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Wednesday, March 08, 2017

What's in Your Genome? Chapter 3: What Is a Gene?

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Here's the TOC entry for Chapter 3: What Is a Gene?. The goal is to define "gene" and determine how many protein-coding genes are in the human genome. (Noncoding genes are described in the next chapter.)

Chapter 3: What Is a Gene?
  • Defining a gene
  •         Box 3-1: Philosophers and genes
  • Counting Genes
  • Misleading statements about the number of genes
  • Introns and the evolution of split genes
  • Introns are mostly junk
  •         Box 3-2: Yeast loses its introns
  • Alternative splicing
  •         Box 3-2: Competing databases
  • Alternative splicing and disease
  •         Box 3-3: The false logic of the argument from         complexity
  • Gene families
  • The birth & death of genes
  •         Box 3-4: Real orphans in the human genome
  • Different kinds of pseudogenes
  •         Box 3-5: Conserved pseudogenes and Ken Miller’s         argument against intelligent design
  • Are they really pseudogenes?
  • How accurate is the genome sequence?
  • The Central Dogma of Molecular Biology
  • ENCODE proposes a “new” definition of “gene”
  • What is noncoding DNA?
  • Dark matter


Graham Jones said...

Typo: "compexity" in Box 3-3.

Larry Moran said...

Thanks. Fixed.

whimple said...

What is the "Dark matter"?

John Harshman said...

It's a bad analogy taken from a real concept in physics. It's generally used by those who want to claim that the bulk of the human genome has mysterious, unknown functions.

anonymous said...

At an "atomic" level ( to paraphrase a physicist metaphor ) a gene ccould be defined as a region of DNA that is transcribed into a stretch of RNA that is "functional"

Of course, that line of reckoning would fall short of the mark in today's day and age.