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Saturday, July 29, 2023

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.


Athel Cornish-Bowden said...

I'm less worried by an incompetent and ignorant student than I am by the people who taught her and the textbooks written by incompetent authors. I abandoned long ago (when I was beginning research) the idea that PhD students senior to me were necessarily more knowledgeable than me. I needed to think about the likely properties of a tripeptide (phenylalanyl-phenylalanyl-glycine, if memory serves), so I went to talk to someone in a group specializing in aminoacid chemistry. I said something about my tripeptide being a zwitterion, and he said it was not possible, as the amino and carboxyl groups were too far apart to interact. Oh dear. That was the end of any idea that people who ought to know more chemistry than me actually did.

Larry Moran said...

I share your concern about the state of science in general. How come nobody around this student raised any concerns about their understanding of junk DNA and the history of the field? How come none of the reviewers of published papers ever question the idea that Francis Crick, Sydney Brenner, Thomas Jukes and others were too stupid to realize than some non-coding DNA could be functional?

John Harshman said...

Looks like some kind of medical (specifically psychiatric) research lab. The farther away from evolutionary biology, the more likely you are to find this sort of thing.

Larry Moran said...


Do you feel the need to post science articles on subjects that are far away from your area of expertise?

I think it's likely that the graduate student thinks this is something they know a lot about. That's very troubling.

John Harshman said...


I think one problem is that people who do molecular biology, especially human-oriented molecular biology, seem to think this is within their area of expertise. Makes some sense, as the best evidence of junk DNA is comparative.

Anonymous said...

Looks like the picture and name of the graduate student has been removed.

John Harshman said...

To clarify: Makes some sense, as the best evidence of junk DNA is comparative...and thus medical researchers focused on human biology could easily be unaware of it.

Athel Cornish-Bowden said...

César: yes, it was the picture that led me to refer to the student as "her". Without the picture, who knows?

Anonymous said...

Can someone explain the current view on Mendelian randomisation regarding junk dna

Larry Moran said...


I'm not sure what you mean by "Mendelian randomness." Can you rephase your question? Are you interested in why junk DNA isn't removed by natural selection?

Anonymous said...

No, I mean Mendelian randomisation method that reliably estimates the effects of a casual variable without the need to conduct a RCT. It relies on random assortment of genes described by Mendels second law of inheritance. Wondering your view point.

Joe Felsenstein said...

Mendelian randomisation method There is a Wikipedia page for an epidemiological method called "Mendelian randomization". When the issue is whether variation in a stretch of putative junk DNA is neutral, I wonder whether vast sampling size of sets of siblings would be needed to detect small fitness differences.

John Harshman said...

I was looking to find reactions to What's in your Genome? on the intertubes and ran into this:!ex%3Ddt%7Dhost&facet.limit=100&facet.mincount=1&

Not currently sure who runs that site, but those are the results of a search for "junk".