The Human Terrain System is a military program to employ anthropologist to help assist and determine the cultural makeup of a given location to better assist the military in furthering their control over a given area.
While this has good effects in reducing numbers of causalities and collateral damage
by reducing the desire for the local population to 'strike back' at the invaders due to cultural miscommunication, it puts the 'anthropology' profession uncomfortably close to the military and puts the profession at risk of being biased and potentially furthering any imperialistic ambition of the state (Turning anthropologist into cultural spies essentially). In addition Human Terrain System programs often work in secrecy, which is totally opposite to the spirit of anthropology.
This understandably worried the international (and American) anthropological research community into criticizing and asking for coworkers to avoid working for such programs.
However while it may be ethical and a moral imperative to boycott such programs. I feel that such action will be as successful as banning napster, yes you can stop it, but it will simply spawn something else more powerful and uncontrollable (which personally for me is a good in in regards to p2p internet freedom, in regards to the death of napster).
Instead, the anthropological research community needs to band together and develop an opensourced organization that will emulate the principle of HTS, but with a focus for maintain ethical conduct of information collection.
To help fund it and maintain its existence, it will employ antropologist to help corporations, NGOs, and police organizations, to assist in understanding local developing countries. The differences is that any findings and reports will be published openly, and if possible in academic papers accessable within the website. Effort should be made to ensure 'grokability' of the findings by average reporters and users (and posted on twitter perhaps).
Profits from the other efforts in this org, will be used to fund extra research in conflict zones and unstable regions (Independent from any competing group, insurgent or military. But maintains dialog with both.), to help promote more informed policy making for all actors in the area. This will hopefully also assist in the 'peace negotiation' if everyone in the region knows the cultural sensitivity of everybody else. It will also assist in empathy building, due to enemies taking time to learn about the other side.
There are obviously more to develop from this concept. Nevertheless I seriously think we need to make this effort work, if we are to protect the academic and ethical integrity of the anthropological profession (And avoid the past tragedy of science being fodder for unethical motives, like how evolution and Darwinism were used to promote racist pseudoscience in the Nazi regime. Which could possibly play a small part for why there are still a lot of resistance against evolution by religious groups. )
After all, we developed science to further the human race, not further a particular agenda (Whether that agenda is 'good' or 'bad' in relative sense).
P.s. The website for this org could be a good opportunity for anthropologist to talk to the general public (e.g. workers for a company wants to know how to respect local customs) via a forum/blog etc...