John Mackey, CEO of Whole Foods, revealed a whole slew of new Whole Foods programs during a talk between him and Michael Pollan, author of The Ominivore’s Dilemma, at UC Berkeley on Tuesday.

One of these programs — dubbed the “Whole Trade Guarantee” — holds some great news in terms of fair trade. John said that Whole Trade Guarantee — which will debut this month — will hold guarantees on five criteria: quality, price (including a fair trade price or better for producers), labor practices, environmental sustainability — and a donation of 1% of sales to a Whole Foods foundation with the goal to help end poverty.

John specified that Whole Foods would be “outsourcing” the labor practices and environmental sustainability guarantees to fair trade — by which I’m guessing John means TransFair USA, which provides fair trade certification for US products — and Rainforest Alliance. In fact, John said that these two certifying organizations will be “competing” for Whole Foods’ certification business.

This nod to fair trade certification is one that’s been conspicuously missing at Whole Foods. While some Whole Foods carry coffee from other companies that are clearly fair trade, at the moment, none of Whole Foods’ store brand coffee — Allegro — carries fair trade certification. Information given out at Whole Foods stores about Allegro coffees have been rather confusing, and at times, misleading, as I wrote about here.

So with this new Whole Trade Guarantee, it seems Whole Foods has changed its mind about fair trade certification, which I like. However, what is this about a competition between TFUSA and Rainforest Alliance? The two organizations have very, VERY different focuses, even as some of their values and criteria sometimes coincide.

Fair trade certification is mostly focused on economic issues surrounding labor and trade; Rainforest Alliance certification hinges on environmental issues that preserve the environment and encourage ecological diversity. Certainly, fair trade practices work to encourage environmentally sustainable practices; the worst pesticides are disallowed, and organic farming is encouraged through an additional monetary premium. And of course, Rainforest Alliance coffee, grown in a well-managed, sustainable way, tends to be of higher quality, fetching farmers a higher price. But fair trade certification doesn’t hold the environmental guarantees that Rainforest Alliance certification does, and Rainforest Alliance certification guarantees neither a minimum price for the farmer, nor any of the other economic development issues that fair trade does address.

I guess I’m saying that while I’m glad that Whole Foods now realizes and acknowledges the importance of third party certification, I have qualms about the fact that Whole Foods seems to be conflating these third party certifications. This can further contribute to consumer confusion. The confusion that encourages consumers think of fair trade and Rainforest Alliance certifications as interchangeable is the same confusion that encourages consumers to think watered-down, in-house criteria — like Starbucks’ own CAFE practices — is similar to third-party certifications.

But we’ll see how it all plays out, once Whole Trade Guarantee rolls out.

During the talk, John also announced a $30 million venture capital fund to invest in unique food artisans around the planet. He also suggested a 5-star rating for organic farms that gives farms higher ratings for superior practices concerning animal treatment to worker compensation, etc. John also wants Whole Foods to create a third-party audited program for the ethical treatment of livestock.

The entire talk’s online, and a fun listen, especially if you’re aware of the history between John and Michael’s exchange regarding ethical food. After the publication of The Omnivore’s Dilemma, which critiqued some of Whole Foods’ practices, John and Michael have engaged in a published debate via their respective blogs. You can catch up on the exchange on Michael’s or John’s blogs.