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In addition to the messages Colin notes, see also Felicity's at <http://www.casi.org.uk/discuss/2000/msg01021.html>.
Is it fair to say that questions raised about "Saddam's Bombmaker" concerned liberties with atmospheric detail, not the substance of the book (the nature of Iraq's program, and the enthusiasm with which Saddam pursued it)? In other words, I don't recall seeing a rebuttal that got to the book's core.
Hamza's co-author, Jeff Stein, is a respected journalist who's also written a nice profile of Denis Halliday <http://www.salon.com/news/1999/01/15newsb.html>. I'd be more suspicious of "Saddam's Bombmaker" had I not unexpectedly heard from Stein himself shortly after emailing him a list of concerns. Stein defended his book, pointedly and with obvious pride (though without specifics).
More ad hominem, there was speculation about "resume inflation" on the part of Dr. Hamza (e.g., was he really the head of Iraq's nuclear program, or merely a mid-level player?). An early characterization of Hamza labels him "a physicist known to have worked on electromagnetic enrichment of uranium" <http://cns.miis.edu/research/iraq/iraqnu95.htm>. However, other bios indicate he headed the weaponization program, though his tenure is unclear (and his difficulties in defecting remains suspicious for one supposedly so highly placed).
I've attached two excerpts from an arms watchdog group where Hamza briefly worked. In these reports, Hamza first discredits the alarmist claims of another defector ; in the second, the ISIS report writers themselves appear to distance themselves from Hamza  .
Economic sanctions are not appropriate as an arms control tool, though that is often the claim made by proponents. Hamza himself is cited saying 'sanctions ... can do little to prevent Saddam Hussein from acquiring a nuclear weapon.' 
Borders remain porous, after all (witness the endless war on drugs). The Nagasaki weapon contained less than 8kg of plutonium, an amount that can be hidden in a soup can. Russia and the U.S. have each declared 50 surplus tons of the material.
Golden Valley, MN USA
"Crying Wolf" About the Iraqi Nuclear Weapons Threat
ISIS Article Review
by Kevin O'Neill, Deputy Director
May 14, 1999
"Certifiable nonsense," says an ex-Iraqi nuclear official about a report that appeared in the March 1999 issue of Reader's Digest and (in excerpted form) in the Wall Street Journal. The initial report, entitled "Is the Bomb Within Saddam's Grasp?" by Kenneth Timmerman, claims that Iraq has acquired a pressurized water reactor (PWR) for its nuclear weapons program and is secretly constructing a facility to enrich uranium.
Khidhir Hamza, a former senior Iraqi nuclear official who defected from Iraq in the early 1990s, now works as a Senior Fellow at the Institute for Science and International Security (ISIS). Timmerman interviewed Hamza for the report, quoting him about Saddam Hussein's single-mindedness to acquire nuclear weapons. However, Hamza says that he told Timmerman that the information about an Iraqi PWR was not credible. Hamza also says that he told the same thing to a Reader's Digest editor when the magazine contacted him to verify his quote. The report was published anyway.
Despite Hamza's conclusions, Reader's Digest reported the story of an Iraqi defector, now connected to the Iraqi National Congress (INC), a principal Iraqi opposition group. The INC defector, identified as a nuclear "technician" who worked on Iraq's uranium enrichment programs, told Timmerman that Iraq had acquired a PWR through contracts with China and North Korea.
According to Hamza, the technician is "a dubious source who should not have been taken seriously." Moreover, Hamza says that the INC lacks the technical background to judge defector information about nuclear activities. Nevertheless, the INC is highly motivated to advance its own agenda against the Iraqi government, even if it means cutting corners around the truth. Hamza says that the INC "shopped the defector around" until it found someone who would accept his story.
Iraq's Efforts to Acquire Information about Nuclear Weapons and Nuclear-Related Technologies from the United States
Prepared under DOE purchase order number DE-AP01-99NN50490.000
David Albright and Kevin O'Neill
Institute for Science and International Security
November 12, 1999
The scope of work for the above-referenced project asks the Institute for Science and International Security (ISIS) to provide a detailed, unclassified report of the efforts by the government of Iraq to obtain information about nuclear weapons and fissile materials production technologies, describing what information Iraq currently has of the U.S. nuclear weapons technology, what information the Iraqis are trying to discover, and how the U.S. might better protect U.S. nuclear weapons information. This report was to be solely authored by Khidhir Hamza, a senior Iraqi nuclear scientist who held several high-level positions in Iraq's pre-Gulf War nuclear weapons program, and to reflect his knowledge and views of the issues; the report was never intended to be a comprehensive assessment of these issues.
To fulfill this project, Hamza drafted a report and was interviewed by ISIS staff on three separate occasions. Transcripts of these interview sessions were produced.
We reviewed a draft report submitted by Hamza, and found much relevant information and insights. However, we regret that we found his report to be deficient in several ways. We also found several inconsistencies in the interview transcripts. However, Hamza failed to respond to comments by us on his draft report or to address the transcript inconsistencies. Despite these shortcomings, Hamza's report and the interview transcripts do address many of the questions asked in the project's scope of work.
This memorandum draws out the main observations from Hamza's report and interviews relevant to the project's scope of work. References are made to Hamza's report and the interviews to illustrate these observations.
Iraq close to building nukes - defector
By Janine Zacharia
WASHINGTON (June 21) - Iraq has all the basic components necessary for a nuclear bomb, but it is unclear whether it has acquired the fissile material to power it, the former head of Iraq's nuclear weapons program said yesterday.
Describing Iraq's nuclear weapons program as "more or less complete," Dr. Khidhir Hamza, who defected from Iraq in 1994, told the American Enterprise Institute that no sanctions or inspectors could thwart the well-concealed Iraqi program.
"The basic bomb components are there in Iraq. The casting is there. One of the casting furnaces was taken out but another one was built... The fuse components are there. Explosives are there. And the initiator for the nuclear reaction is there. So bomb-wise, Iraq is finished. It has the full technology to make a nuclear bomb," Hamza said.
Hamza said he understood that Iraq now has a much better bomb design than the one he was involved in producing, "but the bottleneck remains the supply of fissile material."
If Iraq has managed to purchase such nuclear-ready material, he said, "Iraq has a nuclear weapon by now. If it [has] not, it will have within a short time a nuclear weapon. I expect, another year."
Citing German intelligence estimates, Hamza said Iraq is said to have 1.3 tons of low-enriched uranium and 12 tons of natural uranium, which in their processed form would supply enough material for roughly six bombs.
Now, he said, scientists are focused on adapting the bombs to missiles that can transport them. With continued sanctions making smuggling difficult, Hamza speculated that Iraq is also pursuing a program to develop the technology to produce its own fissile material primarily through what is known as "diffusion."
"Iraq has the material right now, has the technology right now, to go into uranium enrichment if it wants," he said.
Israel bombed an Iraqi nuclear reactor in 1981.
Hamza said the Iraqi nuclear program is so well disguised and dispersed - in hospitals, schools, and small buildings in industrial complexes - that even if UN inspectors, absent since 1997, returned, they would never be able to detect it. And since most of the material necessary for the bomb is already inside Iraq, sanctions, he said, can do little to prevent Saddam Hussein from acquiring a nuclear weapon.
"The program is now harder to target, probably impossible to target," he said.