We use present perfect to talk about actions in the past where the dates is either not important and not known. 'Have been found' though is in its passive form.

"Have been found" is the present perfect continuous and is chosen because there are still archaeological digs happening and pieces are still being found. The idea is that the example allowing for something that happened in the past, at some point. If, however, there was a situation were the time period was more specific the article would use "were found" e.g. "In the 1920's, iron ornaments were found in the Middle East."

In case it helps, some grammar books classify the present perfect tense into four categories. (Of course, it doesn't mean every PP sentence corresponds to only one of these. Often more than one apply.) 1. completion - "I have finished my homework" - I completed it, so there's nothing more to do. 2. result - "I have found my watch" - I found it so I now have it with me. 3. continuation - "I have lived here [I have been living here] for 5 years - it still continues now. 4. experience - "I have been to Japan once" - it's an experience that is part of who I am now. I believe the usage in your example is #2. The writer is supporting his thesis by saying the proof has been found and is available now.