What I'm reading in April

One of my motivations for relaunching Quintessence of Dust was my desire to write about things I'm reading, whether books or articles. So here is a new series, pretty basic: What I'm reading, posted at the start of every month.

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Fiction

Fragile Things by Neil Gaiman

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 about halfway through.

Nona The Ninth by Tamsyn Muir

This is the third in the Locked Tomb Series. The trilogy was recommended by my oldest kid and by my favorite author, Alix Harrow. I've just started and am confused, which is completely normal and exactly what the author intends. As a colleague at PLOS wrote on our scifi/fantasy Slack channel, "the books are emotionally and cognitively demanding." I finished the second book, Harrow The Ninth, a couple weeks ago but one reason I started reading Fragile Things was to give myself a break before diving into Nona. Harrow was intense.

Tomorrow, and Tomorrow, and Tomorrow by Gabrielle Zevin

Recommended by colleagues on the aforementioned Slack channel and in a great review at NPR. Plus, as a bardolator I am doctrinally obligated to read a book with a title like that. I'll start this after Nona (and after a suitable recovery period), probably late in April.

Thoughts on complicity before reading Complicit by Max Bazerman

I have been thinking regularly about complicity for the last several years. It became a central ethical theme of mine in 2016 and it has occupied my thoughts and ideas since. And yet, it recently occurred to me that I seem to be using it as a folk remedy, a kind of folk science in which I use the concept in my thought and sometimes in my conversations as a kind of prop without careful definition of what I mean when I say it. So I decided to work on that, and came home from last month's Tucson Festival of Books with a stack of treasures that includes Complicit by Max Bazerman.

I haven't started it yet (I'm currently slogging through the Six Myths of Evolution mess by Simon Conway Morris). And this means I have an opportunity to do a little experiment. In the spirit of pre- and post-instruction assessments in education, I thought I'd write about what I think now about complicity. Then after I've read the book, I'll write about what I've learned and what has changed.

First, why 2016? It's not that the concept was new to me then. It's that a particular kind of evil was erupting, coincident with my own reflection as a secular humanist (aka atheist) on my many years as a Christian. It was the year of the public emergence of the hate-based cult of Donald Trump, a cult that relies almost entirely on conservative Christianity. Then, as now, I pointed out that Trump is not the cause of the sickness of the right — he's a symptom. The causes include nationalism, racism, ignorance, dishonesty, and fear-based hate. All of those things have deep roots in American conservative Christianity. And for more than 25 years, I had been a part of American conservative Christianity, which I'll call evangelicalism.

On Jane Anger, Shakespeare, apostasy, and blasphemy

Bardolatry has been a cornerstone of Quintessence of Dust since I conceived it. I love the plays, sure, but there's always been something else going on.

"Jane Anger"

Shakespeare is one of those extraordinary phenomena that tempts us to seek extraordinary explanations. Like Harold Bloom, I think of the mystery as essentially unsolvable — Shakespeare is impossible. Complex conspiracy theories about Shakespeare's identity are to me mere acknowledgements that the mystery can't be solved. For me, to attribute Shakespeare to (say) Francis Bacon is to simply rename the mystery. I don't need an answer to "Who was Shakespeare?" It doesn't actually matter to me, because my Bardolatry was never based on facts about the Bard's life.

For a few decades of my life, I was also a Christian. I was comfortable with mystery — about the metaphysical nature of the god I was confessing, stuff like that. Most of my fellow travelers were worried about how to "reconcile" their religious story (about sin and "the fall" and the bible all that) with plain facts about the natural world. I wasn't. One key example: I didn't need an answer to "Who was Adam?" It didn't matter to me, because my willingness to believe in the Christian god had nothing to do with facts about his "life" or about Adam's life. What I did care about was my mistaken belief that this god is worthy of my admiration and worthy of my attention. When I realized he is an insecure loudmouth bully with no capacity for moral responsibility, I ended the toxic relationship almost ten years ago. I won't explore deconversion here; suffice it to say that I concluded that the Christian god is a deviously complex and largely harmful human creation. In religious parlance, this is called apostasy.

The Day Without Yesterday by John Farrell: How did Lemaitre do it?

My first post on John Farrell's The Day Without Yesterday identified two themes the book raises for me: the intellectual milieu into which modern cosmology came to be, and the reasons why Georges Lemaître was able to "lead Einstein and the rest of his generation into a new, truly dynamic model of the universe." (p. 53) The second post looked at the intellectual environment and ended like this:

Some of the greatest minds in human history were overtly resistant to a new model of the universe, a model that was (at least in retrospect) clear from math and physics known at the time. If it could happen to them, it could happen to anyone, and of course it has happened constantly through intellectual history. I think we owe it to Lemaître to reflect on how it will happen again. It has to. Data doesn't wait for minds to be ready.

And yet somehow Lemaître's mind was ready. How? Why?

This question is really interesting to me, and John sets it up brilliantly throughout the book before asking it explicitly in the penultimate chapter (pp. 186-7):

... Lemaître's insights were in fact key in almost all the important milestones of early modern cosmology... He was the first to see how the Einstein and de Sitter models were but two limited cases of a larger body of expanding universe models; he was the first to see that such models had to evolve from a super-dense state; and perhaps most importantly—from the very beginning—he was the first to tie the predictions of relativity about cosmology to actual astronomical observations. How did he do it?

I wrote previously that Lemaître is a scientific hero. It's not enough to point to his scientific accomplishments, which are historic by any account. I think his greatness is magnified by the fact that he stood apart, clear-eyed, amongst a cadre of brilliant minds who were somehow unable to see what he could see. I don't think you can read The Day Without Yesterday without feeling admiration and even awe toward the priest-scientist.

The Day Without Yesterday by John Farrell: "conservatism and hesitation"

In my first post on John Farrell's The Day Without Yesterday, I identified two themes the book raises for me: the intellectual milieu into which modern cosmology came to be, and the reasons why Georges Lemaître was able to "lead Einstein and the rest of his generation into a new, truly dynamic model of the universe." (p. 53) Let's look at that milieu.

The first chapter of the book describes the first time Lemaître and Einstein met in person. Lemaître had published a paper suggesting that the universe was dynamic, indeed that it could be expanding. On meeting Lemaître, Einstein brushed the priest off, even referring to the idea as "abominable." Wow.

Now, John suggests that Einstein was not being a jerk but was instead expressing his personal distaste (revulsion even) to the very notion that the universe was expanding. And this matters because:

The modern world's comprehension of the universe is one of the most fascinating subjects in the history of science. But the history of modern cosmology is one of constant doubt, second-guessing, obstinacy, missed opportunities, distraction, and outright denial. (p. 13, emphasis mine)

To me, that list starts like a normal recitation of human imperfection, hardly remarkable to anyone who has worked in science. Until the end. Obstinacy is bad enough (if fully human) but outright denial? That sounds a bit more serious. And it is.

The Day Without Yesterday by John Farrell: introductory comments

Let's start with full disclosure. John Farrell is a good friend, and we met here at Quintessence of Dust more than 15 years ago. John was one of the first people to read and comment on (and link to) the blog. We share many passions: science, faith/science interactions, writing, the Boston Red Sox, Shakespeare, and Harvard Square. John plays pickup hockey (that's something we don't have in common) and more than once has reminded me (in pubs in Harvard Square) that we are both lucky to have all our hair.

And yet it was not until the last few months that I bought and read his (so far) masterpiece, The Day Without Yesterday. I don't know why it took so long. Surely one reason is that I've only in the last year and a half been reading more books—I've worked as an editor for more than a decade and that means many hours of intensive reading with attendant reading fatigue. But I think another reason—and this is embarrassing to admit—is that I thought I knew the story. Father of the Big Bang, Catholic priest, yeah okay I got it.

I was wrong. And if you think you know the story without reading this book, then you're probably wrong too. The tale is inspiring and exciting, frequently frustrating, and ultimately awe-inspiring, not because of the Big Bang itself (ooooh aaaah) but because the long-overlooked main character, Georges Lemaître, is a hero of science. As I read John's book, I came to think that "Father of the Big Bang" (cutesy double entendre notwithstanding) partially obscures this man's stature as a scientist.

Quintessence of Dust 2023 restart: the what

So, Quintessence of Dust is back in business. (A few days ago, I wrote about why.) Yay! Here are some soon-coming attractions. A couple are book-length projects at various stages of embryogenesis, but the rest are posts and series that represent ideas to dissect/develop and thoughts to get out in the world.

1. My main book project is yet untitled but is well defined enough (barely) to warrant some posts in which I can try out the ideas. The book is about the so-called animal toolkit and the related theme of deep homology. I'll explore those topics then suggest that they tell us something important about the design and evolution of animals. I aim to cause some trouble. And yes, I wrote 'design'.

2. Another less well-developed book idea is tentatively titled "Evolution Is Easy" and that's all you get for now.

3. I just finished The Day Without Yesterday by my friend John Farrell, about the not-well-enough-known cosmologist and priest, Georges Lemaître. I'll write about my impressions of the book and of Lemaître, and I'll try to get John to join in. Maybe an interview of some kind?

4. Other books I've read recently and would like to write about: The Gene's-Eye View of Evolution by J. Arvid Ågren; From Darwin to Derrida by David Haig; and two novels by my current favorite author, Alix Harrow. I just bought (with some hesitation) the new book by Simon Conway Morris, From Extraterrestrials to Animal Minds: Six Myths of Evolution. If the book doesn't piss me off too much,  I'll write about it.

Quintessence of Dust 2023 restart: the why

It's early January 2023, a little before sunset in Tucson. Live image below, showing the glorious Santa Catalina mountains (the snow on the upper reaches is more apparent earlier in the day) and my dinner preparations (shrimp and veggies on the grill).

I've decided to start writing here at Quintessence of Dust, after another long hiatus. Here are some of my reasons.

1. I like to write, and I have things to say, and I self-identify as an author. For eight years, I have co-organized and taught in the Scientific Writing Retreat at Cold Spring Harbor Laboratory. I'm a writer and I need to write, if only for myself.

2. I have an idea for a book, along with some introductory work (but no sample chapters yet) and writing here will help me develop those thoughts. The idea is over twelve years old and has never faded away, which I take to mean that I need to get it out of my system somehow.

3. I have other ideas kicking around in my head and most of them are worth writing about. I have one new intellectual passion that is totally worth writing about: the Sky Islands that nearly surround us here in Tucson.

4. I have an exciting new job with great new people at an organization that's all in for open science. I recently turned over the tens digit on my age-o-meter. My kids will very soon be all out of college. (One is about to start a postdoc!) All of this led, predictably, to a spasm of reflection on projects and vision. One clear result is that I'm feeling more inspired.

An overnight recipe for a new gene: change the frame

Can a new protein-coding gene be born overnight? That's the theme of this series. The answer, remarkably, is yes, and the Arhgap11b gene is the recent case I'm considering. After surveying the ways that this could happen, I narrowed the possible mechanisms to three:

There are really just three kinds of change that can get it done. All three are mutations that change how the DNA sequence that's already there gets decoded into protein. They are: 1) tiny mutations that shift the reading frame; 2) tiny mutations that change splicing; and 3) large-ish rearrangements that create new combinations of code.

Before looking at the details, let's take note of the fact that the genomes of animals and plants typically have gigantic amounts of DNA that does not code for protein. Humans are merely typical in this regard—at least 95% of the human genome is non-coding DNA, but there are organisms with a lot more and some with a lot less. The point here is not about "junk" or function, it's more basic: an animal genome contains vast amounts of DNA that could code for a protein, but doesn't. A new gene doesn't have to be magicked into a genome, by a demon or by a virus. A new gene can enter the gene library simply by becoming a new way of reading a pre-existing text. This is almost certainly how the vast majority of new genes have arisen in animals and plants for at least half a billion years. And the basic mechanism applies to all living things, for 3-ish billion years: any DNA sequence can become a protein-coding sequence, and those that already do code for protein can be straightforwardly modified to make completely different proteins.

Gene-making: some questions answered

In my previous post I attempted to identify all the ways that a new gene can come about, after defining what I meant by "new" and "gene." Two questions came up, one a comment on the post, and the other via Facebook.

1. What about exon shuffling? Isn't that a mechanism by which new genes are made?

Exon shuffling is, roughly, the creating of new coding sequences (genes, as I'm defining them in this series) by the rearrangement of pieces of coding sequence. (An exon is a piece of coding sequence in DNA or RNA.) It's a nice descriptive phrase: the exons are gene pieces, and they can be moved around to make new cominbations that code for new proteins. So is this an additional mechanism for the creation of genes?

No, it's not.