They were familiar with genes that encoded proteins and with a wide variety of genes that produce functional RNAs like ribosomal RNA , transfer RNA, regulatory RNAs, and various catalytic RNAs. It would have been difficult to find many knowledgeable biologists who thought that all genes encoded proteins.
By the 1980s, most knowledgeable biologists were aware of RNA processing. They knew that the primary transcripts of genes could be modified in various ways to produce the final functional form. They knew about alternative splicing. All these things were taught in undergraduate courses and written in the textbooks.
Here's how Michael White views that history in: Your Genes Are Obsolete.
As the century progressed, biologists came to see genes as real physical objects. They discovered that genes have a definite size, that they are linearly arrayed on chromosomes, that individual genes are responsible for specific chemical events in the cell, and that they are made of DNA and written in the language of the Genetic Code. By the time the Human Genome Project was initiated in 1988, researchers knew that a gene was a segment of DNA with a clear beginning and end and that it acted by directing the production of a particular enzyme or other molecule that did a specific job in the cell. As real things, genes are countable, and in 1999 biologists estimated that humans had "80,000 or so" of them.If he means that knowledgeable researchers knew about genes for functional RNAs (e.g. ribosomal RNA genes) then he is right. If he thinks that knowledgeable researchers thought that all genes encoded proteins, then he's wrong.
As for the number of genes, I've addressed this in False History and the Number of Genes, and Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome.
There may have been researchers who speculated about the number of genes in the human genome but surely the only estimates that count are those from scientists who were knowledgeable about the subject. Those experts expected about 30,000 genes based on genetic load arguments and data from the early 1970s on the amount of DNA that was unique. Most of those researchers were expecting humans to have about the same number of genes as fruit flies, or maybe a few thousand more.
Michael White continues ....
Yet, when the dust from the Human Genome Project cleared, we didn’t have nearly as many genes as we thought. By the latest count, we have 20,805 conventional genes that encode enzymes and other proteins. Our inflated gene count, though, wasn’t the only casualty of the Human Genome Project. The very idea of a gene as a well-defined segment of DNA with a clear functional role has also taken a hit, and as a result, our understanding of our relationship with our genes is changing.There are about 21,000 protein encoding genes in our genomes and several thousand more genes that produce functional RNAs. The numbers may be a bit lower than most experts thought, but not by much. No great surprises there unless you count those people who made speculative guesses without knowing the data from the 60s and 70s.
And, there weren't many surprises about defining a gene either.
One major challenge to the concept of a gene is the growing evidence that many genes are shapeshifters. Instead of a well-defined segment of DNA that encodes a single protein with a clear function, we should view a gene as "a polyfunctional entity that assumes different forms under different cellular states," according to University of Washington biologist John Stamatoyannopoulos. While researchers have long known that genes are made up of discrete subunits called "exons," they hadn’t realized until recently the degree to which exons are assembled—like Legos—into sometimes thousands of different combinations. With new technologies, biologists are cataloging these various combinations, but in most cases they don’t know whether those combinations all serve the same function, different functions, or no function at all.Maybe some people didn't know about RNA processing and alternative splicing but many of us did. No surprises there.
We don't know how many genes in the human genome are "shapeshifters" but there's a growing realization that many splice variants are just biological noise due to errors in splicing. Those variants have no biological function. The point is that the definition of "gene" wasn't affected by any discoveries by those who sequenced the human genome or by the ENCODE Consortium.
Our concept of a gene is also challenged by the fact that much of the function in our DNA is located outside of conventionally defined genes. These "non-coding" functional DNA segments regulate when and where conventional protein-coding genes operate. For our biology, non-coding regulatory DNA elements are as consequential as genes, but their properties are even more difficult to define because their function isn’t based on the well-understood Genetic Code and their boundaries are even fuzzier than gene boundaries.No surprises there either. Knowledgeable researchers have known about regulatory sites since the 1960s. Most of them don't incorporate regulatory regions into the definition of "gene." Every gene is going to be associated with regulatory regions that regulate transcription.
I don't see why this well-known fact makes the definition of "gene" obsolete.
As a result, non-coding regulatory DNA elements are much more difficult to count. One consortium of researchers put the number of regulatory DNA segments in the human genome between 580,000 and 2.9 million, while just last month a different consortium claimed that there are only 43,000. Regardless of how you count them, it’s clear that these non-gene regulatory DNA elements far outnumber conventional genes. It is hard not to wonder, then, what good is the concept of a gene if it doesn’t include most of our functional DNA?I think it's totally unreasonable to speculate that every gene would have 20 different regulatory sites scattered around the genome as some of those numbers suggest. If there were only a few near the promoter then this is exactly what we've known for decades and there's no reason to redefine a gene.
Finally, I don't know what Michael White was thinking but I've never heard any knowledgeable scientist say that all functional DNA has to be in "genes." So, what's the problem? If the definition of "gene" wasn't made obsolete with the decades-old discoveries of origins of replication, regulatory sequences, telomeres, and centromeres then what's changed in the past decade?
I don't get it. Why are so many prominent scientists saying that we need to redefine the word "gene"?