The problem with the Darling 58 genetically modified chestnut tree | Hacker News Reader

The problem with the Darling 58 genetically modified chestnut tree

nymag.com

102 pointsjseliger59 comments

For those, like me, who wondered, why not just reclone the original Darling 58?

Here is the answer from TACF: “ Why not then return to the “real” Darling 58? The first reason is that the Darling 58 also uses the 35S constitutive promoter which appears to result in a variety of metabolic costs to the tree and likely causes the majority of performance problems observed in the Darling line. Secondly, there are only a handful, and perhaps even only one, D58 tree(s) in existence. These trees are at either the T0 or T1 stage (the original event and first-generation offspring). If work is to start over at those early diversification stages, it makes sense to focus on new OxO lines that express the gene only in tissues infected with blight. Confining OxO expression to blight infected tissues should reduce the metabolic cost of expressing this gene, thus these new lines are more likely to have enhanced forest competitiveness.”

I’m still confused, why can’t they return to the real Darling 58? Are they saying even the real 58 is not that good, and if they are going to rewind that far back they might as well start from scratch?

I reread the above and realized that TACF isn’t as clear as they should/could be: they are supporting a newer strain, win3.12 [0], which, as alluded to above, expresses the OxO gene only when infected. This is metabolically less expensive. Thus there is no reason to spend effort looking for the Darling 58. I also gather from other sources that the TACF want to downplay that they are switching to this new strain, that this development of finding a bug in Darling 54 is a political salve[1] —- maybe they don’t want to offend somebody?

[0] https://pubmed.ncbi.nlm.nih.gov/34841616/

[1] https://ambrook.com/research/sustainability/GMO-chestnut-con...

Great resources for further reading, thanks. Win3.12 sounds like… a windows version? Lol

Setback in the "American Chestnut Project" - https://news.ycombinator.com/item?id=39044498 - Jan 2024 (2 comments)

Genetic engineering was meant to save chestnut trees. Then there was a mistake. - https://news.ycombinator.com/item?id=38758522 - Dec 2023 (11 comments)

America lost the chestnut, its "perfect tree" - https://news.ycombinator.com/item?id=38754581 - Dec 2023 (176 comments)

TACF is no longer supporting development of D58 American chestnut trees - https://news.ycombinator.com/item?id=38573765 - Dec 2023 (58 comments)

The American chestnut tree is coming back. Who is it for? - https://news.ycombinator.com/item?id=37576771 - Sept 2023 (4 comments)

Technology Puts American Chestnut Trees on the Comeback Trail - https://news.ycombinator.com/item?id=34181235 - Dec 2022 (1 comment)

Biotech chestnut tree poised to restore lost ecosystems and biodiversity - https://news.ycombinator.com/item?id=34143557 - Dec 2022 (1 comment)

Gene editing could revive a nearly lost tree. Not everyone is on board - https://news.ycombinator.com/item?id=32665955 - Aug 2022 (1 comment)

American chestnut tree in Centreville is the 'holy grail' for conservationists - https://news.ycombinator.com/item?id=32621570 - Aug 2022 (155 comments)

American chestnut - https://news.ycombinator.com/item?id=30333498 - Feb 2022 (73 comments)

The demise and potential revival of the American chestnut - https://news.ycombinator.com/item?id=26441593 - March 2021 (86 comments)

Blight wiped out the American chestnut. Scientists are close to bringing it back - https://news.ycombinator.com/item?id=21846891 - Dec 2019 (2 comments)

American chestnut poised for return to America's forests - https://news.ycombinator.com/item?id=13855137 - March 2017 (1 comment)

American chestnut trees are “technically extinct” - https://news.ycombinator.com/item?id=13478910 - Jan 2017 (120 comments)

IMHO this is a romantic effort, no one can plant a tree species at such a scale.

A country of two million people managed to plant six million trees in one day in 2008

https://www.reuters.com/article/idUSTRE4AI49U/

How many of them survived more than a year?

i imagine most of them, Macedonia is not such a dangerous place to live. /s

Many of them. Do you have information about it that the rest of us don't?

"Fifty million trees planted- the government said in 2014- with a success rate of 61% compared to the average European planting success rate of 35%."

> Do you have information about it that the rest of us don't?

No, that's why I asked. I was aware of the less than perfect record elsewhere wondered if they had done better.

Planting trees results in inferior forests. A healthy forest comes from natural forestation that goes through pioneer species stages.

Inferior forests are better than no forests.

You don’t have to take an empty field and plant 100k trees. You can go to where chestnuts used to grow, have some volunteers plant some over time, say 100 every month in an area. Over the course of 10 years, we’ll get some data.

Don’t let great be the enemy of good.

A healthy forest comes from strict conservation laws, confiscation, expropriation, etc. When land is secured, what to plant is a technical detail.

Achieving a good approximation of pristine natural forests might have a lower priority than the variable needs to increase rare plants, provide an habitat for rare animals, make the forest robust against climate and geological hazards, dealing with people with friendly (e.g. edible fruit) or hostile (e.g. thick vegetation to discourage secret hemp cultivation) features, etc.

We routinely plant over a billion trees each year in the USA. Tree planting is a huge industry. We have tractor attachments that can mass plant some species.

I had a friend who planted trees for a summer job. He said it was good money for a summer job and they got paid something like $0.20/tree.

I saw that on tiktok myself. But apparently only the experts at tree planting make good money and it takes a few seasons to get good.

Sometimes, I just have some view of a city, or whatever, look out, quietly scan the horizon and just muse "every tree I see was planted by someone". Someone said "here, there will be a tree" and it was so.

Small ones, big ones. They're just everywhere.

"See that park over there? Someone put every one of those trees in the ground."

Then, as a corollary, one day, a parking lot has several dozen trees. Next day, they're all gone. Week later, a bunch of new ones are back. Guess the old ones were just getting too big.

Friend recently had to take down a 100 year old tree. Was just getting potentially unsafe.

No doubt they'll stick another one in there, and leave it. It'll be there when they pass.

Given adequate rainfall and the right range of soil acidity trees will seed and grow themselves. This town was farm fields in the 1930s. Some trees were planted when the streets were laid out and houses built. Others, particularly ornamentals, continue to be planted. But there are a great number of trees that are volunteers that have been allowed to mature over the last century. Norway maples, sweet gum, tulip poplar, and red oak are particularly good at volunteering.

We have mullberry, maple, boxelder, and sometimes oak trees that spring up everywhere and basically need to be weeded before they get too big. Mullberry is particularly "weedy", a common sight at the edge of fences or in hedges.

I've had health issues for about 5 years, my back yard is a dense forest because I'm not outside editing it back to my preferences.

Trees definitely do not need us.

In a dense cities, the trees you see now that were allowed to grow to maturity were mostly likely planted by a human, with some exceptions of course. Any trees that began to grow organically were probably cut or eliminated.

>Trees definitely do not need us.

Until they do. Eventually bugs and diseases would kill off huge portions of them. Trees would still be around, but it'd definitely be a different mix than we have now. Right now every ash tree in my state is either dead or dying due to beetles, all the chestnuts died when I was a kid, the native oaks mostly only live where they've been planted because anytime one dies a faster growing maple replaces it.

Many do plant themselves. In my city (Atlanta), slash pine, pecan, tulip poplar and mimosa frequently grow as volunteers and get quite large.

This is definitely an odd take, given the 150+ saplings I pull from my meager backyard every spring. I'm still killing off the root system of some Elm trees that were destroyed in 2021 during the big freeze here in Texas. If I didn't keep that in check I'd have dozens of elms at this point.

There definitely is a weird dichotomy between intentionally planted trees and the ones that just randomly show up. Maple trees grow like dandelions here in the midwest.

Hell I've had a little cottonwood tree growing in the corner of my truck bed for 3-4 years. It never gets any bigger but always produces new leaves every spring.

Get one of those fancy scissors, do some pruning and say you're doing this new thing called truck bonsai

Well put.

It's incredible how our minds are unable to grasp timescales greater than a decade. It dawned on me recently. I visited a place that had trees which were roughly my height 10 years ago. It's a genuine forest now.

Trees are perfectly fine with those timescales. Let them be and they will grow.

Another mind-blown moment was when I was visiting a park in Warsaw. Seemed like old-growth forest - little do I know! There was a display nearby which shared, that during WWII, the Nazis cut the park clear because the opposition was hiding in the trees. That was less than 100 years ago.

So, how many do you imagine need to be planted for the species to be self-sustaining?

I mean surely populations would exist, bit the spatial and cultural significance of the species is gone.

And, for how long do we want to believe that environmental change (including fungus) can be frozen in a specific time moment that should be preserved?

Isn’t all the writing about the American chestnut indicative of some on-going cultural significance?

Wasn’t the blight and panic that wiped them out largely a result of human activity?

I think this is one environmental change that happened VERY fast, in which we see our own hand, and that we believe we might still be able to turn back.

But I sense that you see some down side which I don’t see?

I sympathise with the struggle of losing a major specie, and of course the cultural significance is great and will never fully vanish.

One thing is to protect nature, another to reject somehow inevitable change happening all the time.

A legitimate concern could emerge on discussing whether there is no better plan, because IMHO this plan offered false hopes, and perhaps many such restoration plans provide more hopes than quantitative performance indicators.

> the spatial and cultural significance of the species is gone.

If it's ecologically competitive, it will spread again in the fullness of time, no?

Yain, meaning yes and no, because of shifting baselines and other co-occurring dynamics, perhaps there are other natural and man-made uses already taking place?

So this group wants to propagate a GMO to "save" a tree species? Which is of course impossible with current mechanisms. Although it seems that producing a near replacement tree is likely within reach.

But they can't even seem to be sure what edited organism they are trying to propagate? This is why I do not trust GMO stuff. I have no special credentials (just an undergraduate degree) but even at that level it was clearly stated to me that if you're going to do research, you need to keep clear documentation about what you are doing so it is reproducible.

how is GMO different from normal breeding where we hane no clue what mutations happen. Normal breeding doesn't even attempt toestudy for safety.

Yes the science should have been better done but the worst case of GMO is the same as everything else.

For some reason, when you take a process that has traditionally been done with a baseball bat and start doing it with a knife, suddenly everyone comes out of the woodwork to talk about how your knife is too dull and it should either be done with a scalpel or not at all.

Just to tap the brakes for anyone wanting to take your analogy too far: a lot of objections about GMO in general are about the accelerated rate at which the changes can be made, relative to traditional methods (such as breeding). The worry is that we might be introducing altered genomes at a rate faster than we can observe and understand the downstream impacts.

So in those arguments (which are the majority, in GMO debates I've encountered), it's not about the knife being too dull, but being too sharp.

> the accelerated rate at which the changes can be made, relative to traditional methods

Citation needed there. I know the claim is common, but GMO is inserting one known mutation. How many mutations are there from parent to children is not something I can find a citation for, but since most mutations do nothing (or kill the child) there must be a lot of mutations involved in traditional breeding not one which means that GMO is much decelerated vs traditional breeding.

I suppose there's a distinction to be made between quantity and quality of changes, too. Certainly regular sex mixes things up a lot every time, but only within the bounds of the established gene pool (roughly).

Compare this to, say, the famous example of adding firefly genes to tobacco plants, to make them bioluminescent. That's a small change in terms of number of genes, but very "sudden" in terms of how far it is away from the norm — it would have taken a very long time for that to have happened as a result of natural (or even breeding-style) permutations of existing genes. So it's a "big" change in that sense, even if "small" in the other.

As far as citations go, I think the Wikipedia page on GMO foods is decent? [1]

For instance, the "Gene flow" section describes the risk of various unexpected consequences of GMO crops affecting their surroundings: "There are concerns that the spread of genes from modified organisms to unmodified relatives could produce species of weeds resistant to herbicides[303] that could contaminate nearby non-genetically modified crops, or could disrupt the ecosystem,[304][305] "

Of course in general, GMO crops are seen as safe (with lots of of "more long term research is needed" caveats), but the page has various links to concerns and ongoing research along the lines we're been discussing.

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

> how is GMO different from normal breeding where we hane no clue what mutations happen

The answer is in your question. We have no clue.

What we do not know about how living organisms recreate themselves is much more, and more important (IMO) than what we do know.

We know that DNA plays an important role. We also know that DNA is not the whole story.

We know very little about how DNA plays it role. We terribly confused with analogies to coding systems we know about, but it is clearly much more than a code.

The part of reproduction that does not involve DNA is almost a complete mystery.

In normal breeding we do not have to be concerned about what we do not know, when we start changing DNA it becomes very important

We are creating novel self replicating organisms, there is a lot that might go wrong. A very small chance of complete catastrophic results

But, money

> In normal breeding we do not have to be concerned about what we do not know, when we start changing DNA it becomes very important

Normal breeding we are also changing DNA - it is just random uncontrolled mutation.

> Normal breeding we are also changing DNA - it is just random uncontrolled mutation.

That is not paying attention to what I said

> it is just random uncontrolled mutation.

We do not know how genetic changes (evolution) happens, we know it is much more than that

In addition to that there are also methods like atomic gardening which are not considered GMO.

You’ll get a lot of answers to this question, I’ll try to give one that’s distinct from the others:

Practical observation of the two techniques reveals very different outcomes and behaviours. Selective breeding takes time and has intermediate stages that help you see if you’re on the right track. Direct modification: if you get it wrong you’re back to the drawing board.

Worse, legally they’re two very different animals that are treated very differently. If you want big bucks, you want to go the GMO route. The combination of the risky nature with the potential profits makes an ideal environment for malpractice, whether it’s cherry-picking data, deliberately making seeds that aren’t long-term viable or strategies such as long-term pesticides which have a detrimental effect of neighbouring farms.

So in theory, I don’t have a moral objection to GMO. In practice, I can see why the EU banned it.

> Selective breeding takes time and has intermediate stages that help you see if you’re on the right track.

Only if selective breeding needs more than one mutation, otherwise you are just waiting/searching for the desired mutation in a random sample.

> Direct modification: if you get it wrong you’re back to the drawing board.

Either way you are back the the drawing board. Just that with selective breeding you have no idea how much longer you will wait to get the desired mutation.

We have no idea where the smallpox vaccine actually comes from, and it long predates GMO stuff.

Can you explain what you mean by that?

the original vaccine was a live virus, and the only way to grow more of it was to infect people and then harvest it from the pox on their bodies. So many generations of this vaccine virus were passed around this way.

For decades everyone believed it was cowpox, another common virus, but after a while scientists noticed it wasn’t actually cowpox - and modern generic studies show that it doesn’t match any known virus

All of what you said goes against common knowledge of the history of the vaccine. You will have to provide solid sources for your claims in order to not appear as a conspiracy theory peddler.

What you mentioned in the first paragraph is not vaccination, it is called variolation. It predates vaccination by a large margin and was far more dangerous.

> a conspiracy theory peddler.

What conspiracy? It’s a theory of lost knowledge / confusion, but no one is conspiring with anyone.

He asked for a citation. Please provide one.

Okay, I just jumped down a rabbit hole trying to figure out what OP might mean. I think they’ve got it sideways. I think they’re talking about vaccinia, a virus related to cowpox (and smallpox) that form the basis of modern smallpox vaccines. The origin of the virus is, entertainingly, lost to time due to poor record keeping.

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

There’s also “kinepox”, but I _think_ that’s just a different method of cowpox vaccine delivery.

I’m not sure what’s sideways, how is this different from what I said?

Actually, you’re right. With the links it’s clear.

I commented with links to wikipedia’s relevant sections

If scientists found out that it wasn't cowpox and then conspired to keep that fact secret, or conspired to say "we all knew it wasn't cowpox from the beginning", that would be a conspiracy.

wikipedia: “From 1796 to the 1880s, the vaccine was transmitted from one person to another through arm-to-arm vaccination.”

(Variolation used real smallpox, arm-to-arm used the vaccine virus instead) https://en.wikipedia.org/wiki/Smallpox_vaccine#Types

“As medical researchers subjected viruses to serial passage, inadequate recordkeeping resulted in the creation of laboratory strains with unclear origins.[95]: 4 By the late 19th century, it was unknown whether the vaccine originated from cowpox, horsepox, or an attenuated strain of smallpox.”

https://en.wikipedia.org/wiki/Smallpox_vaccine#Origin

Reply on news.ycombinator.com