Life in occupied Poland forced Shahak's mother to pay a Roman Catholic family to hide Israel, whom they returned when she could not afford their safe-keeping him from the Nazis.

[4] As displaced persons, mother and son managed to emigrate to the British Mandate of Palestine, where Shahak's application to join a kibbutz was denied, because he was judged to be physically too slender.

After a religious Jewish education at boarding school in the village of Kfar Hassidim, Israel and his mother moved to the city of Tel Aviv.

[4] In the course of his professional career as a scientist, Shahak's work in organic chemistry produced science about organic compounds of the element fluorine (F), contributed to cancer research, for which he gained an international reputation[5] and included posting as an assistant to Ernst David Bergmann, the nuclear physicist who was chairman (1952) of the Israel Atomic Energy Commission (IAEC).

[8] In 1990, the academic Shahak retired from the faculty of Hebrew University, because of poor health (diabetes mellitus) and greater interest in research work in other fields of intellectual enquiry.

[9] For most of his adult life, Shahak resided in the Rehavia neighborhood in West Jerusalem; at the age of 68 years, he died of diabetic complications, and was buried in the Givat Shaul cemetery.

[4] Shahak had a deep affinity with Spinoza:[10] he always packed a copy of The Ethics in his suitcase for reading during his periodic stints of service in the Israel Defense Forces,[11] and had been writing a book on the philosopher before his death.

He was regularly spat on,[4] frequently given death threats,[4] and decried variously as an Israel basher, self-hating Jew, traitor, and enemy of the people.

[14] In 1969, Shahak and another member of the faculty of Hebrew University staged a sit-down protest against the Israeli government's policy of jailing politically active Palestinian students, by way of administrative detention authorised by state-of-emergency laws; likewise, Shahak supported the political efforts of Palestinian students to achieve equal rights, like those granted to Jewish Israelis, at Hebrew University.

[1] To make public what he considered the anti-Arab and anti-Palestinian legalised discrimination, Shahak published English translations of Hebrew-language reportage about illegal and unjust actions of the Israeli government against the gentile citizens of Israel; Shahak's English reports were intended for the Jewish community of the U.S.[7][9] The translated reports featured headlines such as "Torture in Israel," and "Collective Punishment in the West Bank", which Shahak sent to journalists, academics, and human rights activists, and so ensured that the mainstream population of the U.S. would be informed of the religious discrimination practised by the government of Israel.

[13] As a public intellectual, Shahak wrote about the Israeli government's actions against the non-Jewish citizens of the State of Israel, such as the suppression of freedom of speech and general political activity; land ordinances, living restrictions, and the confiscation of lands from non-Jews; the destruction of houses; legally-sanctioned unequal pay and work restrictions; emergency-defence regulations allowing the summary arrest, detention, and torture of prisoners (civil and military); the collective punishment of communities; the assassinations of leaders (religious, political, academic); racial discrimination in access to education; and the deprivation of Israeli citizenship.

In the book review of a festschrift in honour of Rabbi Elmer Berger Anti-Zionism: Analytical Reflections (1988), Sheldon Richman characterized Shahak's interpretation of Zionism as viewing it as an atavistic reaction against the European Enlightenment's individualism that strove to revive the suffocating world of the Jewish ghetto.

For Richman, Shahak's analysis shed light on the tragic consequences that followed upon the establishment of Israel, as Arabs were swept away to forge a state for Jews alone.

[15] In letters published in the Ha'aretz and Kol Ha'ir newspapers, Shahak criticized the political hypocrisy demonstrated by the radical Left in their uncritical support of the Palestinian nationalist movements.

I have met influential "civil society" Palestinians alive today who were protected as students when Israel was a professor of chemistry at the Hebrew University; from him they learned never to generalize about Jews.

[13][19][20][21] Shahak added that the Beth din, the rabbinical court of Jerusalem, had confirmed that the Orthodox Jew correctly understood Halakha law on Pikuach nefesh regarding non-Jews and the Sabbath, and quoted passages from a recent legal compilation.

[13][21][24][25] The opinions of these rabbis derived from the book Noda B'Yehuda (Known in Judah), in which the 18th-century religious authority Yechezkel Landau said: "I emphatically declare that in all laws contained in the Jewish writings concerning theft, fraud, etc.

In support, he cited Eli Beer, the chief coordinator of Israel's volunteer ambulance service (1,100 medical personnel, 60 per cent Orthodox), who said, "If someone would say we won't save a non-Jewish life on the Sabbath, he is a liar.

He quotes from an official exhortation to religious Jewish soldiers about Gentiles, published by the Israeli army's Central Region Command, in which the chief chaplain writes: "When our forces come across civilians during a war, or in hot pursuit, or a raid, so long as there is no certainty that those civilians are incapable of harming our forces, then, according to the Halakhah (the legal system of Classical Judaism) they may and even should be killed...

[c]The remark regarding children passing a cemetery occurs in Shahak's discussion of passages modified by rabbis who, under pressure from antisemitic Christian authorities such as those in Tzarist Russia, altered the texts, while keeping private copies of the originals which, according to Shahak were restored as the proper manuscript readings and published in Israel after the founding of the state of Israel.

[41] Emanuele Ottolenghi, reviewing Alexander and Bogdanor's book, argued that Jews such as Shahak, George Steiner, Tanya Reinhart, Tony Judt, Avi Shlaim, Seymour Hersh and Daniel Boyarin act as enablers for antisemites, because the rhetoric of antisemitic Jews plays a "crucial role... in excusing, condoning, and — in effect — abetting anti-Semitism."

[43] His death was the occasion of tribute and criticism; the Bar-Ilan University historian Haim Genizi, said that "Shahak's extreme anti-Israeli statements were welcomed by the PLO, and [were] widely circulated in pro–Arab circles", in detriment to the interests of the State of Israel.

Norton Mezvinsky, said that his friend and collaborator was "a rare intellectual giant and a superior humanist"; in that vein, Edward Said said that Shahak was "a very brave man who should be honored for his services to humanity.

[43] Christopher Hitchens considered Shahak a "dear friend and comrade... [who was] a brilliant and devoted student of the archaeology of Jerusalem and Palestine", who, "during his chairmanship of the Israeli League for Human and Civil Rights, set a personal example that would be very difficult to emulate.

"[46] Allan C. Brownfeld, of the American Council for Judaism, recalled a humanist who actively opposed "racism and oppression in any form and in any country"; that Shahak possessed a "genuinely prophetic Jewish voice, one which ardently advocated democracy and human rights.