While the Washington press corps obsessed over Hillary Clinton’s e-mails at the State Department, reporters were missing a far more important story about government secrets. After five decades of pretending otherwise, the Pentagon has reluctantly confirmed that Israel does indeed possess nuclear bombs, as well as awesome weapons technology similar to America’s.

Early last month the Department of Defense released a secret report done in 1987 by the Pentagon-funded Institute for Defense Analysis that essentially confirms the existence of Israel’s nukes. DOD was responding to a Freedom of Information lawsuit filed by Grant Smith, an investigative reporter and author who heads the Institute for Research: Middle East Policy. Smith said he thinks this is the first time the US government has ever provided official recognition of the long-standing reality.

It’s not exactly news. Policy elites and every president from LBJ to Obama have known that Israel has the bomb. But American authorities have cooperated in the secrecy and prohibited federal employees from sharing the truth with the people. When the White House reporter Helen Thomas asked the question of Barack Obama back in 2009, the president ducked. “With respect to nuclear weapons, you know, I don’t want to speculate,” Obama said. That was an awkward fib. Obama certainly knows better, and so do nearly two-thirds of the American people, according to opinion polls.

In my previous blog, “What about Israel’s Nuclear Bomb?” I observed that the news media focused solely on Iran’s nuclear ambitions but generally failed to note that Israel already had nukes. That produced a tip about the Pentagon release in early February.

Yet the confirmation of this poorly kept secret opens a troublesome can of worms for both the US government and our closest ally in the Middle East. Official acknowledgement poses questions and contradictions that cry out for closer inspection. For many years, the United States collaborated with Israel’s development of critical technology needed for advanced armaments. Yet Washington pushed other nations to sign the Non-Proliferation Treaty, which requires international inspections to discourage the spread of nuclear arms. Israel has never signed the NPT and therefore does not have to submit to inspections.

Washington knew all along what the inspectors would find in Israel. Furthermore, as far back as the 1960s, the US Foreign Assistance Act was amended by concerned senators to prohibit any foreign aid for countries developing their own nukes. Smith asserts that the exception made for Israel was a violation of the US law but it was shrouded by the official secrecy. Since Israel is a major recipient of US aid, American presidents had good reason not to reveal the truth.

The newly released report—“Critical Technological Assessment in Israel and NATO Nations”—describes Israel’s nuclear infrastructure in broad terms, but the dimensions are awesome. Israel’s nuclear research labs, the IDA researchers reported, “are equivalent to our Los Alamos, Lawrence Livermore and Oak Ridge National Laboratories.” Indeed, the investigators observed that Israel’s facilities are “an almost exact parallel of the capability currently existing at our National Laboratories.”

The IDA team visited Israeli labs, factories, private companies and government research centers in Israel and relevant NATO nations (details on NATO allies were redacted from the released version). On Israel, the tone of the report was both admiring and collegial. “The SOREQ center,” it said, for instance, “runs the full nuclear gamut of activities from engineering, administration and non-destructive testing for electro-optics, pulsed power, process engineering and chemistry and nuclear research and safety. This is the technology base required for nuclear weapons design and fabrication.”

The IDA team added: “It should be noted that the Israelis are developing the kind of codes which will enable them to make hydrogen bombs. That is, codes which detail fission and fusion processes on a microscopic and macroscopic level.” So far, The IDA estimated, Israel scientists were about where the US had been in the 1950s in understanding fission and fusion processes.

The report does not include a single declarative sentence that directly states the taboo—Israel has nukes—but the meaning is obvious. For many years, scholars and other experts have estimated that Israel has at least 100 to 200 bombs, possibly more.

Some of the IDA’s observations seem to hint at a copy-cat process in which the US government either actively helped or at least looked the other way while Israel borrowed or purloined technologies to establish a parallel nuclear system that looks a lot like America’s. The IDA document does not say anything, one way or the other, on the history of how this happened. But critics of Israel and advocates for banning all nuclear weapons have harbored suspicions for decades.

The Institute for Research: Middle East Policy, Smith said, is pushing another FOIA request aimed at the CIA, hoping to pry open long-secret intelligence investigations about how Israel managed to get the bomb in the first place. The institute is seeking disclosure of a CIA study that supposedly investigated how quantities of uranium were leaked or allegedly smuggled by Israeli agents from a Pennsylvania defense plant to provide seed corn for the Israel bomb.

Smith and others suspect that elements of the US government knew what happened back then or may even have assisted the stealthy transfer. That particular mystery was a hot issue back in the 1970s. It seems likely to get renewed interest now that the pretense of official ignorance has been demolished by release of the 1987 report.

However, the IDA’s most powerful message may not be what it says about Israel’s nukes but what it conveys about the US-Israel relationship. It resembles a technological marriage that over decades transformed the nature of modern warfare in numerous ways. The bulk of the report is really a detailed survey of Israel’s collaborative role in developing critical technologies—the research and industrial base that helped generate advanced armaments of all sorts. Most Americans, myself included, are used to assuming the US military-industrial complex invents and perfects the dazzling innovations, then shares some with favored allies like Israel.

That’s not altogether wrong but the IDA report suggests a more meaningful understanding. The US and Israel are more like a very sophisticated high-tech partnership that collaborates on the frontiers of physics and other sciences in order to yield the gee-whiz weaponry that now define modern warfare. Back in the 1980s, the two nations were sharing and cross-pollinating their defense research at a very advanced level.

Today we have as a result the “electronic battlefield” and many other awesome innovations. Tank commanders with small-screen maps that show where their adversaries are moving. Jet pilots who fire computer-guided bombs. Ships at sea that launch missiles over the horizon and hit targets 1,000 miles away.

I had to read the report several times before I grasped its deeper meaning. The language is densely technological and probably beyond anyone (like myself) who is not a physicist or engineer. The researchers reported on the state of play in electronic optical systems, plasma physics, laser-guided spacecraft, obscure communication innovations and many other scientific explorations that were underway circa 1987.

Finally, it dawned on me. These experts were talking in the 1980s about technological challenges that were forerunners to the dazzling innovations that are now standard. I saw some of these new war-fighting devices in the late 1990s when I wrote a short book on the post-Cold War military struggling to redefine itself when it no longer had the Soviet Union as an enemy (Fortress America: The American Military and the Consequence of Peace).

While reporting on numerous military bases—land, sea and air—I saw some of the early attempts at battlefield communications and guidance systems. A lot of the new stuff didn’t work very well. Soldiers and commanders sometimes had to put it aside or work around it. Drones at that stage were still on the drawing boards, known as UAV’s—“unmanned aerial vehicles.”

The Middle East wars became the live-fire testing ground where new systems were perfected. The consequences of peace were brushed aside by the terror of 9-11. War became America’s continuous preoccupation.

Israel participated importantly in developing groundwork for some of the wonder weapons and, as the IDA survey makes clear, Israeli physicists or engineers were sometimes a few steps ahead of their American counterparts. To be sure, the Israelis were junior partners who brought “technology based on extrapolations of US equipment and ideas.” But the report also observed: “Much Israeli fielded electronic warfare and communications [is] ahead of US fielded equipment.”

On several occasions, the research team spoke of “ingenious” or “Ingeniously clever” solutions that Israeli technologists have found for mind-bending problems of advanced physics. The IDA team also suggested opportunities for American researchers to piggy-back on what Israel had discovered or to team up with one of their R&D centers. Yale’s Office of Naval Research, IDA suggested, should collaborate with the Hebrew University of Jerusalem.

“Scientists at RAFAEL [another Israeli center] have come up with an ingenious way of using the properties of a glow discharge plasma to detect microwave and millimeter waves,” the report said. “The attractiveness of the project lies in the ability of the discharge to withstand nuclear weapons effects.”

This observation gave a me a chill because the earnest defense scientists have yet to find a way for human beings “to withstand nuclear weapons effects.”

It would be good to keep in mind that these extraordinary breakthroughs in technology have one purpose—fighting wars—and are intended to give still greater advantage to advanced nations like the US and Israel that dwarf more primitive adversaries. Many of the new technologies, it is true, will find commercial applications that improve everyday lives (some already have). Yet it is also true that our advances in high-tech killing power have not subdued all the enemies.

They find irregular ways to fight back. They blow the legs off our soldiers. They plant home-made bombs in crowded restaurants. They recruit children to serve as their guided missiles. They capture and slaughter innocent bystanders, while our side merely bombs the villages from high altitude. The victims do not see our way as pristine or preferable. Their suffering becomes their global recruiting.

The highly successful partnership of American and Israeli military science is one more reason it will be most difficult to disentangle from the past and turn the two countries in new directions, either together or separately. But many people are beginning to grasp that lopsided wars—contests between high-tech and primitive forms of destruction—do not necessarily lead to victory or peace. They have led the United States into more wars.