Sky Islands: one of Earth's great evolution laboratories

Let's think of places on Earth where scientists have done great big natural "experiments" on evolution.

Looking east from near the top
of Mount Lemmon, January 2021

Here are some that ought to come to mind (in no particular order other than the first):

1. The Galapagos Islands, with their famous finches and their less-famous tomatoes and all their otherworldly animals, probably belong at the top of the list. Mr. Darwin found inspiration there, but the greatest experiments began more than a century later. I can think of few more inspiring stories of great science done by great people than the lifetime-long work of Rosemary and Peter Grant. If you haven't yet read The Beak of the Finch, get thee to a library or a bookstore.

2. The Caribbean islands, and especially the Bahamas, are a fruitful laboratory for the study of the (rapid) evolution of lizards called anoles. Jonathan Losos was a major figure in launching and leading that subfield, and his 2017 book Improbable Destinies is a great lay-level exploration of evolution and a resounding rebuttal to the random/luck/contingency views associated with Stephen Jay Gould.

3. The Hawaiian Islands are home to hundreds of species of fruit fly (many of them are biology's adored Drosophila) and zero species of ant. These hundreds of species have all evolved in the last 25 million years! Check out the laboratory of Cassandra Extavour at Harvard for a glimpse into the latest research on the evolution of Hawaiian fruit flies.

4. The Great Lakes of East Africa (including Victoria and Tanganyika) hosted one of the most rapid and spectacular adaptive radiations known to humans. Hundreds (likely thousands) of species of cichlid fish live in these lakes, and all of them were "born" in a blink of evolutionary time.

5. The streams of Trinidad are home to guppies, an unremarkable fact until you learn about one of the best-known experiments in the history of evolutionary biology. Over many years, research teams led by John Endler and David Reznick used this natural laboratory to study natural selection (and other topics) in the wild.

There are surely more. But I'm here to tell you about the one that literally surrounds us here in Tucson.

Contemplating libraries in biology. Not that kind. Not that one either.

What is a library? If you ask a biologist (especially a molecular biologist) this question, they are likely to ask for clarification. In their work, they are likely to make regular use of two very different kinds of libraries.

The first is the kind that we've had for millenia: a collection of books, journals, and media that is ordered and curated by people. These are the OG libraries, with 'book' at the very root of the word. They're rapidly evolving in our digital world, but I think they are still essentially what they've always been. Your friend the molecular biologist may not regularly go to a separate room or building to find materials, but they will use the library often.

The second is an extension of the OG concept of a library, but is still called a 'library' by your friend. It contains information, perhaps in vast amounts, but is not ordered or curated. Crucially, it is a specific collection of a particular type of information: genetic information. And while it's neither ordered nor curated, it is physical, and is designed to be searched. The contents of the library might be DNA sequences (genes or even just chunks of some interesting genome) or protein sequences. Unlike your favorite public library, this one doesn't come with a search feature: you have to do that yourself. The process of searching a library is called screening. Your molecular biologist friend can go to the institutional library to read about these kinds of libraries, and find techniques on how to screen one, then perhaps go to a colleague or a vendor to obtain a library. Or she will obtain tools to make one herself.

In my previous post, I talked of an even more radical extension of the concept of a library: a collection of all the versions of any kind of text (a book, a genome, a set of proteins).

The library of possible proteins is beyond vast. Does this cause us to view evolution as harder than it is?

Bates Hall at the Boston Public Library

One of the most effective metaphors for evolutionary change is the image of an exploration of a space, perhaps a map that shows "fitness peaks" or, better, a library of possibilities. The philosopher Daniel Dennett, writing in Darwin's Dangerous Idea, suggested The Library of Mendel as a way of thinking about the total set of possible gene sequences. He was adapting an idea famously employed in a short story by Jorge Luis Borges called "The Library of Babel," which consists of the total set of possible books of a particular length. (This "library" exists on a website designed for creators and researchers.)

Contemplating a space of possibilities—whether that space consists of books written in English (26 letters), or "books" written in the language of DNA (four letters), or "books" written in the language of protein (20 letters)—is both fun and dizzying. The dizziness is induced (for me, at least) by the vastness of these libraries (Babel or Mendel, doesn't matter). How vast? Here is how Dennett describes the Library of Babel's size (italics are his):

No actual astronomical quantity (such as the number of elementary particles in the universe, or the amount of time since the Big Bang, measured in nanoseconds) is even visible against the backdrop of these huge-but-finite numbers. If a readable volume in the Library were as easy to find as a particular drop in the ocean, we'd be in business!

—Darwin's Dangerous Idea, p. 109

Dennett then uses Vast to indicate "Very-much-more-than-astronomically" large and Vanishingly small to indicate the likelihood of something like discovering a "volume with so much as a grammatical sentence in it" in the Library. In other words, we lack words to adequately describe the size of the Library and the improbability of randomly discovering anything coherent inside it.

An extrovert's response to the nightmare of remote work

March of 2020 seems a very long time ago. The coronavirus pandemic was roaring to life in the US, and it had arrived in Cambridge, Massachusetts where I lived and worked. I was leading an international team of editors, half of whom worked in the Cell Press office in Cambridge near the MIT campus. That month, the goal was to flatten the curve, so that our great hospitals and their heroic staffs would not be overwhelmed by COVID patients. There were no vaccines, and we were still wiping down grocery bags because we knew so little about the transmission of the virus. What we knew was that if we stayed away from each other, we would give the virus fewer opportunities to spread. So, early that month, I asked the team to start working from home. About a week later, the whole company moved to working from home.

My bike at Deer Island in Boston

Long before March 2020, I knew I was something of a unicorn in the world of professional editorial work. My colleagues were (and are) generous and committed and brilliant. I think we all had those things in common. But one thing I didn't share with them was my extroversion. I'm a true extrovert, and as near as I can tell I am one of less than a dozen extroverts in the world who work as a journal editor. I'm joking, but I'm serious when I say that when I became a journal editor more than 10 years ago, I stood out immediately among scores of serious introverts. (True story: our open-concept office had "zones" based on noise level, and I was banned from the quiet area. Not just discouraged. Banned.) And so in March 2020, when there were cute jokes going around about how we could be "heroes" by working from the sofa (Google "couch potatriotism"), I was unamused. Working from home meant that I lost my daily bike ride through Cambridge to a bustling workplace full of my friends and colleagues.

Change is hard. Evolution is Easy. Episode 1 of many.

ARIEL: Full fathom five thy father lies.
Of his bones are coral made.
Those are pearls that were his eyes.
Nothing of him that doth fade
But doth suffer a sea change
Into something rich and strange.
—The Tempest, Act 1, Scene 2

I do apologize for this dull cliche, but I know I'm right about this: change is hard. I don't mean that it's hard to adapt after someone or something forces a change on you. That's true too, but it's not my topic here. I'm talking about this: you want to change, or you need to change, or both. You know what the change has to be. Maybe you know what the first step has to be. It's change, and it's hard.

Call it personal growth or self-improvement, or maybe it's habit-breaking or demon-wrestling. Whole libraries could be stocked with materials on how to change. Even when we know we're loved, and believe we're okay, we can see opportunities and challenges that require us to change.

I won't claim to have deep knowledge of the technical literature on how people manage to change. But I do have several decades of experience in the practice of personal growth and change. I have repeatedly faced my need to change, and one of the first lessons I had to learn was the fact that effecting change is a lot harder than it sounds. It's not that easy to face one's need to change but it's vastly more difficult to make it happen. Change is hard.

But evolution is easy.

A blogging festival! I'm in for Blaugust 2023

The messy smelly death of social media is causing a few meaningful losses — most notably damage to or destruction of some online communities that really were valuable. There are some things to lament. Black Twitter, for example, was and is a vibrant and important community. In the Fediverse (aka Mastodon, which is just one part of the Fediverse, but whatever) where I have been camping for several months, I'm listening to and boosting voices that discourage the careless judgment and disparagement of people who want or need to stay with communities in the corrupt plutocrat's broken toy.

But I think the world will be much, much better off without social media as we know it, and much better off without anything that is controlled by uberwealthy unreflective talentless techbros. We'll be better off not just because we'll be free of the immense toxicity created by these rapacious dipshits. We'll also have the chance to create — and recreate — ways of conversing and creating and sharing online. Like... blogging!

Today (almost too late) I learned about Blaugust 2023, a delightfully outfitted and long-running (since 2013!) blogging festival, the major goal of which is to motivate people to create. There's a Blaugchievement list, an extensive prompt list, a Discord server, a dedicated Mastodon account, and a directory. I just signed up for everything! I suggest starting at the media kit.

The basic goal is to post 31 times in August. I'm already at two! I have some topics lined up but I'll dip into the prompt list as needed, and point to interesting work by other participants. See you tomorrow.

What I'm reading in August

One motivation for relaunching Quintessence of Dust was my desire to write about things I'm reading, whether books or articles. So here is this month's entry in my new series, What I'm reading, posted at the start of every month.

---

Fiction

Hester by Laurie Lico Albanese

I bought this book in March at the Tucson Festival of Books after a fascinating event called "She persisted". Even got my copy signed! WBUR loved it. I asked the author whether it would matter that I (unlike, I think, everyone else at the event) have never read The Scarlet Letter and was assured that it would not. I'm a little more than halfway through and I love the book. I think I've read actual accounts of the Salem Witch Delusions (I haven't looked up the history to compare with the book's narrative), and I like the cadence of switching between centuries. A recurring theme is synesthesia, which the central character refers to as "the colors," and there are detailed descriptions of needlework that are a bit challenging.

 

---

Non-fiction

Complicit by Max Bazerman

I wrote about this book and my experiment (before and after reading). The first chapter was harrowing and introduced me to the term "complicitor" and outlines Bazerman's approach, which is case-based and more "practical" than what philosophers do. I should have known that Aquinas was an original source of instruction on complicity, but I didn't. I'm about halfway through.

A Humanist Path: Confucius and Lao Zi for Today by Wei Djao

This book was strongly recommended to me by a friend here in Tucson. My friend has studied with the author, who was partly Tucson-based (and perhaps still is). I'm excited to finally experience the wisdom of these ancient teachers. The publisher's page has a little more information.

You know the ancient struggle between chance and contingency vs. design/structuralism (aka necessity) in evolutionary explanation? How's this for a provocative title of a research paper: "Contingency and chance erase necessity in the experimental evolution of ancestral proteins."

What I'm reading in July

One motivation for relaunching Quintessence of Dust was my desire to write about things I'm reading, whether books or articles. So here is this month's entry in my new series, What I'm reading, posted at the start of every month.

---

Fiction

Hester by Laurie Lico Albanese

I bought this book in March at the Tucson Festival of Books after a fascinating event called "She persisted". Even got my copy signed! WBUR loved it. I asked the author whether it would matter that I (unlike, I think, everyone else at the event) have never read The Scarlet Letter and was assured that it would not. Just started (finally).

Fragile Things by Neil Gaiman

Continued from June. I only recently read American Gods (I know, I know!) and of course loved it. (I was late to the party but at least I read the "author's preferred text.") My brother's favorite book by Gaiman is Neverwhere, and I'll get there, but I grabbed this nice collection of stories and poems at Bookmans and am almost through.

---

Non-fiction

Complicit by Max Bazerman

I wrote about this book and my experiment (before and after reading). The first chapter was harrowing and introduced me to the term "complicitor" and outlines Bazerman's approach, which is case-based and more "practical" than what philosophers do. I should have known that Aquinas was an original source of instruction on complicity, but I didn't.

Design without a designer: explaining and answering some questions

I've been writing and thinking about design in biology since I started Quintessence of Dust. I want to write and think about it a lot more, so in my last post I introduced my view of the concept and pointed ahead to this post, which consists of edited excerpts from some conversations at a discussion forum at the Peaceful Science site. You will find links to those conversations in the previous post. I have removed people's names and lightly edited for clarity. Other people’s words are indented; the rest are mine.

---

I would like to understand better how you think about it because it seems quite different from the way I normally think about it. I would really like learn more about how you see it and expand my understanding of "design".

This is a potentially big interesting deep conversation that is worthy of a dedicated thread with some clear goals. Someday I’ll propose that, since I believe that we can improve the quality and tone of conversations about biological design by getting at least some unbelievers to agree that design in biology is an interesting and worthy question that need not and should not have inherent religious overtones.

I guess my first question for you as you compare your conception of 'design' to mine is this: do you think design is something that is done (by a designer) or do you think it is something that exists and can be detected by humans? Obviously both can be true, but as long as a person believes that 'design' necessitates a 'designer', then they won’t see design the way I do. Because my view is that design exists whether or not it is linked to a designer. To me, it is axiomatic that a mindless process can generate design, not only because we have seen it happen but because there is no good argument to the contrary. It is instructive, IMO, that the "argument" offered to the contrary is something like "all of our examples of design can be traced back to a mind." This is not even an argument.

But what do we mean by 'design'? Here I think we can look at some of the definitions and conceptions offered by the ID movement. I think Behe’s "purposeful arrangement of parts" is a nice start, because it captures something that we all detect when we consider (for example) a molecular machine. Was a bacterial flagellum designed by a designer? I don’t know. Does a bacterial flagellum evince design? To me, the answer is obviously yes.

Design without a designer: the "British tendency" and introduction

One of the most interesting books I've read in the last few years was The Gene's-Eye View of Evolution by J. Arvid Ågren. The author explains the gene's-eye view both scientifically and historically, and I hope to write about the book sometime soon. But for now there's one point he makes that I found fascinating. Citing Kim Sterelny (an Australian philosopher of science who has written on personalities in evolutionary biology, esp. Gould vs. Dawkins), he identifies two major emphases (Sterelny calls them "tendencies") in evolutionary biology: the American interest in diversity and the British interest in design. These are pretty crude distinctions, at least because examplars of the "British tendency" include Americans like Dan Dennett. But the point is that one of two major streams of thought in evolutionary science is the challenge Paley made famous and that inspired Darwin—the one that inspired The Blind Watchmaker and its author. It's the challenge of explaining design in the biological world, and the most notable characters in that story are Brits from three very different generations.

Schematic representations of the type IV filament superfamily of nanomachines, from Figure 1 of Denise et al. 2019

I'm not British (I'm just a wannabe) but I'm drawn to that question too. My interest is probably partly due to my time served as a Christian believer, since the Christian god is a common unworthy beneficiary of the curiosity and wonder that nature inspires in humans. I have always objected to the whole construction: we see cool and extraordinary stuff in nature, we don't seem to have an explanation, so we turn to a god as an "answer." Nothing about those stories appealed to me, not when I was a committed believer and not now that I am an emancipated apostate. One problem, that I've mentioned before, is that I am apparently of the British tendency: I see the design, and I want to explain it. Design is the question, and not the answer to any interesting question. Design is what I see. I don't need a religious apologist to convince me that it exists.