If so, then the medical priests will have earned their respect in every way.  But of course that, too, is a dream.  If all known diseases were cured by one miracle or another, we would still degenerate or even if that could be prevented, we'd be so numerous as to be stacked many-high on top of each other, struggling for food or water and so on--a geriatric nightmare of its own sort.

An ironical year
A century on from Zola's time we may still be at risk of people again turning away from the exaggerated promises of science, and given much of the world today it would be ironic but not so strange if there were a turn to some form of religion or mysticism, some emotional rejection of 'objective' science.  

But there is another sort of irony in the story of Lourdes.  In 1858, eerily reflecting the impending conceptual clash that Zola writes of, while the real Bernadette Soubirous was having the visions that would lead to the pilgrimages to the waters of Lourdes, Charles Darwin and Alfred Wallace publicly announced their discovery of evolution, that directly threatened religious explanations and led steadily to the altars of science instead as a competing explanation for human affairs. 

Zola's touching kind of docudrama makes one aware of the nature of hope, as well as false hope, and our willingness to believe what our particular day's preachers promise.  Zola himself bitterly debunks the claims at Lourdes.  Many of the pilgrims died, some reported improvement (almost always temporary), and only a few were 'cured'.  The trains left somewhat emptier than they were a few days earlier, populated by the returning survivors, still with their ailments, each inspired that the cure will surely happen to them at Lourdes next year!

As described in the link given below, a biography of Zola suggests that he saw a cured case of tuberculosis but changed that to a fatality in his book, to make his main point against superstition. But he was very clear that, as we often see reports today of, for example, placebo effects, it was nervous afflictions (that we refer to by terms like 'psychosomatic') that seemed most likely to be 'cured'.  Real physical problems were not.  The hero in Zola's book, a doubting priest who even had carnal feelings for Marie, understood that that was the nature of her 'cure', but in deference to her faith in Bernadette he made the altruistic decision to let Marie live with her illusions, thus permanently distancing her from his non-belief.

Such a book, though sometimes a bit ponderous in realistic details, is a good reminder of the human rather than just the sociopolitical, economic or even coldly scientific sides of the story.  But this should not take our eye off the importance of keeping science's eye on the proper ball: not that of self-serving empire building and inertia, but of truly addressing human agonies in the best way possible, fallible though we be.

Overall, perhaps we never learn--or, maybe, in being mortal it is not possible that we can learn, and completely accept the grim-reaper's realities that we know, in our hearts, are there.  At least, each of us will have to learn this in his or her own way, at the end.  No miracle can prevent that.

An afternote for fiction lovers
Here is a very nice blog post discussing Lourdes.  The blog is a fine one, about great literature that has survived fads and fashions and stands on its own legs.

Tuesday, September 15, 2015

And there will be humans no more? A review-ish of Greg Graffin's "Population Wars"

Perhaps best known as the leader of Bad Religion, Greg Graffin is also an evolution scholar. His latest book, Population Wars, is out today. 

I was hooked by the description that this is a "paradigm-shifting" book about human behavior, particularly for readers of Dawkins, Diamond, and Wilson. I was surprised at how heavily autobiographical it is throughout. But memoirs do make a lot of sense, given the many fans who are bound to read it, and given how the argument takes shape by the end. 

Graffin is appealing to our inner humans, but without appealing to our inner saps. If I had to sum up the book in one phrase, I'd say it's the least sentimental argument for saving humankind from extinction that you'll ever read. 

That's meant to be entirely neutral, but I don't think I can convey this next thing neutrally: 

I wouldn't have finished reading my advance copy of Population Wars if the publisher hadn't offered me a Q&A with the rockstar.

It wasn't because of his voice. I was thrilled when the first few pages beat just like Bad Religion when the volume's right. 

It was because of the content. I'm not one to throw many punches, let alone at members of my own tribe of evolutionary scientists-slash-authors. But I share this awkward fact (that the only thing that kept me reading this book was my eventual interview with a rockstar) for two reasons: 

Graffin can handle it. And, my experience taught me an important lesson. Because I stuck it out and read through the many pages of cyanobacteria, and the many, many pages of Iroquois history, I was reminded of the importance of learning what we're not necessarily very interested in learning--ever, or at a given moment, or from a particular human's perspective, or whatever. 

Population Wars didn't just teach me new things about natural history,history, and environmentalism, it incidentally taught me something bigger that I think I lost my grip on. It reminded me why we read books.
Books. Neatly stacked and bound piles of paper. This is where so many humans pour our hearts and souls. Whatever one thinks of Graffin's book, it's his blood and guts expertly smeared into teeny tiny perfectly discernible shapes. And you can feel how he honestly believes that humans can figure out a way to prevent our future extinction. That's utterly beautiful even if you don't see things that way. It's there for readers if they stick it out, turn each of those pages, and make it to the end where they can meditate over this human's heart and soul at once. 

When we're finished reading even the best books, the books that light us up from head to toe, we merely shut them and shelve them. CDs of music too. 

We've been married for over seven years and just last week I hear Kevin's "Rockers Galore" for the very first time. It's like a dream mix-tape of The Clash with interviews and it's my new favorite album. It's got Joe Strummer explaining what he was trying to say in Rock the Casbah: "There's no tenderness or humanity in fanaticism.

That fleck of gold was just crammed into a cabinet this whole fucking time? That one sentence that elevates an already great song into the outer dimensions of the rock'n'roll-sphere was hiding in plain sight inside my own fucking house? 

CDs. Books. Even when they're not earth-moving, they contain more human creative and emotional energy than we deserve. But the ones who write them believe that we deserve it, which makes them even more magical. When we leave CDs and books sitting there, unexplored, we're failing humanity.

Population Wars charges us to find the humanity within ourselves to collaborate, globally, as a species to clean up and preserve our planet. Graffin describes how someone can see all of history through an evolutionary lens. His aim is to spread this worldview because it's this perspective, over common ancestry and deep time, that literally unites us as a species, even if we are divided culturally. Unfortunately, saving the planet is too big a job for anything less than all of us. Graffin's book is one voice toward our unification in the face of all the fanaticism.  
This is the first but won’t be the last time I write about the dinner I had with an astronaut. One of the small group of us, one of us who hadn’t walked on the moon, seemed desperate to get an inspired nugget of Truth out of the one man who had. He certainly was a remarkable human, but he clearly wasn’t supernatural. His body language and his seamless diversions showed he was as skilled at avoiding sentimentality as he was oxygen depletion.

In the presence of astronauts and other rockstars people want to have their hearts melted or their minds blown. They want to transcend. To quote Twitter: they want all the feels. When they’re not preoccupied with selfies, they’re begging rockstars for God and they expect to get it. Even in someone’s kitchen, over a casserole and some beers.  Even when they’re hardly fans of Bad Religion and they read its leader’s evolution book? I hope not. I think no one who picks up Population Wars, especially Bad Religion fans, is going to expect kumbaya. Yet, tree-hugging is something for Grateful Dead shows, not punk ones.

Graffin's argument isn't to save the planet for our babies or the polar bears', it's to save the planet because we can. Let's make it our moonshot. Let's boldly go, together, globally, here on Earth. 

That thing that we don't have that could unite us while give us purpose as individuals? That thing that Eggers' protagonist desperately wants? That thing Jon Stewart always talked about? That thing that binds us together with a goal? That thing is saving the species by saving the planet.

And if you're going to save the planet, you've got to learn about things that might not rock you to your core, things that might require more stubbornness than anything to hold your attention. I didn't want to read about Graffin's cyanobacteria. I even got angry about it, but if we're to make a dent in saving the planet, we should be reading about such tedious things. 

Point blank: We humans should be reading as much as we can, whatever we can get our hands on, and without a carrot dangling at the end of the book, without the promise of an interview with a rockstar. 

Because sharing our unique human experiences with one another unites us as humans. 

And also because rockstars go on tour. When you're all done reading and you write to the publicist to say, This is an important book, thank you for sending it to me. I want to write about it. Please set up a Q&A and please send the music that accompanies the book... She is likely to respond with an apology (and without the music too).  

So lessons learned! I read Population Wars and all I got was one brilliant human's heart and soul, one human's bold and hopeful vision for our species.  
Questions for Dr. Graffin

  1. Is Population Wars punk rock?
  2. Both perpetual mutation as well as genetic drift are fundamental to how I have come to understand natural selection as being much weaker than many still believe it to be. However, you have come to this seemingly same conclusion about natural selection without genetic drift and without much consideration of perpetual mutation. Can you help us understand how you did this? And can you explain why you left genetic drift out of your book?
  3. I am drawn to discussions of free will, but it's hard for me to reconcile your argument that it does not exist with the goal of your book urging humankind to save the planet and ourselves. If there is no free will, how will your book's will be done?
  4. What do you want readers to do after reading your book? I'm thinking specifically of the readers who cannot afford to emulate you by building an eco-friendly home and turning down big financial offers from natural gas companies. The book demonstrates your evolutionary worldview, but does not contain many directives. What can we do toward your goal of saving the planet and the species?
  5. How do we join together as a species to accomplish anything together when there's such massive inequality?

Monday, September 14, 2015

Oh Koko!

We'll be sharing much more, in the coming months, about why Anne and I are a wee bit obsessed with Koko the gorilla. She's one of the stars of a project we've got going--a project that will likely diminish our chances of ever meeting the lovely and extraordinary creature.

It's because we've been stalking Koko that Anne and I were perplexed, but not surprised, by this recent piece in The Atlantic:

Click here for the article.

Our eyebrows arched just reading the headline.

It leads a reader to anticipate a conversation with Koko the gorilla, but instead it is mostly an interview with Koko's main human, Penny Patterson. So, I guess the headline is describing what that interview is about--a conversation about conversing. There's no other way to make sense of it. Yet, it's still problematic because gorillas don't converse. Not even Koko.

The piece begins with an anecdote about Koko describing herself with the "queen" sign. Morin, the article's author, follows it with this quote of explanation from Patterson:
Koko understands that she’s special because of all the attention she's had from professors, and caregivers, and the media.
And this is where, to my mind, any interviewer actually fascinated with Koko's mind asks: This is could Koko understand that she receives more human attention than most other gorillas on the planet? And how does she make the connection between this concept, this existence of hers, and that of a queen? When you taught her "queen," what was the definition? 

Unfortunately, this isn't the direction the piece goes. That nugget was a foray into her backstory about her sign language training and her home in California.  And just because the written product of Morin's interview doesn't dive into questions like those italicized up there, it doesn't mean it didn't. But if he did go there, why on earth didn't that gold make it into the piece?

More to the point, why have I never read an interview about Koko that asks penetrating questions about the stories that Koko's humans tell about her mind? Is that nuts and bolts stuff merely uninteresting fodder for readers or is it off-limits to writers who are permitted access? There's an answer at the end of this blog post.

But first, I have more, seemingly infinite, questions... How does Koko's language ability, and let's add Kanzi's too, compare to a highly-trained border collie like Chaser?

Is it categorically different, indicating an actually different kind of cognition?
You might be thinking about this video of Kanzi and saying, yes, yes it's different:

But how is it different? Kanzi is just pairing up two things, which is not really all that different from Chaser getting one toy at a time. It might appear to be more extraordinary than it is because in pairing the two objects for which Kanzi knows the English words, he behaves with them in ways they're meant to be behaved with by people.

That was a sentence worthy of a tinier brain than mine.

What I'm trying to say, poorly, with my human language "abilities," is that grabbing two things, like a soap pumper and a ball, and behaving routinely with one of them (like pumping the soap, which is what one does with a soap pumper) doesn't necessarily require as much human-like comprehension of what Sue's saying as a we might assume--that is, without thinking it through more deeply, or perhaps without trying to think like a dog or like a bonobo, or like a toddler.

Or like a gorilla--a gorilla who's arguably not a gorilla, given she's not socialized like one and given how her humans have admitted that they've intentionally raised her as a human and consider her one:

As they've raised Koko, they've narrated her mind as if it works like ours.This is evident right from the beginning of the interview portion of Morin's article. Patterson is explaining how Koko generalized the sign for "food", saying:
She would perch on this high spot where she could watch people come and go and she would sign “food” to them. It might mean “Give me the treat you’ve got,” or it might mean “I want my toothbrush,” or even just, “Engage with me.” She understood that signs had power. That particular sign got her food, so she wondered, “What else can I do with it?
She did? She wondered? And it was about how to use a sign in different settings to get what she wants? It's not just simply that it's something she could produce and did, in various circumstances? I think describing such processes as "wondering" would be giving humans too much conscious credit most of the time. But it's how we talk about minds. It's how we narrate one another's behaviors, and that of our pets, and that of whatever Koko is.

Often this is lumped into "anthropomorphism" and it's not all bad, but one could argue that it's to be avoided like the plague. If the goal is to understand how an animal thinks, then anthropomorphism risks being more of an obstacle than a helpful metaphor.

Whether the Koko project is scientifically rigorous, I have absolutely no idea. But Patterson's fantasy description of wild gorilla communication rings more of science fiction:
The free-living gorillas might talk about simple things like “Where are we going to get our next meal?” but here [at the research facility] there is so much more to talk about.
Death is one of those things. Here's Patterson's evidence that Koko understands things about death:
The caregiver showed Koko a skeleton and asked, “Is this alive or dead?” Koko signed, “Dead, draped.” “Draped” means “covered up.” 
Again, this is where my dream interviewer asks, What is the connection between "dead" and "draped"? It's even harder to understand the connection between a skeleton and draped. Can you help us understand the logic of her language? 

But we're not given that in this piece.  Morin does follow with "How would Koko know about death?" but it's not demanding a response that gets at the crucial connection between her mind and her signs.

We need to know whether what Patterson says about Koko's mind is true or not and no one seems to be able to  help us learn this. As the piece continues, my desperation for such a person escalates.

Patterson describes how Koko was making a sign that her brother made just before jumping off a rock. It took Koko's people a while to understand what she was trying to say because they hadn't seen her brother do this, but once they saw a film, it was apparent that the sign...
...means “take off” in the sense of “jump off.” Koko wanted us to take off our lab coats.
How does Koko's mind connect "jump off" a rock with "take off" your lab coats? If Morin asked this, he neither published it nor the answer. If Morin asked this question, then he is hoarding the gold all to himself.

The rest of Morin's piece is fascinating, and in parts it's heart-warming, especially if you have a soft spot for gorillas and for people who have those soft spots too. But there's still no conversation with a gorilla, or a conversation about a conversation either.

Read far enough into the article and you'll see what happened to Morin as he prepared to meet Koko:
Patterson cautioned me earlier to refrain from asking Koko questions. I was to let the gorilla take the lead. “She has that royal air about her,” the researcher explained, “and she doesn't entertain questions. Just like you wouldn’t question the queen—Koko is the same way. She’ll disengage.”
So, no conversation is going to be had with an ape, conveniently, because that totally capable ape wouldn't like it if he tried. Hm.

But there would be some lovely and touching moments through the enclosure's fence.

After recounting those, Morin reflects on what I've been discussing:
There was no way to know how much of her behavior was intentional and how much was my own or Patterson’s projection. Allegations of selective interpretation have accompanied ape-language research from the beginning. Still, it was impossible to be there interacting with her, and not feel that I was in the presence of another self-conscious being.
I don't see anything wrong with describing her as self-conscious while also doubting that her mind works like ours.  I live with a one-year old. And even before I had this baby, before I lived with an alien mind, I didn't see anything wrong with this thinking. Morin's final thoughts compare Koko's mind to an alien's, but his piece paints that alien as just another Hollywood humanoid.

When you share the link to Morin's The Atlantic piece on Facebook, the headline in the feed reads: "What gorillas can teach us about being human"

Well, what can they?

I think it's obvious from the article, and from others like it, that Koko is teaching us about our limitations. She's teaching us that we wouldn't care as much about gorillas without her fairytales; that we wouldn't care as much about these truly magnificent animals if they weren't furry humans. And that would be less depressing if we were any good at caring about actual humans.

Thursday, September 10, 2015

What population genetic diversity can and can't tell us

By Anne Buchanan and Ken Weiss

Genetic diversity is indisputably a marker of geographic origin and human migration.  The reason is very simple: new mutations arise independently and, to a great extent uniquely, and they arise in some local area with only a single copy of the newly arisen variant.  Over time, that variant will either disappear (not be passed down to any offspring) or may increase in frequency.  Because humans traditionally had but few surviving children per parent, and mated locally, only slow increases and spread of descendant copies of a variant would occur.  Local areas had a unique pattern of genomic variants and, depending on their population size and structure, different amounts of variation.  Because all humans originated from a smallish emigration from a source population in Africa, there is more, and more complex, genomic variation there than in Eurasia.

Beyond these clear facts about the amount and distribution of human genomic diversity, interpretations of what it means, implies, involves get fuzzy, political, emotional and controversial; race is seen as either a genetic construct or a social one, and it is correlated in some ways with geographic location or origin, so that it is not obvious how genetic variation per se can be interpreted in terms of traits like societal diversity in wealth, achievements and the like.

The danger of course is to assume that geographic correlation of some societal trait with genomic variation is caused by that variation, that is, that societal variation is 'genetic'.  It is natural for some in the developed world to want to see their achievements as being due to inherent genetic traits (read: superiority), and there is a very long history, all the way back to the Greeks in western tradition, to hold such views of inherency.  But this is hard to demonstrate.

An interesting new paper in the September issue of Genetics tries to make some sense of the meaning of genetic diversity ("Genetic Diversity and Societally Important Disparities," Rosenberg and Kang, 2015) by examining "the ways in which population differences in genetic diversity might contribute to consequential societal differences across populations." Rosenberg and Kang assess the importance of genetic diversity in forensics, organ transplants, and genome wide association studies, as well as its contribution to societal disparities.  They conclude that genetic diversity must be taken into account for biological purposes, but they find no association with societal diversity.  Here's why.

Their paper was at least in part occasioned by a controversy over a 2013 report concluding that population genetic variation can be used as a proxy for economic diversity, and success ("The 'Out of Africa' Hypothesis, Human Genetic Diversity, and Comparative Economic Development," American Economic Review, Ashraf and Galor, 2013).  Ashraf and Galor (A and G) write:
This research advances and empirically establishes the hypothesis that, in the course of the prehistoric exodus of Homo sapiens out of Africa, variation in migratory distance to various settlements across the globe affected genetic diversity and has had a persistent hump-shaped effect on comparative economic development, reflecting the trade-off between the beneficial and the detrimental effects of diversity on productivity. While the low diversity of Native American populations and the high diversity of African populations have been detrimental for the development of these regions, the intermediate levels of diversity associated with European and Asian populations have been conducive for development.
And, this was all determined at "the dawn of humankind."  Naturally, and conveniently, a hump-shaped pattern rather than a simple linear one was needed if one had to similarly denigrate Native Americans and Africans.  None of that sort of argument for inherency is qualitatively new but the attempt to make it genetic and hence inherently true had a juicy appeal.  Rosenberg and Kang (R and K), however, apply the same methods to an even larger data set and find no association with economic success.

R and K make it clear that, in their attempt to replicate A and G's study, they are considering within-population diversity, not between.  This is important, because internal diversity is calculated from the population itself, not from a larger collection of populations which has various issues of sample selection, sample size, and the like. Within a population when one can assume approximate random-mating, one can estimate heterozygosity in ways far more unclear when analyzing multiple populations at one go.  So, R and K are calculating expected heterozygosity, "the probability that two draws from a population at a specific site in the genome will produce different genetic types."

Expected heterozygosity follows a consistent geographic pattern,  
...occurring as a function of increasing distance from East Africa, measured over land-based routes. The highest heterozygosities appear in populations from Africa, followed by populations from the Middle East, Europe, and Central and South Asia. Populations of East Asia have still lower heterozygosities, and Pacific Islander and Native American populations, at the greatest geographic distance from Africa over migration paths traversed in human evolution, are the least heterozygous. The linear decrease in heterozygosity with increasing distance from Africa is a strong and replicable
relationship, achieving correlation coefficients near 20.9 in a variety of studies of different genetic markers and sets of populations.
The explanation for the decreasing diversity out of Africa is that each new founding population is a subset of the original group, and thus carries with it less genetic diversity than the non-migrants.

The serial founder model in human evolution. (A) A schematic of the model. Each color
represents a distinct allele. Migration events outward from Africa tend to carry with them only a
subset of the genetic diversity from the source population, and some alleles are lost during
migration events.  (B) An example of the model at a particular genetic locus, TGA012. Each set of
vertical bars depicts the allele frequencies in a population, with different colors representing distinct
alleles. Within continental regions, populations are plotted from left to right in decreasing order
of expected heterozygosity at the locus [equation (3)]. This figure illustrates the loss of alleles across
geographic regions; Native Americans all possess the same allele. The allele frequencies are taken
from Rosenberg et al. (2005).  Source: Rosenberg and Kang, 2015

Other factors influence diversity as well, such as admixture between different groups, but distance from the original source is replicably the primary determining factor.  There are of course geographic irregularities, such as bodies of water or mountain ranges, but the general pattern is clear, consistent with archeology, linguistic patterns, and so on.

Tests of the interaction between genetic diversity and social factors
Genetic diversity is used in forensics to identify a suspect with high probability if the DNA from the crime scene is a perfect match to an individual in the database.  If an exact match isn't found, the DNA profile may be used to identify relatives, which can be done because they will differ by theoretically predictable amounts.  The underlying genetic heterozygosity in a population, however, determines the likelihood that a partial match to a sample is from a genetic relative.  In a low diversity population, risk of a false positive is higher than in a high diversity population, because in the former a higher fraction of individuals will share each allele, which will mean it is less informative.

The different levels of genetic diversity in different populations means that the usefulness of DNA for identification purposes varies between populations.  And, populations are unequally represented in forensic databases.  That is a social issue, not a biological one, and doesn't obviate the relationship between genetic diversity and identification of social relationships.

Genetic diversity is important in determining matches for the purpose of organ transplantation, particularly bone marrow.  Here, higher diversity populations will have lower match probabilities -- that is, it's most difficult to find a match when diversity in the population is highest, and the difficulty descends with decreasing diversity.  These are rather clear issues.

The difficulty is greater when populations are less likely to be well represented in match databases, which is, again, a social issue.
...the chance that no donor match is found is greatest for African Americans, followed by the Asian-American, Hispanic, Native American, and white groups. As in the forensic case, the population genetics of genetic diversity, together with societal factors that vary across populations, contributes to the quantity of ultimate interest. Both genetic diversity and its interaction with factors that affect participation in transplantation are important in increasing the probability that any given recipient can find a successful match.
Genome wide association studies searching for alleles associated with disease rely on the relative proximity of SNPs, or DNA markers, with disease alleles.  In populations with high genetic diversity, in African populations, or among African Americans, because of the longer history of genomic recombination events that scramble nearby nucleotide variants over the generations, results in lower linkage disequilibrium (LD), so that the proximity of markers to causal alleles can't be relied upon with the same likelihoods as in more recent populations.  One needs more marker test sites to find the LD one needs to make associations with traits, for example.  R and K report that it has been estimated that 96% of subjects in GWAS are of European ancestry. The social implications of this are that disease alleles are even less likely to be identified in high diversity populations than in others.  The vast majority of GWAS and similar findings can be extrapolated only with great and unknown uncertainty at present (though many still attempt it, in what can be called expeditions of wishful thinking).

So, these are three examples of situations in which differences in genetic diversity between populations, interacting with social diversity, can have important social implications -- false positives in forensics, low probabilities of transplant matches, and low likelihood of inclusion in genetic research.
Each of these settings involves a problem that is fundamentally biological—DNA-based identification, transplantation, and genetics of disease. In each setting, principles from population-genetic theory in which aspects of genetic diversity feature prominently underlie the contribution of genetic diversity: theories of forensic and transplantation matching explicitly produce an inverse relationship between match probabilities and genetic diversity, and GWA statistics rely on models of the decay of genetic diversity and production of LD during migrations.  
Back to economics
R and K then return to the societal economics question, to re-examine whether population-level biological determinants are relevant to economic development, asking whether population genetic diversity is as useful when applied to a discipline in which population genetics theory is not relevant. Among other things, there are dangers of being statistically misled by phenomena such as Simpson's paradox and the ecological fallacy.

A and G used a small amount of genetic data to calculate genetic heterozygosity for a small number of populations, and imputed heterozygosity for many more based on geographic distance from Africa. Imputation generally takes sites found in one study that didn't look for variation between them, and assumes the states of those internal sites based on studies of other pouplations where they were typed.  This is a common, if iffy practice, in GWAS, but at least works reasonably well when the samples are from the same geographic area, such as Europe. It is sometimes needed because different GWA studies of a given trait use different marker sites (because they use different genotyping platforms).

R and K recalulated the results by using actual genetic data for more populations, but retaining the same analytic methods used in the original study.  So, rather than actual data for 53 populations in 21 countries, R and K used genetic data from 237 populations in 39 countries.  And they found no effect of genetic diversity on economic success.

Further, they chose multiple different samples of 21 countries, and found a significant effect in at most 27% of them.  Thus, three quarters of the time, had A and G chosen a different sample subset, they would have found no effect.  And, conclude R and K, even if the assumption that studying population genetic diversity and its effect on economic development is valid, the effect didn't persist for an expanded set of populations and countries.  While genetic diversity affects differences between populations in a variety of other ways, when the effect is biological and population genetics theory applies, economic success is not one of them.  "[P]rinciples of population genetics produce no theory of the economic development of nations..."

It is of course plausible that overall variation patterns include variation that leads one population, overall, to have more, or less, of some societal attribute.  One can always construct post hoc stories that fit social prejudices, for example.  But plausibility is not the same as truth, and one can -- and should -- ask why the investigators are making their societal assertions in the first place.  Generally, we know the answer, and it isn't very savory.

Monday, September 7, 2015

How do we know what we think we know?

Two stories collided yesterday to make me wonder, yet again, how we know what we think we know.  The first was from the latest BBC Radio 4 program The Inquiry, an episode called "Can we learn to live with nuclear power?" which discusses the repercussions of the 2011 disaster in the Fukushima nuclear power plant in Japan. It seems that some of us can live with nuclear power and some of us can't, even when we're looking at the same events and the same facts.  So, for example, Germans were convinced by the disaster that nuclear power isn't reliably safe and so they are abandoning it, but in France, nuclear power is still an acceptable option.  Indeed most of the electricity in France comes from nuclear power.

Why didn't the disaster convince everyone that nuclear power is unsafe?  Indeed, some saw the fact that there were no confirmed deaths attributable to the disaster as proof that nuclear power is safe, while others saw the whole event as confirmation that nuclear power is a disaster waiting to happen.  According to The Inquiry, a nation's history has a lot to do with how it reads the facts.  Germany's history is one of division and war, and nuclear power associated with bombs, but French researchers and engineers have long been involved in the development of nuclear power, so there's a certain amount of national pride in this form of energy.  It may not be an unrelated point that therefore many people in France have vested interests in nuclear power.  Still, same picture, different reading of it.

Cattenom nuclear power plant, France; Wikipedia

Reading ability is entirely genetic
And, I was alerted to yet another paper reporting that intelligence is genetic (h/t Mel Bartley); this time it's reading ability, for which no environmental effect was found (or acknowledged).  (This idea of little to no environmental effect is an interesting one, though, given that the authors, who are Dutch, report that heritability of dyslexia and reading fluency is higher among Dutch readers -- 80% compared with 45-70% elsewhere -- they suggest because Dutch orthography is simpler than that of English.  This sounds like an environmental effect to me.)

The authors assessed reading scores for twins, parents and siblings, and used these to evaluate additive and non-additive genetic effects, and family environmental factors.  As far as I can tell, subjects were asked to read aloud from a list of Dutch words, and the number they read correctly within a minute constituted their score.  And again, as far as I can tell, they did not test for nor select for children or parents with dyslexia, but they seem to be reporting results as though they apply to dyslexia.

The authors report a high correlation in reading ability between monozygotic twins, a lower correlation between dizygotic twins, and between twins and siblings, and a higher correlation between spouses, which to the authors is evidence of assortative mating (choice of mate based on traits associated with reading ability).  They conclude:
Such a pattern of correlation among family members is consistent with a model that attributes resemblance to additive genetic factors, these are the factors that contribute to resemblance among all biological relatives, and to non-additive genetic factors. Non-additive genetic factors, or genetic dominance, contributes to resemblance among siblings, but not to the resemblance of parents and offspring.  Maximum likelihood estimates for the additive genetic factors were 28% (CI: 0–43%) and for dominant genetic factors 36% (CI: 18–65%), resulting in a broad-sense heritability estimate of 64%. The remainder of the variance is attributed to unique environmental factors and measurement error (35%, CI: 29–44%).
Despite this evidence for environmental effect (right?), the authors conclude, "Our results suggest that the precursors for reading disability observed in familial risk studies are caused by genetic, not environ- mental, liability from parents. That is, having family risk does not reflect experiencing a less favorable literacy environment, but receiving less favorable genetic variants."

The ideas about additivity are technical and subtle.  Dominant effects, that is, non-additive interactions among alleles within a gene in the diploid copies of an individual, are not inherited as additive ones are (if you are a Dd and that determines your trait, only one of those alleles, and hence not enough to determine the trait, is transmitted to any of your offspring).  Likewise, interactions (between loci), called epistasis, is also not directly transmitted.

There are many practical as well as political reasons to believe that interactions can be ignored.  In a practical sense, even multiple 2-way interactions make impossible sample size and structure demands.  But in a political sense, additive effects mean that traits can be reliably predicted from genotype data (meaning, even at birth): you estimate the effects of each allele at each place in the genome, and add them to get the predicted phenotype.  There is money to be made by that, so to speak.  But it doesn't really work with complex interactions.  Strong incentives, indeed, to report additive effects and very understandable!

Secondly, all these various effects are estimated from samples, not derived from basic theory about molecular-level physiology, and often they are hardly informed by the latter at all.  This means that replication is not to be expected in any rigorous sense.  For example, dominance is estimated by the deviation of average traits in AA, Aa, and aa individuals from being in 0, 1, 2 proportions if (say) the 'a' allele contributed 1-unit of trait measure.  Dominance deviations are thoroughly sample-dependent.  It is not easy to interpret those results when samples cannot be replicated (the concepts are very useful in agricultural and experimental breeding contexts, but far less so in natural human populations). And this conveniently overlooks the environmental effects.

This study is of a small sample, especially since for many traits it now seems de rigueur to have samples of hundreds of thousands to get reliable mapping results, not to mention a confusingly defined trait, so it's difficult, at least for me, to make sense of the results.  In theory, it wouldn't be terribly surprising to find a genetic component to risk of reading disability, but it would be surprising, particularly since disability is defined only by test score in this study, if none of that ability was  substantially affected by environment.  In the extreme, if a child hasn't been to school or otherwise learned to read, that inability would be largely determined by environmental factors, right?  Even if an entire family couldn't read, it's not possible to know whether it's because no one ever had the chance to learn, or they share some genetic risk allele.

In people, unlike in other animals, assortative mating has a huge cultural component, so, again, it wouldn't be surprising if two illiterate adults married, or if they then had no books in the house, and didn't teach their children that reading was valuable.  But this doesn't mean either reading or their mate-choice necessarily has any genetic component.  

So, again, same data, different interpretations  
But why?  Indeed, what makes some Americans hear Donald Trump and resonate with his message, while others cringe?  Why do we need 9 Supreme Court justices if the idea is that evidence for determination of the constitutionality of a law is to be found in the Constitution?  Why doesn't just one justice suffice?  And, why do they look at the same evidence and reliably and predictably vote along political lines?

Or, more uncomfortably for scientists, why did some people consider it good news when it was announced that only 34% of replicated psychology experiments agreed with the original results, while others considered this unfortunate?  Again, same facts, different conclusions.

Why do our beliefs determine our opinions, even in science, which is supposed to be based on the scientific method, and sober, unbiased assessment of the data?  Statistics, like anything, can be manipulated, but done properly they at least don't lie.  But, is IQ real or isn't it?  Are behavioral traits genetically determined or aren't they?  Have genome wide association studies been successful or not?

As Ken often writes, much of how we view these things is certainly determined by vested interest and careerism, not to mention the emotional positions we inevitably take on human affairs.  If your lab spends its time and money on GWAS, you're more likely to see them as successful.  That's undeniable if you are candid.  But, I think it's more than that.  I think we're too often prisoners of induction, based on our experience, training, predilections of what observations we make or count as significant; our conclusions are often underdetermined, but we don't know it.  Underdetermined systems are those that are accounted for with not enough evidence.  It's the all-swans-are-white problem; they're all white until we see a black one. At which point we either conclude we were wrong, or give the black swan a different species name.  But, we never know if or when we're going to see a black one.  Or a purple one.

John Snow determined to his own satisfaction during the cholera epidemic in London in 1854 that cholera was transmitted by a contagion in the water.  But in fact he didn't prove it.  The miasmatists, who believed cholera was caused by bad air, had stacks of evidence of their own -- e.g., infection was more common in smoggy, smelly cities, and in fact in the dirtier sections of cities.  But both Snow and the miasmatists had only circumstantial evidence, correlations, not enough data to definitively prove their were right.  Both arguments were underdetermined.  As it happened, John Snow was right, but that wasn't to be widely known for another few decades when vibrio cholerae was identified under Robert Koch's microscope.

"The scent lies strong here; do you see anything?"; Wikipedia

Both sides strongly (emotionally!) believed they were right, believed they had the evidence to support their argument. They weren't cherry-picking the data to better support their side, they were looking at the same data and drawing different conclusions.  They based their conclusions on the data they had, but they had no idea it wasn't enough.  

But it's not just that, either.  It's also that we're predisposed by our beliefs to form our opinions.  And that's when we're likely to cherry pick the evidence that supports our beliefs.  Who's right about immigrants to the US, Donald Trump or Bernie Sanders?  Who's right about whether corporations are people or not?  Who's right about genetically modified organisms?  Or climate change?  Who's right about behavior and genetic determinism?  

And it's even more than that! If genetics and evolutionary biology have taught us anything, they've taught us about complexity.  Even simple traits turn out to be complex.  There are multiple pathways to most traits, most traits are due to interacting polygenes and environmental factors, and so on. Simple explanations are less likely to be correct than explanations that acknowledge complexity, and that's because evolution doesn't follow rules, except that what works works, and to an important degree that's what is here to be examined today.  

Simplistic explanations are probably wrong.   But they are so appealing.