Tuesday, May 2, 2023

Chapter 11: Zen and the Art of Coping with a Sloppy Genome

The title comes from Zen and the Art of Motorcycle Maintenance, one of the most popular philosophy books of all time. The theme of my book is very different; it's about the idea that life at the molecular level is very messy and error-prone and looks nothing like a well-constructed Swiss watch. The author of Zen writes a number of short essays called Chautauquas and I'm going to close this book with a few of my own. (pp. 297-298)
The limitations of genomics
Genomics focuses on a global analysis of the entire genome rather than on specific genes. Genomic studies collect large amounts of data that may be useful in uncovering new features and in forming new hypotheses but those hypotheses still need to be tested at the level of individual genes. Genomics workers often believe they have discovered novel features of the genome that overthrow old ideas—features such as tens of thousands of noncoding genes, abundant alternative splicing, and huge amounts of regulatory sequence—but they have only discovered data that may or may not point to new features pending closer analysis. (pp. 299-302)
The function wars
The ENCODE publicity campaign kicked off an extended discussion about the meaning of the word function—a discussion that Alex Palazzo calls the 'function wars.' The new function wars drew in philosophers who have been debating the meaning of function for many decades. The wars are over and the most reasonable definition of molecular function is the maintenance definition that describes functional DNA as DNA that is currently maintained by natural selection (purifying selection.) (pp. 302-307)
[ENCODE and their current definition of "function"] [Identifying functional DNA (and junk) by purifying selection] [The Function Wars Part IX: Stefan Linquist on Causal Role vs Selected Effect] [The Function Wars Part VIII: Selected effect function and de novo genes] [The Function Wars Part VII: Function monism vs function pluralism] [The function wars are over] [Philosophers talking about genes] [When philosophers write about evolution] [When philosophers talk about genomes]

Scientific revolutions
The scientific literature and the popular press are full of reports of scientific revolutions that have just overthrown some old paradigm causing the textbooks to be rewritten. That's not how science really works. Most scientific revolutions develop slowly over a period of many years as more and more data causes us to revise our old ideas. Many of the so-called revolutions reported in the popular press are actually paradigm shafts, not paradigm shifts. The concept of junk DNA refers to a real revolution in our thinking about genomes. It developed over many years in the 1960s and 70s but it failed to convince most biologists. All of the announcements about disproving junk DNA are fake revolutions and paradigm shafts. (pp. 307-311)
[ENCODE and their current definition of "function"] [University press releases are a major source of science misinformation] [Press release from the Francis Crick Institute misrepresents junk DNA]
No comfort for Intelligent Design Creationists
Intelligent Design Creationists have been predicting for years that most of our genome would turn out to be functional. They interpret recent results to be a vindication of their prediction. I hope I've demonstrated that they are wrong. (pp. 311-312)
[Religion vs science (junk DNA): a blast from the past] [Stephen Meyer "predicts" there's no junk DNA] [Do Intelligent Design Creationists still think junk DNA refutes ID?] [You need to understand biology if you are going to debate an Intelligent Design Creationist]
Scientific controversies
There is a genuine controversy over the amount of junk DNA in the human genome but the existence of this controversy is hidden from the general public because most scientists ignore it. Why do most scientists refuse to even consider the idea that our genome could be full of junk? I outline four reasons for this behavior. (pp. 321-315)
[Scientists say "sloppy science" more serious than fraud]
Coping with a sloppy genome
I hope I've convinced you that it's possible to live with the idea that 90% of our genome is junk. (p. 315)

Notes for Chapter 11 (pp. 333-334)

References (pp. 335-358)

Index (pp. 359-372)

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