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Comment by chiefalchemist | Hacker News Reader

> "Use it or lose it" applies to genes as much as (or maybe even more than) anything else. Genes involved in biological processes are lost if the trait they confer is unused or unnecessary."

Why would this be true? Can't a gene be dormant? Or perhaps over-ridden but another gene or genes?

Or is, over the long haul (read: __many__) years any and all genes will naturally mutate (that is, be lost). Then if the "replacement" is more advantageous, the replacement will persist.

Fair enough. But that's not use it / lose it per se. It's still in use, but less so (and is over time replaced).

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It's that second one. Geneticists talk about genes being "conserved" when they are needed, and use the level of conservation to understand how essential a gene is to the functioning of an organism. For example, hemoglobin genes are highly conserved across all animals, because any mutation there is likely to produce an unviable organism.

If something is not conserved by selection, then the default is for it to be overwritten. So more like "need it or lose it". But I feel like that's pretty close to the article's phrasing.

It's simpler than this: If you can obtain a nutrient from the environment, then the machinery to make it yourself breaking won't kill you.

Same way mammals keep losing vitamin C synthesis when they settle on a diet that's rich in it.

This isn't "use it or lose it" this is just "lose it and don't die". Having the synth path is better, dying is worse.

> Same way mammals keep losing vitamin C synthesis when they settle on a diet that's rich in it.

This is a terrible example; all mammals eat a diet rich in vitamin C, but loss of the ability to synthesize it is quite rare, being restricted to some primates, some rodents, and most bats.

https://en.wikipedia.org/wiki/Vitamin_C#Biosynthesis

It was a breakthrough when scurvy was observed in guinea pigs in 1907. Before that time, it had never been observed outside of humans, though it is known in humans for most of recorded history.

Most animal diets are not rich in vitamin C. Meat and leaves have minimal vitamin C for example. Humans evolved to conserve vitamin C and eat a much wider diet than most mammals. Without that deer for example might occasionally get enough Vitamin C, but would quickly get scurry at various times of the year.

> Meat and leaves have minimal vitamin C for example.

A human can eat nothing but fresh meat without suffering from scurvy. And in fact, a diet of fresh meat is sufficient to cure scurvy in a human already suffering from it. You could argue that humans conserve vitamin C better than lions do, but you can't argue that lions are eating a diet that is not rich enough in vitamin C to support an animal that can't synthesize its own. It's not an issue of the amount in the diet.

While you make a significant distinction in that evolution does not necessarily make a decision to eliminate unused traits, most traits that consume resources and energy do get culled as it almost universally improves survivability.

After all, one of the things that's so hard for us to grok about evolution is that it's not a goal-oriented process in any way. It's not engineering, it's the process of random chance and what can persist.

For example, a lot of people think that all our junk DNA actually does something profound and important, and while some of it probably does have a purpose we don't yet understand, I think it's almost certain that any process that makes a bunch of random decisions that are mindlessly culled by environmental forces will inevitably generate some flotsam and noise in its code. It's kind of like training AI; it definitely won't give you the most minimalist method of carrying out that task, but it will eventually find some way to carry it out. Almost as a brutal, automatic tropism.

Yes. I agree. My issue was with the phrase "use it, or lose it." As you said there's plenty of "left over" genes. They're not lost. What's happened is their traits have been replaced by a more advantageous trait. The former might still be useful, but the latter are more so and become the majority, so to speak.

The “survival of the fittest” phrase is a huge disservice to generations of students.

Traits that are maladaptive are culled. Ones that have no effect are preserved, increased or diluted depending entirely on what other genes they appear with. Not the gene themselves.

If pale eyes were not beneficial in northern latitudes, we would still have blue eyes because the norsemen had them, and they were very successful. That gene will stick around until something forces it out of the pool because there is otherwise nothing to stop it.

In the simplest case there is a default state (e.g. eyes have color of whatever pigment just happen to be produced there as a sideeffect of important genes). And then there are genes that override this default. They may disable the normal pigment genes, they may produce additional pigment, they may break down pigment. These genes can then exist in variants (alleles). Following the example, they may produce pigment molecules with different colors.

In the absence of selection pressure the override genes will mutate randomly. The end state of that process are broken genes that don't do much of anything (loss of function), and so the color goes back to the default.

For human eyes, the default is blue eyes and there are then some genes that overrides this by producing melanin, which turns the eyes brown.

This is purely hand-waving, but one scenario where natural selection loses the gene is where the expression of the NIN gene created a vulnerability for a virus/bacteria/fungi that would kill out the plant. Considering the gene involves a pathway that hosts symbiotic relationships with micro-organisms, it seems possible.

In such a scenario, the only surviving, reproducing individuals would have mutated in such a way to suppress expression of the gene. (Again, there is no evidence of this, it's just conjecture)

> Considering the gene involves a pathway that hosts symbiotic relationships with micro-organisms, [the expression of the NIN gene created a vulnerability] seems possible

Ha—the plants were hosting an API for the bugs.

this quote seems rather poor for this particular case, since, nitrogen fixation is more than "just a gene", it's a symbiotic relationship with an invasive bacterium that has its own agenda.

However, in general the concept of drift causing loss is solid; guinea pigs and humans have both independently lost the ability to create their own vitamin c. It's possible that some rather successful member of the species for some other reason (stronger, smarter, or just sexier) happened to have the vitamin c gene loss, and the need for vitamin c just wasn't pressing enough to overcome the other appeal.

Another version of this is that the Vitamin C gene itself mutated into something useful, or that not having it was in and of itself a small benefit given ample dietary C. A quick google shows there has been some speculation about this, but nothing definitive.

Over the long run it’s entropy working against a simple cost benefit analysis. If there is a sufficient multigenerational selective advantage the the gene will he preserves. If not, then there is no positive selection and it’ll accumulate mutation.

My guess is complexity. Any gene still in there is a gene that can go wrong. Purging unuseful ones minimises risk.

It seems to me that it a gene gets disabled, but still physically exists, random mutation will eventually scribble over it, as mutations there wouldn't affect the survival of an individual. So dormant genes will eventually disappear.

It's because of genetic drift.

If there is no selection happening on the gene, then the relative distribution of that gene in the population effectively drifts at random.

So yes, a gene can definitely be dormant, but it can also be lost if it's not actively being selected for.

There's no guarantee that the gene will be lost if it's not used, but it's definitely a possibility that increases with time.

gases expand, unless something stops them. mutation is like brownian motion.

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