Another failure: "The Mysterious World of the Human Genome"

The Mysterious World of the Human Genome
by Frank Ryan
William Collins, an imprint of Harper Collins, London UK (2015)
ISBN 978-0-00-754906-1

This is just another "gosh, gee whiz" book on the amazing and revolutionary (not!) discoveries about the human genome. The title tells you what to expect: The Mysterious World of the Human Genome.

The author is Frank P. Ryan, a physician who was employed as an "Honorary Senior Lecturer" in the Department of Medical Education at the University of Sheffield (UK). He's a member of The Third Way group. You can read more about him at their website: Frank P. Ryan.

The first seven chapters are about the history of DNA. Ryan doesn't really tell us anything about what's in your genome until chapter 8. According to Ryan, the publication of the draft human genome sequences in 2001 led to several breakthroughs. Here's how he puts it on page 128.

The word 'breakthrough' is often misused in relation to scientific discovery, but here, indeed, was real breakthrough after breakthrough. And the breakthroughs presented a very much unprepared world of science with not one but three major surprises, each a challenging new mystery.

Regular readers of Sandwalk can probably guess what the three breakthoughs are because we've heard about them time and time again from amateurs who write about the human genome. Here's the list.

1. Biochemists had figured out that there are about 100,000 proteins in human cells so they expected about the same number of genes. "It was an almighty shock" to discover that there are only 20,500 genes.
2. The second major shock was that viruses or virus-like entities make up 45% of the genome.
3. The third breakthrough is that 50% of the genome "appeared to code for nothing that we recognized at the time."

Frank Ryan suffers from a familiar syndrome called the The Deflated Ego Probblem. He describes his problem on page 130 ...

The paltry 20,500 genes seemed downright humiliating. To put it into perspective, we had roughly ten times as many genes as an average bacterium, four times as many as a fruit fly, and just twice as many as a nematode worm. In term of genes, we seemed hardly more complex than these humble life forms. A related revelation was the number of genes we have in common with these simpler organisms. We now discovered that we share 2,758 of our genes with the fruit fly and 2,031 with the nematode worm: and the three of us—human fly and worm—have 1,523 genes in common.

The truth is that the number of genes was pretty much what was expected by the experts [False History and the Number of Genes 2010] [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. And the truth is that "only" 1500 shared genes seems very low.

But if you were one of those scientists—like Frank Ryan—who didn't read the scientific literature, then you may have been under the false impression that humans need many more genes to make them feel important. In that case, your deflated ego needed puffing up so you had to come up with one or more of the seven possibilities that scientists use to rationalize the "shocking truth."

In Ryan's case, he tells us that the explanation was alternative splicing.

... understanding of how exons and introns work now affords an explanation of how just 20,500 genes could possibly code for 80,000 to 100,000 proteins.

A gene which, for example, had 14 exons separated by 13 introns, is likely to code for more than one protein. All that is necessary is that the regulatory mechanisms, which decide on which exons to splice together to make the messenger RNA, choose different combinations of exons. We now know that this is exactly what happens. The ability of a single gene to code for more than one protein is known as 'alternative splicing.' (p. 135)

There are two things wrong with this description. First, human cells do NOT contain 80,000 - 100,000 different proteins. Second, alternative splicing is a real phenomenon but it only applies to a small number of genes. It is simply not true that most, or even many, human genes are spliced to produce different proteins [see Alternative Splicing]. Most examples of different forms of mRNA are just splicing errors that are never translated.

The number of virus sequences in the human genome is not a problem according to Frank Ryan. He tells us that several new genes have evolved from virus sequences and there may be many more.

In 2001, when the first draft of the complete human genome showed that roughly 45 per cent of the human genome appeared to be made up of retroviruses, or virus-like entities, such as LINES and SINEs, some biologists dismissed this huge genetic inheritance as junk, the graveyard of past viral infections. But today we have become a good deal more cautious in our interptetations.

The truth is quite different. The experts expected that most of our genome would turn out to be junk and that's exactly what was revealed when the human genome sequence was published. Half of our genome is composed of bits and pieces of ancient transposons. They look like junk and detritus and that's exactly what they are. Some small bits have secondarily evolved a function but the vast majority is still junk.

What about the rest of the genome? That's the subject of the third "breakthrough." Frank Ryan tells us that most of this DNA is required to regulate the expression of the 20,500 protein-coding genes. Some of that regulation involves epigenetics. Some of it contains stretches of DNA for ribosomal RNAs and tRNAs and some of it is devoted to a "surprsing variety of RNA molecules that did not code for proteins, but nevertheless had important roles to play in the control and expression of genes" (p. 188). There's a special class of these RNAs ...

... there is another more astonishing class of non-coding RNAs that regulates the human genome, a relatively new discovery that explains that mysterious black hole in the 2001 draft genome—the 50 per cent of our human DNA that was left a baffling blank. (p. 189)

He's talking about long non-coding RNA or lncRNA. After dutifully covering the few well-known examples of functional lncRNAs, Ryan continues with ...

Inspired by these discoveries, scientists began to search for more of these long non-coding RNA molecules to discover that they are transcribed pervasively throughout mammalian genomes. In time, lncRNAs were duly recognised as part of a newly recognised and very powerful epigenetic regulatory system, giving rise to an explosion of new research. This exciting new venture is still taking place as I write, but already we know that our human genome, like that of all plants and animals, contains vast number of long and small non-coding RNAs within which the lncRNAs comprise a class of their own, ranging in size from 200 to more than 100,000 nucleotides long. (p. 192)

You won't be surprised to discover that Frank Ryan repeat the myth that a gene was defined as protein-coding and you won't be surprised to learn that the recent discovery of genes for functional RNAs was a revolutionary finding that changed the way we look at genes.

The truth is far different. We've known about genes for functional RNAs since the 1960s and knowledgeable scientists since that time have never claimed that all genes have to encode proteins. We've known about a variety of small functional RNAs since the late 1970s—Sidney Altman got a Nobel Prize for one of them in 1989.

More of these small functional RNAs were discovered in the 1990s (a small surprise) but no knowledgeable scientist can defend the claim that most of our genome is devoted to their production.

The book closes with several chapters on the evolution of humans and the human genome. This is where Frank Ryan promotes his view of evolutionary change. His view includes mutation but also three other important mechanisms of change; epigenetics, symbiosis, and hybridization (of different species) (= MESH).

Epigenetics is trivial and unimportant in evolution. Symbiosis happened only a few times in three billion years. Hybridizations are one-off events that occur only once in every 10-100 million years, if at all. Mutations happen all the time.

Frank Ryan's goal is laudable ...

I set out to write this book from the premise that it would attempt to provide a non-scientific reader with a basic understanding of how his or her own genome works. I can only hope that I have succeeded in that aim. The very notion that we might understand the evolution, structural make-up and detailed function of the genomes that code for life, including our own human genome, is of epochal importance not only for science but also for all of us. I hope it has become clear that such understanding is important, since it must be for society in general, and not scientists alone, to decide where we go from here. (p. 298)

He has not succeeded. I don't say this just because I disagree with him. I'm certain that most of our genome is junk and unlike him I don't think the ENCODE Consortium was correct. That's not the issue. Frank Ryan is free to promote the minority view that most of our genome is functional but as a scientist writing for the general public he is obliged—in my opinion—to present the facts as fairly and objectively as possible. He has not done this. He doesn't present any of the evidence for junk DNA and he doesn't reveal to his readers any of the scientific objections that weaken his position.

Consequently, he leaves his readers with the impression that scientists have uncovered lots and lots of function in our mysterious genome. That means his non-scientific readers do not understand the real science behind the human genome after reading his book.

It's another failure, just like Nessa Carey's book Junk DNA: Why there is more to the human genome than meets the eye and John Parrington's book The Deeper Genome: A Journey Through the Dark Matter of the Genome. This is not how good science writers are supposed to behave.

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