Plants repeatedly got rid of their ability to obtain their own nitrogen | Hacker News Reader

Plants repeatedly got rid of their ability to obtain their own nitrogen

arstechnica.com

135 pointscurtis53 comments

> "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).

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.

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.

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.

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.

I wasn't taking too much care of the grass and fertilizing it and after a few years I started seeing more and more clover. It turns out clover fixates nitrogen from the air. The clover took over in some areas almost completely. After a while I started liking how clover looked.

This happens on my parents' lawn too. I don't understand though, if grass grows better than clover in nitrogen-rich soil, why doesn't the grass come back once the clover has replenished the nitrogen?

If you overseed with grass seed it will. Grass and clover makes a really nice sward. When I had a lawn (more than 10 years ago!), I eventually realised the beauty of this. Mix in camomile for an even lusher, softer lawn. Let it grow long enough for the clover and camomile to flower and it's amazing. The longer grown inhibits other weeds. It's practically maintenance free -- just run over it with a push mower every once in a while.

On farmland, the nitrogen from the clover reaches the grass after it has been eaten by sheep/cows and then excreted - either directly or by the farmer spreading manure.

The ability to synthesize compounds is often lost when those compounds abound in the organism's environment because synthesis consumes energy and an organism's energy budget is limited.

Examples from the animal kingdom include frugivorous humans lacking the ability to synthesize vitamin C, and cats lacking the ability to synthesize taurine.

As I said in a sibling, this reason is more complex than it has to be.

If you can suffer a mutation and not die, because you can obtain the nutrient from food, then you can have offspring who have the same non-fatal problem.

There's no budgeting involved and whether the conditions that make this a reduction in fitness occur or not is a fluke. Vitamin C synthesis turned out to be a big deal for humans once we started going to sea.

I'm going to take a wild guess and say that this is due to low CO2 levels. Plants evolved and are use to 1200ppm CO2 level. The current levels 300-400ppm 1/4 to 1/3 of their normal level, they are starving. Its amazing they are actually surviving. Probably going to get downvoted to hell but science is science.

> Plants evolved and are use to 1200ppm CO2 level [...] they are starving [...] science is science.

Well, that's certainly a novel kind of pseudoscience pro-emission bullshit, I'll give you that.

Unfortunately -- by your logic -- both of us are simply fancy Coelacanths which "evolved and are used-to" briny sea water as our "normal" environment, which is why it's so difficult to type this with my flippers while suffocating on dry land.

No, wait, that's not true, because evolution is a constant process and doesn't just happen once and stop. I can take a literal breath of relief.

So let me get this straight. You reject the relevance of higher CO2 Levels in the past because it's too long ago. Then you point out that evolution is an ongoing process, but apparently it's too slow to accommodate a rapid rise in CO2 Levels. Is that correct? If so, it's not wrong, but it seems a little like mental gymnastics to fit a particular idea.

> You reject the relevance of higher CO2 Levels in the past because it's too long ago.

I reject his weird concern-trolling, regarding a category of "starving plants" which are necessarily extinct and have been for many millions of years. Since they do not live anymore, it makes any "more CO2 makes them happier" appeal ridiculous.

> apparently [evolution is] too slow to accommodate a rapid rise in CO2 Levels

Evolution "accommodates" rapid changes that harm a species via DEATH AND DISRUPTION. As we are both members of the supposedly-dominant species right now, surely you'd agree that generally has more risk than reward, and that we'd rather not have population die-backs from famine or economic losses from cities built in the wrong place.

> cats lacking the ability to synthesize taurine

Where, in the wild, do find their plentiful taurine?

Small mammals!

And birds and insects!

CHEEZBURGRZ

Nitrogen is usually a limiting factor, but freeloading is often a viable strategy if there is a cost involved.

I wonder if the symbiotic bacteria provide other benefits, such as fighting off other bacteria that would attack the plant.

Fava beans! Easy to grow, fun to watch, nice flowers, tasty, and big nitrogen nodules.

A fun thing about them (in the PNW at least) is that you can plant piles of them in fall and they will grow with very little assistance (or watering since it rains so much) and you'll have heaps upon heaps of beans in spring.

I planted $10 of Windsor beans 2 years ago and ended up drying about 300-400 seeds (far more than $10 worth) and still had too many to eat. Some of my new son's first solid food was a hummus made from those same dried beans (really delicious!).

Such a fun plant to grow. Processing the beans is a bit of work, but wow, it's worth it. Unparalleled flavour in the bean kingdom.

Although it’s worth pointing out that about 1 in 10 people suffer from Favism (1),which is sort of rough.

1. Glucose-6-phosphate dehydrogenase deficiency, leading to hemolytic anemia.

Plus they pair well with a nice chianti.

I feel like this pairing lacks a protein to really balance it out.

Fava beans have a fair amount of protein in 'em already!

Perhaps a sweetbread of some sort?

Where do you buy some? There's a little playground behind my building with a few trees and I'd love to add some plants and see them grow eventually.

Couldn't it be as simple as as a selection of ample seed production over ample nitrogen availability in an environment where adequate sunlight was more often a limiting factor than adequate nitrogen. It takes significant energy to produce the root exudates that encourage and feed the specialized symbiotic bacteria that will fix some amount of nitrogen for the roots. The plant already needs lots of energy to build it's carbon structure and immune system. Then more energy for seed production, which is the most important of all. This energy has to come from sunlight. In growing competition with other taller plants and trees, sunlight is often greatly diminished. The plants that 'stopped' producing these exudates and used the available energy in structural fitness / robust seed production were able to compete more effectively as a species over a larger area.

This may be an evolutionary stable strategy (https://en.wikipedia.org/wiki/Evolutionarily_stable_strategy).

If nitrgoen-fixating species already cover N% of the niche, other species may not be pressed too hard to retain their own nitrogen-fixing ability.

Yay for outsourcing.

How do non-symbiotic plants normally process their nitrogen into ammonia?

Article didn’t mention.

Ammonia and other nitrogen containing molecules are already in soils in varying quantities and are taken up by the roots like other nutrients.

This article is showing its biases. You only need to fix nitrogen in a monoculture, and rather than giving up on that idea they’re going to keep trying to make plants that are everything to everyone.

If your ecosystem contains nitrogen fixers you can scavenge nitrogen from your neighbors. In some cases this could be construed as a second symbiosis: A vining legume is working with the bacteria for nitrogen and its neighbors for loft. It has access to more sunlight in the spring, and can lay down more nitrogen before the trees wake up. At which point the trees have access to more nitrogen for manufacturing leaves.

To my way of thinking, this makes a ton of sense.

I don't think Darwin got it right. It's not "survival of the fittest". It's "survival of that which can find its place in an ecosystem".

I think it's "Survival of the Fittest Ecosystem," actually. So not like, "Humans are fittest," but instead, "Human eating corn cow sheep soy etc. while building machines is fittest"

It's interesting how selection acts at different levels. Individuals are reasonably good at enslaving their cells so they cooperate (when they don't, they get cancer).

But cooperation between individuals is much less effective, not to mention between species. An ecosystem is incapable of enforcing a contract between species to prevent a selfish species from destroying the whole thing.

That's basically what it meant in the first place. It's "fittest" in the older and broader sense of "fit": suitability for a task, role, or purpose.

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