Christmas in the Kenya highlands

No matter how many times I come up into the highlands of the Central Province of Kenya it never fails to surprise me how little the place looks like “Africa.” The main cash crop is tea (there is also some pyrethrum still around, but tea largely displaced it in the 50s and 60s), giving the landscape something of a south Asian vibe. Tea is grown both in large plantations and by smallholders like my mother-in-law Hilda.

Her food cropping system at Gataka (Gitiha, Githunguri, Kiambu District) on the other hand, would not be out of place in Mexico. She grows potatoes, maize, beans and pumpkins, which all go into making the staple food called “irio” — basically mashed potatoes coloured with the pumpkin leaves and encrusted with the beans and maize. Some farmers grow sweet potatoes and taro where it is warmer and wetter. There are scattered plum and pear trees in my mother-in-law’s cabbage and kale fields, which would look like Europe if not for the reddish tropical soils. She stall-feeds her six Friesian cows on maize stalks, the smaller potatoes and napier grass, although they are also let loose in a grassy paddock for a few hours a day. She has a woodlot of Australian species, mainly blue gums and black wattle, used mainly for firewood.

Hardly a cultigen of African origin among that lot: “lost crops of Africa” indeed! Of course if you dig a little deeper you do find some local plants being used. A few weedy leafy greens among the potatoes, some local trees in the small remaining patches of native forest and hedges, yams here and there perhaps. But the overall look of the agriculture surely owes more to the “Columbian exchange” and the globalizing tendencies of colonialism and missionary activity than traditional African crops. An object lesson in global interdependence in genetic resources. When I’ve pointed this out to the people here in the past the first thing they always asked me was “so what did we grow before?”.

A good question. Sorghum and finger millet instead of maize, I suppose, cowpeas for beans and yams for potatoes. No sense in going back to that wholesale, of course, but certainly more could be made of some local resources, hence the considerable — and successful — recent work on African leafy vegetables and local fruits. Actually one of my sisters-in-law did try to grow vegetable Amaranthus up here. There is a weedy type among the potatoes, but she got the seeds of a larger-leaved, erect, single-stemmed variety from her mother and sowed them in a corner of a cabbage field. Unfortunately, germination was poor and nothing much came of the experiment. We’ll see if we can source some better seeds from somewhere. Will keep you posted.

Now I’m off to Christmas dinner of roasted goat and irio. Happy holidays!

Fermenting the biofuel revolution

Part 2 of my musings on bioenergy is now available. This ramble looks at a novel form of breeding yeast, persuading it to make many more errors as it copies its DNA, and thus throw up lots of mutants for engineers to select among. The result is a yeast of unparalleled potency that would have been all but impossible to produce by tinkering with one gene at a time. And that leads into a consideration of some of the policy aspects of biofuels, such as what poor people will eat when the bioenergy industry is paying more than double today’s price for food in order to turn that food into fuel.

Biomass and bio-energy

We alluded last week to a new paper showing that prairie grasses are a far better source of biomass for energy than anything else currently around. There’s obviously a lot to be said, but rather than clutter up the pages here (our goal is two longer articles a month) I decided to use my own blog to publish a slightly closer look at bio-energy and to link from here to there. So what are you waiting for, go on over and read it. I’ll add links to the other parts as I publish them there.

Geotagging biodiversity

These days, if I’m 10 km NE of Suva on the road to Nausori, Northern Division, Fiji, and want to take a picture of the tropical countryside, after snapping away I can also pull out my little GPS machine and determine my position exactly as degrees of latitude and longitude – 18.075S, 178.525E, as it happens. And that’s much handier for sharing information about geographic locations, something that has become a lot easier – and popular – since the launch of Google Earth. What I’ve just done on the road to Nausori is called geotagging, or georeferencing. That just means adding information about locality – ideally latitude and longitude coordinates – to media like websites, RSS feeds and indeed images. Once your images are geotagged with coordinates and uploaded to Flickr, for example, you can display them in Google Earth – or a geographic information system (GIS) – to show where you took them. Pretty cool way to tell your family about your recent vacation. Soon, digital cameras will have a built-in GPS (many mobile phones already do), and the geotagging will be automatic.

Conservationists are also very keen on geotagging, but geotagging organisms is not as easy as photos. We have huge repositories of specimens of plants and animals at our disposal, both live and preserved, in things like herbaria, natural history museums, botanic gardens and genebanks. And associated with these specimens is usually a certain amount of data: things like the name of the species, the name of the collector, the date the specimen was collected and the place where it was found. These collections and their data are a very precious resource for taxonomy, ecology, conservation, agricultural development and other types of work, but they would be more valuable still if the data were available electronically to a greater extent. Many genebanks and herbaria have not yet placed the information found on the labels stuck on their seed containers and specimens sheets into a database, for example, although to be fair some have, and have even made that information available on-line.

However, even when the label information is digitized, the locality information is very rarely in a form that you can plug directly into Google Earth. That’s because, typically, the locality information – which may have been collected long before the GPS receiver became so readily accessible – doesn’t include latitude and longitude coordinates. It’s much more likely to just have the kind of information I started this post with: “10 km NE of Suva, on road to Nausori, Northern Division, Fiji.” Armed with that kind of text description, a good map, and perhaps some guesswork, you can of course derive the coordinates. But imagine doing that for all the pressed plants or germplasm accessions in even a smallish herbarium or genebank. Doesn’t bear thinking about. And there’s no guarantee that someone else presented with the same locality description in another herbarium or genebank would get the same answer.

Enter the Biogeomancer project. A global consortium of natural history scientists and experts in geospatial data, its goal is to “maximize the quality and quantity of biodiversity data that can be mapped in support of scientific research, planning, conservation, and management.” One of the main ways it does this is by developing tools to automate the geotagging process.

These tools first break down – parse – the textual locality description into its components, and look up the key locality name (Suva, in our example) in electronic gazetteers, which are lists of locality names with their coordinates. They then apply the offset implied by the phrase “10 km NE” to the locality’s coordinates, according to specified methods and standards, even providing an estimate of accuracy. Finally, they validate the results, for example by checking that the final coordinates are on land (assuming the specimen is a terrestrial organism!), between Suva and Nausori, and in the Northern Division of the country called Fiji.

Automated geotagging should cut down the time necessary to process a specimen from 5-10 minutes to fractions of a second, while adding to the repeatability and accuracy of the process. That means that data exchange will be easier, and that it will be possible to combine data coming from different institutions in a single analysis with more confidence that the quality of the data from different sources will be comparable.

Biogeomancer expects to have a “workbench” available to automate georeferencing by the end of 2006. I’m sure many botanists and zoologists will jump on it, but genebanks will probably be a bit behind. They don’t seem as wired into the latest bioinformatics developments as museums and herbaria. Maybe this post will help a bit.

Nutrition genes feed fantasy

Scientists in the US and Israel have discovered a gene that can boost the protein, iron and zinc levels of modern wheats. It is present in wild emmer wheat (Triticum turgidum ssp. dicoccoides) but somewhere along the way to modern bread and pasta wheats became non-functional. Inserting the gene into modern wheat — by normal breeding, they hasten to say, not genetic engineering — raises the protein and minerals by about 10 to 15 per cent. Modern wheat does have genes that are similar to the “wild” gene, which has been called Gpc-B1 for its effect on grain protein content. Blocking the activity of those genes in modern wheats causes the plants to live longer, but depresses the amounts of protein, iron and zinc even further.

Uauy2Hr The science of the discovery is intriguing. At the simplest level, Gpc-B1 seems to control not only the time at which the flag leaf, the big leaf just below the ears of grain, dies, but also the movement of protein, iron and zinc from the flag leaf into the grain. The actual research paper, in the 24 November issue of Science, requires a subscription to read, but you can find more from the University of California Davis’ press release and some press reports.

To be honest, I had expected more press coverage, not least because this is the third report in a week or so that sheds light on genes and nutrition, but it may be early days yet. The first, genetically engineering cotton seeds to get rid of a harmful compound called gossypol (once considered a contender for a male contraceptive) did indeed get a massive amount of attention. The second, a technical tour-de-force that showed where seeds store iron and how more of it can be made available to the plant and to people who eat the plats (or possibly just the germinating seeds) more or less vanished without trace. But all the coverage I have seen stressed one thing: world hunger.

One in three children worldwide is underweight and malnourished, and “hunger claims the lives of 20,000 children a day”. Two billion people suffer micronutrient deficiencies. The idea that a gene, or genes, can solve these problems at a stroke, as it were, is appealing. Wheat supplies roughly a fifth of all the calories people eat. Boost the protein and mineral content just a little, the argument goes, and you go a long way to eradicating malnutrition. Fix the staple crops — usually by genetic engineering, but that’s irrelevant — and you fix the problem.

Personally, I think this misses the point completely.

So nu-food wheat boosts protein and iron by 10 to 15 per cent? A dish of pumpkin leaves, preferably cooked with a little oil, delivers much more iron and a healthy dose of protein, with roughly twice the daily requirement for vitamin A thrown in for good measure. And the pumpkins are already being grown in places where these deficiencies are acute. Millets not only deliver better nutrition than wheat, they also offer farmers a much greater income and do much less damage to the environment.

All around the world, there are diverse, often local, crops — fruits and vegetables, cereals, legumes, other grains — that offer a far better deal nutritionally and environmentally, but that have suffered under the hegemony of the big three; wheat, rice and maize. But the silver bullet approach continues to dominate so much agricultural research.

The Bill and Melinda Gates Foundation, for example, gave US$ 7.5 million to develop a super-cassava. Cassava is a vitally important calorie crop in Africa, but it doesn’t contain much in the way of protein or micronutrients. It can be toxic. And it is susceptible to virus diseases. So the Gates Foundation asked scientists to fix those deficiences. And the scientists are only too happy to oblige. “Eventually, we’d like to bring all of these traits together into one variety of cassava,” Richard Sayre, the scientist leading the team, said.

Gates presumably gets the best advice money can buy, but this is woefully outmoded. Sayre is a plant breeder. Has he never heard of southern corn leaf blight, the disease that wiped out half the US maize harvest in 1970? How come? Because maize breeders had used a nifty little gene, called Texas male sterile, to ease the job of making hybrids. For years, schoolchildren and college kids in the midwestern states had made handy money in the summer wandering up and down rows of seed corn de-tasseling — castrating — the mother plants, so that only the pollen from the father plants went into the seeds. The male sterility gene did the job genetically, depriving those kids of an income but making maize-breeding more efficient. And making all the maize that contained the gene susceptible to southern corn leaf blight. Boom — an epidemic.

Genetic uniformity inevitably leads to increased vulnerability to pests and diseases. And genetic diversity, in and of itself, is an effective weapon against pests and diseases. This is not the place for an extended discussion of that basic premise. My intention is simply to point out that magic bullet solutions — for wheat, for cassava, for rice, for anything — contain the seeds of their own destruction. That is true of the whole of agricultural history. The first farmer to select an improved wheat from the wild emmer growing all around, for example, took the first step onto a treadmill. The thought of a single variety of Gates über-root over-running Africa conjures, for me, a vision of the Irish Potato Famine, in spades. Likewise, a nutritionally improved wonder wheat will do almost nothing sustainable to feed the rural poor.

Their salvation lies in diversity. Crop diversity. Species diversity. Nutritional diversity. One could do an awful lot in that direction with $7.5 million plus a bit of whatever else is going into making magic bullets.

To be fair, the scientists who discovered the grain protein content gene in wild wheat are very circumspect about the prospects. The gene, they say “may contribute” to the more efficient manipulation of senescence and nutrient remobilization in crops, and this may “translate into food with enhanced nutritional value”. But that modesty doesn’t last long. Nor, I suspect, will the improvements being sought.

Picture shows wild emmer wheat in its natural habitat north of the Sea of Galillee, Israel, courtesy of Zvi Peleg and Assaf Distelfeld.