ChatGPT lies about junk DNA

I asked ChatGPT some questions about junk DNA and it made up a Francis Crick quotation and misrepresented the view of Susumu Ohno.

We have finally restored the Junk DNA article on Wikipedia. (It was deleted about ten years ago when Wikipedians decided that junk DNA doesn't exist.) One of the issues on Wikipedia is how to deal with misconceptions and misunderstandings while staying within the boundaries of Wikipedia culture. Wikipedians have an aversion to anything that looks like editorializing so you can't just say something like, "Nobody ever said that all non-coding DNA was junk." Instead, you have to find a credible reference to someone else who said that.

I've been trying to figure out how far the misunderstandings of junk DNA have spread so I asked ChatGPt (from OpenAI) again.

Q: What is junk DNA?

ChatGPT: Junk DNA is a term used to refer to non-coding DNA sequences in an organism's genome that do not code for proteins and whose function, if any, is not yet fully understood. These sequences were once thought to have no biological function and to be "junk" or remnants of evolutionary processes. However, recent studies have shown that some non-coding DNA sequences play important regulatory roles in gene expression and have other biological functions. The term "junk DNA" is therefore controversial and is no longer used frequently in scientific literature.

This misconception seems to be quite common. Many people think that the term 'junk DNA' was a synonym for 'non-coding DNA' and that the recent (?) discovery of functional non-coding DNA means that there's no such thing as junk DNA.

Q: Which scientists thought that all non-coding DNA was junk?

ChatGPT: The idea that non-coding DNA, especially repetitive DNA sequences, was "junk" and had no functional significance was proposed by molecular evolutionary biologist Susumu Ohno in 1972, in his book "Evolution by Gene Duplication." This idea was further popularized by British geneticist John Mattick in the 1990s. However, as more research has been conducted on the genome, it has become clear that non-coding DNA plays important structural and regulatory roles in gene expression, and the term "junk DNA" is no longer considered an accurate description.

Susumu Ohno never said that all non-coding DNA was junk. He published several papers where he discussed regulatory DNA and whether a large proportion of the genome could be devoted to regulation. At no point did he ever suggest that regulatory DNA doesn't exist therefore all non-coding DNA is junk.

John Mattick is a big fan of regulatory sequences—he thinks that a large percentage of the genome is dedicated to producing non-coding regulatory RNAs. He is partially responsible for spreading the rumor that scientists in the 1970s said that all non-coding DNA was junk but he has never documented that claim because it's false. It's very difficult to show on Wikipedia that Mattick is distorting the truth.

ChatGPT concludes, again, that the discovery of functional non-coding sequences, such as ribosomal RNA genes (1960s), means that the the term "junk DNA" is no longer an accurate description of non-coding DNA. That statement could only be true if someone had claimed that all non-coding DNA is junk.

Q: Can you find a direct quotation by Susumu Ohno saying that all non-coding DNA was junk?

ChatGPT: Yes, in his 1972 book "Evolution By Gene Duplication", Susumu Ohno stated the following: "The earthworm, being a more primitive animal, should have a more primitive genome, just as it has a more primitive anatomy. But we know from our studies on nucleic acids and proteins that this sweeping generalization is not quite correct; some of the most advanced animals seem to have many apparently useless DNA sequences... the earthworm probably has no room for 'junk' DNA in its genome."

This is one of the earliest examples of the hypothesis that non-coding DNA is non-functional or "junk", which was proposed by Ohno in the context of comparing the genome of the earthworm to that of more advanced animals.

I don't have Ohno's book but I don't need it since the quotation does not answer the question.

Q: Are there any other scientists who said that all non-coding DNA was junk?

ChatGPT: Yes, there were other scientists who shared the view that much of non-coding DNA was useless, non-functional and even redundant. One of the prominent scientists who argued for the idea that non-coding DNA was "junk" was Francis Crick, co-discoverer of the structure of DNA. In his 1970 article "Central Dogma of Molecular Biology", he suggested that "the information content of the nucleus has been shown to be almost entirely independent of the cytoplasmic environment, which emphasizes the isolation of the genetic material from the operational proteins of the cell... My own belief is that these sequences are in fact junk, partly to allow mutations to occur without lethal effect, and partly as merely redundant copies of functional sequences elsewhere in the DNA."

In addition to Crick, scientists like Leslie Orgel and Walter Gilbert also proposed the idea that much of non-coding DNA was non-functional in the 1970s and 1980s. However, it is worth noting that as more genomic data has become available, our understanding of the functions and roles of non-coding DNA has evolved and expanded beyond the simplistic "junk" label.

I have Crick's 1970 paper and there is nothing in that paper that's remotely similar to the quotation that ChatGPT attributes to Crick. I was unable to find any source for that "quotation." It's true that there were scientists (Leslie Orgel, Walter Gilbert) who thought that most of the non-coding DNA was non-functional but that's not the question that I asked and it's not the position that ChatGPT is defending.

There are two lessons here: (1) Don't trust ChatGPT, and (2) ChatGPT is probably spewing back the common misunderstanding of junk DNA. If Wikipedia is ever going to be a reliable encyclopedia then one of it's primary goals must be to refute misunderstandings and misconceptions but that doesn't jibe with the Wikipedia culture.

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