Monday, September 29, 2014

Predicting future environments: it's impossible in principle

We often caution here on MT about predicting the future.  There's an idea afoot that once we know our genomes we'll be able to predict who will get what chronic disease, even when the disease is the result of genes interacting with environmental factors.  Or even multiple genes and multiple environments.  But, as we've often said, making such predictions with known accuracy is impossible in principle.  And here's why.

A BBC television series in the 1970's, "A Taste of Britain," hosted by Derek Cooper, set out to document traditional foods and food practices in Britain before they disappeared.  The long-running BBC Radio 4 show, "The Food Programme," revisits this series by traveling to the places documented 40 years ago to find out what became of the foods, the people, and the traditions the original program had captured on film.  "A Taste of Britain Revisited" is a fascinating glimpse into traditional foods and how they've fared in the intervening years.

Cooper urgently tracked down cockle pickers, sewin fishermen, truffle hunters, cheese makers, colliers wives, makers of Yorkshire Pudding, makers of Welsh cakes and laverbread, and more, certain that the traditions he was documenting would soon be lost.

Cockle pickers, Wales: Daily Mail, 2008

Fishing for sewin (sea trout) in traditional coracles, Wales; Wikipedia
And some were.  Once miners were moved into council housing in Yorkshire, away from coal-fired ovens, Yorkshire Pudding was never the same.  Native English crayfish will soon be extinct because a heartier North American variety has taken over, bringing a virus that kills the natives with it.  Cooper filmed the last traditional hearth in Wales, which was replaced but something more modern just weeks later.

And some have changed. The traditional Dorset Blue Vinny cheese that Cooper was told he was eating was in fact a second-rate Stilton, the real thing not having been made since World War II when the making of soft and semi-soft cheeses was banned, and only hard, transportable cheeses like cheddar could be made, to be sent to the cities.  But the recipe for Blue Vinny was found in the 1980's, and the cheese revived.  Cockles were in short supply in the 1970's and had to be imported.  The numbers increased for a while after that, fell and increased again, but now aren't as plentiful as they were, and cockle gatherers don't go to the beach by horse and cart any longer.

Horse and Cart on Beach, William Ayerst  Ingram; Wikipedia

And some have remained the same, but the economics have changed.  Welsh laver, or seaweed, is now being sold in Japan, when just 40 years ago getting it to London was a major accomplishment.   Businesses have been bought up by foreign companies.  A Spanish company now buys British cockles, and they are now being canned and sold in Spain. "Cans is something we never thought we'd put cockles into, but if that's the way they want them, that's the way they can have them."

So, Cooper wasn't entirely right that he was documenting the final days of many traditions and foods, though he was certainly documenting change.  I don't know what he thought was going to replace traditional foods, but perhaps the biggest change over the last 40 years was the rise of processed foods.  Whether or not he foresaw that I don't know, but even if he or anyone else had, the health effects couldn't have been predicted.  Indeed, even with all the evidence before us, we can't really say what the health effects of any of the specific changes have been.  Yes, people are more obese, have more heart disease, stroke, hypertension, cancers and so on, but in a very real sense, a major 'cause' of these diseases is control of infectious diseases.  

But, that's not the real point of this post.  The point is that it looks as though the common, late onset chronic diseases we are dying of now are the result of complex interactions between genes and environment.  Epidemiologists have been trying to identify environmental risk factors for decades, with only modest success -- meaning that it's not clear that we know which aspects of our environments are linked with risk.  But even if we did, these two series of programs on traditional foods in Britain make it clear that while we may fit today's disease cases to yesterday's exposures, it's impossible to predict what people will be eating not far into the future, so that even if we do identify risk alleles and risky environments, we don't know that carriers of that allele will still be exposed to risky environments not many years from now.  So, we can't predict their disease with more than retrospective accuracy, when we know from experience that risks of the same traits change rapidly and substantially.

Here's an example.  Type 2 diabetes has risen to epidemic levels in Native American populations, and Mexican Americans who are admixed with Native Americans, since World War II.  The nature of the disease and the pattern of the epidemic suggests that a fairly simple genetic background may be responsible.  But, even if so, that's only in the provocative environment of the last 60 or so years.  That's because there was little to no type 2 diabetes in Native Americans, or Mexican Americans, before then, yet whichever alleles are responding now, leading to glucose intolerance and so forth have basically not changed in frequency. It's the environment  -- diet and exercise, presumably -- that has changed.  This epidemic could simply not have been predicted 60 years ago, even if we'd been genotyping people then, because whatever risk alleles are now responsible were not causing disease before the environment changed.

So, the promise that genotyping every infant at birth will allow us to predict the late onset, complex diseases they will eventually have is unlikely to be met.  Instead, for many or most complex traits, it's an illusion that's being sold as fact.


Edward Hessler said...

This is a great essay and very much in the spirit of TMT. I went to the BBC and listened for a while to radio with me making the images.

I'm so glad when I learned of this...another time-capsule from which we cannot make rational predictions, no matter we want to, but from which we can investigate continuity and change.

Reminds me, in a way, of Gould and Eldredge

I thought of the Opies work on play--the games and the rhymes (rhyming games). I still go to the library to browse this literature and thankful for their thorough and loving documentation. Here, you will find an excerpt from one of the volumes published by New York Books.

However, it merely scratches the surface of their work. Archives in England include papers and recordings.

( < >)

Anne Buchanan said...

Thank you, Ed. Yes, exactly, about predictions.

And thanks for the link to the Opie's work. Was their purpose to catalogue traditions before they died out, as Derek Cooper's was, I wonder? In any case, an equally valuable time-capsule.

Edward Hessler said...

I don't think this was their intention/motivation (to record traditions before they died out). Their career aim and interests/scholarship--folklorists of children's rhymes, games, etc. is what drove them.

This Wiki link tells you more than you want to know but I love their comments on how they worked together, not too many paragraphs in.

Your father would love, I think, some of the rhymnes and I'd guess that some kids would, too but probably not all.

There have been two position papers by early childhood groups released recently which emphasize the importance of play, something I fear is disappearing as we push educational expectations and readiness progams and assessment ever downward.

Childhood is a time of its own, well some of it should be.

Anne Buchanan said...

Rowing across the Atlantic in a very small boat? Indeed! Even more difficult if they only discussed their work late at night!

I will send the link to my father. I think you're right that he will love the rhymes.