Idiosophy

A physicist loose among the liberal arts

Author: Joe Page 3 of 30

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Ethiopia in Old English

This may be my new favorite Tolkien quote. It’s a refutation of scholars who thought the sigel in “Sigelwara-land” meant the sun:

The Ethiopians did not dwell in the sun, or have any such relation to it as exists between wara and its accompaniment in other compounds. They may have dwelt uncomfortably near it (east or west, the direct south seems to have been thought too hot even for them), but they were none the less earth dwellers, slowly roasted perhaps, but not cremated; they were not salamanders.

I think we have here a glimpse into the English mind-set that caused the UK Foreign Office to give 19th-century embassy staff  in Washington DC a pay augmentation because of the hazardous tropical climate. [citation needed]

Sunshine icon that is black with a white face

Bayes and the Bees

Over on Mastodon, I was alerted to a paper about bee populations on the prairie.1 The authors demonstrate that after the prairie is burned, ground-nesting bees move in in greater numbers than in similar patches of un-burned prairie. This is good stuff — it’s another contribution to our growing understanding that wildfires play a constructive role in the ecology of grasslands. (So say both the National Park Service and the Nature Conservancy, among others.)  This paper is very well done. The next time I think my job is tedious and nit-picky, I can think of these researchers examining bees under a microscope to see whether their mandibles are worn down from digging holes.

box-and-whisker plots of nest count and effective number of species

Figure 3 from Brokaw et al.

I’m writing this post because the graph of their primary result makes me sad. The results they’re showing are for matched sets of burned and un-burned plots at four sites. On the left, graph (a) shows their estimate of the number of active subterranean bee nests. On the right, (b) shows the “effective number of species” calculated by a tricky mathematical process2 from the sample of bees they caught.3

The authors want to show that there’s a significant difference between the burned (orange) and unburned sites, but this graph doesn’t do that. The horizontal line indicating the mean of each case is inside the range of the other case.  Putting a couple of asterisks at the top of  plot (a) (which was statistically significant) doesn’t help the visual impact of the overlapping boxes. I guess we could read the text around the figure to find out what tests they used and why they think the difference is significant, but then what’s the figure for? It’s supposed to be worth a thousand words.

Eight histograms

Plot of Table S3 from Brokaw et al.

Fortunately, this is an open-access paper and the authors have made their data available. Here are their data, as histograms of the number of nests they found in each of the sixteen samples at each of their four sites. The top row, burned, looks like they might have more nests than the bottom row, especially in the first and third sites (Devil’s Run and Miller), but the differences in sites 2 and 4 are harder to see. The main purpose of statistics is to make sure I’m not fooling yourself when I look at a graph, and this is an ideal place for it.

As it happens, my old computer joined the bleeding Choir Invisible a couple of weeks ago, and I’m just getting the new one properly furnished. I installed Richard McElreath’s “rethinking” package for R last night, so I’m all set to do some statistics.  Let’s see what I can do with Brokaw’s bees.

First, the number of nests they find is an integer. If we can make one more assumption, we can do a lot more with the data on hand. I’m going to say that the chance that a nest appears in a given sample site is independent of whether there’s already a nest there or not. I think this is pretty good. Their sample sites are squares 2-4 feet on a side. Every bee’s nest I ever dug up was a few inches across (the exact sizes were hard to determine while I was running away).4 The number of nests maxes out below 16, which means they’ve all got at least a foot between them. I think this is a good approximation.  [Edited to add: The Principal Investigator informs me that the things I dug up are wasp nests, which is indicated by the fact that I needed to run away. Bee nests are only a couple of millimeters across, the bees aren’t harmful, and the assumption is even better than I thought.]

That assumption lets us do a simple model: The number of nests they found is distributed according to a Poisson distribution. Poisson distributions have one parameter, the log of whose mean is a different number for each site, plus a constant for whether the site was burned or not. Prior distributions for all parameters were uninformative gaussians. The burning-constant is assumed to be the same for all sites. Here’s what comes out of the model.

Poisson regression results are a lot clearer than the box plots.

Posterior distribution of the parameter for each site and treatment.

This graph makes it clearer how good Brokaw et al.’s research finding was. There’s no question here — using a Bayesian Poisson regression model eliminates almost all the overlap between burned and unburned results. The burning-constant is +82%, with a 95% confidence interval from +45% to +227%. (Some of those peaks are really broad.) That is, regardless of which site we start at, the number of nests we’d expect to see in a recently-burned site would be 82% higher.

How good is the Poisson assumption? Pretty good, based on just looking at how far apart the nests are. One other argument, though: this model would break down if there were lots and lots of bee nests, but in that case we wouldn’t be worried about whether we were harming bee populations by stamping out grass fires, and nobody would have done these measurements in the first place.


Notes

Look, Ma! I’m on a podcast!

I don’t talk about my job much, because getting permission to release things to the public is a gigantic pain. But this time someone else did all the work.  Here’s a podcast about one of my co-workers. She’s talking about a cool thing she’s doing with graph theory:

Episode 16

The coolest figure from “Graph Theory as a Mathematical Model in Social Science”

My role in the podcast is to be an authoritative old geezer who tells amusing stories about what graphs are good for. As it happens, I started my experiments in 21st-Century graph theory right here on the blog. I do a lot of it at my job now, because I happened to be thinking along those lines when a problem came across my desk that needed graphs. And it took off from there. There are a lot of people thinking about how the humanities can play a bigger role in engineering, as engineers make decisions they think are independent of squishy, qualitative stuff.  I’m not sure this is what they’re referring to.

Funny coincidence: Corey Olsen was saying something similar in the Mythgard Academy “Alice” class the other night, except he was talking about English and chemistry.

 

Military Engineering in Literature

Aragorn: “Men are better than gates, and no gate will endure against our Enemy if men desert it.” 1

Christine de Pizan: “Even the strongest city will fall if there is no one to defend it.” 2


 

Alice Breaks a Law of Physics

It’s been fun going Through the Looking Glass with the Mythgard Academy. In my own (frequent) readings, I tend to focus on the mathematical jokes1, so the way Corey Olsen takes apart the verses is new to me.

I love the idea that the mirror is playing a substantial role. Tweedledum and Tweedledee are characters in a poem in our world. It’s in trochaic meter, with lines of four feet and three feet alternating. The poem they recite to Alice, which necessarily comes from their world, is in iambic meter, with lines of four feet and three feet.2 They’re mirror images!

Also, the way cause and effect get reversed is fun. The White Queen can remember either way through time, and Prof. Olsen makes the excellent point that when Alice thinks of a nursery rhyme from the primary world, and then the events happen to the characters around her, that’s the same phenomenon. She can remember things that haven’t happened yet.

Tenniel's illustration of the Lion and the UnicornReversal of poetic meter also happens, though less perfectly, in “The Lion and the Unicorn”. Suppose we use “+” to indicate a stressed syllable and “-” to indicate unstressed.3 The pattern of stresses in “The Lion and the Unicorn were fighting for the crown” is “-+-⁠-⁠-+-⁠-⁠-+-⁠-⁠-+” which my ear splits up into (-+-⁠-)(-+-⁠-)(-+-⁠-)(-+). That is to say, I hear it as a four-syllable foot. Now, I know that real scholars think the rhythm of the end of the line is important and the beginning is not, but that’s not how I hear things. I hear the rhythm established at the beginning as dominant. A change in rhythm within a line sounds like it’s at the end. 4

In the second line of “L&U”, Prof. Olsen talked quite a bit about the “all ’round the town”. One of the students asked why the first syllable was missing from “around”, which with the would have made it a nice alternation of stressed and unstressed syllables. But that’s not what this poem is about. This poem is about four-syllable feet. All ’round the town is “++-+”, which is what we get for the rest of the verse, like “Some gave them brown.” This latter foot is related to the first foot “-+-⁠-” by a mathematical transformation: exchange stressed syllables for unstressed, and reverse the order in time.

But wait a minute — there’s a symmetry of nature called CPT Symmetry that says if you exchange positive charges for negative (Charge), flip a system in a mirror (Parity), and reverse the flow of time (Time), all the laws of physics are the same. We’ve done all three here, so the plum-cake should act the same as it does in our world. At least, I hope we have done all three — if she’s just flipped Time and Parity, Alice has entered a world of antimatter and boom! the book would be much shorter. Slicing a plum-cake after it’s handed round is un-physical.

Now, we might be tempted to excuse Lewis Carroll on the grounds that quantum field theory wouldn’t be invented for half a century after the publication of Through the Looking Glass, but your humble Idiosopher respectfully submits that an author so skilled at time reversal should have remembered it.


 

Information, Data, Information

I’m catching up with A Collection of Unmitigated Pedantry. They have a guest post from James Baillie about prosopography from a few weeks ago. I did not know that prosopography has expanded from family relationships to more general connections. In fact, it seems to have crossed over into graph analysis. I hope they have taken Frank Harary’s appeal to heart and aren’t just drawing pictures, but are also using the mathematical power of a graph.

There’s interesting stuff there about medieval Georgia1, but the larger point Baillie gets across is about data-driven historical research: “a data structure or a block of code are things that make implicit and subjective arguments about how to see the world.” This is a good point, which I’ve lived in another context. In our modern world, data are everywhere. The job of combining data and synthesizing information from them employs a lot of people.

A historian has to do the reverse task as well, though. The evidence that we are given from the past is not data, pace2 the dictionary, we aren’t given data; we’re given information. We have immensely-powerful tools for processing digital data, which everyone should apply wherever they can. In order to exploit the power of data processing, though, a lot of human thought has to go into creating the database.

This is the way it used to be. The word “analysis” referred to the step where observations of the real world were cut up into data, then “synthesis” was how we reassembled the data into a theoretical framework.3 Our world of ubiquitous surveillance has greatly reduced the first step, causing us to put the lion’s share of our effort into the second. If we’re not careful we can lose sight of all the thought that needs to go into observation and analysis, and misinterpret what we’re seeing when we look at the synthesis. Good job by Baillie putting out that reminder.


 

Who’s Smarter?

I have recently made the acquaintance of a Philological Crocodile, who raises an interesting question: Are scientists really smarter than scholars of the humanities? 1 And then the crocodile chomps it to bits.  As it happens, I have an opinion on this question. Fortunately, I commit neither of the sins he excoriates.

I know a lot of really smart people on both sides of the divide. The humanities scholars are better at arguing. The scientists accomplish more, so we look smarter. This appearance can be traced to one underlying fact: in the sciences we have an objective standard for what is “true”. No theory ever completely passes that test, but a lot of ideas fail it. In the humanities, nothing seems ever to be completely decided. Any theory is as good as the person arguing for it.

This has an immediate practical consequence. Those who purport to study the humanities must learn centuries of earlier work and include it in their research. A dissertation in the humanities has hundreds of pages of description of earlier thoughts on the subject, accompanied by acknowledgements or refutations. The sciences carry little of that baggage. Because a scientist can be proven incorrect or irrelevant, all the previous thinkers and researchers who have turned out to be wrong can be ignored. Therefore, the sciences can progress faster.

Disseration is very thin

My dissertation; banana for scale

A visit to our Physics Department library in the 1980s gave me a lasting impression of this phenomenon. One bookcase held printed copies of all the doctoral dissertations in the history of the department. Most were about a centimeter thick. These were written by people who had made a significant original contribution to our knowledge of the natural world. A couple were 7-10 cm thick. These were dissertations for degrees in education or philosophy of science.

Mine was 133 pages long, double-spaced, and that includes the ancient tradition that figures should be on their own page and the caption on the facing page. My references were numbered 1 through 64.  Can you imagine anyone getting past a humanities review committee with 64 citations? Citations to the committee-members themselves probably have to be more than that.

So that’s my resolution of the whole argument. Scientists look smarter if we’re measuring achievement, but humanities scholars look smarter when we argue with them. If the humanities had a way to prove someone definitively wrong, future researchers could ignore anyone in that category and everyone could save a lot of time. It invites speculation — what would the humanities look like, if they advanced like the sciences do?

Surveying Twitter Replacements

light-blue bird in extremely poor healthTwitter is going downhill. I’ll stay there as long as I can, but I’ve been looking for a new place. I’m back from safari. Here’s my report on a few alternatives. I’ve visited Reddit and Imgur as well, but they seem qualitatively different from an actual twitter successor.

Micro.blog

Been there: Since 2018. Cost: Everybody pays $5/mo. Activity level: Quiet.

The place’s affect is weirdly decaffeinated. The population trends younger X to Millenials.  People here don’t like my jokes much.

This is the most interesting place from the social/software point of view. You’re not supposed to be a mere consumer of social media and clicker of hearts. Your posts to micro.blog are actually links to a real blog in an old-fashioned web-ring. Things you post here, i.e. to your micro-blog, will show up in a Google search. Every account has a built-in podcasting capability, too, though I’ve never used it. The site doesn’t have passwords; the server sends an e-mail with a link to click every time you log in. The iOS app is good (and you stay logged in). You can’t “like” a post; you have to say something nice instead. Nobody uses hashtags; they use emojis instead. Supports markdown for formatting posts.

I’ve only found one interesting professor to follow on this site. Lots of photographers.

Counter.social

Been there: Since April. Cost: Free, but I pay $5/mo for Pro membership. Activity level: Firehose

The friendliest social network. Everybody there seems cheerful and they’re promiscuous with upvotes and shares. It’s run by a famous hacker (all by himself). Counter.social is built on the Mastodon platform. When I joined I thought it was part of the Mastodon fediverse, but they’ve had a disagreement, so it went its own way. That means you can’t follow other Mastodonians from here. The Jester is so serious about keeping misogynists and fascists out that he’s blocked entire countries. I trust the security on this site. Somebody may try to get in, but I pity the fool. There are places for Virtual Reality chat rooms on the site. If anybody has ever used them, I haven’t seen it.

Update: you can get to CoSo from the web. Here I am, and here’s Corlin who clued me in.

No academics here. It’s mostly for everyday life and snarking about politics. A stranger once congratulated me for a “Tolkien deep cut” on this site. It was a quote from LotR.

Mastodon

Been there: 1 week. Cost: I’ll start chipping in if I like the place. Activity level: Firehose.

I’m on the universeodon server, which I can’t spell. I chose it because a couple of people from my Twitter feed are there. This site is the closest to reproducing my Twitter timeline. People I follow are here, as well as quite a few people I never followed because all their tweets got retweeted to me anyway. Old-timers use pseudonyms; twitter refugees use their real names. The program has gotten a bad rap on Twitter but I haven’t had any problems with it. I use the web interface because I haven’t heard enough good things about the app. Weirdly, “log out” is under the Preferences menu. Is that an omen?

The hard part is choosing a server, but it doesn’t matter if you don’t pick the ideal one. They’re interconnected really well. All the admins seem to be suffering a mild case of shock these days. If things coalesce in a few months, we can all get together somewhere.

I’ve found lots of interesting professors to follow. Humanities Commons runs its own Mastodon instance, invitation only, but they’ve had a really bad week for crashes.

Post.news

Been there: 1 day. Cost: complicated. Activity level: Garden hose.

Intended to be a place for grownups. You have to ask to join, but if they let me in they must not be too picky. (Write something interesting in the box where they ask you who you are; it helps.) People mostly use their real names. In terms of appearance, Post looks like Apple where Mastodon looks like Linux. It’s a private, for-profit company like Twitter that’s planning to make money off its users’ network.

The site is changing by the hour – things that were bugs this morning are fixed now. Supports markdown for formatting posts. The unique feature here is that you can tip the writer for a good post. 1 point is a US penny; everybody gets 50 of them to start with. This might be a good way to pay writers who only occasionally come into my sphere of interests. People here like my jokes. I had followers within a few hours of joining.

So far it’s mostly journalists, humorists, and people with cats and dogs. This might turn into my new “front page”.

Idiosophical Tag Cloud

I’ve just handed in my essay for Gardeners of the Galaxies. But before I did, I ran it through the JSTOR Text Analyzer to see if there was anything I’d missed. It found me a paper I’d never heard of that was relevant enough to include.

In the process it produced a list of relevant tags. My first reaction to it was, “What in the world did I just write?” My second reaction was, “Mission Accomplished!”

topics covered in the essay

Hobbits and their Soil

Tom Hillman’s latest post cites C.S. Lewis citing Tolkien musing about the effect of living in one place and eating local produce for generations. Maybe, the musing goes, that is the source of hobbits’ apparent power to resist evil.

As it happens, I was just reading about the dangers of eating locally. William Albrecht wrote a famous paper1 about the sorry condition of the teeth of military recruits during World War 2. The men with the worst teeth were geographically concentrated in areas where the combination of soil mineralization and rainfall caused calcium deficiency. Eating locally was the source of the problem. In our modern food system, we eat food from all over, so this doesn’t happen so often.Calcium shall be my shield

But then it struck me: I’ve never heard of the Native Americans who originally lived in the Appalachians having dental problems. Google Scholar only finds a few skeletons, explicitly described as anomalous. Bad teeth are found in only the descendants of European colonists. Eliot’s line about how ‘We are synthetic men, uprooted’ seems to be applicable in more places than just the Shire.

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