Uncommon Ground

Academics, biodiversity, genetics, & evolution

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I am a snoot

I have little trust in people who don't use the Oxford comma.

From grammarly.com

Last Friday I confessed to my obsession with grammar and usage. In response, Alex Buerkle (@disequilibber) passed along a link to a wonderful article by David Foster Wallace describing the state of the “language wars” in the early 2000s. If you’ve never heard of the language wars or of the epic battle between prescriptionists and descriptionists, you may not find the article all that interesting, but it really struck a chord with me. I am a snoot.

A SNOOT can be defined as somebody who knows what dysphemism means and doesn’t mind letting you know it.

OK. Maybe I’m not really a snoot. I had to Google “dysphemism” – a derogatory or unpleasant term used instead of a pleasant or neutral one, such as “loony bin” for “mental hospital” – and I probably won’t brag about knowing the definition now (and I doubt that it will enter my regular vocabulary). So maybe it’s more accurate to say that I have a lot of sympathy with snoots. If you want to understand that means, I’m afraid you’ll have to read Wallace’s article. Here’s the link: http://harpers.org/wp-content/uploads/HarpersMagazine-2001-04-0070913.pdf Bottom line: Grammar and usage matter, because they convey a lot about us. The dialect we choose to use says a lot about who we are and about who we think our audience is.

Reproducibility is hard

Last year, the Open Science Collaboration published a very important article: Estimating the reproducibility of psychological science. Here’s a key part of the abstract:

We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. There is no single standard for evaluating replication success. Here, we evaluated reproducibility using significance and P values, effect sizes, subjective assessments of replication teams, and meta-analysis of effect sizes. The mean effect size (r) of the replication effects (Mr = 0.197, SD = 0.257) was half the magnitude of the mean effect size of the original effects (Mr = 0.403, SD = 0.188), representing a substantial decline. Ninety-seven percent of original studies had significant results (P < .05). Thirty-six percent of replications had significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.

Since then, reproducibility has gained even more attention than it had before. My students and I have been taking baby steps towards good practice – using Github to share code and data (and versions), using scripts (mostly in R) to manipulate and transform data, and making the code and data freely available as early in the writing process as we can. But there are some important things we don’t do as well as we could – I’ve never tried using Docker to ensure that all versions of the software we use for analysis in a paper are preserved, I’m as bad at writing documentation for what I’m doing as I ever was (but I try to write my code as clearly as possible, so it’s not too hard to figure out what I was doing.

I need to do better, but Lorena Barba (@LorenaABarba) had a article in the “Working Life” section of Science that made me feel a bit better about how far I have to go. Three years ago she posted a manifesto on reproducibility. In her Science piece, she describes how hard it’s been to live up to that pledge. But she concludes with some words to live by:

About 150 years ago, Louis Pasteur demonstrated how experiments can be conducted reproducibly—and the value of doing so. His research had many skeptics at first, but they were persuaded by his claims after they reproduced his results, using the methods he had recorded in keen detail. In computational science, we are still learning to be in his league. My students and I continuously discuss and perfect our standards, and we share our reproducibility practices with our community in the hopes that others will adopt similar ideals. Yes, conducting our research to these standards takes time and effort—and maybe our papers are slower to be published. But they’re less likely to be wrong.

Barba, L.A. 2016. The hard road to reproducibility. Science 354:142 doi: 10.1126/science.354.6308.142
Open Science Collaboration. 2015. Estimating the reproducibility of psychological science. Science 349:aac4716 doi: 10.1126/science.aac4716

On commas and grammar

I have little trust in people who don't use the Oxford comma.

From grammarly.com

I admit it. I am obsessed with grammar and usage. I own all four editions of Fowler, and I also own Follett, Garner, two or three editions of Strunk and White, and many other usage manuals. I am also a big fan of the Oxford comma. So I was pleased to see Kathleen Parker’s column in The Washington Post last week. Here’s why:

[Grammar] matters because good grammar conveys a great deal about a person.

Quality is in the details — and attention to commas, semicolons, dangling participles, gerunds and the proper placement of quotation marks says to the reader that this person is careful, considerate (because bad grammar is painful to the discerning eye), and (there’s that Oxford comma) competent.

“Grammar is credibility,” says Amanda Sturgill, an associate professor of communications at Elon University, where I recently spoke. “If you’re not taking care of the small things, people assume you’re not taking care of the big things.”

Noise miners

I’ve pointed out the problems with small, noisy samples using simulations (here, here, here, and here). But I’ve also learned that stories are far more persuasive than facts, and I’ve learned that I’m not good at telling stories. Fortunately, there are some people who tell stories very well, and John Schmidt is one of them. Here’s how his recent story, Noise Miners, starts.

What most people don’t understand about noise is how hard it is to find the good stuff.

You can get noise anywhere; most noise is just sitting on the ground, waiting for you to pick it up. Coincidences — “coinkidinks”, as collectors sometimes call them — can be had by the dozen just outside your front door. As I arrived in this small university town, home to one of the largest noise mines in the country, I planned to see how the high-quality noise was dug, and to learn about the often-forgotten people who dig it for us.

Follow the link and read the whole thing if that piques your interest.

Plants can be endangered too!

Yes. I know that if you’re reading this, you already know that there are thousands of endangered plant species in the world. You may even know that I’ve spent a fair amount of time thinking about how to protect them and how to prevent those that have small populations from declining even further. So why the title? Two reasons:

First, Mung Balding and Kathryn Williams have a very nice article in Conservation Biology explaining why plant blindness is such a problem. Here’s the abstract:

Plant conservation initiatives lag behind and receive considerably less funding than animal conservation projects. We explored a potential reason for this bias: a tendency among humans to neither notice nor value plants in the environment. Experimental research and surveys have demonstrated higher preference for, superior recall of, and better visual detection of animals compared with plants. This bias has been attributed to perceptual factors such as lack of motion by plants and the tendency of plants to visually blend together but also to cultural factors such as a greater focus on animals in formal biological education. In contrast, ethnographic research reveals that many social groups have strong bonds with plants, including nonhierarchical kinship relationships. We argue that plant blindness is common, but not inevitable. If immersed in a plant-affiliated culture, the individual will experience language and practices that enhance capacity to detect, recall, and value plants, something less likely to occur in zoocentric societies. Therefore, conservation programs can contribute to reducing this bias. We considered strategies that might reduce this bias and encourage plant conservation behavior. Psychological research demonstrates that people are more likely to support conservation of species that have human-like characteristics and that support for conservation can be increased by encouraging people to practice empathy and anthropomorphism of nonhuman species. We argue that support for plant conservation may be garnered through strategies that promote identification and empathy with plants.

Second, Robbie Blackhall-Miles (@fossilplants) has a passionate post in Gardens (the gardening blog at The Guardian) describing just how repugnant the trade in endangered plant species is.

Buying just one orchid illegally on the internet from Indonesia or a few snowdrops dug from the wild in Bulgaria fans the flames of a trade that has dire consequences for the world’s plant life. Buying one of these plants is exactly the same as buying a carved piece of ivory, a tiger skin or a gram of ground rhino horn. Wouldn’t you think twice about doing that?

OK. I can’t help myself. There’s a third reason. When you hear the phrase “endangered species” do you think of an orchid or a cycad, or do you think of a panda, a rhino, or a tiger? If a picture of an animal popped into your head first (and not just an animal, but a mammal), it shows how much work we have to do.

Balding, M., and K.J.H. Williams. 2016. Plant blindness and the implications for plant conservation. Conservation Biology doi: 10.1111/cobi.12738

Terry Tempest Williams on wilderness

From The Hour of Land: A Personal Topography of America’s National Parks:

The legacy of the Wilderness Act is a legacy of care. It is the act of loving beyond ourselves, beyond our own species, beyond our own time. To honor wildlands and wild lives that we may never see, much less understand, is to acknowledge the world does not revolve around us. The Wilderness Act is an act of respect that protects the land and ourselves from our own annihilation.

The Wilderness Act

Naomi Oreskes and Erik M. Conway on the nature of science and science policy

I read Merchants of Doubt several years ago. If you haven’t read it yet, I urge you to buy a copy now (or check it out from your local library) and read it immediately. I was thumbing through some notes recently and ran across this passage that sums up the nature of science and its relationship to policy very nicely.

All scientific work is incomplete – whether it be observational or experimental. All scientific work is liable to be upset or modified by advancing knowledge. That does not confer upon us a freedom to ignore the knowledge we already have, to postpone action that it appears to demand at a given time. “Who knows,” asks Robert Browning, “but the world may end tonight?” True, but on available evidence most of us make ready to commute on 8:30 the next day.

This is only one of many gems in Merchants of Doubt. Read it and share it with your friends and family.