RNA demethylation increases rice and potato yields 50% | Hacker News Reader

RNA demethylation increases rice and potato yields 50%

nature.com

190 pointsmleonhard167 comments

Interestingly, DNA methylation seems to be a good indicator of aging and possibly even play some active role in the aging process.

https://en.wikipedia.org/wiki/Epigenetic_clock

https://www.nature.com/articles/d41586-019-02638-w

https://www.npl.washington.edu/av/altvw211.html

Epigenetics seems to be a field with some low-hanging fruit still available. Perhaps even significant "fruit" such as tissue regeneration in adult humans.

But I do not want to speculate about validity of this particular result. Incidentally, both rice and potatoes spike my blood sugar a lot, so I only consume them infrequently. I wonder how many other people suffer from the same effect without knowing. And thus, what the overall effect of cheaper rice and potatoes on health of the population would be.

(I am neither diabetic nor prediabetic and my normal fasting glucose is between 4.0 and 4.7 mmol/L, far into the healthy territory. Most other foods rarely spike it beyond 7.5. Rice can easily reach 11.)

I would guess that cheaper rice and potatoes would not have a great effect on the health of the population, since they're already consumed in vast quantities due to being the cheapest things available. Lack of them generally isn't what causes food cravings though, so being cheapest by a larger margin seems unlikely to shift behaviour by much.

To share a personal anecdote on the subject: I consumed cheap carbohydrates mostly out of a sense of duty to my own pocketbook for the longest time, because I didn't believe someone with my rather voracious appetite could afford to eat just meat and vegetables. When I tried cutting out cheap carbs like rice and potatoes as an experiment, I found my appetite diminished and I consumed no more meat and vegetables than I had before.

This thread seams to be missing the point... With cheaper rice and potatoes, more people in the world can avoid going hungry. The net result is a less impoverished global society.

Alternatively, more land can be reforested and given back to wildlife.

How many people in the world starve because rice and potatoes are too expensive for them? Outright famines are becoming very rare and those that still happen tend to be caused by logistical problems.

We have been galloping into the "obesity is a bigger problem than starvation" territory for decades and we are not far from the end position. Everywhere but Subsaharan Africa, an obesity pandemics is raging. We should not ignore its cost, either human or financial. A wealthy society which suffers from a lot of obesity is de facto impoverished, too.

I would like us to concentrate on lowering the price of foods that contain more nutrients. Things like avocados have become less available to the poor in the last decades, thus stripping them of valuable source of protein, fat and vitamines.

> I would like us to concentrate on lowering the price of foods that contain more nutrients.

Potatoes are rich in nutrients especially if you eat them whole. They are also rich in fiber and starch as a complex carbohydrate takes a long time to be broken into glucose and therefore is not prone to spiking glucose.

There is a reason potatoes have been a staple food for such a long time. If you don't eat them over processed, it's a cheap and relatively healthy food. The whole low-carb diet thing really is a fad.

Cheap proteins remain available in the form of chickpeas and lentils. Avocadoes are just inherently costly to produce and hard to store.

I know that whole potatoes are fairly nutritious, but I suspect that most of the surplus is going to end up in a highly processed form that suits human tongue better at the cost of quality. Such as fries.

>Potatoes are rich in nutrients especially if you eat them whole. They are also rich in fiber and starch as a complex carbohydrate takes a long time to be broken into glucose and therefore is not prone to spiking glucose.

Generally speaking, yes absolutely. What happens in a case like this article, though? Is the 50% increase in biomass matched by an increase in nutrient uptake from the soil/growth medium? What are the chances these bigger potatoes are actually less nutrient dense?

I would like to see a histogram of worldwide BMI. Are we past the point where world median BMI is over 25?

I am not sure if taking BMI histograms worldwide makes sense. Human populations differ and East Asians tend to suffer from complications of obesity from lower BMIs than the rest of the world [0]. Do it region-wise, if needed.

[0] https://www.who.int/nutrition/publications/bmi_asia_strategi...

> Outright famines are becoming very rare

Add climate change and the story may change a bit. Its a good thing to be better at making foods that are the backbone of (many people's) diets. We need other things too, but that doesn't make this less beneficial.

I am not sure that's entirely correct.

India for example, where rice is the staple food has one big problem for feeding people. And it doesn't seem to be having not enough rice. The problem seems to be infrastructure. IIRC India in raw numbers is totally able to feed everyone using just their own production. But there are literally tons of rice rotting away being unable to reach the people in need because of the bad infrastructure.

Old article so maybe things have changed already: https://www.thestar.com/news/world/2011/07/17/why_india_cant...

Then again this is just from 2020: https://www.indiatoday.in/india/story/chhattisgarh-16000-sac...

The net result is even more overpopulation.

Decrease in population is not driven by food availability. People have less kids when they don't need them to ensure their subsistence in old age. You want the world population to decrease? Raise the standard of living in poor countries and work on lowering child mortality.

I don't disagree, my comment was specifically about cultures where overconsumption is the norm. Which aren't necessarily the ones most of us would expect.

source: https://en.wikipedia.org/wiki/List_of_countries_by_obesity_r...

I do agree cheaper unprocessed food is a net gain. However consider this:

https://www.forbes.com/sites/timworstall/2011/09/22/there-ar...

> Incidentally, both rice and potatoes spike my blood sugar a lot, so I only consume them infrequently.

Have you tried 'true' brown rice (the one which takes ages to cook)?

Not yet, but I will. It is on my curiosity list.

That is neat, but we should also look at the amount of fertilizer this change will cause. We are already running soil at the redline and we have more trouble getting the fertilizer into the soil in a healthy way. If this ends up killing the soil 5 years faster through overutilization, it really isn't an improvement as it takes a ton of effort and time to revitalize soil.

> We are already running soil at the redline

This is not a scientific statement at all; it's an attempt at an analogy that doesn't work. Farming w/ intensive fertilization doesn't "kill soil"; the soil is basically just a substrate to hold water and fertilizer, and a ton of farmland in the US is basically this. It's not natural, but it's a steady-state.

And if the change here just makes the potato and rice more efficient, you could get similar yield improvements from organic farming. Just rotate a legume in every few years, you're not going to break the ecosystem by growing potatoes faster.

> The soil is basically just a substrate to hold water and fertilizer,

This view is incredibly harmful. What lives in the soil is important too, small animals, insects, mushrooms... And the soil supports this. The density, temperature, texture are all factors to it.

Every time I get to the US, I'm aghast at the pitiful taste of the fruits and veggies. The way you are growing things produces volumes yes, but of tasteless empty shells of a plant.

Of course then you put sugar on everything because the raw thing is aweful to eat.

So you get obese people with nutrient deficiency, on top of a dead soil that is an ecological disaster.

Seing only one dimension of something or maximizing productivity always leads to some kind of unbalance, and the effects are far reaching.

I have experimented with Hydroponics for vegetables and herbs and it all boils down to a science. We know exactly what nutrient ratios a plant needs, at what stages, and so on, and when done in a controlled environment plants are much healthier and have more consistent yields. There is no “magic” to soil, it’s a chemistry problem. After my experiences people who talk about the soils being “depleted” or whatever sound anti-science to me.

We are good at growing a lot of food because big ag has figured out the science and is really damn good at it. In fact it is a miracle; only a few short generations ago famines were a common occurrence. Consistency of flavor and yield reigns supreme, because when someone orders a Big Mac or a Bud Light they want it to taste the same every time.

Now of course, there is a whole organic and craft market segment for people who disagree with that premise and it’s served quite well in the US for those who want to pay for it.

There is also a role for microbes in soil, which is an active area of research. Here’s some science on it, as an example:

https://ohioline.osu.edu/factsheet/SAG-16

I would say that’s more than just chemistry, unless you mean chemistry in a sense that’s so general the statement becomes a tautology.

If the chemistry is perfect, why are store bought and fast food tomatoes so bland, for instance? I haven't been scientific about comparing them but the difference in flavor in garden grown tomatoes seems pretty pronounced.

Because they are different tomatoes, selected for long storage on shelves in shop, not for taste. Your garden tomato will be much tastier, but will start to spoil sooner.

Interestingly enough consumers drove the market for tasteless tomatoes. customers bought more tomatoes that were more brightly colored and more round, which drove selection for these characteristics

Hmm, maybe because they can't select for taste? If it was possible to get sample of tomatoes or other vegetables before buying, maybe things would change?

Producers want to sell more, therefore they select varieties that look pretty, that are uniform in color and shape, they will also select varieties that keep for a long time for transport, or that grow bigger and ripen faster for better yields, being measured only by weight. Lots of factors but none related to taste or nutritional value. The consumer has very little say in all this.

Nope. I've seen many times seeds from letfover of tasteless salads grow into delicous plants after being just throw away in a fertile garden.

And honestly I met so many farmers that have no idea what tomatoes should taste like it's not even funny. Dining at their table, I hear them rejoice the produce in their plate is so good while I cringe because they feels like clown noses compared to the real thing.

Just like people can't fathom that we used to have bird migrations that cover the entire sky, people don't realize what we have lost with food. And they think they do, they think you are some kind of bragging posh to tell them that that's not supposed to be like this.

But I ate strawberries from my mother in law garden yesterday. It felt like eating sweets.

I haven't eaten some like that for 20 years, and I'm a very picky buyer.

Her soil is full of life.

Fruits and vegetable have been selected for being awesome for centuries. If you treat them well, you will not want to eat a kit kat instead.

But I don't blame the kids that do: currently, the kit kat tastes way better that whatever they have for lunch.

The tomato thing is no mystery - superparkets sell tomatoes taken off the vine weeks before they a ripe, because a ripe tomato is very gentle and will not survive handling.

And the message you are replying to is correct, supermarket tomatoes are different variety, farmers get paid for mass, not for taste.

Supermarkets have giant charts that determine shape, roundness, and colour of tomato. They will buy perfectly round, red tomato that tastes like water. They will not buy an ugly but tasty tomato from a farmer.

Are they the same varieties? Vegetables grown to be sold in stores are selected largely fit their shelf lives, to minimize the loss during the lengthy distribution and sale process. Your garden grown tomatoes are probably a different variety... and almost certainly much fresher.

No, 2 years ago I ate amazing cherry tomatoes from a friend garden. He told me he didn't plant them, they came out themself out of the shitty store bought ones that he discarded one day.

The variety matters, but that's not the end of the story.

The other issue with many plants is that they're picked before they're ripe - if you'd eat it straight away, you'd wait longer before picking and it would be tastier, but as you want them to survive transportation and long waiting in store shelves, you're picking them long before they're fully ripe.

Of course, it's a collection of things, but it's not true for tomatoes in can, which you can put in right after the harvest. And my ex house mate cans from the garden would always feels like fruit juice while the supermarket one, well...

Tomatoes can crossbreed, so the seeds of one plant are not necessarily the same variety as the parent.

The tomatoes you find in a shop have been picked before they are ripe so that they ripen during transport. This improves yields and reduces spoilage and bruising.

However, it results in a tomato that - while it looks like a normal tomato - the sugars and other flavours don't develop in the same way, rendering it bland.

If you want to buy tomatoes that taste good, you can get them from a farmers market and they will taste a lot better - even if grown in the same soil with the same techniques as the supermarket tomatoes. Alternatively canned/frozen/preserved tomatoes tend to be made with naturally ripened tomatoes. Obviously you can't really used those tomatoes the same way you'd use a raw tomato, though.

This isn't specific to tomatoes, many commercial fruits and veggies are picked before they're ripe.

> There is no “magic” to soil, it’s a chemistry problem.

Soil biology is no "magic" though.

> Now of course, there is a whole organic and craft market segment for people who disagree

It's almost as if you were suggesting that organic regenerative ag is based on some sort of non-scientific cult but that's not really the case.

> It's almost as if you were suggesting that organic regenerative ag is based on some sort of non-scientific cult but that's not really the case.

From an agricultural stand point not necessarily from a consumers who are passionate about it perspective, there's a huge amount of culty anti science.

Maybe but we are discussing agricultural production techniques here, not marketing

Mehhhhhh...organic and / or natural anything is based on separating fools from their money. That's not to say that there aren't small numbers of highly informed people who understand what "organic" agriculture is doing, it's to say that the vast majority of people who believe things about "organic" foods believe wrong things. It's conflated with naturalness marketing woo.

That’s irrelevant though, because in this thread we are discussing agricultural production not marketing.

Thinking this way is the exact problem. You believe you know what a plant needs but that's not true. We don't even know how plants "works" entirely.

There's one easy proove, anything grown the way you describe taste like nothing compared to an healthy plant. Quality farming is not about volume or look but the actual quality of the produce.

I wouldn't call what you say science at all. As soon as you state that you know everything and that someone who disagrees is anti-science is just plain arrogance, not science. If you're really interested in science though, please read the huge amount of research on soil and plant that has been done since the 1950's so that you catch up at least....

Edit: Forgot to mention something, soil is not only for plants, there's a whole ecosystem that depends on it and need to be taken into account

Someone in my family is a “plant reader” , he goes all over the world to help with production methods. He can just look at plants, examine it by hand and tell you what the plant needs. It’s quite incredible really. He always says all the factors need to be right, it’s a question of balancing.

That's sounds quite interesting. Never heard of this activity before. I'll look into it definitely!

Too much scolding, too little substance. As soon as people relegate to taste, I tune out. Taste is a first world problem and highly subjective.

You mean taste, one of the sense that makes us what we are today? The thing that humanity and other animals have used to analyze what they feed themselves with?

I'm not talking about eating for pleasure, but you can definitely taste that something is wrong with industrially grown veggies and fruits (and the same apply for animal farming).

He's talking about the raw ingredients not some hyper processed supermarket food. If there is something wrong with the raw ingredients I think it is fair that we try to figure it out.

Food pleasure from taste is one of the most basic pleasure and so available to everybody and essential for your well being. The fact that immigrants continue to cook like where they are from for most of their life is a rebuttal to your statement. Food quality is of global importance, most problem with food production comes from disorganization and incentives or lack of it not from lack of production.

"anything grown the way you describe taste like nothing compared to an healthy plant"

That's absolutely not true, it's been tested by thousands of people and you can try it yourself. Taste is affected by variety and ripeness, waay before it has anything to do with the soil.

I've tasted it, and agree with your parent. Most people just have no idea what their food is supposed to taste like, so if you give them decent tomatoes, they will think they are amazing.

Do your study in the south of italia in the summer for a fair fight.

So https://en.wikipedia.org/wiki/Terroir is just marketing?

I partially disagree. For decades the taste of tomatoes coming out of Dutch greenhouses has been considered as 'underwhelming'. At least for small cherry tomatoes that is not the case anymore, they are usually superior to the stuff that comes from Spain. Furthermore all sorts of so called 'cultured' berries are often acceptable now, year round.

Don't know about nutrients though, since I have no real means to check for that.

So it seems, at least for some plants it is possible to selectively breed them over long times to make them adapt to greenhouse/hydroponics/etc without losing their taste.

And I remember the real taste of berries, because I picked them in the wild in forests in my youth, and sometimes, though much less often even now.

> This view is incredibly harmful. What lives in the soil is important too, small animals, insects, mushrooms...

I want to highlight that it's a relatively recent discovery that almost all plants live in a symbiotic relationship with fungi (Mycorrhiza) in the soil, which I wasn't taught in school.

Plants can also live without, but the existence of Mycorrhiza fungi impacts plant productivity and robustness.

[1] https://en.wikipedia.org/wiki/Mycorrhiza

https://phys.org/news/2021-07-cyborg-soil-reveals-secret-mic...

"people with nutrient deficiency"

Nutrients in plants decreased by small amount, but fresh plants in our diet decreased by 90%. Never in history have humans consumed exclusively fried chicken and deef fried potato. The diets are the real culprit.

There are complex factors, for example our supply chain takes tomatoes before they are ripe - a ripe tomato is so soft, it's impossible to get to the consumer in one piece

People eat fried chickens because their greens taste like crap while the fried chicken taste good even with a crap chicken.

Give a person delicious plants, and they will eat them.

The soil is not a mere substrate, it is an entire ecosystem into itself. Topsoil depth is directly correlated with crop yield, and top soil depth has been shrinking. It takes atleast 50 years, often longer, to turn shit soil into good top soil worth anything and it requires sacrificing a lot of the yield to do so.

Growing alfalfa would help, but that is often not that profitable compared to reaping the soil and throwing on more artificial fertilizer until the soil is garbage.

People have done it alot faster than 50 years.

Method boils down to, no till, plant a mix of cover crops, and don't plant mono culture. Ended up getting a inch of top soil a year.

plant a mix of cover crops

You're starting halfway on the track. Most things you plant in arid soil won't grow, which is the situation where the GP started from. Sure, once you have a soil quality where your crop mix grows, it will take less than 50 years.

"How to get an inch of topsoil?" - "first, have an inch of topsoil" isn't really the scenario the GP was thinking of.

The prairies in Canada/US are very arid, and they have no problem growing things.

> It takes atleast 50 years, often longer

Or, crazy idea, just do exactly what we do with fertilizer. Identify what's missing, prepare it en masse, and add it back in. This could include microbes, minerals, certain types of organic material, you name it. As our understanding of a system improves so too does our ability to efficiently manipulate it to achieve the end result that we want.

You don't understant the volumes involved in farming, 4 inches of soil * area of 1000 hectares = 3 million tons of material.

No one suggested replacing the soil wholesale. I described additional things which might be incorporated into existing fertilizers in the future. I believe many of them already include organic matter of various sorts.

For the record, I believe you drastically underestimate our current practices and capabilities. We've been performing nitrogen fixation on an industrial scale since the early 1900s.

You are talking about replacing 30% of topsoil, thats how much organic matter as a percentage of soil you need to have for soil to be soil and not sand.

Its not about capabilities, ita about cost.

No, it's exactly what you suggested. Let's say you can get a microbial solution manufactured in a lab. You still have to distribute it and let it "grow" into the soil. That is exactly the opposite of what you said you wanted though. It's not the instant application process that fertilizers have. Therefore you actually do need to supplement the soil wholesale for an instant result. Waiting for the "dumb bacteria" to do their job costs money so it won't happen.

Why is it hard to restore topsoil?

Soil depletion / degradation is definitely something we should be paying more attention to. A couple recent HN threads on the topic:

"Organic and regenerative agriculture are revitalizing rural Montana economies" - https://news.ycombinator.com/item?id=27809279

"Have Fruits and Vegetables Become Less Nutritious? (2011)" - https://news.ycombinator.com/item?id=25032337

What do you think happens when soil is loosened to mix in fertilizer, and a large amount of rain / wind happens?

A plant that creats more biomass is not going to deplete soils. In fact it might restore soils by fixing more carbon from the atmosphere and adding more organic material in the form of roots and shoots.

The biggest problem with fertilization and why it is applied annually is that it is very mobile and washes away in the rain or breaks down or evaporates.

Doesn’t the biomass get dumped into the soil in a different place? You grow something, pick it, ship to a different country.

At a minimum, the roots are left in the soil.

Normally other parts of the crop are left in the field too, like leaves and stems and whatever else doesn't sell.

Not to forget that nowadays plants are optimized for high yield. I’d imagine the fruit/stem biomass ratio is becoming higher.

It needs to create biomass from something.

The main content of plant-created biomass comes from atmospheric CO2 and water, not from soil (well, roots extract water from the soil, but that's not what we mean by soil depletion). A significant minority is nitrogen, which either needs nitrogen-fixing plants (which extract it from atmosphere) or fertilization.

If the end-product is more carbon and nitrogen, doesn't that also mean it's less nutrient dense in other important micronutrients?

There is a long term trend that vegetables are getting less nutritious, yes. And it is speculated that it is because of soil depletion.

https://www.cookinglight.com/eating-smart/nutrition-101/frui...

Increasing the efficiency on existing farmlands should be the goal. Best way to reduce harm to the soil, ecosystem, nature is if we didn't require that much land. Maybe we can't decrease our usage just yet, but we can increase the efficiencies and decrease the demand for more farmland. Even an organic farmland is desert compared a forest.

I understand your point, but at the same time i don't know of an industry where increasing efficiency has lead them to think "now we can use less".

I don't follow, forests are great but if the farmland you are using gets ruined you need to do something... right now something is usually more petro-fertilizer and pesticides, and occasionally more traditional methods at smaller scales.

It's great if you can use less land for farming, but if concentration leads to the land being damaged beyond repair then what's the point? You'd just have to turn unused land into farmland, and if you're doing that you may as well use crop rotation intentionally.

If you need to deposit massive amounts of natural gas (used to make hydrogen used to make ammonia) on a small amount of land instead of using a larger amount of land and using slower methods to get nitrogen in the soil... there is surely a stable point where the soil is continually usable without needing a lot of fertilizer.

Yes, it seems to me increased efficiency would best be spent on fallowing the fields to allow the soil to regenerate.

Demethylation: [...] removal of a methyl group (CH3) from a molecule. https://en.m.wikipedia.org/wiki/Demethylation

Is anyone familiar with this process and can explain this paper to me like I'm five? :)

Unfortunately don’t have time to check out the paper, but vaguely I am aware that methyl groups are like an accessory that can be attached or detached (by the cell, normally) to an arbitrary section of DNA within your chromosome. And it can be used in this way for regulation of DNA expression. Because when the methyl group is there it’s harder for that section of DNA to be read (transcribed) because the methyl group is physically in the way. The train can’t run on the track because there’s a big rock on it

DNA is like code, but then there’s this whole meta level of DNA regulation that determines whether each section of code is used, and how much

So by demethylizing some section of the DNA, implicitly that means the scientists made that section of DNA be used more often. And it just so happens that when that section of DNA is used more often it contributes to various processes that ultimately end up with the plant organism as a whole producing more “yield”, or parts of the plant that we like to eat

https://en.m.wikipedia.org/wiki/DNA_methylation

Wow. Thanks for the explanation. It seems to me then that this result is a slam dunk Nobel. Yield improvement without the GMO stigma.

How is removing (obfuscation!?) smth from the DNA not genetic modification?

In dealing with methylation one doesn't add to or remove the "code" to synthesize any particular protein from the cell(s) of the organism, the DNA/genes per se remains intact. The process inhibits / allows synthesis of particular proteins from the genes/DNA.

Think of it like software -- by flipping an A/B Switch in software configuration you don't add to or remove from a program, you merely turn on/off certain features. Same with methylation -- it's the A/B Switch for protein synthesis, FWIU.

I think most lay people would view this as genetic modification, or at least "genetic manipulation", which might be even scarier.

Having said that, I'm pro-GMOs and always roll my eyes when brands go out of their way to say that they proudly don't use GMOs.

Technically correct might be the best kind of correct, but i doubt it will change hearts and minds.

It's enough to circumvent regulations for marking products as GMO.

The EU definition is "organisms in which the genetic material (DNA) has been altered in a way that does not occur naturally by mating or natural recombination". https://publications.jrc.ec.europa.eu/repository/handle/JRC5...

I'm honestly not sure which side of the definition this falls under. It certainly doesn't occur naturally.

Yeah, seems like a case for the lawyers.

No, they are changing DNA, they are adding DNA code that does the demethylation of RNA.

It's like adding code to the compiler so it produces different assembly from the same higher level code. But it's still added code because the compiler itself is in the codebase.

Because it’s epigenetics! No novel gene sequences are introduced. Just a change in what natural genes are expressed and at what levels.

How novel is the idea then?

No. The FTO gene from humans was inserted into the genome of these plants. That gene produced a protein that performs RNA demethylation, which isn't even epigenetics, because epigenetics is the set of extra stuff that happens on DNA, not RNA.

Oh my bad I didn’t read the full article. Of course, insertion of a gene to do demethylation would be genetic modification.

Methylation groups are considered meta-genetic I thought. Sort of like dog-earring a base pair.

edit: epigenetic, not metagenetic

This is GMO. They added a human gene to rice and potatoes to get the improved yields.

People that dislike GMO aren't going to be any happier about adding _human_ genes to plants.

As long as it’s not round up ready or otherwise encourage more pesticid use I’m cool with it

Or making the plant produce pesticide of its own, causing bugs to develop resistance to measures needed by organic farmers, and also dosing humans with what would otherwise be easily rinsed off.

I'm looking forward to the day when we can collectively disentangle GMO from all of the other negative practices of big ag. I don't see a reason why responsible genetic modification can't be a part of a sustainable and equitable future agricultural system.

"Genetically modifying food to increase yield is good for the environment" is a true statement, but you're going to need an awfully good PR firm to persuade the public it's true...

Yeah exactly. And not only yield, but natural pest resistance, etc. I'm also imagining how genetic modifications might eventually be environmentally beneficial in the context of whole-ecosystem engineering if/when we ever move beyond a monocrop model, such as modifying native organisms to counter invasive species, etc. Admittedly a bit sci-fi currently but in principle possible!

Can you explain the link between the methylation and adding that gene?

The gene that was added is translated into a protein that floats around the cell doing the RNA demethylation. The plants already have other genes that produce proteins that did that, but adding another one has an effect.

Edit: correction - thanks Scaevolus, my mistake.

Now it makes sense, thanks!

I'm surprised the plant lives at all in that state... One would imagine RNA methylation is used for all kinds of logic and mechanisms in plant cells, so arbitrarily removing them all would break stuff.

It would be like a programmer saying "let's just comment out every line of code starting with "if" in the windows source code, and then see if it boots faster!

Plants already have proteins that do this [1], but modifying them or adding new ones can affect phenotype as shown by this study.

[1] https://www.frontiersin.org/articles/10.3389/fpls.2019.00500...

As long as this technology is not used to prevent country farmers to store their own seed whenever they want, and make it only legal to purchase 'Monsanto approved' seeds, I am completely fine with this.

In this case it's RNA not DNA.

Demethylating DNA is like uncommenting a line of code; demethylating RNA is like uncommenting compiled/assembly rather than the source.

Thank you for this incredible analogy.

Oops, thanks

I can't explain the paper, but if DNA is genetic ROM, methylation is like one bit of RAM available on each digit [*].

Most of the cellular machinery tries pretty damn hard to make exact copies of DNA. The methylation bits, by contrast, get deliberately flipped on and off all the time.

[*] Technically only A and C can accept methylation, but in a double helix you'll always have either an A or a C on one side or the other at every position (A pairs with T, C pairs with G).

Deliberately flipped based on what?

That is an area of very active research.

I mean the exact chemical mechanism for the flip is some enzyme, and the flip certainly affects gene expression. As to why the cellular systems flip these bits, great question :)

I am going to ask a noob question: if this change is beneficial to plants, why has it not occurred already by natural mutation?

Evolution can be blind "hill-climbing", so if it's a step towards "local maximum", why has it not already been taken? Is it not a "local" step (i.e. hard to occur naturally) or not "towards maximum" (i.e. good for the farmer but not for the plant)

Maybe not enough time has passed.

That's a soft restatement of 1: Is it not a "local" step

I think demethylization would very much be a smooth direction of descent to produce more fruit. It's just that the production of more fruit is not beneficial.

Yes, the consensus seems to be for 2: this change is not seen in the wild as it not beneficial there. i.e. it is not towards in a wild plant's local maximum of producing most offspring given limited resources.

Perhaps after a few generations there is damage that would otherwise have been protected; or maybe the unmethylated FTO protects from adverse weather / environmental conditions that are not normally present in greenhouses.

Either of those could prove catastrophic, so I don't think yours is a noob question - unfortunately, I am also a noob.

> if this change is beneficial to plants, why has it not occurred already by natural mutation?

Because plants in the wild aren't selected for producing as much rice/tuber as possible. They're selected for being able to survive and reproduce, which only goes hand-in-hand up to a point, after which the plant would just be wasting nutrients.

The amount of nutrients available to a plant in the wild might also be far from 'greenhouse conditions', so even if it was beneficial to the plants they wouldn't be able to do so anyways.

So it's 2: this change is not in the wild plant's best interests, for being able to survive and reproduce in the wild. In that case the dial is best set to a lower level of resource utilisation, that still produces sufficient offspring.

Seems like an appeal to nature fallacy. If humans are ensuring that the plants reproduce, you don’t need to ‘set the dial lower.’ Almost all of our fruits and vegetables provide more nourishment than their naturally occurring counterparts. This is merely a continuation of that process.

I do not think that I'm saying what you seem to be replying to. I merely asked why this mutation has not occurred in the wild if it is beneficial in the wild. And it was answered that it is not beneficial, in the wild.

Farmed crops have different characteristics to wild plants, due to selection by the crop eaters. We know this very well. The same selection by crop eater is present in plants with berries where the seeds are dispersed by birds. The "appeal" and "fallacy" is you reading in a subtext that was not intended.

I think the error is one of imagining evolution finds maxima of this sort. It just finds acceptable local values that are good enough to survive generation to generation.

Ex) Biological immortality seems like a great trait for animals to have but precious few have it.

> Biological immortality ... but precious few have it.

Because it is not "within reach" as a local maximum.

It's not necessarily beneficial to plants from an evolutionary point of view, in that it doesn't necessarily help them reproduce. Evolution's 'objectives' (of course, they're not really objectives) are very different to humanity's on most food plants. Even ignoring genetic engineering, most of our current food plants aren't particularly similar to their wild ancestors, and the changes generally aren't for the better if you're only concerned with plant reproduction.

Amusingly enough, the FTO gene was one of the earliest genes where a link was found between common variants and a trait in humans[0]. Different subtypes of FTO influence your chance of putting on weight. The newspapers at the time (2007) had headlines like "Fat gene found". Interesting to see that adding it to potatoes makes them put on weight too.

[0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646098

> We demonstrate that the presence of FTO stimulates root meristem cell proliferation and tiller bud formation and promotes photosynthetic efficiency and drought tolerance but has no effect on mature cell size, shoot meristem cell proliferation, root diameter, plant height or ploidy

Looks promising but I wonder what impacts this will have on the nutritional content?

Without some analysis, it's not clear to me that it's not just water weight. They did say the cell size is similar to normal which could be a proxy for that.

50% increase in yield is impressive. That's about what the C4 rice initiative had promised. (And C4 rice is still years away of being a reality, IIRC.)

I, for one, welcome our new potato-human hybrid overlords.

There's a Mr. Potato Head joke in here somewhere.

The line between veganism and cannibalism is getting blurry.

Time for a certain Church to declare growing potatoes a murder.

A tenth of what they claim would be Nobel prizing winning.

But it has ties to Western Universities, it's not straight out fiction. [1]

Not that it matters, but nutrients are claimed to be the same

And it in theory works with many plants, think flowers, drugs, wood.

Even their claim deeper roots would help with carbon sequestration.

What would it do to a Sequoia?

[1] https://news.uchicago.edu/story/rna-breakthrough-crops-grow-...

We don't need this. We don't have a productivity problem.

We have problems transporting food; in organising food production; food waste; carbon abuse transporting food just because "it's cheaper to make it over there"; in food cultures that ignore seasonality etc.

I would expect a 50% increase in yield change like this to lead to no academic paper, but instead rapid rapid black market distribution around the world, while someone gets rich to the tune of billions of dollars...

The fact they wrote an academic paper instead tells me it probably has some big downside...

Maybe its 50% more carbs, without any more iron or potasium uptake.

I've got a feeling that, provided the minerals you care about are in the soil, it would be pretty straightforward to selectively breed to get more of them into the leaves, probably with a small yield penalty.

I think just nobody who farms these crops directly cares about these minerals because that isn't what earns them more on the rice exchange.

Or very limited upside, potatoes yield is already high enough to remove a lot of nutrients from the soil. The limiting factor may not be plant yield at all but access to nutrients or water.

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