Uncommon Ground – Academics, biodiversity, genetics, & evolution

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One way that I’m using Claude

Like many people, I often ask Claude or ChatGPT a simple question that I might once have investigated using a search engine. That’s useful, but not particularly creative. For the past month or month and a half, though, I’ve been using Claude in a way that some of you might find useful.¹

I use Endnote as my bibliography manager,² and I use Obsidian to manage a large collection of markdown notes. Here’s how I use Claude to link the two of them.

Export all references in the Endnote database to a text file using the BibTeX export format. That retains all of the bibliographic information. It also includes the abstract for any references that has one.
The first time through I prompted Claude to scan the BibTeX export and (a) retain only those records that include an abstract and (b) write each BibTeX record to a file with a name based on the citation within my Obsidian vault.³ Now I prompt Claude to scan the BibTeX export and (a) retain only those records that include an abstract and that haven’t already been added to my Obsidian vault and (b) write the new records to the vault, adding a letter to the year for disambiguation where necessary.

Now I have a bunch of bibliographic records where I can easily search abstracts as well as authors and titles. More importantly (for me), when I open a specific record, theSmart Connectionscommunity plugin shows me notes in my Obsidian vault that are similar to the one I’m looking at with a numerical score that depends on the degree of relationship. The image below is a screenshot of what this looks like for a paper by Daniel Schreider that recently appeared in Genetics.

Assuming that there is a “some of you” who read entries here. ↩
Yes, I know that Clarivate is evil, but I’ve been using EndNote for at least 20 years, maybe 30. Old habits die hard, and I’m sure you could mimic everything I describe here in your bibliography manager. And in case you’re wondering, I Clarivate won’t pay me for mentioning Endnote, and I won’t get any money from them if you click on that link and decide to buy it. ↩
I use <author>-<year>-<source>. ↩

kent November 9, 2026 Productivity 0 Read more >

International Fountain Pen Day

The first Friday of November is International Fountain Pen Day, and I felt compelled to celebrate by giving myself an early holiday present.

That’s a photo of the Pilot Justus 95, black with gold trim that I just ordered. I clipped it from the Pen Botique site where I bought it. I already own a Namiki Falcon and a Pilot Metal Falcon, both of which are among my favorites.¹ In fact, the Justus 95 looks a lot like my Namiki Falcon, but that’s not why I bought it. I bought it because the Justus 95 has an adjustable nib. It can be adjusted to be hard or soft. I’ll probably set it to hard most of the time, but when I feel like having a little fun and having my line width vary a little more than usual, I’ll switch to soft.

Don’t count on it, but it’s possible that I’ll post a writing sample that shows the difference after my new pen arrives next Wednesday.

Why do I mention the Namiki Falcon? Because Ryosuke Namiki founded Pilot, and Namiki is owned by the Pilot Corporation (https://en.wikipedia.org/wiki/Namiki). I could also have mentioned that I own a Namiki Vanishing Point. ↩

kent November 6, 2026 Uncategorized 0 Read more >

Against falsificationism

In The Logic of Scientific Discovery Karl Popper proposed that falsifiability solves both the problem of distinguishing science from pseudoscience¹ and the problem of induction, the observation dating to Hume if not before, that you cannot justify generalizations with the same logical certainty that you can justify the conclusion of a syllogism. Even though you’ve seen the sun rise every morning as have millions of people before you, it is possible (even if highly improbable) that it won’t rise tomorrow morning.

Consider a simple syllogism, this one an example of a pattern known asmodus ponens:

All human beings are mortal.
I am a human being.
Therefore, I am mortal.

The defining characteristic of a logically valid syllogism is that if the premises are true—“All human beings are mortal.”, “I am a human being.”—then the conclusion must be true, where “must” has the same logical force as the assertion that “equals” does in 2 + 2 = 4.

Your belief (and mine) that the sun will rise tomorrow morning is justified, but our belief doesn’t carry with it that degree of certainty, because we can imagine that the sun might not rise tomorrow morning. Earth might explode in the next 12 hours.² So no matter how many times the sun has risen before, it might not rise the next time.

Falsifiability solves the problem of induction by arguing that inductive reasoning should not be the goal of science. What science can establish with certainty is which hypotheses are false. Popper argued that science advances by excluding more and more false hypotheses. And he argued that pseudoscience is characterized by theories unconnected to data or observation or connected only through special pleading, paying attention only to some of the evidence.

The logic of falsification is simple. Consider the hypothesis “All swans are white.” If that hypothesis is true, we can construct the following syllogism.

All swans are white.
This bird in front of me is a swan.
Therefore, the bird in front of me is white.

Well, if you’re a birder or you’ve been to souther Australia, you know that there’s a species of swan there, Cygnus atratus that is black. Thus, we can conclude with logical certainty that the hypothesis, “All swans are white,” is false. That’s how falsification works.

But there’s a problem with what I just wrote. Given the structure of the argument, if the bird in front of me is black, we know that at least one of the two premises must be false, but we don’t know which one. Even worse, it’s possible that I wrongly asserted that the bird in front of me is black. Maybe it’s a white bird that’s been dipped in black dye. There’s nothing in the logical structure of those premises that tells us which of those possibilities is right, only that one of them must be. We haven’t advanced nearly as far as we thought.

We depend on our background knowledge to judge whether our observation is wrong and whether one or both of our premises is wrong. More precisely, as a knowledge community, the group of people interested in and expert in the subject of our hypothesis use their shared background knowledge and experience to determine the appropriate conclusion, possibly after a lot of argument and additional observation.

Falsification isn’t as simple as people often think.

The demarcation problem ↩
I’m writing this a little before 7:00pm EST, and the sun is expected to rise tomorrow at 6:23am EST. ↩

kent November 2, 2026 Philosophy of science 0 Read more >

The trouble with wilderness

In an earlier post on industrial tourism, I struggled with how to balance the desire many of us have to protect wilderness with our concern for those who cannot enjoy its pleasures. I argued that those of us who want to protect wilderness must recognize and respect the values of those who want easier access just as much as they must recognize ours. I also argued that we need to trust one another. I don’t know how we build trust, but I have two ideas to share that might help us understand each other better.

The first idea traces to William Cronon and his essay The trouble with wilderness: or, getting back to the wrong nature:

The more one knows of its peculiar history, the more one realizes that wilderness is not quite what it seems. Far from being the one place on earth that stands apart from humanity, it is quite profoundly a human creation—indeed, the creation of very particular human cultures at very particular moments in human history. It is not a pristine sanctuary where the last remnant of an untouched, endangered, but still transcendent nature can for at least a little while longer be encountered without the contaminating taint of civilization. Instead, it’s a product of that civilization, and could hardly be contaminated by the very stuff of which it is made. (emphasis added)

Those of us who value wilderness have to recognize that valuing wilderness is a recent historical development. Cronon argues that before the 19th century wilderness “was a place to which one came only against one’s will, and always in fear and trembling.” Wilderness became a place that we value because most of us were no longer struggling against a wild nature to survive. It became a place we had left behind, a place we could value because it no longer threatened us. Wilderness is there because we made it, not because we discovered it.

Those who value access wouldn’t understand any of that. They may never have had a pleasant experience in wild nature. They still see it as forbidding and threatening. Think of a friend or a relative whose idea of nature is a well-manicured public park or golf course. They might be literally frightened for their life if they were to find themselves on a hiking trail in the Rocky Mountains.

At the same time, we need to recognize that

A man could be a lover and defender of the wilderness without ever in his lifetime leaving the boundaries of asphalt, powerlines, and right-angled surfaces. We need wilderness whether or not we ever set foot in it. Edward Abbey, Desert Solitaire , p. 162

So the person who doesn’t place a value on wilderness now, might be persuaded to change their mind. But we’ll only be able to persuade them if they trust us, and we’ll only be able to persuade them if we trust them enough to open our minds to the possibility that we might learn something from them too. We’ll especially need to keep in mind Jonathan Franzen’s advice.

We can’t make a reader care about nature. All we can do is tell strong stories of people who do care, and hope that the caring is contagious.

Franzen was writing about nature writing, but the same principle applies to conversations about nature. We have to meet people where they are, not where we want them to be. We have to hope that if we tell strong stories of people who care about wilderness, the caring will be contagious.

kent October 26, 2026 Environment 0 Read more >

Nature writing

Who am I to give advice on nature writing? No one. I couldn’t write a readable essay about nature if my life depended on it. But I have read a lot of nature writing,¹ and more importantly I was recently reminded of Jonathan Franzen’s essay, The problem of nature writing. I won’t offer my own advice about nature writing, I’ll just pull a couple of suggestions from Franzen’s essay, and I won’t be at all offended if you follow the link to Franzen’s essay and never return. He is, after all, an accomplished writer.

The phrase under the title captures Franzen’s key insight:

To succeed—to get people to care about preserving the world—it can’t be only about nature.

To succeed, nature writing has to capture not only those of us who are already captivated by it, but also those who think they don’t care about it, maybe even those who find nature scary (or at least messy). And how do we do that? By telling stories. Stories capture an audience.² So nature writing needs to be story telling, but not just any story.

Narrative nature writing, at its most effective, places a person (often the author, writing in first person) in some kind of unresolved relationship with the natural world, provides the character with unanswered questions or an unattained goal, and then deploys universally shared emotions—hope, anger, longing, frustration, embarrassment, disappointment—to engage a reader in the journey.

Effective nature writing involves a story about people, usually the author. Whether it’s Thoreau at Walden Pond, Abbey at Arches, or Dillard at Tinker Creek, effective nature writing tells a story about the author and their intense personal relationship with nature.

We can’t make a reader care about nature. All we can do is tell strong stories of people who do care, and hope that the caring is contagious.

If you’ve read this far, you owe it to yourself to read Franzen’s essay. It’s not long, and you’ll learn much more from it.

Henry David Thoreau, John Muir, Aldo Leopold, Edwin Way Teale, Edward Abbey, Annie Dillard, Robin Wall Kimmerer, and others ↩
If you don’t believe me, read through a few of the articles on Randy Olson’s Substack, ABT Agenda ↩

kent October 18, 2026 Writing 0 Read more >

More thoughts about industrial tourism

Edward Abbey was undoubtedly right about industrial tourism. It deadens us to the world, and it disconnects us from the sublime. But does that mean that all national parks should ban cars? Protecting wild areas where human influence is minimal is undoubtedly important, and Abbey is right that cars trailers “tend to separate [us] from the world around [us].” But cars also provide access to parts of the world that some people would never see without them. Cars and wildness are incompatible. How do we choose between them?

The answer can’t be that every national park must completely exclude cars, if only because we’d have many fewer and much smaller national parks than we do now. The answer also can’t be to allow cars anywhere we can build a road, because that tramples on the interests of many people, like me, who value wildness. The answer must be that we balance the need for wildness with the need for access. But how do we do that?

The first step must be for those of us who value wildness to understand that there are those who value access as much as we value wildness and that their interests deserve respect from us in the same way that our values deserve respect from them. That is very hard. I shudder when I see a hillside covered with ATV or dirt bike tracks, but the people who made those tracks are people—human beings who deserve to be treated with the same respect and dignity that expect from them. Given enough time I might be able to persuade them that their interests would be better served by enjoying the outdoors on foot or on horseback. But until I succeed, I have to respect their interests and seek a way to accommodate them without doing unreasonable damage to my own. Of course, they must do the same with me—respect my interests and find a way to pursue theirs that leaves wild spaces for me.

That first step is big. It requires trust on both sides. It requires me to trust that ATV riders will respect my interests because if I don’t trust them, I can’t trust any agreement we reach. If I don’t trust them, I will believe that they are taking advantage of me even if I can’t see how they’re doing it. And they, of course, have to trust me for the same reason. If you think about it a bit more, that first step I proposed is really the second or third step (and there are more steps to come).

The first step is to recognize that the problem isn’t to choose between cars and wildness. It is to find the balance between cars and wildness. Or to say it differently, it is to realize that cars and wildness are only partially incompatible.

The second step is to build trust among those with different interests. In taking the second step, we’ll cycle back and forth between building trust and building understanding. We may even circle back to the original conflict and find a new way to describe it that makes our interests more compatible than we originally thought.

kent October 12, 2026 Environment 0 Read more >

Do we need to worry about writing?

Joe Cruz, Chair and Professor of Philosophy and Chair of Cognitive Science at Williams College, writes that “we think best by speaking, answering and defending our ideas.” He points out that good teachers rarely, if ever, read lecture notes verbatim. Instead, they speak extemporaneously, engage students in discussion and debate, and guide students to mastery through practice and feedback. But he misses several important points.

First, Cruz minimizes the challenge of implementing the practice he recommends: 45-minute oral exams of each student in a course. He admits “there will be challenges of scale,” but he teaches at a college where the total enrollment is about 2300. The two introductory courses for biology majors at UConn enroll over 600 students per semester. That’s 450 hours of oral examinations per semester. If you wanted to schedule all of those exams in final exam week, that’s 9 hours a day for 10 examiners. If the examiners were graduate assistants, it would take 22 1/2 of them. They can’t work more than 20 hours per week.¹

Second, Daniel Drezner argues more effectively than I can that “writing is pretty damn important.” If you need to be convinced of that, click through to read his post on Substack. Cruz admits that “writing remains an essential life skill, and we will continue to do it,” but he underestimates how important it is and how important practice is to doing it well.

Third, Cruz seems to miss the point about “writing is thinking.”² John Warner puts it much better than I do:

One of my mantras about writing is that writing is thinking. Writing is simultaneously the expression and the exploration of an idea1. As we write, we are trying to capture an idea on the page, but in the act of that attempted capture, it’s likely (and even desirable) that the idea will change.

Writing your ideas down forces you to struggle with them. You can’t write a clear sentence or paragraph unless you understand, really understand what you’re writing about.

Fourth, discussion and debate involving people who genuinely seek knowledge enhances understanding because both sides see in real time where the holes in their arguments are. But discussion and debate also favor those who are quick on their feet. A faulty argument produced quickly and expressed confidently often prevails over a sound argument produced later.³ I worry about the weight quick responses get in discussions and debates. Would you rather listen to someone who responds quickly but is wrong or someone who responds slowly but rarely makes a mistake?

Our graduate students are unionized, and the 20 hours per week of assistantship duties is mandated by the contract, but it is also consistent with longstanding practice based on the federal requirement that international graduate assistants work no more than 20 hours per week. ↩
I say “seems to miss” rather than “misses” because Cruz is obviously very smart. I find it difficult to believe that he doesn’t understand the point I’m about to make, but his op-ed provides no evidence that he understands it. ↩
Or a sound argument that isn’t produced at all because the debate has moved on before the person with the sound argument had a chance to express it. I won’t claim that all of my arguments are sound, but anyone who’s been in a graduate seminar with me knows that I am often silent. It’s partly because I want students to take the lead, but it’s also because I don’t think quickly. Unless the subject is something I am already intimately familiar with and have well-formed opinions on, I am not likely to have an observation worth sharing before the discussion has moved in a direction that makes my observation relevant. ↩

kent October 5, 2026 Academics 0 Read more >

Industrial tourism

A Google search returns a list of sites that describe industrial tourism as “a type of travel that involves visiting active factories, decommissioned industrial plants, craft workshops, and industrial heritage sites to learn how things are made and explore economic history”¹. I think of it differently.

I first encountered the phrase in Edward Abbey’s Desert Solitaire, a chapter entitled “Polemic: Industrial Tourism and the National Parks.” Abbey’s polemic is directed at mechanized tourists, those who visit national parks in cars, trucks, and recreational vehicles and who rarely stray beyond the most convenient paths.² His complaint? “Industrial Tourism” is a threat to the national parks. Why? Because

A weird, lovely, fantastic object out of nature like Delicate Arch has the curious ability to remind us—like rock and sunlight and wind and wilderness—that out there is a different world, older and greater and deeper by far than ours, a world which surrounds and sustains the little world of men as sea and sky surround and sustain a ship.

Industrial Tourism deadens us to the world out there. It disconnects us from the sublime. Industrial Tourists see beautiful things, but they miss the sublime, which is “vast and mysterious, while the beautiful tends to be confined and groomed.”³

Congress recognized that places without industrial tourism should be protected when it passed the Wilderness Act of 1964.

In order to assure that an increasing population, accompanied by expanding settlement and growing mechanization, does not occupy and modify all areas within the United States and its possessions, leaving no lands designated for preservation and protection in their natural condition, it is hereby declared to be the policy of the Congress to secure for the American people of present and future generations the benefits of an enduring resource of wilderness. (Section 2(a))

It defined wilderness as a place “where the earth and its community of life are untrammeled by man, where man himself is a visitor who does not remain” (Section 2(c)).⁴

Abbey proposed three principles to govern the future of national parks:

No more cars in national parks.
No more new roads in national parks.
Put the park rangers to work.

He was confident that millions of citizens would embrace the “adventure, difficulty, and challenge” of parks in which visitors traveled only by foot, horseback, muleback, or shuttle. I admire the vision he describes, but I do not embrace it.

He dismissed those “unwilling to crawl out of their cars,” either forgetting or ignoring those whose abilities do not allow them to travel far from their car. He avoided the dilemma of simultaneously protecting wilderness for those who can enjoy it and providing access for those who cannot hike or climb.

From that AI Overview that Google provides. ↩
Before going further, I should confess that I will soon be an industrial tourist. On Wednesday, my husband and I will fly to Salt Lake City. From there we will drive to Zion, Bryce, Capitol Reef, Canyonlands, and Arches National Parks. We will only drive through Capitol Reef on our way from Bryce Canyon to Moab, and we will spend no more than a day in each place. ↩
Marcus Willascheck, Kant: A Revolution in Thinking, Harvard University Press, 2023. ↩
In 1964 even most scientists would probably have imagined that there were places in the world without human influence. We know better now. ↩

kent September 28, 2026 Environment 0 Read more >

And another thought about AI and education

Now that I’ve started, I can’t stop seeing new angles on this topic.

I just started Adam Gopnik’s The Real Work. It’s a book-length meditation on how to find mastery in your life.¹ He’s talking about mastery on page 2, but he could have been talking about effort and satisfaction in learning:

What really moves and stirs us is accomplishment, that moment of mastery when suddenly we feel that something profoundly difficulty, tenaciously thorny, has given way, and we are now the Master of It, instead of us being mastered by it.

That’s what we need to inspire in our students, a feeling of mastery, that they are masters of the subject, not the other way around.

“The real work” is a phrase magicians use when talking among themselves about their craft. It is, in Gopnik’s words, “what makes a magic effect magical.” ↩

kent September 23, 2026 Academics 0 Read more >

A bit more about AI and education

Education is like the gym. No one lifts weights because they from the floor because they are trying to move them. They lift weights because they’re strengthening their body to meet challenges they don’t know about yet. Education strengthens the mind for mental challenges we haven’t anticipated.

That’s not a new analogy. I’m sure you’ve read it before. I mention it because Dan Rockmore¹ has a nice essay in The New Yorker making the point again: “Should the classroom be more like the gym?”

The great challenge of teaching is not to transmit information—machines do that cheaply now—but to engineer those moments of genuine understanding reliably enough that students come to crave them. The intellectual equivalent of the body’s feedback is real and, when it arrives, more powerful than any endorphin.

Rockmore is the William H. Neukom 1964 Distinguished Professor of Computational Science at Dartmouth. https://faculty-directory.dartmouth.edu/daniel-rockmore ↩

kent September 22, 2026 Academics 1 Read more >