Plagiarism at a glance

I reported yesterday on a thesis, Studies of Active Information in Search, I retrieved from the BEARdocs archive at Baylor. If the document is authentic, then Distinguished Professor of Engineering Robert J. Marks II, a.k.a. the "Charles Darwin" of intelligent design, approved extensive plagiarism of publications he coauthored with William A. Dembski.

Here are images, purposefully low in resolution, of pages 1-7 of the 8-page introduction. Passages plagiarizing papers by Dembski and Marks are highlighted in color. Those copied from papers by the thesis author (with Dembski and Marks as coauthors) are "lowlighted" in gray. The gray areas are hard to see, and some of you have suggested that they should be white. But I emphasize that the bibliography does not include the papers, and that Dembski's name is omitted from the copyright release forms in the appendix. I call shenanigans.

There are also comment boxes in my annotation of the document. They indicate the sources of the copied passages, and I include that content here to cover myself legally. Most of you will want simply to glance at the images, and gauge the scale of the plagiarism.

YELLOW: I give a reference list below.
PURPLE: Begin at first sentence of [1].
YELLOW: Begin at paragraph 2 of [1]. A period has been changed to a colon, and "no free lunch theorem" has been capitalized.

GRAY: First sentence of [4].
RED: Begin at third complete paragraph of second page of [1].

GRAY: Points (a-c) here come from the third sentence of [3].
GREEN: Begin about midway in the second column of [1], with "can" changed to "often" in the last sentence.

BLUE: Begins with the third sentence on the second page of [1].
PURPLE: Skip 3 sentences, arriving about midway in the first column of second page of [1].
GRAY: First 3 paragraphs of [4], with one awkward sentence rewritten. This gray passage runs to the end of the thesis section.

PURPLE: Opening of Sect. II-A of [2], with a period changed to colon, and with a reference deleted. Note that the copied period in the equation should have been changed to a comma.

YELLOW: The fourth sentence in column 2 of [2], with one reference removed. Note that the period at the end of the equation is copied, and that the "bits" should have been inserted ahead of the period.
RED: Skip two sentences following Equation (3) [(1.3) here] in [2].
GREEN: Begin with second sentence, third paragraph of Sect. II of [2]. The colon prior to the equation is changed to period here.
BLUE: Begin with third sentence following Equation (2) in Section II-A of [2], eliminating initial clause, and changing "for" to "of."
PURPLE: Begin with last paragraph of first column of page 2 [2].
YELLOW: Begin with the second sentence of footnote 3 of [2].

RED: Begin with second sentence, column 2, second page of [2]. Note that exogenous information is given above (1.2), so the copy here of the definition in [2] is redundant.
GREEN: Begin with last sentence of first full paragraph in column 2 of page 2 of [2], and move footnote 4 into the body.
BLUE: [blue highlighting, yellow box by mistake] Second full paragraph in second column, second page of [2]. Here "dB" is changed to "decibels," and "instead" is changed to "rather."

Conclusion

It seems to me that 4+ pages are highlighted. In other words, at least half of the introduction is copied from papers by Dembski and Marks. If Marks in fact approved this, then he has suffered a serious lapse in ethics.

References

[1] William A. Dembski and Robert J. Marks II "Conservation of Information in Search: Measuring the Cost of Success" IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, vol.5, #5, September 2009, pp.1051-1061, http://evoinfo.org/publications/cost-of-success-in-search/

[2] William A. Dembski and Robert J. Marks II, "Bernoulli's Principle of Insufficient Reason and Conservation of Information in Computer Search," Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA - October 2009, pp. 2647-2652, http://evoinfo.org/publications/bernoullis-principle-of-insufficient-reason/

[3] [Student], William A. Dembski and Robert J. Marks II, "Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism," Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA - October 2009, pp. 3047-3053, http://evoinfo.org/publications/evolutionary-synthesis-of-nand-logic-avida/

[4] [Student], George Montañez, William A. Dembski, Robert J. Marks II, "Efficient Per Query Information Extraction from a Hamming Oracle," Proceedings of the 42nd Meeting of the Southeastern Symposium on System Theory, IEEE, University of Texas at Tyler, March 7-9, 2010, pp.290-297, http://evoinfo.org/publications/efficient-per-query-information-extraction-from-a-hamming-oracle/

“Charles Darwin” of intelligent design condones plagiarism at Baylor?

Last year, “intelligent design” creationist William A. Dembski, Research Professor of Philosophy at Southwestern Baptist Theological Seminary, said of one of his coauthors at Baylor University, “[Student] — With pro-ID graduate students like this, Darwinian profs don't stand a chance.” Well, [the student] evidently went on to defend a master’s thesis, Studies of Active Information in Search, in the Fall semester of 2010. I downloaded it from Baylor’s document archive, and had only to read to the bottom of the first page to discover plagiarism.*

Almost half of the first chapter is copied, without citation or sign of quotation, from

• William A. Dembski and Robert J. Marks II, Conservation of Information in Search: Measuring the Cost of Success, 2009
• William A. Dembski and Robert J. Marks II, Bernoulli's Principle of Insufficient Reason and Conservation of Information in Computer Search, 2009

[Edit 3/24: Actually, at least half is copied, as you easily can see in my markup of the text.] According to the signature page, Marks, who holds the rank of Distinguished Professor of Engineering at Baylor, served on the thesis committee. Yes, I am referring to one of the twenty most influential Christian scholars — the “Charles Darwin” of intelligent design.

Most of the thesis is copied from two published conference papers, and from an article that had been accepted for publication:

1. [Student], William A. Dembski and Robert J. Marks II, Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism, 2009
2. [Student], George Montañez, William A. Dembski, Robert J. Marks II, Efficient Per Query Information Extraction from a Hamming Oracle, 2010
3. George Montañez, [Student], William A. Dembski, Robert J. Marks II, A Vivisection of the ev Computer Organism: Identifying Sources of Active Information, accepted August 27, 2010; published December 15, 2010

Not only are these papers not cited, but they also are not listed in the bibliography.

Chapter 2 is essentially (2), beginning with the fourth paragraph, and skipping Section II. (The first three paragraphs are in Chapter 1.) It corrects errors that I identified here at Bounded Science. More than half of the paper is mathematical analysis that is beyond most master’s students in computer science. I would guess that [the student’s] contributions were programming, data gathering and visualization, and paper preparation. If I am right, then it is inappropriate for the thesis to give the impression that [the student] did the math.

Chapter 4 is (1) with Section I eliminated, and with several small changes. It haplessly ends with “we have not explored in this paper.” (For those of you who are not scholars, I should explain that theses are not referred to as papers.)

Chapter 3 is not so simply related to its source, presumably because its author is not the lead author of (2). Almost all of its text is present in the article. But the chapter reorders passages of the article. Most notably, it moves empirical results ahead of theoretical analysis, and introduces awkward forward references to the analysis. Also, there are occasional replacements of words with synonyms, as well as deletions and insertions of short phrases. All in all, the chapter looks like the work of someone who was trying, pathetically, to make copy-and-paste pass for original writing. (Seventeen years of teaching experience are talking here.)

Chapter 5 is a double-spaced, one-page conclusion.

Some universities limit how much of a thesis may come from published work, but I can find no indication that Baylor is one of them. Yet the thesis does not state that the chapters are excerpted from published and forthcoming papers. Instead there is an appendix entitled ”Copyrights” that gives, without explanation, copyright release forms bearing the titles, but not the complete lists of authors (required by the publisher), of (1) and (2). Guess which author is missing? Yes, that would be William A. Dembski. I suspect that the forms on file with the publisher bear his name.

To get a hint that Dembski deserves credit for contributions to the thesis, you have to click the Show full item record button of the entry for the thesis in the BEARdocs system, and then figure out the meaning of the identifier.citation fields providing full citations of (1) and (2). In my opinion, burying this information in the metadata of the document retrieval system is unethical.

The copyright release forms indicate that the authors retain the right to use the published material in derivative works, “provided that the source and any IEEE [Institute of Electrical and Electronic Engineers] copyright notice are indicated.” So the thesis perhaps does not violate the copyrights of the publisher. But there is much more to academic integrity than not breaking the law. When you draw on a source, you cite it, even if you are one of the authors. When you copy from a source, you indicate clearly what you are copying. It would have been so easy to end the introduction of the thesis with an indication that Chapter 2 is excerpted, with emendations, from (2), and that Chapter 4 is excerpted from (1). As for Chapter 3, the author should have written it from scratch, and should have cited (3) in all places where the work was not his own.

Now, should you believe that self-citation and self-quotation are optional in scholarly writing, go back to the beginning of this post. It is unethical for a thesis committee member to condone plagiarism, even if it is plagiarism of his own work. The unacknowledged use of (3) in the thesis is egregious. It is clearly wrong to draw on the work of others, and not indicate that you are doing so. (For those of you who are not scholars, I should mention that references to forthcoming publications are common.) There is no wiggle room here. If the document is authentic, then both [the student] and Marks are out-of-bounds ethically. And one really must wonder what was going on with the chairman of the thesis committee, associate professor of computer science Greg Hamerly. Was Marks the de facto chairman? Had Hamerly even bothered to read the handful of papers on active information? If he had, then he is complicit. If he had not, then his performance was shabby, to say the least.

The contact information below should come in handy for any journalist who wants to work on the story. And I encourage readers to let Baylor administrators know what a blight on the reputation of the school the thesis is. Click here now to open your default email application and address the dean of the graduate school, J. Larry Lyon. You will CC the executive vice president and provost, the dean of engineering and computer science, and the chairman of the computer science department.

---

Thesis author:
[Student]

Thesis committee member:
Robert J. Marks II, Ph.D.
Distinguished Professor of Engineering
(254) 710-7302
Robert_Marks@baylor.edu

William A. Dembski, Ph.D.
Research Professor of Philosophy and Director of the Center for Cultural Engagement
Southwestern Baptist Theological Seminary
817-923-1921 ext.4435
wdembski@designinference.com

J. Larry Lyon, Ph.D.
Dean of the Graduate School
Baylor University
(254) 710-3588
Larry_Lyon@baylor.edu

Elizabeth Davis, Ph.D.
Executive Vice President and Provost
Baylor University
(254) 710-7803
Elizabeth_Davis@baylor.edu

Benjamin S. Kelley, Ph.D., P.E.
Dean of Engineering and Computer Science
Baylor University
(254) 710-3871
Ben_Kelley@baylor.edu

Signed to approve thesis as department chairman:
Donald L. Gaitros, Ph.D.
Professor and Chairman of Computer Science
Baylor University
(254) 710-3876
Don_Gaitros@baylor.edu

Thesis committee chairperson:
Greg Hamerly, Ph.D.
Associate Professor of Computer Science
Baylor University
(254) 710-6846
hamerly@cs.baylor.edu

Thesis committee member:
[completed Ph.D. and joined Baylor in 2009]
Young-Rae Cho, Ph.D.
Assistant Professor of Computer Science
Baylor University
(254) 710-3385
Young-Rae_Cho@baylor.edu

---

* I emphasize that my remarks are contingent on the authenticity of the document residing in Baylor’s BEARdocs archive on March 19, 2011. When possible, I assess the thesis I retrieved, and not persons. I have verified that Baylor requires entry of theses into BEARdocs. A metadatum indicates that the thesis was added on January 5, 2011, which is consistent with December 2010 graduation. I contacted [the student] by email to ask if the document were the final draft of his thesis, and he responded, “I have not verified the document, but it should be the final draft.”

Join together to report scholarly misconduct?

Edit (9 Oct 2009): Friends and respected acquaintances have persuaded me to rebut the article of Dembski and Marks in the peer-reviewed literature, and not to fuel the "Expelled" propaganda campaign of the intelligent design movement by lodging complaints of scholarly misconduct.

In my opinion, Dembski and Marks engaged in scholarly misconduct in their article Conservation of Information in Search: Measuring the Cost of Success. I will respond by lodging complaints with the academic institutions that employ the authors. I had planned on supplying readers with contact information and encouraging them to send their own letters of complaint. Now I believe that letters with many signatories would command more respect.

At most academic institutions, there are established procedures for responding to credible allegations of scholarly misconduct by faculty members. Allegations are typically reviewed by committees comprised mostly of ordinary faculty members — people who generally want to make fair decisions. Perhaps Dembski is safe. It would be nonetheless interesting to see a "secularized" Baptist university sanction one author, and a Baptist seminary let the other off the hook.

I must emphasize that the issue is not ID per se. Deceptive manipulation of a scholarly forum to advance any socio-political agenda whatsoever is wrong. As some of you know, I actually protested Baylor University's refusal to let Bob Marks display his "Evolutionary Informatics Lab" webpages with the standard disclaimer promulgated by the American Association of University Professors. What animates me to demand academic freedom is precisely what animates me to demand academic integrity.

Technical language goes nowhere with administrators and academic integrity committees. Furthermore, people may have a hard time seeing that Dembski and Marks misconstrued Dawkins. Here are some transgressions that are relatively easy to establish:

1. The authors analyze two closely-related computational methods without giving their conventional names, without indicating that they have been analyzed many times in the literature, and without citing prior analysis. This is egregious in light of the fact that their analyses did not appear in the paper until I explained one of the methods to Marks, provided its name, suggested analyzing it, and indicated that there were many analyses of it in the literature.
2. The authors mathematically formalize a computational method described informally in a popular-science book by Richard Dawkins, and attribute their formal method to Dawkins. That is, they mention neither that they are disambiguating an ambiguous text, nor that their disambiguation is highly controversial. This is egregious in light of the fact that Dembski has offered elsewhere several distinct interpretations of the text, and has emphasized its ambiguity.
3. The authors falsely attribute the term partitioned search, an apt name for their own formalization, to Dawkins. The attribution heightens the impression that they are relating straightforwardly Dawkins' precise meaning.

Speaking to motivation is tricky, but necessary, I think:

1. The authors submitted the article to a broad-scope journal with editors unlikely to recognize methods coming from the field of evolutionary computation. They evidently did not want to draw attention to the fact that parts of the paper needed the scrutiny of specialists in evolutionary computation. One of the analyses is a rehash of old results, and the other has no apparent utility in engineering.
2. Dembski has engaged in what he calls "cultural war" for many years, and the prominent atheist and evolutionary biologist Dawkins is his arch enemy. Dembski's socio-political ends take precedence over academic honesty in the article. He could not score a categorical hit on Dawkins without unequivocally representing Dawkins' work as something he and Marks knew how to analyze. In fact, the dubious interpretation makes for a very simple analysis. Following publication of the article, Dembski revealed his agenda on the Web:

   Our critics will immediately say that this really isn’t a pro-ID [intelligent design] article but that it’s about something else (I’ve seen this line now for over a decade once work on ID started encroaching into peer-review territory). Before you believe this, have a look at the article. In it we critique, for instance, Richard Dawkins METHINKS*IT*IS*LIKE*A*WEASEL (p. 1055). Question: When Dawkins introduced this example, was he arguing pro-Darwinism? Yes he was. In critiquing his example and arguing that information is not created by unguided evolutionary processes, we are indeed making an argument that supports ID.

   But soon after that, Dembski emphasized the ambiguity of Dawkins' description of his computational method, and decided that Dawkins used a method other than the one he and Marks analyzed — a method much harder to analyze. He also reported that he had communicated recently with Dawkins on the matter, and this brings to the fore the question of why he did not ask Dawkins for clarification prior to publication of the article. Evidently getting an unqualified "critique" of Dawkins through peer review was more important than honestly reporting that he and Marks had analyzed a mathematically convenient interpretation of Dawkins.

Some rumination

Dembski and Marks write, "Partitioned search [12] is a 'divide and conquer' procedure best introduced by example." Italicizing the term and placing a reference immediately after it is significant. By convention, this indicates that the term comes literally from the indicated source. There is, of course, no instance of "partitioned search" in reference [12], The Blind Watchmaker. Students might claim plausibly that they did not know the convention, but not a pair of highly experienced scholars.

There is utterly no way to warp Dawkins' description of how his Weasel program operated into D&M's partitioned search. Perhaps I'm underestimating the academic integrity committees. If they saw Dawkins' description of the Weasel program juxtaposed with D&M's description of partitioned search, they might sense that something's rotten in Texas.

How would an honest and responsible scholar go about disambiguating an algorithm in a popular science book? Obviously he would contact the author, if possible. Dembski has communicated with Dawkins plenty of times in the past, and has communicated with him about the Weasel program since publication of the article. Considering the controversy over the Weasel program, there was absolutely no justification for excluding Dawkins from the loop. This lends credence to the claim that Dembski and Marks chose to engage in false attribution because it served an ulterior purpose.

D&M did not know how to analyze the active information of Dawkins' algorithm, so they pinned on Dawkins an algorithm they felt was "close enough," and that they knew how to analyze. (I am sure that they did not know how to analyze Dawkins' algorithm because the article includes an analysis of a restricted form of it.) Whether partitioned search was "close enough" or not is irrelevant. The issue is that D&M had no justification for flat declaration that it was Dawkins' algorithm.

Back to the task

It would be good, I think, to mail a cover letter, a synopsis of the allegations like that I provided above, and somewhat detailed evidence. For instance, I would quote from my email to Marks, as in my last entry. It would be nice if Wesley were to provide a synopsis of Dembski's weaseling on the Weasel. I can give a succinct and simple explanation that D&M analyzed the (1,2)-ES and the (1+1)-ES, as well as a demonstration that they needed to keep reviewers from looking at prior analyses of ES's.

What I have in mind is to prepare the materials, put them on display for comments, revise, and then solicit signatures. I'd like to hear if you think many people would join in if I prepared something along the lines of what you've seen here. Should I just go it alone?

ADDENDUM

See Jeffrey Shallit's remarks on acknowledging priority at Recursivity.