How could a graduate student at King's College in London not know the difference between junk DNA and non-coding DNA?

There's something called "the EDIT lab blog" written by people at King's College In London (UK). Here's a recent post (May 19, 2023) that was apparently written by a Ph.D. student: J for Junk DNA Does Not Exist!.

It begins with the standard false history,

The discovery of the structure of DNA by James Watson and Francis Crick in 1953 was a milestone in the field of biology, marking a turning point in the history of genetics (Watson & Crick, 1953). Subsequent advances in molecular biology revealed that out of the 3 billion base pairs of human DNA, only around 2% codes for proteins; many scientists argued that the other 98% seemed like pointless bloat of genetic material and genomic dead-ends referred to as non-coding DNA, or junk DNA – a term you’ve probably come across (Ohno, 1972).

You all know what's coming next. The discovery of function in non-coding DNA overthrew the concept of junk DNA and ENCODE played a big role in this revolution. The post ends with,

Nowadays, researchers are less likely to describe any non-coding sequences as junk because there are multiple other and more accurate ways of labelling them. The discussion over non-coding DNA’s function is not over, and it will be long before we understand our whole genome. For many researchers, the field’s best way ahead is keeping an open mind when evaluating the functional consequences of non-coding DNA and RNA, and not to make assumptions about their biological importance.

As Sandwalk readers know, there was never a time when knowledgeable scientists said that all non-coding DNA was junk. They always knew that there was functional DNA outside of coding regions. Real open-minded scientists are able to distinguish between junk DNA and non-coding DNA and they are able to evaluate the evidence for junk DNA without dismissing it based on a misunderstanding of the history of the subject.

The question is why would a Ph.D. student who makes the effort to write a blog post on junk DNA not take the time to read up on the subject and learn the proper definition of junk and the actual evidence? Why would their supervisors and other members of the lab not know that this post is wrong?

It's a puzzlement.

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What's in Your Genome?: 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?
Chapter 5: The Big Picture
Chapter 6: How Many Genes? How Many Proteins?
Chaper 7: Gene Families and the Birth and Death of Genes
Chapter 8: NoncodingGenes 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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Zach Hancock interviews me on his YouTube channel

We had a good time talking about junk DNA, alternative splicing, and science misinformation.

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The evolution of genomic complexity explained by Zach Hancock

Zach Hancock has posted another YouTube video. This one is about the evolution of genomic complexity. Have you ever wondered why eukaryotic biochemistry is so much more complex than the same processes in bacteria? Maybe it's because bacteria have highy efficient biochemistry and eukaryotes have evolved bigger, more complex structures by accident. This is a video about evolution by accident and the evolution of complexity in the absense of positive Darwinian selection.

You can learn about constructive neutral evolution and the origin of introns and the spliceosome. You can learn why eukaryotic ribosomes are so much bigger and more complex than bacterial ribosomes. As a bonus, you can learn how structures showing irreducible complexity arose quite naturally in the absence of any supernatural intervention.

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James Shapiro doesn't like junk DNA

Shapiro doubles down on his claim that junk DNA doesn't exist.

It's been a while since we've heard from James Shaprio. You might recall that James A. Shapiro is a biochemistry/microbiology professor at the University of Chicago and the author of a book promoting natural genetic engineering. I reviewed his book and didn't like it very much—Shapiro didn't like my review [James Shapiro Never Learns] [James Shapiro Responds to My Review of His Book].

Gert Korthof reviews my book

Gert Korthof thinks that the current view of evolution is incomplete and he's looking for a better explanation. He just finished reading my book so he wrote a review on his blog.

Scientists say: 90% of your genome is junk. Have a nice day! Biochemist Laurence Moran defends junk DNA theory

The good news is that I've succeeded in making Gert Korthof think more seriously about junk DNA and random genetic drift. The bad news is that I seem to have given him the impression that natural selection is not an important part of evolution. Furthermore, he insists that "evolution needs both mutation and natural selection" because he doesn't like the idea that random genetic drift may be the most common mechanism of evolution. He thinks that statement only applies at the molecular level. But "evolution" doesn't just refer to adaptation at the level of organisms. It's just not true that all examples of evolution must involve natural selection.

I think I've failed to explain the null hypothesis correctly because Korthof writes,

It's clear this is a polemical book. It is a very forceful criticism of ENCODE and everyone who uncritically accepts and spreads their views including Nature and Science. I agree that this criticism is necessary. However, there is a downside. Moran writes that the ENCODE research goals of documenting all transcripts in the human genome was a waste of money. Only a relatively small group of transcripts have a proven biological function ("only 1000 lncRNAs out of 60,000 were conserved in mammals"; "the number with a proven function is less than 500 in humans"; "The correct null hypothesis is that these long noncoding RNAs are examples of noisy transcription", or junk RNA"). Furthermore, Moran also thinks it is a waste of time and money to identify the functions of the thousands of transcripts that have been found because he knows its all junk. I disagree. The null hypothesis is an hypothesis, not a fact. One cannot assume it is true. That would be the 'null dogma'.

That's a pretty serious misunderstanding of what I meant to say. I think it was a worthwhile effort to document the number of transcripts in various cell types and all the potential regulatory sequences. What I objected to was the assumption by ENCODE researchers that these transcripts and sites were functional simply because they exist. The null hypothesis is no function and scientists must provide evidence of function in order to refute the null hypothesis.

I think it would be a very good idea to stop further genomic surveys and start identifying which transcripts and putative regulatory elements are actually functional. I'd love to know the answer to that very important question. However, I recognize that it will be expensive and time consuming to investigate every transcript and every putative regulatory element. I don't think any lab is going to assign random transcripts and random transcription factor binding sites to graduate students and postdocs because I suspect that most of those sequences aren't going to have a function. If I were giving out grant money I give it to some other lab. In that sense, I believe that it would be a waste of time and money to search for the function of tens of thousands of transcripts and over one million transcription factor binding sites.

That not dogmatic. It's common sense. Most of those transcripts and binding sites are not conserved and not under purifying election. That's pretty good evidence that they aren't functional, especially if you believe in the importance of natural selection.

There's lot more to his review including some interesting appendices. I recommend that you read it carefully to see a different perspective than the one I adocate in my book.

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

In last chapter of my book I try to convince readers that biochemistry, molecular biology, and evolution are sloppy processes and the idea of a sloppy genome is a logical consequence of evolution. The chapter contains Chautauguas on genomics, the function wars, intelligent design creationists, and scientific controversies.

Click on this link to see more.
Chapter 11: Zen and the Art of Coping with a Sloppy Genome

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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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