The Best of Quintessence of Dust

When I started Quintessence of Dust during a sabbatical year in the summer of 2007, I thought of it as a place to discuss science in the context of evangelical Christianity, and envisioned topics ranging from evolution to developmental biology to neuroscience. All of those topics interface with Christian belief in ways that can elicit fear and drama, and I covered all of them at times on the blog. But during its initial run of 5 years, Quintessence of Dust became best known, I think, for two things: 1) critiques of creationism, especially of the Intelligent Design (ID) movement; and 2) science writing on topics in evolutionary biology.

It's no fun to read the error-filled emanations from the ID movement, and even less fun to critique them. It's way more fun (and much more edifying) to read about how the world works. During those first 5 years, when I wrote about how evolution works I created some pieces that I am still excited about. Two of them were honored by inclusion in science blogging anthologies, but that leaves several others that still have some spark. A few were even peer-reviewed, meaning that I asked the expert whose work I was describing to read the post and offer feedback and/or correction. Although I converted many of the best posts to PDFs and have now published them on my website, there's no good way to find the posts here on the blog. At least until now: here is an annotated list of the Best of Quintessence of Dust, 2007-2012.

1. They selected teosinte...and got corn. Excellent!

Teosinte and primitive maize
(photo by John Doebley).

This is by far the most widely read and popular post on Quintessence of Dust. It describes a famous example of "evolution in action," that of the generation of modern corn from an ancestral plant called teosinte. The post was included in the 2007 edition of The Open Laboratory, an annual anthology of the best science writing on blogs.
The post was inspired by a lecture I heard at the 2006 Annual Meeting of the Society for Developmental Biology, and established basic evolutionary biology as a theme on my blog. The teosinte-to-corn transition is an example of very fast, very significant evolutionary change, in a form that is easy to see and understand. The title is a bit silly, I'll grant (it's a blog, and it was a long time ago), but the piece is the best of Quintessence of Dust.

2. How the bat got its wing

This post discusses the publication of a landmark paper in evolutionary developmental biology, known as evo-devo. The details are fascinating, and the post explains all of them. The paper, about the development of bat wings, was the first to show how a new biological feature can arise from changes in regulatory DNA elements as opposed to changes in standard genes. If this all sounds a bit nerdy and techie to you, read the post. It's super interesting—after all, it's about bats.

3. Alu need to know about parasitic DNA: Introduction to Alu elements

This is one of my personal favorite posts. It was the first in a series on Alu elements, which constitute a form of parasitic DNA found in the human genome. The series addresses misinformation about "junk DNA" that has long been a centerpiece of creationist propaganda, and culminates in a post that reviews a paper about the role of Alu elements in human blindness. This opening post, introducing Alu elements, explains what they are and why this matters in any discussion of "junk DNA." Anyone who talks about the human genome—or any other mammalian genome for that matter—without discussing mobile genetic elements is someone unqualified to discuss the topic.

4. What a selfish little piece of...

Read this post if you think you know what the phrase "The Selfish Gene" means. You will probably discover that you were wrong about what "The Selfish Gene" means. Even if you do currently know what that phrase means, you'll enjoy reading about a classic example of a selfish gene. Or, as I describe it:

"But can we picture a gene that actively harms its host in order to get ahead?

At first, this might seem ridiculous. How can harming the host help a gene propagate itself? We can talk about the examples above, and explain each through some reproductive benefit or trade-off. But I'm not talking about negligence here; I'm talking about harm. Well, okay. I'm talking about killing babies."

Normal tomato leaf (left)
compared to Darwin's tomato leaf

5. Finches, bah! What about Darwin's tomatoes?

This is cool little post, also about evo-devo, and also anthologized in The Open Laboratory, this time the 2008 edition. Big evolutionary changes can result from small genetic changes. Really cool.

6. Which came first, the bird or the smaller genome?

This is the first science writing I did at Quintessence of Dust, and I think it has aged well. It discusses a paper that tackled the interesting question of how and when bird genomes became so much smaller than those of their fellow vertebrates. This post has fossils, and dinosaurs, and genome analysis. And it was peer reviewed by the first author of the paper.

7. Clone wars, or how evolution got a speed limit

This post is about a phenomenon in evolutionary genetics that is hugely important but not well known even among biologists. It is regularly asserted that evolution will automatically go faster in very large populations, because it is naively assumed that a huge number of available mutations automatically means better odds on getting from one evolutionary point to another. It's not true. Check it out.

Embryo photomontage,
by Pavel Tomancak

8. It's just a stage. A phylotypic stage. Part I.

This is the first in a series on a remarkable pair of papers that appeared together in Nature in December of 2010, on the subject of the "phylotypic stage." This sounds all jargony and obscure, but it's really interesting—it's roughly about whether the sequence of events in the development of an animal embryo reflects something about the evolutionary history of that species. The question has an eventful history with some memorable characters. The two Nature papers nailed the answer to the question, in brilliant experiments that could only have happened in the 21st century.

9. Gene duplication: "Not making worse what nature made so clear"

This post is a bit too technical, but I like it because of the topic (specific experimental analysis of evo-devo concepts) and because it was peer-reviewed by one of the authors, in this case a bit of an idol of mine, Sean Carroll.

10. How to evolve a new protein in (about) 8 easy steps

This post is pretty technical too, but the subject is the work of one of the stars of evolutionary genetics, Joe Thornton of the University of Chicago. The post describes one of his groundbreaking papers, and then I asked him to look it over. This led to another case of peer review of one of my blog posts, and led to a followup post about Joe's comments on my piece.

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This Best of Quintessence of Dust page grew out of my work to get my work ready for a better venue, after Scribd became a pay-to-read site. My main site now hosts all of my writing.

All of the posts in this collection were written while I was a scientist at the Van Andel Research Institute and a professor at Calvin College. All are licensed for reuse with attribution (CC-BY 3.0) by Stephen Matheson (see more on the Rules page).

Page created 6 February 2016. Revised 18 August 2019.