Amjad Barham’s article in support of the recently-declared boycott of Israeli academic institutions is one of the more thoughtful to come out of the controversy, and deserves an equally thoughtful response.

I have had extensive experience coordinating and studying Israeli-Palestinian joint academic projects, and I think it is important to show how this boycott, in fact, seriously harms Palestinian interests and set back the possibilities of genuine peace and attainment of Palestinian rights.

Along with many others, I view current Israeli policy as disastrous, and see the continuing occupation, under whatever names, harming both Israelis and Palestinians. Along with many other academics, I strongly support the Arab League Initiative as a basis for negotiations, leading to the establish-ment of a Palestinian state alongside Israel, with East Jerusalem as its capital. Many of us are on record strongly condemning Israeli brutality in attacks and ordinary encounters. But we equally condemn Palestinian attacks on Israelis, which have killed thousands over the years and helped to perpetuate Israel’s fortress mentality.

Having lived in Israel through two years of the second intifada, when suicide bombings were a weekly and sometimes daily occurrence, I am acutely aware how such attacks prevent even the thought of peace and coexistence.

Much of my work to counter these trends has been carried out through organising and conducting joint academic projects between Israelis and Palestinians and, on occasion, other Arab academics. Unfortunately, Dr Barham’s claim that far too few Israeli academics have protested Israeli policies is absolutely correct; similarly, only a small percentage of Israeli and Palestinian academics have even met each other, let alone participated in joint projects.

Yet Dr Barham’s article assumes a single explanation that defies history and fact. Palestinians are not pure victims: Israelis are not solely aggressors. Israelis are also under attack and have a right to defend themselves. While I accept that the continuation of occupation is the single most important fact in the perpetuation of the conflict, anyone who has lived among Israelis understands why so many see its continuation as defensive, even if they disagree, as I do.

Dr Barham, like many Palestinians, sees complete opposition to the army, to the government and to all Israeli policies as the only possible moral behaviour. This view makes Israel into a monochromatic society obsessed only with oppressing and exploiting Palestinians. That wrong-headed outside view helps perpetuate the conflict, not solve it.

The simple political fact is that the conflict will not end until both Israelis and Palestinians accept, publicly and unequivocally, the legitimacy of Israel and Palestine, and are convinced that the other side accepts it as well. This is not a call to wait forever until this happens. On the contrary, a political process could and should start today to create the political basis for a Palestinian state. But this will not take place while most Israelis are convinced that Palestinians, and much of the Arab and Muslim world, wants only to outlaw and then destroy Israel. And outlawing is exactly what boycotts are about.

It is completely wrong to state that Israeli academics have not been “a bastion of dissent or a force of opposition to state policies”. It is a fact that much of the political as well as intellectual leadership of the opposition to the occupation has come from academics from the 1970s through today, a source of continual anger and irritation to the Israeli right-wing.

One example of this is the “Proposed Guiding Principles for Dialogue and Cooperation”, recently prepared under the auspices of Unesco by Walid Salem and Edy Kaufman. It develops a code of ethics that would guide both sides in dealing with the other, including steps to ensure freedom of movement and academic freedom, which have been frequently threatened and abused.

But perhaps worst of all, the strategy of the boycott assumes that ignoring Israeli concerns and simply applying external pressure will have political results. Instead, it completely undercuts the arguments of those of us who are trying to shape an atmosphere of legitimacy.

Palestinians are thus following in the footsteps of the failed Israeli policies from 1948 until the Oslo accords of 1993, whereby Israel ignored the existence of a Palestinian people and tried to deal with everyone else except the accepted Palestinian leadership. The boycott proponents now believe, against all the evidence, that external pressure will force a change in Israeli policies. Instead, such actions strengthen hardline forces by convincing centrist Israelis that there is no alternative to fighting for their existence.

Now the boycott strategy is frequently based on a flawed analogy with South African apartheid. As my colleague and friend Benjamin Pogrund has written in these pages and elsewhere, as repressive and oppressive as the occupation is, and as unfair as many Israeli laws are even to Palestinian citizens of Israel, the bases, legality and purposes of the two regimes are completely different. And there is no reason to believe that pressures of this sort will be anything but counterproductive.

There is, of course, a special pleasure in striking out at your adversary at a safe distance. It can seem much more satisfying than the messy business of understanding your opponent’s fears and concerns, recognising your own partial responsibility for creation and perpetuation of the conflict and seeking to compromise issues that both sides consider existential. Among other things, it exposes you to opprobrium from your own side and seems to sully the purity of your own cause.

But this tangled conflict does not have one author or one solution. Recognition of the shared responsibility in both its genesis and its resolution, which requires legitimation rather than de-legitimation of the other side, is the only practicable and effective way to proceed.

· Paul Scham is adjunct scholar at the Middle East Institute in Washington, D.C and co-editor (with Walid Salem and Benjamin Pogrund) of the book Shared Histories: A Palestinian-Israeli Dialogue (2005).