Author: Mike White

Genomes, Books, and Science Fiction

The Legacy of Slavery in African American DNA

This week at Pacific Standard,  I discuss a recent study that examines the influence of slavery and its discriminatory aftermath in the genetic diversity in over 4,000 African American genomes. One of the most striking results of the study is probably the most obvious: On average, about 15% of the DNA of African Americans is of European origin – and, according the researchers’ best statistical model, that European DNA largely dates back to before the Civil War. That was a time when interracial sexual relations overwhelmingly took the form of whites raping black slaves. After the Civil War, according to the model, admixture between blacks and whites dropped off sharply.

Like I said, it’s not particularly surprising, but the breadth of the genetic legacy of slavery is striking.

The study makes some other intriguing suggestions about African American genetic history, especially regarding the enormous demographic shift of the Great Migration (~1915-1970), when 6 million African Americans left the South and settled in other parts of the country. The big takeaway from this study is that African American genetic history is one of coercion: coerced migration and coerced sex over a relatively short period of time, which left strong signals in the genetic diversity of present day African Americans.

Aside from the historical aspect, studies like this matter if African Americans are going to participate in the ongoing development of personalized genomic medicine. Because the genetic structure of the African American population differs from that of whites, African Americans have different genetic risk factors for disease – and even different risk variants for the same diseases. Studies like this lay the groundwork for an inclusive practice of genomic medicine.

Sunday Science Poem: Darwin and Happy Endings

Wisława Szymborska’s “Consolation” (2002)
henri_rousseau_-_fight_between_a_tiger_and_a_buffaloEvolution has always been more controversial socially than scientifically. After Darwin published the Origin, the idea that all species descended from common ancestors was quickly accepted by most biologists (though his proposed mechanism of evolution, natural selection, remained controversial until the 20th century). Socially, however, evolution was and remains difficult for many people to swallow. The literalist beliefs of religious fundamentalists of course conflict with evolution. But even among those who don’t have a particular religious axe to grind, discomfort is not uncommon. Evolution in practice is brutal: we posses our unique adaptations – our brains, our opposable thumbs, our ability to talk, to socialize, to feel, see, and touch – thanks to the selective death of billions of organism over eons.

In her hilarious poem “Consolation”, the late Nobel-winning Polish poet Wisława Szymborska ironically contrasts the brutality of the real world in which evolution plays out, with the romantic world we construct for ourselves. She portrays Darwin, the great thinker who first grasped the harsh reality of evolution, as someone who escapes by reading novels with only happy endings.
Consolation

Darwin.
Supposedly for relaxation he read novels.
But he had a requirement:
they couldn't end sadly.
If he happened on one,
he flung it furiously in the fire.

True or not –
I gladly believe it.

Roaming in his mind over so many times and places
looking back on all the extinct species,
such triumphs of strong over weak,
so many tests of survival,
sooner or later all in vain,
that at least in fiction
and its micro-scale
he had a right to expect a happy ending.

And so necessarily: sunrays behind a cloud,
lovers together again, kin reconciled,
doubts dissolved, faith rewarded,
fortunes recovered, treasures dug up,
neighbors regret their mulishness,
good names restored, greed put to shame,
old maids married to respectable ministers,
schemers expelled to the other hemisphere,
forgers of documents cast down the stairs,
seducers of virgins hurrying to altars
orphans taken in, widows embraced,
pride humbled, wounds mended,
prodigal sons invited to the table,
the cup of bitterness poured into the sea,
tissues wet with tears of reconciliation,
universal singing and music-making,
and the puppy Fido,
lost already in the first chapter,
let him run home again
and bark joyfully.

Translation from the Polish by Michael A. White (2016)
Image: “Fight Between a Tiger and a Buffalo”, Henri Rousseau (1908), via Wikimedia Commons.

Sloppiness vs Reproducibility

I’m not a big fan of reproducibility projects. Shoddy papers shouldn’t be tolerated, but the truth is that sometimes rigorously done research isn’t reproducible — and when that happens, science gets interesting. It should go without saying that a peer-reviewed paper isn’t a guarantee of truth. If done properly, a paper is a record of a rigorous attempt to discover something about the world, no more, no less. What we believe about nature should reflect the accumulated evidence of many researchers and many papers, and that means the scientific literature should reflect our latest tentative, bleeding-edge thinking, even at the risk of being wrong. It’s counterproductive to hold up publication until some other lab reproduces your result, or to retract papers that don’t hold up, unless they had clear methodological flaws or artifacts that should have been caught in review.

Two recent articles capture what I think is the right attitude on reproducibility. First, as David Allison and his colleagues write, as a community of researchers, editors, and reviewers, we’re not doing as well as we should be when it comes to meeting high standards for best statistical and other methodological practices:

 In the course of assembling weekly lists of articles in our field, we began noticing more peer-reviewed articles containing what we call substantial or invalidating errors. These involve factual mistakes or veer substantially from clearly accepted procedures in ways that, if corrected, might alter a paper’s conclusions.

There is no excuse for this kind of sloppiness.

On the other hand, here is Columbia’s Stuart Firestein:

The failure to replicate a part or even the whole of an experiment is not sufficient for indictment of the initial inquiry or its researchers. Failure is part of science. Without failures there would be no great discoveries.

So yes, let’s clean up science by rooting out obvious “invalidating practices” that all too often plague papers in journals at all tiers. But let’s not be naive about how science works, and what the scientific literature is supposed to be. To paraphrase what  I wrote recently, if some of our studies don’t turn out to be wrong, than we’re not pushing hard enough at the boundaries of our knowledge.

GMO wild organisms: As if GMO crops weren’t controversial enough…

The big biotech controversy of last year was over the ethics of using CRISPR to edit human embryos – something which a team of Chinese scientists did last April. The possibility of designer babies led to a major scientific summit meeting, hosted by the National Academy of Sciences, during which the attendees concluded that “It would be irresponsible to proceed with any clinical use of germline editing” until safety concerns are allayed and society comes closer to an ethical consensus.

While the world was fretting about edited embryos, scientists introduced an even more ethically fraught biotechnology: gene drives, a tool to genetically modify organisms in the wild. Gene drives have the potential to do a lot of good, by controlling disease vectors like malaria-bearing mosquitos. But if you thought GMO crops were controversial, just wait to see how people react to GMO wild organisms.

I cover the new CRISPR-based gene drive technologies in my latest Pacific Standard column. Here’s the tl;dr version: Gene drives can do a lot of good, but because they are simple to make, and because their consequences aren’t confined by political borders, we’re going to have a hell of a time ensuring they’re used responsibly.

How to advance science by failure

Stewart Firestein has a provocative piece in Nautilus on the role of failing well in science:

As your career moves on and you have to obtain grant support you naturally highlight the successes and propose experiments that will continue this successful line of work with its high likelihood of producing results. The experiments in the drawer get trotted out less frequently and eventually the drawer just sticks shut. The lab becomes a kind of machine, a hopper—money in, papers out.

My hope of course is that things won’t be this way for long. It wasn’t this way in the past, and there is nothing at all about science and its proper pursuit that requires a high success rate or the likelihood of success, or the promise of any result. Indeed, in my view these things are an impediment to the best science, although I admit that they will get you along day to day. It seems to me we have simply switched the priorities. We have made the easy stuff—running experiments to fill in bits of the puzzle—the standard for judgment and relegated the creative, new ideas to that stuck drawer. But there is a cost to this. I mean a real monetary cost because it is wasteful to have everyone hunting in the same ever-shrinking territory…

How will this change? It will happen when we cease, or at least reduce, our devotion to facts and collections of them, when we decide that science education is not a memorization marathon, when we—scientists and nonscientists—recognize that science is not a body of infallible work, of immutable laws and facts. When we once again recognize that science is a dynamic and difficult process and that most of what there is to know is still unknown.