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Monday, January 29, 2024

"People also ask" about junk DNA

I'm interested in the spread of science misinformation on the internet. The misinformation about the human genome is a good example that illustrates the problem. There are many other examples but I happen to know a lot about this particular one.

Anyone trying to find out about junk DNA will find it impossible to get a correct answer by searching the internet. The correct answer is that the amount of junk DNA in the human genome is controversial: some scientists think that most of our genome is functional while others think that as much as 90% is junk. The scientific evidence strongly favors the junk side of the controvesy and that's very well explained in the Wikipedia articles on Junk DNA and Non-coding DNA.

The Wikipedia article on junk DNA comes up at the top of the list when I use Google to search for "junk DNA." That's the good news. The bad news is that the rest of the page is full of articles debunking junk DNA and implying that most of our genome has functions that have recently been discovered. But this isn't the only problem. The top of the page also has a "People also ask" section with questions about junk DNA. These questions come from a Google algorithm that searches the internet for questions related to your search query. When you click on the answers to these questions, you'll find that they are invariably mined from articles disputing the idea of junk DNA

I suspect that most people will click on the short answers to these questions instead of reading the Wikipedia articles. They will get a very distorted view of junk DNA and come away with the idea that there's no such thing. This is one way that Google reinforces scientific misinformation.

I'm going to give my own answers to these questions because I'm told that blogs are a significant source of information for the Google search engine. Maybe my answers will eventually appear under "People also ask." It's worth a try.

Why is 98% of our DNA called junk DNA?

Less than 2% of the human genome encodes proteins and some people assumed that the remaining 98% was called junk DNA. However, no knowledgeable scientist ever claimed that 98% of our genome was junk so this is an unfortunate myth that has propagated among opponents of junk DNA. The proponents of junk DNA have always argued that 10% of the genome is functional and this includes at least 8% of the non-coding DNA.

What is a junk DNA?

Junk DNA is defined as DNA that has no biological function. Proponents of junk DNA claim that less than 10% of the human genome has a well-defined function and the rest is junk. Opponents of junk DNA argue that we don't know the function of much of the genome but there's evidence suggesting that it might have an unknown function.

Is junk DNA harmful?

Junk DNA has no function so it is not harmful. However, mutations in junk DNA can be harmful if they create a new site that interferes with normal gene function.

Why is it no longer called junk DNA?

There are many scientists who continue to use the term "junk DNA" because they think it's a good way to describe non-functional DNA in the genome. Opponents of junk DNA believe that the term is no longer useful.

What is the junk DNA controversy?

The controversy is about the amount of junk DNA in the human genome. Some scientists, especially experts in molecular evolution, think that most of our genome is junk but other scientists dispute this claim.

Does junk DNA have a purpose?

Junk DNA does not have a purpose because, by definition, junk DNA is non-functional DNA. Sometimes new functional elements are found in DNA that was thought to be junk and sometimes DNA that was thought to be functional turns out to be junk.

Can junk DNA be removed?

One of the operational definitions of junk DNA is DNA that can be removed without any noticeable effect on the individual or the species. Several experiments have demonstrated that junk DNA can be deleted. Any DNA that causes harm if removed is not junk DNA.

Does everyone have junk DNA?

If proponents of junk DNA are correct then everyone has lots of junk DNA in their genome.

What is junk DNA now called?

In the early 1970s junk DNA was defined as DNA that has no function. The definition has not changed since then.

Is most of the human genome junk DNA?

Many scientists think that 90% of the human genome is junk. Other scientists dispute this claim.


John Harshman said...

I tried asking "What is junk DNA?" and here's what I got:

First, a short definition: "genomic DNA that does not encode proteins, and whose function, if it has one, is not well understood." Not good, but it gets worse.

Wikipedia was the fourth result. The first three were all bad in different ways:

"So-called junk DNA plays critical role in mammalian development"

"Junk DNA, in reality, activates under stress. It is just dormant archaic DNA."

"In genetics, the term junk DNA refers to regions of DNA that are noncoding."

Stewart Hinsley said...

I asked Bing Copilot "what is Junk DNA". It cites Wikipedia for all but the last paragraph (which is cited to an article at Quanta Magazine).

"Junk DNA, also known as non-functional DNA, refers to DNA sequences within an organism’s genome that do not have any relevant biological function. Most organisms, including humans, have some amount of junk DNA in their genomes. This non-functional DNA can include pseudogenes (inactive remnants of once-functional genes) and fragments of transposons and viruses. However, it is possible that some organisms may have substantial amounts of junk DNA.

The concept of junk DNA has a long history. In the late 1940s, geneticists such as J.B.S. Haldane and Hermann Muller predicted that only a small percentage of the human genome contains functional DNA elements (genes) that can be destroyed by mutations. These predictions were based on the estimated mutation rate in humans and the species’ ability to tolerate deleterious mutations. Muller even suggested that the human genome could only contain about 30,000 genes.

However, our understanding of junk DNA has evolved over time. Repetitive DNA, which makes up a significant portion of genome size differences, was discovered and attributed to the C-value paradox. While some scientists believed that repetitive DNA might regulate gene expression, others considered it nonfunctionalTomoko Ohta proposed the nearly neutral theory, which explains how slightly deleterious junk DNA could be maintained in species with small effective population sizes.

In summary, junk DNA represents portions of the genome that lack a known biological purpose, but ongoing research continues to reveal complexities and surprises related to noncoding DNA and RNA."

popgen wannabe said...

I find that it's impossible to get a grip on the concept of junk DNA online, and perhaps even elsewhere unless you are a specialist on that topic. The views presented on this blog seem among the most sensible to me.

Tangentially related, has anyone read this new book?

The review already seems a bit misleading to me, and I don't know if I trust the reviewer's description of the state of evolutionary biology.

Larry Moran said...

@popgen wannabe

Several of us have been working on correcting Wikipedia articles so that the correct view of junk DNA is covered. Check out the one on Junk DNA.

I read Denis Noble's review of Philip Ball's book. It's not surprising that Denis Noble would write a favorable review of a book that promotes his own strange view of biology. Noble tries to shoehorn all of biology into human physiology and the idea that our behavior is more than the action of our genes (duh!).

My copy of Ball's book, "How Life Works," won't arrive for another few weeks. I'll have more to say about it later but I'll post something about it soon to alert readers.

Anonymous said...

is the answer to "can junk dna can be removed" entirely correct? I can't imagine removing any 90% of dna would be entirely harmless just by the virtue of new proximity of literally everything else causing new cis interactions. Or is that already accounted for in the definition of junk dna since deletions of large sections of dna has been tried before and that sort of thing simply doesn't happen as often as I intuit it would?

Or as a thought experiment, if I add a beneficial gene that by some molecular circuitry, is only expressed when the genome is as long as it is now, did I eliminate the concept of junk dna under the current definition?

Larry Moran said...


I suspect you are correct when you say that instantly removing all the junk DNA would probably be harmful. However, that can't be an argument for function and against junk DNA because it's an unrealistic scenario.

When I say that junk DNA is DNA that is not under purifying selection it implies, correctly, that it could be deleted without harm but for this to happen naturally it would have to happen gradually over many generations so the organism could adjust gradually to a smaller genome.

Yeast is a good example of an organism that has shed most of its junk DNA, including introns, over the course of 100 million years or more. Pufferfish is another example.

Your thought experiment would challenge the concept of junk DNA. If such a gene exists, it would mean that there is merit to bulk DNA hypotheses and even though the sequence of bulk DNA is not under purifying selection, its presence is under purifying selection.

Do you think that either of those points counts as a good argument against junk DNA and in favor of a fully functional genome, or are you just nitpicking over the precise meaning of the words 'function' and 'junk'?

Anonymous said...

A bit of nitpicking and a bit of questioning my intuitions. The answer just sounded a bit too ambitious.

Under that light I don't think the thought experiment would change all that much since it only introduces a specific point of failure to exaggerate the issue and would likely be similarly able to adapt to gradual reductions in the amount of DNA if any possible path in evolution was silly enough to keep it for long at all.

But then it'd also be interesting to know the minimal scaffolding required to keep all current regulatory structures if one wanted to craft a minimal genome for anything with large amounts of junk at any given moment.

Larry Moran said...

@Anonymous: I count scaffold attachment regions (SARs) as part of the functional genome. (There are other names for these sequences.) I count required spacers, including those necessary to separate functional elements, as part of the functional genome. None of them seem to account for more than a tiny fraction of the genome so they can easily be included in the 10% that's functional.

I have never seen a rational argument in favor of the idea that a large fraction of the genome is required to organize chromatin. None of them pass the Onion test.

Stewart Hinsley said...

The thought has crossed my mind that removing (or adding) large chunks of DNA might mess up the synchronisation between DNA replication and the rest of the cell cycle.

Against, polyploid plants seem to be mostly unaffected.

For, in some high induced polyploid crosses (in the dodecaploid range) in Triticae some of the constituent genomes are systematically eliminated.

Even if the effect was real it seems a stretch to describe it as a bulk DNA function.

Anonymous said...

What I meant by scaffolding here was anything that'd be needed to prevent any detrimental effects from removal of all junk dna all at once at point of a history of a genome before it can be.. yeastified with time. I'll admit that it is not particularly useful nor biologically meaningful