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Comment by Retric | Hacker News Reader

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.

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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.

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.

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.

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