Category Archives: Curiosities of Nature

Reupping:Why reproducibility initiatives are misguided

I’m reposting this two-year old piece, because it’s worth reminding ourselves why exact replication has, with minor exceptions, never been an important part of science:

In my latest Pacific Standard column, I take a look at the recent hand-wringing over the reproducibility of published science. A lot of people are worried that poorly done, non-reproducible science is ending up in the peer-reviewed literature.

Many of these worries are misguided. Yes, as researchers, editors, and reviewers we should do a better job of filtering out bad statistical practices and poor experimental designs; we should also make sure that data, methods, and code are thoroughly described and freely shared. To the extent that sloppy science is causing a pervasive reproducibility problem, then we absolutely need to fix it.

But I’m worried that the recent reproducibility initiatives are going beyond merely sloppy science, and instead are imposing a standard on research that is not particularly useful and completely ahistorical. When you see a hot new result published in Nature, should you expect other experts in the field to be able reproduce it exactly? Continue reading

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A Long View of the Scientific Revolution

wotton Been eager to get this doorstop of a book, which sat on my shelf for most of 2016:  David Wotton’s The Invention of Science. I’ll have more to say later, but for now, a few pages in, it’s clear that Wotton really takes the long view on science. “It is far too soon to say” how the Scientific Revolution will turn out:

But since 1572 the world has been caught up in a vast Scientific Revolution that has transformed the nature of knowledge and the capacities of humankind. Without it there would have been no Industrial Revolution and none of the modern technologies on which we depends; human life would be drastically poorer and shorter and most of us would live lives of unremitting toil. How long it will last, and what its consequences will be, it is far too soon to say; it may end with nuclear war or ecological catastrophe, or (though this seems much less likely) with happiness, peace and prosperity.

Reading Regulatory DNA, or My Attempt to Explain What I Do

At the end of October, our paper on gene regulation in the retina was published in Cell Reports. (We paid good money for open access, so go ahead, click the link – there’s no paywall.) Our editor asked us if we wanted to try two things to help explain our work to our broader audience. The first is Figure360, a brief video guide to one figure in our paper. This is still fairly technical; it’s how I might explain our work in a conference poster presentation.

The second way we were invited to explain our work was in an informal post on the Cell Reporter blog. Here I tried to explain what we did in a way that would make sense to my mother. (Who has a bachelor’s degree in biology, so at least I had a chance)  My mother’s response: “I read it 3 times to better understand it.  It is a difficult topic.” In other words, I failed to make sense…

It’s not the most jargon-free thing I’ve written, but for your edification and enlightenment, I’m posting the link here. Check it out to understand massively parallel reporter gene assays and our Goldilocks theory of gene expression.

 

 

Climate change has altered nearly all of the planet’s ecosystems

It looks like we’re going to have a climate change denier heading up the EPA, Oklahoma’s attorney general Scott Pruitt, who has spent the Obama administration suing the agency he will now lead. So we’ll be hearing a lot about whether the science is “settled” and the uncertainty in climate scientists forecast.

As you listen to these debates, the thing to know is that climate change isn’t just about what might happen in the future. It has already radically altered the planet in ways that may be invisible to those of us who live in wealthy countries, but not to just about all life on Earth. As a recent review of the documented biological impacts of climate change puts it, “Climate change impacts have now been documented across every ecosystem on Earth.”

Last month I wrote about this story for Pacific Standard. The key point is one to keep in mind as we confront denialism in the Trump administration:

The consequences of widespread and rapid changes to something as complex as the world’s ecosystems are difficult to predict. The unpredictability of these consequences has been used as an excuse to dismiss them and paint scientists as alarmists. But unpredictability is exactly what should concern us: Our civilization, including our agriculture, water usage, population geography, and public-health measures, are adapted to fit the global climate that we live in. The prospect of further broad, unpredictable shifts to the world’s ecosystems should spur us to action, not complacency. As the authors of the Science paper write, “humanity depends on intact, functioning ecosystems for a range of goods and services.” For most life in those ecosystems, climate change is not a future event, but a present reality.

 

 

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.