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Part XVII: The Nature-Science Case (3195 查看)

March 10, 2013 06:41PM
【Note: The PDF file is more reader-friendly. Click the title to open it.】


Shamelessness Shouldn’t Be Anyone’s Nature
──An Open Letter to Nature (Part XVII) & to Science (Part II)


Xin Ge, Ph. D.

Columbia, SC, USA



【Summary】On Sept. 6, 2001, Fang published an article in Southern Weekend. About two thirds of the article was plagiarized from three articles published on the websites of Nature and Science.


【Content】

Fang’s Plagiarism History: The Nature-Science Case

The Story
Self-admission
Low Level Plagiarism
A Complete Comparison between Fang’s article and the articles he plagiarized
Notes


Fang’s Plagiarism History: The Nature-Science Case

As mentioned before, Fang published 4 articles in Southern Weekend from August 30, 2001, to the end of the year, and all of them were plagiarized from western media. The Science case I introduced in the previous part was the first case discovered, but not the first plagiarism Fang committed. In this part, I’ll introduce a case Fang committed simultaneously against Nature and Science.


Major characters: the 3 victims and the thief
From left: Dr. Philip Ball, whose “A new hope for travelling salemen” was published on Nature’s website on July 8, 1999; an anonymous author, whose “New path lays DNA puzzles bare” was published on Nature’s website on August 14, 2001; Ben Shouse, whose “With Genomes, Less Can Be More” was published on Science’s website on August 15, 2001; and Fang Zhouzi, who plagiarized the above three authors on September 6, 2001.


The Story

At the turn of the centuries, genomics was arguably one of the hottest terms in both science literature and high-tech industries. Apparently trying to take advantage of the situation, Fang, who had no training whatsoever in either genomics or bioinformatics, suddenly became a “universally acclaimed” (有口皆碑的) bioinformatician and a consulting scientist working for a mysterious U. S. Bio-info or bioinformatics company[1]. Correspondingly, Fang published several articles about the human genome project, at first to laud it, then to derogate it. His attitudinal change had nothing to do with science, instead, it had everything to do with his personal relationship with Dr. Yang Huanming, the leader of China’s human genome project[2].

On September 6, 2001, Fang published an article in Southern Weekend, entitled “Place Chinese Postmen in the Genome.”[3] The article contains 6 paragraphs, 33 sentences, and 1,553 Chinese characters (excluding punctuation marks). In the first half of the article, Fang introduced the two approaches of genome sequencing, i. e. Human Genome Project’s hierarchical shotgun sequencing and Celera’s whole genome shotgun sequencing. Then, Fang began to talk about the difficulty of assembling the sequencing data into genomic sequence. After that, Fang introduced a genome assembly program EULER, which was based on solving an Eulerian, instead of a Hamiltonian, path problem.

According to Fang, EULER was developed in “the lab of Pavel Pevzner, of the University of California, San Diego.” Fang was apparently referring to the paper entitled An Eulerian path approach to DNA fragment assembly, published on August 14, 2001, in PNAS (98:9748-9753). However, among the 3 authors listed in the paper, two, including the corresponding author and the contributing academician, Dr. Michael S. Waterman, were from University of Southern California. Then, how could Fang attribute the intellectual property to “the lab of Pavel Pevzner” at UCSD? Obviously, Fang even didn’t read the paper when he wrote his article, and what he wrote was copied from someone else’s article(s).

Indeed, about two third of Fang’s article was plagiarized from three articles, two published on Nature’s website, one on Science’s website. Specifically, Fang’s plagiarism distributed in 5 paragraphs (83%), and 19 sentences (58%) and 1,019 characters (66%) of Fang’s article were derived from direct translation. More specifically, Fang wrote 2 sentences, 179 characters by translating Ben Shouse’s With Genomes, Less Can Be More (ScienceNow, 15 August 2001); 2 sentences, 91 characters by translating Philip Ball’s A new hope for travelling salemen (Nature News, 8 July 1999); 14 sentences, 648 characters by translating an anonymous author’s New path lays DNA puzzles bare (Nature News, 14 August 2001), and 1 sentence, 101 characters by translating the two Nature articles (see figure below).


Fang’s plagiarism in his Place a Chinese Postman in the Genome
Among Fang’s 1,553 Chinese characters, 1,019 characters (colored) were derived from direct translation of three articles published on the websites of Nature and Science, without attribution. The colors of the plagiarized text correspond to the colors of the three articles being plagiarized, listed at the bottom. The characters in red are those plagiarized from the two Nature News articles. (The punctuation marks and blank spaces in Fang’s article were removed to generate the continuous 1,553-characters text.)


Self-admission

Unlike in the Science case in which Fang denied any wrongdoing at least six times, somehow Fang admitted his plagiarism in this Nature-Science case, although subconsciously. In “New path lays DNA puzzles bare,” there were the following two sentences:

“Chief among these is that large genomes such as ours are very repetitive, like a jigsaw with many identically shaped pieces. Sequencing errors compound the problem - you don't know whether you're looking at different stretches of DNA or not.”

Fang’s translation was:

“In addition, because of sequencing errors, a sequence could have different sequencing results─namely, sequences with slightly different sequencing results might not belong to repetitive sequences; instead they are the same sequence─, which compounds the problem.” (Sentence #18, see the comparison table below.)

When I discovered the case back in November, 2010, I thought Fang either didn’t understand the original article, or he thought that all repetitive sequences were imperfect repeats, so I wrote a few words to laugh at his stupidity[4]. Fang never responded to my article directly, just like he is not responding to my open letter to Nature─every part of the letter has been sent to him directly─, but one of his follower did. That guy calls himself james_hussein_bond, and he was the one who fired the first shot in Fang’s Across the Pacific Campaign against Dr. Xiao Chuanguo in October, 2009, by spreading rumors about Xiao’s procedure in a spina bifida patient website based in the U. S.[5]. james_hussein_bond knew almost nothing about genomics, but he was stupid enough to “stand up” for his “great leader,” tried his best to demonstrate that the person who misunderstood the Nature article was not Fang, but Yi Ming[6]. By doing that, this follower admitted that Fang translated the Nature article, but he denied that Fang translated the article wrong. The funny thing was that Fang published that article on the New Threads the next day, and then on his blog a few days later[7]. Apparently, Fang would rather admit his plagiarism than admit his ignorance. The psychology behind the weird behavior is in fact quite simple: Fang steals because of his ignorance (plus laziness), by admitting his stealing, Fang was hoping he could hide his ignorance, because subconsciously, Fang believes stealing is a lesser crime, while ignorance would disqualify him from science writing completely.

However, Fang’s article was saturated with ignorance. For example, anyone with some basic knowledge in graph theory should know that the so called “Chinese postman problem” has nothing to do with “Chinese postmen,” rather, it is a mathematical problem about route inspection, or postman tour, which was first studied by a Chinese mathematician[8]. So, why did Fang want to “place Chinese postmen in the genome,” and for what?

Also, Fang translated the phrase “the Medical Research Council's Human Genetics Unit in Edinburgh” in Ben Shouse’s article into “Edinburgh’s British Medical Research Council's Human Genetics Unit” (sentence #10 in the table below), obviously not knowing MRC is a national research institution in UK. For the same reason, Fang translated “UK Medical Research Council's Laboratory of Molecular Biology in Cambridge” in “New path lays DNA puzzles bare” into “the molecular biology laboratory at the University of Cambridge” (sentence #33).

Low Level Plagiarism

In the previous part of the letter, I deliberately avoided discussing Fang’s low level plagiarism, because his “advance plagiarism” was more prominent in that case. However, in this case, it was low level plagiarism which was more prominent. Why? Because Fang knew little about genomics, none about graph theory, therefore he was unable to “advance” the originals. Let’s take a look at a few examples.

Fang’s 10th and 11th sentences were as following:

“At the Genome Informatics Conference held on Aug. 9, Edinburgh’s British Medical Research Council’s Human Genetics Unit revealed their independent test of the two sequences, the results were surprising. A research team at the University of Edinburgh independently sequenced a 6.9-megabase region of human chromosome 4, and then used it as the standard to compare the sequences published by Human Genome Project and Celera. The results showed that although Celera left more gaps, they made half as many ‘misassemblies’ as Human Genome Project, about 2.08 misassemblies per megabase.”

They were translated directly from Ben Shouse’s article, With Genomes, Less Can Be More:

“At the Genome Informatics Conference here on 9 August,...the Medical Research Council's Human Genetics Unit in Edinburgh, described an analysis of a 6.9-megabase stretch of chromosome 4....The region...had been sequenced independently ...at the University of Edinburgh....

“... compared the sequences published by Celera Genomics and the publicly funded Human Genome Project (HGP), using the ... data as a yardstick. Contrary to speculation, Celera's approach ...yielded better data than the ...approach used by HGP. ...Celera made half as many ‘misassemblies’...as the public effort did, logging 2.08 misassemblies per megabase.”

The fact is, besides being published online, Mr. Shouse’s article was also published in Science magazine[9]. On Sept. 28, 2001, Science published a letter from the Edinburgh group “to set the record straight”: they claimed that they didn’t sequence the “6.9-megabase stretch,” and the stretch was not even 6.9-megabase, but 5.8-megabase. Also, the group refuted Mr. Shouse’s statement that Celera’s result was better than that of HGP’s, since the former had used latter’s data for their assembly[10]. In other words, both the wording and the mistakes were the signature of Mr. Ben Shouse’s article, and Fang duplicated both.

Also, in sentences #25-26, Fang wrote:

“Recently, the lab of Pavel Pevzner at the University of California, San Diego, announced in PNAS that they had found a new way to assemble the genome. They cut the DNA fragments one more time, cut them into smaller fragments of equal size. In this way, they transformed the hamiltonian path of genomic sequences into a ‘eulerian path’.”

They were the direct translation of the following sentences in New path lays DNA puzzles bare:

“By breaking the chunks of DNA into smaller fragments of equal size, Pavel Pevzner, of the University of California, San Diego, and his colleagues have transformed the hamiltonian path of genome sequencing into a 'eulerian path'.”

As mentioned above, by translating “Pavel Pevzner……and his colleagues” into “the lab of Pavel Pevzner,” Fang showed unequivocally that he didn’t read Dr. Pevzner’s PNAS paper. Similarly, by translating “breaking the chunks of DNA into smaller fragments of equal size” into “cut the DNA fragments one more time into smaller fragments of equal size,” Fang showed that he didn’t understand what he was talking about. Apparently, the Nature article was saying it figuratively, and in practice, it was done mathematically. And Fang thought that the DNA was “cut” into “equal size” physically and experimentally, because he used the term “cut” (切割) twice, which was the same verb he used in sentences #3, #6, #8, #15, and #16, meaning physically cutting the DNA molecules. Also, Fang used the term “lab” (实验室) without any basis, indicating he thought the DNA was experimentally cut in a laboratory. Is anyone aware of a technique which could “cut DNA fragments into smaller fragments of equal size”?

In summary, Fang’s knowledge in this case was merely enough for low level plagiarism, insufficient for “advanced plagiarism,” and absolutely inadequate for independent science writing. In other words, without plagiarizing, Fang could not write Place Chinese Postmen in the Genome based on his understanding of an original research paper.








Notes

[1] On June 15, 2001, Science Times published a report, Facing China’s Academic Corruption: Spreading Salt on the Ulcer, in which it says: “Especially in the area of biology, which is Fang Zhouzi’s specialty, and Fang is still engaging in consulting work in biological information in the United States, therefore he is universally acclaimed in this area.” (Original Chinese: “尤其是在生物学领域,这是方舟子本人的专业,而且至今他在美国从事的也是生物学信息咨询工作,因此在这方面是有口皆碑的。”) Fang re-published the report on his New Threads on June 20, 2001. ( See: 于彤:《直面中国学术腐败:在溃疡处撒“盐”》,2001年6月15日《科学时报•读书周刊》). Many people believed that so called “work in biological information” meant bioinformatics. For Fang’s relationship with that bio-info or bioinformatics company, see Part VI of this letter.

[2] There are many evidences showing that Fang’s relation with Dr. Yang deteriorated suddenly in the mid of 2000, and Fang’s attitude toward human genome project changed coincidently with that relation deterioration. For detail, see: Yi Ming. The Feud between Drs. Fang Zhouzi and Xiao Chuanguo. pp.200-202. (亦明:《方舟子陷害肖传国始末》200-202页).

[3] Fang Zhouzi. Place Chinese Postmen in the Genome. Southern Weekend, September 6, 2001. (方舟子:《在基因组上安置中国邮差》, 2001年9月6日《南方周末》).

[4] My original Chinese: “可笑的是,这位‘有口皆碑’的‘生物信息学家’,在抄人家的科普文章时,都会抄错。比如,在上面引用的第一段文字中,方舟子写道:‘而且,由于测序错误的存在,对同一段序列可能会有不同的测序结果——换言之,略有差异的测序结果可能不是属于重复序列而是同一序列,这就使得问题变得更加复杂。’假如你对这段话的意思摸不着头脑,千万不要怪罪自己太笨,或者知识不足。即使是对基因组学略有研究的亦明兄(在笔者的《高级植物分子生物学》中,专门有基因组学一章)对此也是一头雾水。实际上,《自然》的文章是说,当你拿到两段相同的DNA序列之时,你搞不明白他们到底是同一个东西,还是来自位于基因组不同区域的重复序列。而因为测序本身不是百分之百的准确,会使略有不同的序列相同,或使完全相同的序列略有不同,因此这样的麻烦更为棘手。也就是说,方舟子这个‘文抄公’连‘二道贩子’都算不上,因此只能说是一个‘头道骗子’。” See: Yi Ming. Fang Zhouzi Plagiarized Journal Nature in 2001. [www.rainbowplan.org], Nov. 15, 2010. (亦明:《方舟子九年前曾抄袭〈自然〉杂志》, 2010年11月15日虹桥科技论坛).

[5] For Detail, see: Yi Ming. The Feud between Drs. Fang Zhouzi and Xiao Chuanguo. pp.292-293. (亦明:《方舟子陷害肖传国始末》292-293页).

[6] james_hussein_bond’s ignorance in genomics was indicated in his first draft of his article, “Whether It Is Fang Zhouzi’s Fault if Fang Expert Yi Ming Does Not Understand a Popular Science Article?” posted hours after my article was posted. He revised the first versin after someone pointed out the mistakes in it. The links to the two versions are: [www.xys.org], and [www.xys.org].

[7] See: james_hussein_bond.《“方学家”亦明读不懂科普文章是否该算作方舟子的错?》, XYS20101116; james_hussein_bond.《“方学家”亦明读不懂科普文章是否该算作方舟子的错?》, Fang’s blog on sina.com, Nov. 21, 2010.

[8] See: [en.wikipedia.org].

[9] Shouse, B. 2001. Less can be more, U.K. study finds. Science 293:1238-9.

[10] Semple CA. et al. 2001. Comparing human genome mapping data. Science 293:2394-5.



被编辑2次。最后被亦明编辑于08/05/2013 07:19AM。
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