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Comment by dkoston | Hacker News Reader

How naive or arrogant do scientists have to be to think that we have “junk” DNA that doesn’t affect how we develop? Wouldn’t it be much more useful to classify things we don’t understand as “unknown purpose X” so that more people are inclined to study them?

/end venting

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The word junk does not appear in this paper. They talk about noncoding regions, noncoding mutations, and noncoding genome.

More generally, the term "junk DNA" was coined to refer to a specific type of noncoding DNA. These two articles give the historical background for the term:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014423/

https://judgestarling.tumblr.com/post/64504735261/the-origin...

Agreed, maybe I misspoke but I wasn’t aware of any place I said it did.

“Junk DNA” is a well accepted term by the scientific community and public.

https://www.scientificamerican.com/article/what-is-junk-dna-...

Humorous take on my point: https://www.amazon.com/Junk-DNA-Journey-Through-Matter/dp/02...

I think my main point was missed which is: “labeling something as non useful and leaving it out of the majority of DNA sequencing as a result has made large swathes of the scientific community unaware of how non coding DNA works within the DNA ecosystem”. I think it’s unfortunate that the community doesn’t label this as “exciting area of unknown science” which would encourage investigation.

> labeling something as non useful and leaving it out of the majority of DNA sequencing as a result has made large swathes of the scientific community unaware of how non coding DNA works within the DNA ecosystem

This is simply not true. Noncoding RNA and in particular regulatory regions have been known and studied for many decades. The reason we know less about them than about genes has multiple reasons, foremost the difficulty in studying them (large-scale studies have only recently become possible). But it has nothing to do with “ignorance”, or with the label “junk DNA” (the SciAm article you link to is utterly wrong to claim otherwise).

Furthermore, although I also think the name has issues (but mostly in science communication), scientists don’t just “assume” that intergenic, non-regulatory DNA regions are unimportant. They have good reasons, backed by evidence, to think so. I’m actually in the camp that thinks that stochastic biochemical function is potentially important (and I used to study repeat elements) but even so there’s almost certainly very little “exciting … unknown science” in junk DNA.

I have to disagree. Whole genome sequencing has only been prevalent in the past few years. I can agree that much of this has to do with the cost and complexity involved and the rise of new techniques and more computing power has opened up whole genome sequencing which has only been around since 2003 (1) and has been highly expensive and not used frequently until recently (2).

The majority of research I’ve come across in the past decade has been still focusing on DNA microarrays and qPCR which are focused on coding DNA. Perhaps I’m not seeing all the papers published for the studies you are familiar with and as such have a bias to believe that only a small portion of research is using NGS and is focused on non coding DNA.

1 https://www.yourgenome.org/facts/timeline-history-of-genomic... 2 https://academic.oup.com/hmg/article/25/R2/R157/2198171

Well my own research has focused completely on noncoding DNA. So yes. It exists.

Ok, we'll replace junk with noncoding above.

Junk DNA means non coding and without benifit. Due to the random nature of mutation such sequences are expected. However, verifying any specific sequence is useless is difficult.

One important consideration is sequence length may have value even if the content is meaningless. Another is random sequences may aid long term adaptation even if they don’t currently do anything. So, if anything Junk is a fairly descriptive term as you may eventually use stuff from a Junk Drawer even if it’s not currently useful.

I don’t believe it exists without benefit. Nature can certainly phase parts of our system out over time (appendix) but to say it is without benefit is a bold statement. I’d argue that we simply don’t know the purpose and dismissing it as non-beneficial is arrogant or naive. Science should be based around evidence rather than lack of.

What is the benefit of having an arch in the nose vs not having one? Or the benefit in light brown hair vs dark brown hair? Or the benefit in light brown eyes vs dark brown eyes?

How about the benefits in male pattern baldness where some of the hair on the scalp is affected by high levels of DHT and some aren't? How about diffused baldness where the way in which a person balds isn't in one particular place and is all over the scalp randomly?

These are all visual, observable examples. But when looking at individual genes, I'm sure you can appreciate that randomness inserts itself there as well - randomly, and not necessarily with any benefit. I don't think its arrogant or naive to appreciate that we are a set of random mutations, some of which have helped us become extremely successful in nature, but some of them don't have those benefits and only survived through luck or selection of other genes in the person they cohabited.

I can absolutely appreciate that we are a series of mutations.

To say that there is no benefit or detriment to having an arched nose or not also seems naive. It’s likely that the shape of your nose can affect how much air passes to your lungs, how likely it is to be sun burnt or not, and many other things. Just because the values or benefits might be minuscule compared to other things doesn’t mean they do not exist. Tiny optimizations are common in all systems and they should not be overlooked.

To say that massive portions of our DNA “have no benefit” without having proof of such, seems naive to me. It’s ok for others to disagree; clearly the majority of the scientific community does. It’s just unfortunate that we have been ignoring the possibility that this large portion of our DNA could have effects on our system. In the article above, it’s not benefits that matter but risks. We shouldn’t only care about parts of our body that may bring benefit but also those which may harm us.

As far as baldness goes, this is a trait that could be seen as a benefit. Some females may desire a mate with high levels of DHT and baldness is a good indicator that a being has high levels. There are many visual traits (see birds) that allow the narrowing of selection for potential mates.

Evolution is not a process of finding a global optimum, just a local one. And traits which have no impact on the chance for a species to reproduce just get carried along for the ride.

An obvious example of this is the Laryngeal nerve. Fish evolved with this nerve being a simple straight line between the brain and larynx. However, in animals which evolved from fish and have necks, we see that the nerve is "trapped" under the aortic arch in the thorax. So this nerve ends up looping through your neck to reach your thorax. Giraffes have this nerve going all the way down their neck and back up again. But this inefficiency has no impact on the survival chances of a species (if your neck is severed you're dead regardless of whether you have an additional nerve running through it) so it's stuck around.

So, there definitely are traits which objectively have no benefit or detriment and have just stuck around. You could argue even some late-life conditions which are detrimental also "stuck around for the ride" because people late in life don't reproduce and thus there is no evolutionary mechanism to affect such traits.

Sure, I even made this point when I pointed out that the appendix has gotten carried along for the ride in another comment.

Do you really believe that 75-98.8% of our DNA serves no purpose and is being carried along for the ride? That doesn't seem like a small inefficiency.

Why would you assume a high grade of efficiency, let alone perfection?

I’m assuming more than 2% efficiency would be achieved. I could be wrong but why would I assume that when most other systems in the body are massively more efficient that DNA would be the outlier?

> To say that massive portions of our DNA “have no benefit” without having proof of such, seems naive to me.

What makes you think scientists have no proof? The whole reason we know junk DNA has no important function for cell biology is that there’s good evidence that says so. There’s some wiggle room with the details but the general picture of this won’t change, and this has been studied for a long time and is fairly well understood.

Whole genome sequencing on humans has only existed for 16 years (1). In 2003, the cost was prohibitive until NGS (next generation sequencing) techniques became commercialized. We can definitely disagree here as 15 years of research which in my worldview is focused mostly on coding DNA and karyotyping doesn’t seem like much to draw this conclusion. There’s plenty of decades old science that has shifted or been rewritten due to the rise of new techniques related to faster computing power.

It’s quite possible that I’m biased based on the labs I’m familiar with and papers I’ve been reading. I just haven’t seen the focus that you are talking about.

1 https://www.yourgenome.org/facts/timeline-history-of-genomic...

Junk DNA has already been studied before whole-genome sequencing existed, and evidence from NGS not only hasn’t overturned that research, it has largely corroborated it. And as for personal biases, I’m a staunch defender of the ENCODE research so I’m certainly not biased in favour of the concept of junk DNA.

Interesting. I may be biased in the other direction after reading "The Epigenetics Revolution" and "Junk DNA" by Nessa Carey.

ENCODE is such an amazing project! Also, thanks for your research on non coding DNA.

But junk is perjorative word which suggests that it is entirely disposable even desirable to remove. That may turn out to be true but the experiment required to prove that thesis would require closely observing a biological systems evolution and disease evolution for some length of time, with "junk" DNA somehow removed and repressed. It may turn out to be a sort of filler with certain characteristics that work out to have repercussions for longer term genetic dynamics, and it may not. Since we cant tell yet, the name for it is very presumptive.

> But junk is perjorative word which suggests that it is entirely disposable even desirable to remove

That's subjective.

> It may turn out to be a sort of filler

Yes, that's understood and recognized in every analysis.

> the name for it is very presumptive.

Naming is hard. The lowest common denominator (least amount of thought/simplest concept) will almost always persist. It's not like someone is wringing their hands in the background imagining they have fooled the scientific community.

Junk (and/or noncoding) DNA provides necessary structure for our chromosomes, spacing for transcription, and some defensive properties.

There are many benefits beyond just that of coded information storage, which people are focused on here in this thread.

Personally I think it's both naive and arrogant to assume that because something is called "junk DNA", that means that the scientific community as a whole have decided to never consider whether it has any impact. There are all sorts of weird terms-of-art in science and I find it quite frustrating that armchair-scientists think they know better purely based on the words that happen to be used.

Actually, “junk DNA” was assumed to have no function decades ago. That’s why it got the name. That’s what I was taught in college 15 years ago.

Subsequently it was discovered it does have a very important function.

Scientific understanding evolves.

What you were taught in college 15 years ago is still correct. Junk DNA does not have “a very important function”. The “subsequent discoveries” were, by and large, just a failure in science communication. Junk DNA is still non-functional, very little has changed. We know this because it’s not preserved evolutionarily. By contrast, “important” DNA is preserved from mutation (this is called “negative” or “purifying” selection) because mutating it is almost always bad for the individual. What has changed is twofold:

* We have a better handle on what constitutes noncoding, non-junk DNA. The proportion of DNA thus labelled has grown slightly (but only slightly!). We were always aware of its existence but we previously couldn’t study it easily. There are very good reasons to think that the proportion won’t grow much further. The rest is still junk DNA.

* We know more about how new genetic function can evolve using the raw genetic material in junk DNA, and how junk DNA might interfere with the proper function of cells, in particular in the presence of pathogens. But, again, the principle of this was already known (or, partially, at least strongly suspected) decades ago. It was just not studied, and we’re now able to study it better.

But our fundamental understanding of junk DNA hasn’t changed.

Many noncoding DNA sequences must have some important biological function. This is indicated by comparative genomics studies that report highly conserved regions of noncoding DNA, sometimes on time-scales of hundreds of millions of years. This implies that these noncoding regions are under strong evolutionary pressure and positive selection.[47] For example, in the genomes of humans and mice, which diverged from a common ancestor 65–75 million years ago, protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented in noncoding regions.[48]

Noncoding DNA ≠ junk DNA! In fact, the latter is a subset of the former. Confusing the two is understandable since even scientists occasionally play fast and loose with the terms but scientists nevertheless understand that they are different. To cite from the same article you’ve cited:

> When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA".

And this is by no means a new discovery, functional noncoding DNA has been known for as long as junk DNA.

Maybe my wording wasn’t clear. I never implied that everyone is ignoring non coding DNA. My point was that it seems naive or arrogant to label something as “not useful” rather than “use unknown”. It makes it less likely that a larger amount of people will investigate it.

I think you should also use some data to back up your point because it’s my understanding that the majority of DNA sequencing ignores non coding DNA and the article makes the same point. You also have no idea what field I work in so I’d suggest perhaps asking before coming to the conclusion without any data.

As far as I can tell, the preferred scientific term is "non-coding DNA," with "junk DNA" being a sensational term that gets more traction in the media.

Here’s the Wikipedia quote:

It’s not all non-coding DNA that is “junk”, just the stuff that “has no purpose”.

I’m arguing that it is much more likely that we don’t understand its purpose and should treat it as such rather than dismissing it as “junk”.

I like the use of “junk” DNA only because it reminds people how much we don’t know. It wasn’t that long ago the term was used because that’s DNA was assumed to be useless.

How is that naive or arrogant?

As it seems to imply that this area of our DNA has no significant value. It seems highly unlikely to me that there is a large mass of DNA in our body that doesn’t affect our overall system. I relate this to people believing for long periods of time that animals cannot tell time or remember things for long periods of time and then later realizing that they can do both.

If we were given an explanation of "this type of DNA used to do X but since Y happens, it is no longer used", I'd be more apt to believe in "junk DNA". Without explanation for what it is for or what it was for, saying it is junk seems naive.

The history of science, and especially biology, suggests that there is a lot of stuff which isn't understood very well. Seeing no importance in an aspect of the natural world can be as much a comment on experimental design and human knowledge ("knowing what to look for") as on the phenomenon ostensibly being studied. Typically "being able to observe an effect" is contingent on some other dependent scientific "knowledge".

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