Dr. Steven Jones has published a new paper called "Revisiting 9/11/2001 --Applying the Scientific Method" at the Journal of 9/11 Studies, the introduction follows, download the attached PDF for the full article.
In this paper I focus on the application of the scientific method to the study of what really happened on 9/11/2001, particularly in the destruction of the World Trade Center buildings . There is something here to look at in depth: this is serious business. It is not just "nutty fringe science" or "conspiracy theory" that can be rejected without even considering the data. There is need for scientific scrutiny as I hope to demonstrate in this paper. In fact my colleagues and I now feel that we have sufficient data to conclude that the collisions of jets with the two Towers are NOT sufficient to explain the complete and rapid collapses of both Towers and WTC 7. We conclude that the evidence is compelling that the destruction of the WTC buildings involved planted cutter charges (such as explosives and incendiaries). We will consider this evidence. 
1 This paper is based on a talk I gave at the University of California at Berkeley on November 7, 2006, with important updates.
2 See http://journalof911studies.com/volume/200609/Why_Indeed_Did_the_WTC_Buildings_Completely_Collapse_Jones_Thermite_World_Trade_Center.pdf
. Fortunately, there is now a body of extensive research gathered in the peer-reviewed books cited above and in the Journal of 9/11 Studies. That is the way science proceeds, with observations, hypotheses, experiments and published papers. For a more extensive treatment of the study of 9/11 events than can be provided in one paper, I refer the reader especially to http://journalof911studies.com/
. Here you will find an ever-expanding set of papers relating to the study of "What really happened on 9/11/2001?" The issue, however, is not just understanding, but also a quest to seek justice based on the findings.