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The long-range implications are probably good news, actually!
In a weird way, the news of a nationwide organic milk shortage actually warms my heart. It means that there is such a strong market for organic milk that not only is it possible to create a shortage, but that shortage even makes the national news! Considering how hard it has been to convince the average American of the benefits of organic food and agriculture, this milk shortage is kind of a win, if you think about it.In a nutshell, demand has outstripped the national supply of organic milk, and things are looking a little rough in 2012 for organic milk fans. Part of the problem is the length of time it takes to be certified organic. It takes a lot of time, money, and paperwork to be certified organic.
To make things worse, some dairy farms refuse to pursue organic certification, in the belief that "if your farm is certified organic, you can't give a cow antibiotics if she gets sick." I live in an area with a lot of dairy farming (Skagit Valley, about 70 miles north of Seattle) and I have heard this rationalization from many people - including dairy farmers.
The truth is that yes, you are allowed to medicate sick livestock. You just have to keep them separated from the rest of the herd while they are being treated, and dump any milk they produce. Obviously, farmers would be doing this anyway, because you can't sell milk from a sick cow. So the end result is exactly the same as ordinary conventional farming practices.
Another problem is that feed prices have risen faster than milk prices. Consumers are still somewhat price-conscious when it comes to organic items, and frankly we may not be willing to pay what organic milk is worth. The price of cattle feed like hay and feed corn has risen dramatically in the last few years, which is pinching everyone - not just end consumers questioning the price of a loaf of bread, but farmers trying to feed their livestock. A lactating milk cow requires a lot of feed in order to keep producing milk!
(Incidentally, this NPR news story cheekily advises against stockpiling organic milk, because it's perishable. However, you can store milk in the freezer. Remove the caps of plastic jugs to allow room for expansion; cardboard half-gallons will be fine.)
The organic milk shortage is primarily affecting Horizon and Organic Valley, both of which are national distributors. You will no doubt have better luck sourcing organic milk locally - keep an eye out at your local farmer's market for local dairies, and ask around!
