Monday, March 20, 2017

Correcting the correction of a video about evolution

Charlie McDonnell is the author of a book called Fun Science: A Guide To Life, The Universe And Why Science Is So Awesome. He made a video on misconceptions about the theory of evolution (see below). Sally Le Page (below left) is an evolutionary biologist working on her Ph.D. at Oxford (UK). She noticed a few problems with the McDonnell video so she made one of her own to correct the misconception in the first video. Now it's my turn to correct the misconception in the video that corrects the first video!

Sally Le Page highlights six misconceptions in the McDonnell video. She points out that none of them are very important—they are "little niggles"—but she still thinks a comment is necessary. (I agree.)

Wednesday, March 08, 2017

What's in Your Genome? Chapter 4: Pervasive Transcription

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]. Chapter 3 defines "genes" and describes protein-coding genes and alternative splicing [What's in Your Genome? Chapter 3: What Is a Gene?].

Chapter 4 is all about pervasive transcription and genes for functional noncoding RNAs.
Chapter 4: Pervasive Transcription
  • How much of the genome is transcribed?
  • How do we know about pervasive transcription?
  • Different kinds of noncoding RNAs
  •         Box 4-1: Long noncoding RNAs (lncRNAs)
  • Understanding transcription
  •         Box 4-2: Revisiting the Central Dogma
  • What the scientific papers don’t tell you
  •         Box 4-3: John Mattick proves his hypothesis?
  • On the origin of new genes
  • The biggest blow to junk?
  •         Box 4-4: How do you tell if it’s functional?
  • Biochemistry is messy
  • Evolution as a tinkerer
  •         Box 4-5: Dealing with junk RNA
  • Change your worldview


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
  • Alternative splicing
  •         Box 3-2: Competing databases
  • Alternative splicing and disease
  •         Box 3-3: The false logic of the argument from         complexity
  • Gene families and 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

Monday, March 06, 2017

What's in Your Genome? Chapter 2: The Big Picture

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 2.

Chapter 2: The Big Picture
  • How much of the genome has been sequenced?
  • Whose genome was sequenced?
  • How many genes?
  • Pseudogenes
  • Regulatory sequences
  • Origins of replication
  • Centromeres
  • Telomeres
  • Scaffold Attachment regions (SARs)
  • Transposons
  • Viruses
  • Mitochondrial DNA (NumtS)
  • How much of our genome is functional?


What's in Your Genome? Chapter 1: Introducing Genomes

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 1.

Chapter 1: Introducing Genomes
  • The genome war
  • What is DNA?
  • Chromatin
  • How big is your genome?
  • Active genes?
  • What do you need to know?