Genetic engineering fails to overcome the flaws of monoculture

I saw an interesting story on the Independent today, claiming that pests are developing resistance to the Bt proteins genetically engineered into some crops. Here is the link:

Worm evolves to eat corn that was genetically engineered to kill it

Although the Independent has gone downhill over the last few years and is rapidly descending into red-top rag territory, I don't see any reason to doubt the story, since evolved resistance is what you'd expect to happen over time.

The reason I think this story is interesting is that it highlights the downsides of misapplying our understanding of genetics. I am not necessarily against genetic engineering for some purposes - fixing genetic diseases in people has my complete support, and introducing genes for some traits into food would be OK too. I have no problem with anyone trying to genetically engineer bigger tastier potatoes for example.

An example of corn monoculture

The problem is when genetic engineering is used to promote and enable the "exterminate everything else" monoculture approach of modern farming. This is doomed to fail because ultimately the pests don't really have anywhere else to go. If you give a plant better disease resistance in a varied ecosystem, the pests will move onto other plants, but if you only grow one plant across wide areas, then the pests must adapt or die. And there are good reasons to expect that adaptation should generally be possible, such as the following:

1. The plant itself must tolerate any toxic chemicals it contains or that are applied, so the chemical cannot be inimical to basic life processes without killing the desired crop

2. Some part of the plant will be consumed by humans, and therefore must also be non-toxic to humans.

3. Plants have been engaged in chemical warfare against pests for as long as both have existed, and yet pests still exist

4. Many plants depend on a supporting web of other life, from pollinators to soil micro-organisms, and in this case any chemical weapon must be selective. Pests may be able to copy non-affected organisms.

The attempt to wipe out all the pests while at the same time retaining a non-harmful, edible plant appears to me to be a war that we simply can't win. The best that can be attained is the fluctuating stalemate which has held throughout history, with one side gaining a temporary advantage for a while which is then neutralised by changes in predator populations or changes in the plants themselves.

Genetic engineering plants to either contain or tolerate poisons is just a risky way to gain a temporary advantage, since there is a high risk of these poisons having adverse effects either on other parts of the ecosystem (e.g. pest predators, beneficial soil microbes, ...) or even on people themselves. How many chemicals were used for decades in the belief that they were safe, only for scientists to later show that they increased the risk of cancer or some other health problem?

A much better approach to pest control is:

1. diversify away from monoculture - give the pests more targets so they either can't specialise, or if they do they cannot wipe out your entire crop

2. Encourage predator populations to maintain a limited but constant stock of pests instead of insisting on complete extermination. This means providing predator and beneficial species with habitat and uncultivated spaces.

3. Use limited and targeted chemicals only when necessary, accepting that they do harm as well as good

But this won't happen as long as the model is industrial monoculture agriculture, where the goal is to minimise the human labour in farming, and to de-skill and automate the process as much as possible.

Global gardens

I was thinking earlier today about the diverse origins of the various plants in our garden. The following is off the top of my head with a bit of googling where I wasn't sure:

North America

Saskatoon
Oregon Grape
Jerusalem Artichokes
Aronias / Chokeberries

South America

Fuchsia

Asia

Goumi
Goji berry
Apple - according to Wikipedia, the main ancestor of malus domestica grows in Kazakhstan.
Pear (?) - according to Wikipedia, the genus originates in China, but it's been widespread across Europe and Asia for a long time
Rugosa Rose
Blueberry Honeysuckle
Flowering quinces
Japanese wineberry

Middle East

Medlar - still popular in Iran!

Europe

Pear (?) - Pears have been in Europe for a long time, but the genus originates in China 
Plum (?) - Does anyone know the exact origin of prunus domestica? It's assumed to be some kind of hybrid...
Cherry
Rosemary
Sage
Thyme
Blackcurrant - also in parts of Asia
Red/whitecurrant
Sweet Cicely
Lemon Balm
Bay Tree

Widespread

Raspberries - various native species across much of the world
Blackberries - various native species across much of the world
Gooseberry - Europe and parts of Africa and Asia. I think there is some cross-breeding with related American species for disease-resistant cultivated varieties.
St John's Wort - across Europe and Asia

Admittedly the list of European plants is longest, which is what you might expect since the UK is part of Europe. But I think it's quite impressive how many of the plants are actually from a very long way away from here originally.

Jerusalem Artichokes

Jerusalem Artichokes - At best a distant relation to true artichokes

As part of filling up the new garden with edible plants, I've been looking for Jerusalem Artichoke tubers to plant. And it turned out to be a bit of a struggle... I remember a few years ago seeing them everywhere, but this year I had to try several garden centres to find them. And it is the season to plant them right now, since the RHS and a number of other reputable websites say March - April.

Having tracked them down, I had to decide where to plant them. And this is where I hit contradictory advice. One of the things which originally attracted me to Jerusalem Artichokes was that numerous sources described them as:

1. Prolific / high yielding
2. Unpicky as to site / soil
3. Tolerating partial shade
4. Spreading to a form a dense cover, invasive if not controlled
5. Casting dense shade below that suppresses (other!) weeds

For example, here is what Patrick Whitefield has to say about them:

The best place for them is either just to the north of the forest garden where the ground is shaded by the trees, or in some place that is shaded by buildings or other tall vegetation. An acquaintance of mine who had an awkward patch in his garden, overshaded by laurel bushes, found that Jerusalem artichokes were the only food plant he could grow there with any success.

...

They are very tough plants, tolerant of poor soils and needing little in the way of cultivation. 

With this idea of their requirements, I had planned to put them in a slightly shady corner, between two hedges, currently overrun with ground elder. My cunning plan was to use them as a crop of last resort for a difficult area, and to try to use them as a barrier to either keep the ground elder in that corner or at least slow down its spread a bit. I had a good two or three square meters partially cleared and ready to go.

But then I read the planting advice on the packet containing the tubers. This advice could be summarised as:

1. Plant them somewhere sunny
2. Keep soil around them moist
3. Keep the soil around them clear of weeds
4. Feed them with compost, manure or fertiliser

This could basically be summarised as "coddle the plants". This is a far cry from a lot of what you can read online, which describes the plants as basically indestructible.

So which set of requirements is correct? It seems to be quite common in gardening that one and the same plant can be described in very different terms by different sources. I think that this is basically because there are so many variables involved that often it's not clear why a plant succeeds in one location but not another, and people then incorrectly extrapolate from their experience. In the case of plant suppliers, I think they also tend to play it safe to avoid complaints.

Anyway, I decided to just go ahead and give it a try. 15 tubers are now planted in my slightly shady three square meters, partially cleared but with ground elder roots still lurking in there somewhere. Hopefully I'll be able to report a dense Jerusalem Artichoke thicket in a few months.

Song of the Day - It Will Not Be Forgotten

Song of the Day - Heathaze

Beware the fisherman who's casting out his line
Into a dried up river bed
But don't try to tell him 'cause he won't believe you
Throw some bread to the ducks instead, it's easier that way
Feel like an alien, a stranger in an alien place

Song of the Day - Blue Skies for Everyone

Probability in TV and Economics

In TV, nothing proves how clever you are than spouting off probabilities. "I estimate a 75.2% chance of destruction!" cries Mr Spock when encountering some new alien, or perhaps "There's a 30% chance he's guilty" from a university boffin on a show like Numb3rs. There's just one problem with this: it's complete and utter bollocks.

The problem is that in real world complex situations, there is basically no way of accurately estimating probabilities. In situations where the rules are simple and known, probabilities can often be calculated, but when you move to a situation where a lot of information is hidden, estimated probabilities are more or less meaningless.

If we go back to Mr. Spock and his attempts to estimate how likely James T is to get everyone killed, the following might be major stumbling blocks:

1. Often, the knowledge of the enemy is very limited. If your overall probabilities involve decisions by living beings, then you need to be able to assign probabilities to the different decisions they might make.

2. The number of variables quickly becomes impossibly large - not only do you have to worry about the probability of the enemy captain making decisions, but also the competence of the guy actually firing the guns. For example, if the gunner falls asleep on the job 50% of the time, then this has a major impact on the probability of the Enterprise getting blown up.

And so on. Of course, Mr. Spock can try to make assumptions, but if you make big assumptions you cannot rely on the result. For example, Mr. Spock might assume that the enemy captain has a very low probability of making suicidal decisions, but if the enemy happens to believe that a flock of beautiful virgins are waiting for him in the next life he might actually not be bothered by an "everybody dies" result. You could say that Mr. Spock's original probability estimate was reasonable given his knowledge, but it was also useless precisely because of his lack of knowledge.

This same issue plays out in economics. Economists assume that:

1. everyone is rational
2. people make decisions that maximise something ("utility") over time

How does (2) work in an unpredictable world? Economists say that people maximise "expected utility", e.g. the average result of their actions. The problem with this is that, in order to know the average or expected result, people would need to know the probability of all the different possible outcomes of their choices. Is this really possible?

Most economists basically assume it is. Keynes said it wasn't, because the future is unknowable - not only can you not know what will happen, you can't even know with any accuracy the probability of any particular thing happening. The reason is that the world is so extremely complex that building any kind of model of it without a vast number of basically untestable and unjustifiable assumptions is impossible. People are too limited in perception, knowledge, and processing power to accurately calculate the probability of far future events.

Of course, people can try to estimate probabilities anyway, and big financial institutions do use statistical models, but if those probabilities are based on a larger number of assumptions, any of which could be invalidated at any time by events, it means that people's probability estimates are extremely volatile and their decisions might suddenly swing strong from one direction to another. In this situation, using a model is not really any better than just using your gut.

Thus, what people do is use heuristics and make a guess. This is reasonable because doing better is impossible, for the reasons just discussed. It does however make planning less of a pure scientific exercise, with one correct answer, and turn it into a subjective area where it is impossible to prove which plan is the best. And because people tend to make the same (incorrect) assumptions, it also means that crowds tend to show volatile and herd-like behaviour, which then causes "irrational" booms and crashes which the models don't predict.

And that's why Mr. Spock is spouting nonsense to look clever, and how economists oversimplify the world in their models.