Category: Information

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How would you PageRank genebank accessions?

Various friends have sent me, over the past few days, different takes on a recent paper which used the Google PageRank algorithm to identify the most “important” species in food webs, perhaps because they know I’m a sucker for examples of cross-pollination between disciplines. The BBC had its say, and also ScienceDaily, among others. I posted the ScienceDaily article on Facebook, as I am wont to do when I think something is interesting — maybe even have a gut feeling it might be relevant to agrobiodiversity conservation — but don’t know quite what to make of it. Sure enough, someone left a comment that he thought the algorithm was a secret, which was also my understanding: Google don’t want people to manipulate the rank of their web pages. But then someone else came in and said that the basics of how the thing works are in the public domain.

To prove it, he provided a link to an American Mathematical Society article entitled How Google Finds Your Needle in the Web’s Haystack. Which is why I love social networking, but that’s another story. Now, that article is definitely NSFW, unless you work at the American Mathematical Society, so think twice before clicking, but here’s the lede:

Imagine a library containing 25 billion documents but with no centralized organization and no librarians. In addition, anyone may add a document at any time without telling anyone. You may feel sure that one of the documents contained in the collection has a piece of information that is vitally important to you, and, being impatient like most of us, you’d like to find it in a matter of seconds. How would you go about doing it?

And I thought to myself: just change that 25 billion, which of course refers to the number of pages on the internet, to 6.5 million or 7.2 million or whatever, and the guy could just as easily be talking about accessions in the world’s genebanks.

Now, basically we search for the germplasm we need by starting with a big dataset and applying filters: wheat, awnless wheat, awnless wheat with such and such resistance, awnless wheat with such and such resistance from areas with less than x mm of rainfall per annum, and so on. Would it make any sense to rank the accessions in that initial big dataset? On what basis would one do that anyway? That is, what is the equivalent of hyperlinks for accessions? Because the essence of PageRank is that important pages receive lots of hyperlinks from important pages. So, numbers of requests? Amount of data available on the accession? But wouldn’t that just mean that only the usual suspects would get picked all the time? Genetic uniqueness, perhaps, then? That would be turning the algorithm on its head. Looking for lack of connections rather than connections to other accessions. You could in fact have different ranking criteria for different purposes, I suppose.

Ok, now my brain hurts. This cross-pollination stuff can be fun, but it is hard work.

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Nibbles: Chickens, Peppers, Treaty, Breadfruit, Preservation, Food systems, Adaptation, Yam multiplication

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Talking about prairie restoration

“Not long ago, it was assumed that once a prairie was plowed up for row crop agriculture, there was no way to get the plant and animal species back again,” said Chris Helzer of The Nature Conservancy. “But now we’ve got the technology and experience to successfully harvest and plant seeds from hundreds of plant species. So in cases where it makes sense to do that kind of restoration, we can re-establish that diverse plant community.”

And that, as we’ve seen, includes a whole bunch of crop wild relatives. Wonder if the folks talking about this in Aurora, NE will give them their due. In fact, I wonder if restoration ecologists in general give any sort of special consideration to CWRs in their work. If you know, tell us.

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Indigenous food systems documented

FAO has a book out called Indigenous Peoples’ Food Systems, published with the Centre for Indigenous Peoples’ Nutrition and Environment (CINE). There’s an informative interview with Barbara Burlingame, senior nutrition officer at FAO and coordinator for the book, on the FAO InTouch website. Unfortunately, this is only available internally at FAO, for reasons which elude me. Here’s a few of the interesting things Dr Burlingame had to say.

We wanted to showcase the many dimensions of these traditional food resources, breaking them down by nutrition, health, culture and environmental sustainability. So much knowledge of early cultures is contained within traditional foods and their cultivation, and they have a direct impact on the physical, emotional, mental and spiritual health of indigenous communities. Indigenous foods can have important nutritional benefits, for example. For instance plant foods are generally viewed as good sources of carbohydrates, vitamins and minerals. These foods also provide important economic benefits, such as helping create self-sufficient communities and establishing a strong foundation of food security.
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We believe the information can be a help to those in nutrition, agriculture, environmental and health education, and science, including policymakers. Nutritionists can use the information to try and correct imbalances in certain regions. For example, we discovered in research that the Pohnpei district community in the Federated States of Micronesia was severely deficient in vitamin A, despite the fact that a species of banana rich in vitamin A beta-carotenes was indigenous to the region. Once we determined the nutritional composition of the banana, we were able to educate the people about its benefit and encourage them to eat the local fruit, which helped reverse the deficiency.
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Yes, another book is under way that focuses more on nutrition and public health. It will look at policy dimensions, stemming the tide of obesity in indigenous peoples, the value of indigenous weaning foods for babies, and a ‘go local’ campaign in Micronesia encouraging communities to eat local food items. We will also continue in our efforts in integrating elements of biodiversity into all aspects of nutrition.

“Go Local” of course refers to the campaign to promote traditional foods in the Pacific spearheaded by Lois Englberger and her colleagues at the Island Food Community of Pohnpei, who have appeared frequently on these pages. It’s great to see my old friends from the Pacific getting this kind of international exposure for their efforts, and making a difference beyond their immediate region.

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