Snowy Thoughts on the Scientific Revolution

Snowed in here on Presidents Day, I won’t claim to be quite as inspired as Descartes meditating in his overheated cabin, but I do have some thoughts to share.

Recently I read a number of books and book chapters on the Scientific Revolution. I wanted to know, what exactly changed in our society’s approach to knowledge? We have modern science today, and in the year 1500 the prevailing approach to knowledge in Europe was something else. What changed and why?

Obviously that’s a big topic and historians of the scientific revolution have tackled this problem from a variety of angles. There were social changes and institutional changes, including those associated with the Reformation and the Renaissance, there was the invention of movable type, the European discovery of the Americas, various technological changes, especially in glassworks that led to the construction of the first telescopes, mircoscopes, and barometers. There is a lot of fodder here for historians, and it would be too simplistic to ask, what was the one thing that caused people to empirically study the world around them? The Scientific Revolution is not about the defeat of superstition by reason (though David Wootton, in his wonderful history, The Invention of Science, argues that the Scientific Revolution led educated people to give up on their beliefs in witches, werewolves, magnets neutralized by garlic, etc.). Nor is it about people deciding to start observing the world – Aristotle himself, as well as many of the Medieval scholastics were very careful observers of nature.

Three of the books I’d recommend are:

  1. Peter Dear’s Revolutionizing the Sciences, a concise book intended as kind of a textbook that neatly asks what it meant to know something in 1500 versus what it meant to know something in 1700. Overall, this book most directly gets at my interests.
  2. Steven Shapin’s The Scientific Revolution. Shapin has some notoriety for his relativist take on science, but this is a worthwhile book. The philosopher Peter Godfrey-Smith, in his textbook on the philosophy of science, says this is not a good history of the scientific revolution, but it’s an interesting book nonetheless. I agree that this is worth reading. Shapin considers what was considered worth knowing and why during the Scientific Revolution. The answer to this kind of question naturally involves a discussion of social changes, which of course were critical in the development of science. My criticism is that this book is too focused on changes in rhetoric alone (largely about the metaphor of a clockwork universe). When you view the Scientific Revolution as largely a rhetorical battle, you miss the impact of the new, quite radical empirical discoveries that occurred during the 16th and 17th centuries.
  3. David Wootton’s The Invention of Science. Hands down, this is the best history of the Scientific Revolution out there. It is carefully argued, with its claims backed up much more by extensive evidence than in any other broad book on the subject. Wootton’s unique approach is to understand the conceptual changes of the era by studying linguistic changes, made possible by online, searchable texts. Wootton uses the changing use of words like fact and discovery (and not just in English!) to chart conceptual changes. Wootton also, much more directly than any other historian that I read, directly engages with claims made in the philosophy of science. For example, the discovery of the complete phases of Venus, which was flat-out incompatible with the Ptolemaic system, led to a more silent paradigm shift than Thomas Kuhn would have predicted.

In any case, this is a long wind-up to the main point of this post. As complex as the Scientific Revolution was, for me the most interesting take is this: In the 17th century, the Aristotelian understanding of what it means to know something was replaced by a new understanding that largely still holds in modern science. Here’s what Aristotelians thought of what was called scientia:

The medieval Latin scientia, although cognate with the modern English “science,” referred to any rigorous and certain body of knowledge that could be organized (in precept though not always in practice) in the form of syllogistic demonstrations from self-evident premises. Under this description, rational theology belonged to scientia – indeed, it was the “queen of sciences” – because its premises were the highest and most certain. Excluded, however, were disciplines that studied empirical particulars, such as medical therapeutics, natural history, and alchemy, because there can be no absolute certainty about particular phenomena. (“The Age of the New”, Katherine Park and Lorraine Datson, Cambridge History of Science: Early Modern Science).

For Aristotelians, empirical disciplines were not science because their findings couldn’t be demonstrated with certainty. The Scientific Revolution turned this conception of knowledge upside down: empirical findings of non-self-evident phenomena became more reliable than syllogistic demonstration from self-evident premises. Aristotelians assumed most interesting phenomena were common knowledge, and all we needed to do was reason about them. The new meaning of the word ‘science’, however, was something else: discovery of new phenomena through experiment and explaining them with mathematical principles.

In other words, the old scientia was this: logical demonstration from self-evident principles to achieve certainty. The new science was this: fallible conclusions based on the empirical discovery of new phenomena beyond our everyday experience.

What this means is that, by giving up the need for absolute certainty, we managed to figure out the most reliable way to discovery knowledge that humans have ever hit upon.

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 “Reupping:Why reproducibility initiatives are misguided”

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.