Chapter 10: Turning Genes On and Off

Francis Collins, and many others, believe that the concept of junk DNA is outmoded because recent discoveries have shown that most of the human genome is devoted to regulation. This is part of a clash of worldviews where one side sees the genome as analogous to a finely tuned Swiss watch with no room for junk and the other sees the genome as a sloppy entity that's just good enough to survive.

The ENCODE researchers and their allies claim that the human genome contains more than 600,000 regulatory sites and that means an average of 24 per gene covering about 10,000 bp per gene. I explain why these numbers are unreasonable and why most of the sites they identify have nothing to do with biologically significant regulation.

This chapter also covers the epigenetics hype and restriction/modification.

Click on this link to see more.
Chapter 10: Turning Genes On and Off

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Chapter 9: The ENCODE Publicity Campaign

In September 2012, the ENCODE researchers published a bunch of papers claiming to show that 80% of the human genome was functional. They helped orchestrate a massive publicity campaign with the help pf Nature— a campaign that succeeded in spreading the message that junk DNA had been refuted.

That claim was challenged within 24 hours by numerous scientists on social media. They pointed out that the ENCODE researchers were using a ridiculous definition of function and that they had completely ignored all the evidence for junk DNA. Over the next two years there were numerous scientific papers criticizing the ENCODE claims and the ENCODE researchers were forced to retract the claim that they had proven that 80% of the genome is functional.

I discuss what went wrong and lay the blame mostly on the ENCODE researchers who did not behave as proper scientists when presenting a controversial hypothesis. The editors of Nature share the blame for not doing a proper job of vetting the ENCODE claims and not subjecting the papers to rigorous peer review. Science writers also failed to think critically about the results they were reporting.

Click on this link to see more.
Chapter 9: The ENCODE Publicity Campaign

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Chapter 8: Noncoding Genes and Junk RNA

I think there are no more than 5,000 noncoding genes but many scientists claim that there are tens of thousands of newly discovered noncoding genes. I describe the known noncoding genes (less than 1000) and explain why many of the transcripts detected are just junk RNA produced by spurious transcription. The presence of abundant noncoding genes will not solve the Deflated Ego Problem.

This chapter covers the misconceptions about the Central Dogma and how they are incorrectly used to try and discredit junk DNA. The views of John Mattick are explained and refuted. I end the chapter with a plea to adopt a worldview that can accommodate messy biochemistry and a sloppy genome that's full of junk DNA.

Click on this link to see more.

Chapter 8: NoncodingGenes and Junk RNA

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Chapter 7: Gene Families and the Birth & Death of Genes

This chapter describes gene families in the human genome. I explain how new genes are born by gene duplication and how they die by deletion or by becoming pseudogenes. Our genome is littered with pseudogenes: how do they evolve and are they all junk? What are the consequences of whole genome duplications and what does it teach us about junk DNA? How many real ORFan genes are there and why do some people think there are more? Finally, you will learn why dachshunds have short legs and what "The Bridge on the River Kwai" has to do with the accuracy of the human genome sequence.

Click on this link to see more.

Gene Families and the Birth and Death of Genes

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Chapter 6: How Many Genes? How Many Proteins?

Here's a link to the summary of what's in Chapter 6. The important topics are the correct definition of "gene" and the number of protein-coding genes. I explain the false history concerning the number of genes that were predicted when the human genome sequence was published. This is the chapter that introduces the Deflated Ego Problem.

The last half of the chapter covers introns and why most intron sequences are junk. There's an extensive discussion of alternative splicing and why most genes are NOT alternatively spliced in spite of what you might have been taught.

Chapter 6: How Many Genes? How Many Proteins?

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Chapter 5: The Big Picture

Here's a link to a summary of what's in Chapter 5. It lists the main components of the human genome and concludes that less than 10% of the genome is functional. In other words, 90% of your genome is junk!

Chapter 5: The Big Picture

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Chapter 4: Why Don't Mutations Kill Us?

Chapter 4: Why Don't Mutations Kill Us?

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Chapter 3: Repetitive DNA and Mobile Genetic Elements

See Chapter 3: Repetitive DNA and Mobile Genetic Elements

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90% of your genome is junk

If you are interested in learning more about junk DNA here's some links to relevant information.

Prologue
Chapter 1: Introducing Genomes
Chapter 2: The Evolution of Sloppy Genomes
Chapter 3: Repetitive DNA and Mobile Genetic Elements
Chapter 4: Why Don't Mutations Kill Us?
Chaper 5: The Big Picture
Chapter 6: How Many Genes? How Many Proteins?
Chapter 7: Gene Families and the Birth and Death of Genes
Chapter 8: Noncoding Genes and Junk RNA
Chapter 9: The ENCODE Publicity Campaign
Chapter 10: Turning Genes On and Off
Chapter 11: Zen and the Art of Coping with a Sloppy Genome

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