Coyne quickly corrected that omission with a post the next day: The Neutral Theory: a genuinely important supplement to evolution’s “Modern Synthesis”.
Comfort made many mistakes but one of them was praising Philip Ball's book How Life Works. This prompted Ball to respond to my blog post by giving us a link to his own review on the Scientific American website: The Selfish Gene, revisited.
I wasn't impressed by that review either and I pointed out that some of the problem is related to how you define the term "gene." Ball doesn't do a good job in any of his writings - for example, he misrepresents the history of the definition of "gene" by claiming that the original 1960s definition was restricted to protein-coding genes. He attributes that definition to Francis Crick. This allows him to advance his agenda of showing that the old fuddy-duddy scientists were wrong about genes and genomes and recent discoveries have overthrown the old paradigms. (He sees himself as part of the revolution.)
Ball defended his writings by claiming that it's very difficult to write for a general audience and I shouldn't be so picky about how to define a gene.
Well, as it turns out, I've also tried to write something for a general audience only I tried to be historically and scientifically accurate as well.1 Here's what I wrote in my book - please let me know if you think I did an adequate job on a difficult topic.
"Ball is one of the most meticulous, precise science writers out there. He is the antithesis of hypey, "dumb-it-down" reporting. He is MUCH more credible than you are, Laurence."
John Horgan July, 2024
I’m going to be talking a lot about genes so it’s a good idea to describe how genes work and how we define them. Here’s a good working definition of a gene, “A gene is a DNA sequence that’s transcribed to produce a functional product.” I’ll discuss some controversies about the definition in Chapter 6 but, for now, let’s just accept this definition. It’s what most biochemists and molecular biologists mean when they talk about genes. (Chapter 1: p. 21)
Defining a gene
In Chapter 1 I defined a gene as a DNA sequence that is transcribed to produce a functional product and this is the way genes have been described since the 1960s by many scientists who have thought seriously about the subject. There are lots of textbooks that use a similar definition. Kostas Kampourakis in Making Sense of Genes concludes that the most acceptable definition of a gene is the one that includes production of both proteins and noncoding RNAs (see the quotation at the beginning of this chapter).
Therefore, in this book I will consider genes as DNA sequences encoding information for functional products, be it proteins or RNA molecules. With “encoding information,” I mean that the DNA sequence is used as a template for the production of an RNA molecule or a protein that performs some function Kostas Kampourakis (2017)
The idea here is that the primary gene product is RNA and any segment of DNA that’s copied into RNA (transcription) qualifies as a gene as long as the RNA has a biological function. That last bit is important because there are sequences of DNA that are transcribed but the RNA doesn’t do anything. Transcribed pseudogenes are an example but so are many spurious or accidental transcripts that happen quite frequently when the transcription machinery makes a mistake. Those bits of DNA are not genes even though they are transcribed.
There are very few definitions in biology that are absolute. In fact, one of the main reasons why biology is so difficult is because it is full of exceptions to the rule. In the case of genes, the exceptions are well-known; they include the fact that some genes are made of RNA not DNA—the genes of coronavirus are an example. There are also more complicated exceptions such as cases where several different protein-coding regions are transcribed together to produce a long RNA where several different regions can be translated simultaneously. These complexes are called operons and they are common in bacteria. The problem here is that we will often want to refer to each protein-coding region as a separate gene. There are also rare examples of two separate DNA sequences that are transcribed to produce RNAs that are then joined together to make a functional product; strictly speaking, neither of the separated DNA sequences qualifies as a gene.
What this means is that the best definition of a gene is only a “working definition” because there is no definition that covers all cases. This drives philosophers crazy but biologists are used to such ambiguity.
The molecular gene and the Mendelian gene
The gene I’m talking about is the “molecular gene” (a gene that corresponds to a particular DNA sequence in the genome) but geneticists often talk about another kind of gene called the “Mendelian gene.” Both definitions are used in the scientific literature and they do not overlap. I will use the molecular definition in this book but keep in mind that there are lots of functional DNA sequences that are not genes by this definition.
The Mendelian gene concept is frequently used by geneticists and evolutionary biologists. It’s a nebulous ill-defined unit as seen in the definition used by Richard Dawkins in his book The Selfish Gene. To him, a selfish gene is any bit of chromosome that’s subject to natural selection. This would include centromeres, origins of replication, and regulatory sequences that are not genes by the molecular definition. When Dawkins talks about the “selfish gene,” he’s talking about a unit of selection and not the molecular gene. The “selfish gene” is just a convenient metaphor as he makes abundantly clear in his book.
To be strict, this book should be called not “The Selfish Cistron” nor “The Selfish Chromosome”, but “The slightly selfish big bits of chromosome and the even more selfish little bit of chromosome.” To say the least this is not a catchy title so, defining a gene as a little bit of chromosome which potentially lasts for many generation, I call this book “The Selfish Gene.” Richard Dawkins (1976)
Dawkin’s book, The Selfish Gene, has been voted the most inspiring science book of all time in a 2017 poll by the Royal Society of London. This is a problem because the book only deals with the Mendelian gene so the general public (and many scientists) are not familiar with the molecular definition and the distinction is crucial. It’s also a problem because the concept of the selfish gene is highly adaptationist—it’s all about natural selection—and you will never understand genomes if that’s all you know about evolution.
In the debate over the definition of a molecular gene, I favor a definition that focuses on RNA as the functional product because I think this definition captures the essence of what most scientists believe when they talk about genes as functional entities. This includes scientists who may slip up from time to time by restricting their gene talk to protein-coding genes. When you ask them in private, it turns out they are well aware of ribosomal RNA genes and a host of other nocoding genes. Sometimes scientists just forget to be precise when talking about genes and they give the impression that there’s only one kind of gene; namely, the ones that encode proteins. (Chapter 6: pp. 137-138)
1. The top three requirements for good science writing are: accuracy, accuracy, and accuracy.
1 comment :
That's a very nice summary!
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