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The Ward Churchill academic misconduct investigation concerned charges of plagiarism, fabrication, and falsification against Churchill at the University of Colorado at Boulder, where Churchill was a professor at the time. On May 16, 2006, the investigative committee released its findings that Churchill had engaged in academic misconduct and had been "disrespectful of Indian oral traditions."

The University's Standing Committee on Research Misconduct voted that Churchill should be dismissed. Chancellor Phil DiStefano then recommended to the University's Board of Regents that Churchill be dismissed. After an investigation of Churchill's past research, Churchill was fired by the University on July 24, 2007 for research misconduct, including plagiarism, fabrication, and falsification.

Subsequent to his firing, Churchill sued the University for damages and reinstatement. According to Churchill's lawyer, "the search for professional misconduct was simply a pretext for a foregone decision to get rid of him." On April 1, 2009, a Colorado jury found that Churchill had been wrongly fired. At the verdict, Churchill's counsel asked Judge Larry J. Naves of Denver District Court to order reinstatement, in light of the verdict. On July 7, 2009, Naves vacated the monetary award and declined Churchill's request to order his reinstatement, deciding the university has "quasi-judicial immunity". On February 18, 2010, Churchill appealed the judges decision.

Background
On September 12, 2001 Ward Churchill published a controversial essay about the September 11, 2001 attacks, entitled "Some People Push Back: On the Justice of Roosting Chickens". In that essay, Churchill argued that American foreign policies provoked the attacks and questioned the innocence of some of the 9/11 victims, characterizing them as part of the infrastructure of an imperialist government, and as "little Eichmanns". National attention was drawn to the essay in January 2005, when Churchill was invited to speak at Hamilton College in New York as a panelist in a debate titled "Limits of Dissent".

Hundreds of relatives of 9/11 victims protested against Churchill's scheduled appearance at Hamilton. Joan Hinde Stewart, Hamilton College president, said that the college was committed to his right of free speech and would not be rescinding the invitation. As publicity about this controversy grew, the Colorado Legislature unanimously passed a resolution labeling Churchill's remarks "evil and inflammatory." Colorado Governor Bill Owens, a Republican, stated Churchill should be fired and asked the university to dismiss him. New York governor George Pataki, also a Republican, called Churchill a "bigoted terrorist supporter." Conservative bloggers such as Little Green Footballs and Free Republic began posting hundreds of comments critical of Churchill, and two days later the national media took note, followed by local media in Colorado and in the Hamilton College area.

The nationwide attention to his 9/11 essay led to a greater examination of other works by Churchill as well as the man himself. On February 3, 2005, the University of Colorado at Boulder Board of Regents ordered a 30-day internal review to determine if Churchill's "conduct, including his speech, provided any grounds for dismissal for cause". During this probe, allegations, both old and new, were raised against Churchill accusing him of academic fraud and plagiarism, and questioning his claims of American Indian heritage. In response, Churchill agreed that plagiarism would qualify as academic misconduct, but publicly challenged anyone to find plagiarism in his work. The media took up the challenge, and a number of allegations of research misconduct were made. Conservative commentators publicized the allegations of bad scholarship by Churchill, including Bill O'Reilly and Ann Coulter; others, such as David Horowitz, continued to criticize Churchill's inflammatory remarks. Emma Perez, chair of the Ethnic Studies Department at the University of Colorado, wrote that the effort to fire Churchill was part of "the neocon battle for dominance in academe" through "forcing and then manipulating this 'investigation' of Ward's scholarship."

On March 24, 2005, University Interim Chancellor Philip DiStephano held a press conference to announce the results of the seven-week preliminary review of professor Churchill. "While there are limits to the protections afforded by the Constitution, our review has determined that those limits have not been exceeded in professor Churchill's case," Mr. DiStefano said, noting that the review panel found that Mr. Churchill committed no violation in describing some victims of the terrorist attacks as "little Eichmanns." The same panel, however, referred for further investigation the allegations of plagiarism and Indian heritage misrepresentation. DiStefano submitted a list of research misconduct allegations to the Research Misconduct Committee, and a six person inquiry subcommittee was appointed to conduct a preliminary evaluation. The committee declined to address the issue of Churchill's ethnic heritage. On August 19, 2005, the inquiry committee reported that it found seven of the allegations merited further investigation.

Smallpox blanket genocide
In at least six different essays, Churchill alleged that the United States Army deliberately distributed smallpox-infected blankets to the Mandan Indians at Fort Clark in 1837 to spark a smallpox "pandemic" and that hundreds of thousands of Indians died of smallpox as a consequence. Other scholars who have studied this episode agree that smallpox killed many Indians in this time frame, but deny that there is any evidence to support Churchill's allegations of deliberate genocide by means of smallpox blankets. They also charge Churchill with exaggerating the death toll and with falsifying the sources he cites in support of his claims. Professor Thomas Brown wrote in the journal Plagiary that, "Every aspect of Churchill's tale is fabricated.

In November 2004, Guenter Lewy, a professor emeritus of political science at the University of Massachusetts Amherst, published an essay about American Indians and Genocide. Lewy says of Churchill's assertion that the U.S. Army intentionally spread smallpox among American Indians by distributing infected blankets, "we know of but a single instance of such warfare, and the documentary evidence is inconclusive." Lewy calls Churchill's estimate of 100,000 deaths during the 1836-1840 smallpox epidemic "obviously absurd", but notes that two scholars support Churchill's claim.

In an article in the journal Plagiary, entitled "Did the US Army Distribute Smallpox Blankets to Indians? Fabrication and Falsification in Ward Churchill's Genocide Rhetoric", Lamar University sociology professor Thomas Brown accused Churchill of fabricating the incident and falsifying his sources. Brown argues that Churchill's claim that his cited source—Russell Thornton—supports Churchill's smallpox blanket allegations is a falsification of Thornton. Brown also charges Churchill with fabricating the presence of US Army personnel on the scene, with fabricating the distribution of blankets taken from a military infirmary in St. Louis, and with concealing evidence in his possession that disconfirms his allegations. Three of the authors that Churchill cites in support of his smallpox thesis, Evan Connell, RG Robertson and Russell Thornton, have rejected Churchill's interpretation of their work. Thornton characterized Churchill's smallpox thesis as "fabrication."

In an interview in 2005, Churchill stated that he had obtained documentary evidence confirming his description of events at Fort Clark.

The May 2006 report by the Investigative Committee of the Standing Committee on Research Misconduct at the University of Colorado corroborated Churchill's critics. The committee concluded that for over a period of 10 years, Churchill consistently falsified his sources and fabricated claims regarding the Fort Clark epidemic. The committee criticized Churchill for failing to recognize and correct his errors, and for his insistence that he intends to republish his indictment of genocide in the future without substantive changes. The committee also criticized Churchill for answering his critics with ad hominem attacks instead of reason and evidence.

Additionally, the committee found Churchill guilty of serious research misconduct in his claims that John Smith initiated a smallpox epidemic against Wampanoag Indians when he visited New England in 1614. The committee found that the source Churchill cited for his claim (Manitou and Providence: Europeans, Indians, and the Making of New England, 1500–1643 by Neal Salisbury) actually gave evidence contrary to his claim, namely that Smith viewed the Indians as a potential source of labor to be exploited militarily (rather than exterminated) and that the epidemic did not break out until at least eighteen months after Smith had left the area. Based on these and other inconsistencies, the committee determined that Churchill had fabricated this event and cited sources in a misleading way.

General Allotment Act
In two articles published in the 1990s, University of New Mexico law professor John P. LaVelle, an enrolled member of the Santee Sioux Tribe of Nebraska, alleged that Churchill has repeatedly published false claims about the General Allotment Act, mistakenly attributing a "blood quantum" standard of Indianness to the Allotment Act.

Churchill in his defense acknowledges that the term "blood quantum" is not used in the General Allotment Act, but maintains that the term is an accurate summary of the what he describes as the eugenics component of the Act. According to Churchill, "[Under] blood-quantum standard… through intermarriage, future generations of Indians would be of progressively less native blood, until they couldn't meet the legal standard and tribes would disappear altogether."

The Investigative Committee of the Standing Committee on Research Misconduct at the University of Colorado, released in May 2006, agreed with LaVelle that the blood quantum requirement is not present in the Dawes Act, and that Churchill had repeatedly misrepresented the requirement as falling within the Act itself. The Committee also observed that most tribes did choose to impose blood quantum standards for tribal membership during the historical era of the General Allotment Act, and that Churchill's larger argument thus had some validity, even though he misrepresented the contents of the Act.

LaVelle agrees with Churchill that the Act represents "a contemptible effort by Congress … to strip Indian tribes of all collectively held lands, force Indian people to assimilate into white society, and generally undermine the tribes' territorial sovereignty." However, LaVelle argues that Churchill has falsified the Act in order to support his eugenics charges. LaVelle notes that the Code of Federal Regulations gave tribes free rein to define their membership in any way they choose for the purposes of allotment, and that the tribes themselves have chosen to set blood quantum standards for membership. LaVelle argues that Churchill's attack on the tribes' standards constitutes an attack on tribal sovereignty. LaVelle complains that Churchill disguises his attack on tribal blood quantum standards by falsely attributing the source of those standards to the Allotment Act.

According to LaVelle, Churchill has not responded directly to LaVelle's specific charges to explain in detail how the Act introduced a blood quantum. LaVelle went through Churchill's works essay by essay, and says that Churchill had not cited evidence for his claim that the Allotment Act imposed a blood-quantum standard: This lack of a supporting citation is explained by the fact that ... the (Dawes Act) never contained any such federally imposed eligibility 'code' at all.  LaVelle states that part of his initial concern was that Churchill's claims about the Dawes Act—which LaVelle characterizes as a "hoax"—were "seeping" into the scholarly literature.

Churchill responded to LaVelle's critique by comparing the number of times his articles have been cited to the number of times LaVelle has been cited: ''In academia, you measure the influence of your publications via what's called the "Citation Index," that is, a literal count of the number of times your material is cited by others. Neither of LaVelle's essays on the Allotment Act, the first of which came out in the American Indian Quarterly almost a decade ago, has ever been cited by an Indian legal scholar.'' Churchill acknowledges elsewhere that LaVelle's work on the Allotment Act has been cited by two scholars; but uses a phrase from Robert Porter, in describing LaVelle's legal interpretation as being designed to "put a happy face on colonialism." Churchill claims of his own citation that he was "as of mid-2001, the most cited ethnic studies scholar in the country". The Investigative Committee concluded that Churchill had fabricated his claim that the GAA contains a blood quantum, and had falsified his evidence in support of that claim. Specifically, the committee stated that Churchill used as "independent" evidence for his claims two essays that Churchill later described as having been ghostwritten by himself "from the ground up." (See Annette Jaimes and Rebecca Robbins, below) The committee also criticized Churchill for answering his critics with ad hominem instead of reason and evidence.

Findings of plagiarism
The University of Colorado's Research Misconduct Committee concluded that Ward Churchill plagiarized the writing of three different authors.

Annette Jaimes and Rebecca Robbins
John LaVelle was the first to publicly note that several of Churchill's essays share similarities with an earlier essay by Annette Jaimes, Churchill's ex-wife. Additional plagiarism allegations stem from portions of an essay Churchill published in 1993 that closely resemble a 1992 essay published by Rebecca L. Robbins. However, "LaVelle did not accuse Churchill of [plagiarizing the Jaimes passages], one of the most serious offenses in academia. On the contrary, LaVelle speculated that Churchill might have been the author of all the works. The ideology, rhetoric and writing style" of the Jaimes piece are 'interchangeable' with positions that Churchill takes in his books, LaVelle wrote".

Churchill also asserts that he himself is the original author of the material in question, and thus has not plagiarized either Jaimes or Robbins: "I'm free to make disposition of my ideas and my material any way I see fit… That's my understanding of the situation… If there's an issue around that, then there's an issue around that." Churchill says that he ghostwrote the material to help Jaimes' career: "All you need to do is take a piece of Annette Jaimes' material, which is published—and she's published things that I didn't (write) – take her stuff, stack it up next (to mine), set it side by side, and read the two… You tell me who's writing this. We don't need to get into forensics to do it."

Jaimes denies that Churchill wrote the material in dispute, and calls him "a liar." Jaimes complains that Churchill is jeopardizing her career to defend himself from the plagiarism allegations, and said "He's despicable." Robbins has refused to comment publicly on the matter, but Jaimes says that she saw an early draft of Robbins' essay, and that the matter in question is original to Robbins.

Because both Robbins and Jaimes refused to testify for the committee, it took Churchill's word that he was the original author of the essays published under Robbins and Jaimes's names. However, the committee still found Churchill guilty of "serious research misconduct" with regards to the Robbins and Jaimes essays, for failing to follow accepted practices of attributing authorship, and for citing in works published under his own name to these essays that he had ghostwritten, as if they were independent sources.

The Water Plot
University of Colorado's Research Misconduct Committee also investigated allegations that Churchill plagiarized a pamphlet entitled "The Water Plot"—originally published by Dam the Dams, a Canadian activist group in 1972—and republished it under his own name several times.

Churchill first re-published the "Water Plot" essay in 1989, when he credited the piece both to the original authors as well as to the "Institute for Natural Progress." In three subsequent publications, twice in 1993 and once in 2002, Churchill took sole credit for substantially the same essay. Churchill says that he did not plagiarize the essay in 1993, but rather that the editors of Z Magazine incorrectly excised Dam the Dams from the byline. Churchill also says he did not plagiarize in 2002, because he added additional material of his own to the essay, and because he cited Dam the Dams as one of his sources in the footnotes.

The University of Colorado's investigative committee determined that Churchill repeatedly plagiarized the Water Plot pamphlet, and that Churchill's "misconduct was not accidental, but deliberate."

Fay Cohen
The University of Colorado's investigative committee determined that Churchill had plagiarized the work of Professor Fay G. Cohen of Dalhousie University, Nova Scotia, and republished it in a book edited by his wife Annette Jaimes. The previous year, Churchill had edited his own book of collected essays, which had included Cohen’s chapter on fishing rights. Churchill then solicited Cohen’s essay for republication in his wife’s book. Cohen refused to grant Churchill and Jaimes permission to republish the essay.

In Jaimes’ book, the essay in question is attributed to the "Institute for Natural Progress," the same pseudonym under which Churchill had previously published the disputed "Water Plot" essay. In the back matter, Jaimes writes that Churchill "assumed the lead role in preparing" the essay; he characterized his role as similar to a newspaper’s "rewrite man," who takes materials gathered by others and works them into a final version for publication.

After the Jaimes book was published, Cohen asked lawyers at her university to assess her rights in the matter. An internal Dalhousie University report concluded that "[t]he article … is, in the opinion of our legal counsel, plagiarism," Dalhousie spokesman Charles Crosby said, summarizing the report's findings in an interview with the Rocky Mountain News.

Churchill says that he has not committed plagiarism because he never said he wrote the essay. The CU investigative committee found Churchill's defense "implausible," observing that Churchill did claim authorship of the essay in his official Faculty Report of Professional Activity for the year 1991, followed by the parenthetical notation "for the Institute for Natural Progress." The committee concluded that Churchill's involvement in plagiarizing Cohen's essay constitutes an act of research misconduct.

Result of Investigation
At least nine misconduct charges against Churchill have been submitted to the University of Colorado's Standing Committee on Research Misconduct. The Investigation Subcommittee determined seven of the submitted allegations were worth investigating. The Committee has defined its jurisdiction narrowly in Churchill's case, limited to the three dimensions of research misconduct that are specified in the University of Colorado at Boulder’s Administrative Policy Statement on Misconduct in Research and Authorship. The Standing Committee has declined to pursue charges of copyright violation that do not meet the legal definition of "plagiarism". The Committee's investigative subcommittee completed its investigation into the seven charges of plagiarism, fabrication, and falsification, brought by Professors Brown, LaVelle, Cohen, Kevin Vaughan of the Rocky Mountain News, as well as Churchill's alleged plagiarism of the "Water Plot" pamphlet and the Fay Cohen essay.

A May 9, 2006, final report by the University of Colorado's Standing Committee on Research Misconduct stated that Churchill had falsified and fabricated information, and plagiarized two different essays.

The University released its investigative committee findings on May 16, 2006. The committee agreed unanimously that Churchill had engaged in "serious research misconduct," including four counts of falsifying information, two counts of fabricating information, two counts of plagiarizing the works of others, improperly reporting the results of studies, and failing to “comply with established standards regarding author names on publications.” The committee was split with regard to what sanctions to recommend: two recommending against dismissal because the misconduct was not serious enough; two recommending temporary suspension and one recommending dismissal.

Following the sub-committee report's release, Churchill called the report "self-contradictory" and "patently false".

The Standing Committee on Research Misconduct also disagreed on what sanctions should be imposed on Churchill. On June 13, 2006, they voted six to three in favor of recommending dismissal. Additional charges of misconduct were tabled pending the outcome of an additional investigation initiated as the first investigation concluded. Churchill was fired in July, 2007, thus mooting any investigation of the additional charges.

In defense of the investigation, University of Colorado President Hank Brown, a former Republican senator, stated that the firing of Churchill was necessary to protect the integrity of the university's research. Brown also stated that Churchill "did not express regret, did not apologize, did not indicate a willingness to refrain from this type of falsification in the future."

Lawsuit by Churchill
Following his dismissal, Churchill immediately filed a lawsuit against the university claiming that he had been fired for exercising his right to free speech. His lawsuit, filed in Denver District Court, charged that after the essay came to light, “the university vowed to examine every word ever written or spoken by Professor Churchill in an effort to find some excuse for terminating his employment.” The lawsuit sought unspecified damages and reinstatement. University spokesman Ken McConnellogue said the school stands by the decision to fire Churchill. In an interview with the Rocky Mountain News, Churchill's lawyer David Lane stated that Churchill's primary motive for the lawsuit is reinstatement as opposed to a cash settlement. Patrick O'Rourke, serving as university counsel, stated that "A jury of faculty members found research misconduct. We don't believe he is a scholar that should be re-employed, and we believe the jury will conclude the same."

In April 2009, a Denver jury awarded Churchill $1 in damages, finding that the college wrongfully fired him. As one of the jurors said later in a press interview, "it wasn't a slap in his face or anything like that when we didn't give him any money. It's just that David Lane kept saying this wasn't about the money, and in the end, we took his word for that." At the verdict, Churchill's counsel asked Chief Judge Larry J. Naves of Denver District Court to order reinstatement in light of the verdict.

On July 7, 2009, Judge Naves found that the defendants were entitled to quasi-judicial immunity as a matter of law, vacated the jury award of $1 and determined that the University does not owe Churchill any financial compensation. Naves also denied Churchill's request to order reinstatement at CU. In February, 2010, Churchill appealed the judge's decision.

The Colorado Court of Appeals upheld Judge Naves' decision that the CU Board of Regents had "quasi-judicial immunity." Churchill attorney David Lane is quoted as saying that he will seek to have the decision reviewed by the Colorado Supreme Court, and predicted that the matter will eventually be decided by the United States Supreme Court. In February 2011, Churchill filed a petition for writ of certiorari to the Colorado Supreme Court.

On September 11, 2012, Churchill lost his appeal to the Colorado Supreme Court against previous rulings that the university does not have to rehire him. His lawyer filed a petition for a writ of certiorari to the Supreme Court of the United States on December 10, 2012 with a response due on January 11, 2013. The petition was denied in April, 2013.

Reactions to the University of Colorado Investigation
Emma Perez, the chair of the Ethnic Studies Department at the University of Colorado, stated that Churchill is innocent of the misconduct charges, and that the CU investigation was politically motivated by outrage against his 9/11 essay. A second category of observers either take no position on the issue of Churchill's alleged misconduct, or state that while Churchill is probably guilty of research misconduct, the circumstances surrounding CU’s investigation warrant leniency regarding sanctions against Churchill. Thomas Brown, a longtime Churchill critic, argues that while the investigation may have been politicized, Churchill’s alleged plagiarism is the central issue, and that sanctions are warranted.

A statement issued by the Foundation for Individual Rights in Education agreed that while Churchill's freedom of speech was protected, freedom of expression did not excuse any academic misconduct and that Churchill's free speech protections should not insulate him from allegations of academic misconduct. Similarly, Eugene Volokh, writing in the Huffington Post, agreed with the University's assessment that, "public figures who choose to speak out on controversial matters of public concern naturally attract more controversy and attention to their background and work than scholars quietly writing about more esoteric matters that are not the subject of political debate." Volokh concluded, "That seems to me to be exactly what happened here. Unfortunately for Ward Churchill, it turns out that his scholarship couldn't bear the attention that his statements prompted." Others who have criticized Churchill with reference to the University of Colorado investigations include Alan Dershowitz, Jessica Corry and Peter Worthington

The American Civil Liberties Union expressed support for Churchill, stating that the "poisoned atmosphere in which this investigation was launched ... irretrievably tainted the process." Similarly, at least 50 scholars and organizations including Hamid Dabashi, Richard Falk and Howard Zinn also wrote in support of Churchill citing academic freedom and freedom of expression issues.

The Colorado Conference of the American Association of University Professors issued a report on November 11, 2011, stating that "Because of the University of Colorado's indifference to the ideals of academic freedom ... the Colorado Conference of the American Association of University Professors (AAUP) recommends that any faculty seeking employment accept a position at the University of Colorado only as a last resort." In response, a University of Colorado campus spokesperson said that the cases had no bearing on the issue of academic freedom, and were certainly not related to each other.