Enjoying the end of summer

We’re having some glorious end-of-summer weather here in Switzerland. Yesterday, a friend and I rode down to the river, and our horses enjoyed splashing around in the water.

I would argue that riding can also be a reflective ecological method, although it does require a bit more active focus than does relaxedly strolling along. But it also changes your perspective. You’re higher up, for one thing – closer to the tree branches and farther from the ground-dwelling insects (which are usually what capture my attention). For another, you are an intimate part of another creature’s experience. You realize that literally every plant has a risk of herbivory. You appreciate how deeply ingrained the flight instinct is in prey animals. Your attention is drawn to sounds before you have actually heard them.

Anyone who interacts with horses know that they are intelligent, opinionated, and communicative, and here is some supporting evidence. A research team in Norway taught a group of horses to use a set of wooden boards with different symbols to ask to have their winter blankets put on or taken off. All the horses learned what the symbols meant and applied what they had learned in order to be comfortable in different weather conditions.

(I’ll let you know how that goes with my horse!)

Beauty, sexual selection, and meditation

I recently finished the audiobook of “Why Buddhism is True” by Robert Wright. I also recently started reading “The Evolution of Beauty” by Richard Prum, and I think there are ideas in the latter that could inform the former. Of course, when one, as Wright does, writes a book that includes arguments about natural selection, a fuller discourse on evolution helps.

In this case, I noticed that Wright discussed natural selection to the neglect of other evolutionary forces. Continue reading

Musings on human evolution

I love when science provides space for fun, and it so often does. Some time ago, I read Richard Lenski and Terence Burnham’s 2017 paper in the Journal of Bioeconomics entitled “Experimental evolution of bacteria across 60,000 generations, and what it might mean for economics and human decision-making,” (1) and it was one of those papers where I could tell that they had a blast writing it. They give an overview of the Long-Term Evolution Experiment (LTEE), which Lenski has running for longer than I have been alive (if it were a scientist, it could be applying for postdocs by now), and how understanding how bacteria evolve may or may not help us understand some of the random stuff people do.

Because, as behavioral economists know, the random and illogical things that people do actually show patterns and have plausible and increasingly evidence-backed explanations (yes, I am a fan of the Freakonomics Radio podcast).

My favorite point that Lenski and Burnham make in the paper is that many of the human inventions that we consider commonplace and integral to our lives, like stock exchanges, colonoscopies, and agriculture, have in an evolutionary sense not been around for very long. Continue reading

Thoughts on reading the Introduction to “The Structure and Confirmation of Evolutionary Theory” by Elisabeth A. Lloyd

1.

Lloyd describes J. J. C. Smart’s opinion that biologists use statistics only to do significance testing on experimental data and not to extract trends and create generalizable models of underlying fundamental processes as scientists in other disciplines (notably physics and chemistry) do.

In my experience of learning statistics and talking with others about statistics, this is not an entirely unfair accusation. The only statistics I learned during my undergraduate studies in biology were related to basic significance testing (e.g. t-tests and chi-squared tests) and how to formulate hypotheses testable by these methods. It wasn’t until after completing my masters degree that I have started to learn in depth, through self-motivated study, about linear modeling, how that relates to principles of experimental design and power analysis, and how to generalize responsibly. Continue reading

Playing with neural networks – new scientific names for bacteria

It was recently Valentine’s Day, and I came across the story of an AI that had come up with some innovative messages to print on candy hearts. Over Christmas, my sister (who never fails to bring joy into my life) had shown me a new Harry Potter story that had been written by an AI, and I was extremely taken with this new source of mirth in my life. Needless to say, it wasn’t long before I wondered whether I could put neural networks to my own uses.

Via an aiweirdness post about recipes, I found the open-source neural network code that Janelle Shane used, and I thought I should give it a try. After some struggle learning how to navigate in Mac’s terminal and figuring out all the things I had to install to get the model to run – I did it. I ran a neural network! My fiancé learned to code his own neural networks a few months ago just for fun, so I was expecting it to be a much more involved process. But karpathy did the hard work of writing the neural network code; I just had to implement it. Continue reading

Why is showering bad for our skin bacteria? (evolutionary questions)

After reading Alanna Collen’s 2015 book 10% Human: how your body’s microbes hold the key to health and happiness, I have become interested in, among other topics featured in the book, the work of the AOBiome company. Collen mentions this company in the context of aspects of our modern lifestyle which may be detrimental to the beneficial microbes that live on and in us. In this particular case, it is the practice of showering every day with body soap and deodorant that may be disproportionately displacing certain types of bacteria that process ammonia and help control the bacteria responsible for giving us body odor. AOBiome proposes that by replenishing these ammonia-oxidizing bacteria (AOBs) on our skin, we can reduce or eliminate the need for deodorants and showers. We can also replenish them through contact with soil or untreated (an unpolluted) water, according to Collen. I have read up on AOBiome a bit, and their scientific logic seems sound and is backed up by pilot studies they have done (see end for links). However, I have some questions about the evolutionary biology side of things: Continue reading

Nicco’s list of notable female scientists

My lab recently went on a retreat, during which each lab member gave a presentation or led an activity on the topic of their choice (one colleague of mine led us in a ballet tutorial, another in a “choose your own adventure” Youtube video series). One presentation that I found particularly inspiring was simply a list of several female scientists and their important contributions to their fields. This is not the first time I have encountered such a list, but it is the first time that I was familiar with more than one or two of the names on it. I’m not particularly conversant in the names and deeds of my scientific forebears (a fact which I am working to remedy), so this has never surprised me. But this time I knew of 6 of the 13 of the scientists we talked about! That means I’ll be asking for seven biographies for my birthday this year… Continue reading

How fast is evolution?

This question came up during a class I took during my masters studies at the ETH Zurich. What is the maximum speed of evolution? On what factors does it depend? We discussed the idea that selection curbs the speed of evolution, acting as a brake by removing some phenotypes from the population and preventing evolution from continuing down those trajectories.

In that case, evolution without brakes means evolution in the absence of selection. All individuals reproduce in a statistically equal way, and individuals carrying mutations that in the real world would be lethal have just as many offspring as anyone else.

If we think of evolution in terms of travel through sequence space, then we can ask what affects the speed of that travel. Imagine that we start with a single reproducing genotype GREEN of length K in an environment that imposes no restrictions on population size or anything else.

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First grant

sword and shield medieval fencing

As a sophomore at Sweet Briar College, I received an honors grant to study the recreation and practice of Western European historical swordsmanship. Here is a video of me talking about the experience at the Pannell Scholars Fair in the spring of 2013, and here is an article with a few highlights.

So my professor has this to look forward to when I defend my PhD –> xkcd: Thesis Defense

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