Creationism Slips Into a Peer-Reviewed Journal

Reports of the National Center for Science Education
Title: 
Creationism Slips Into a Peer-Reviewed Journal
Author(s): 
Steven L Salzberg
Volume: 
28
Issue: 
3
Year: 
2008
Date: 
May–June
Page(s): 
12–14, 19
This version might differ slightly from the print publication.
A strange thing happened in the scientific literature recently. A pair of creationists, who have seemingly legitimate scientific credentials, attempted to publish some creationist assertions in a peer-reviewed journal. Their effort was nearly successful, mostly because they hid their pseudoscience in the middle of the article, surrounded by legitimate scientific discussion of unrelated topics. Luckily, they were caught just in time, and it turned out that they were pretty clumsy. In fact, if they had been just a bit more clever, they might have gotten away with it.

First, let us examine the facts: the two authors, Mohamad Warda and Jin Han, submitted a review paper to the mainstream journal Proteomics. This is a well-regarded journal, with a distinguished editorial board, which focuses on novel technologies for studying the protein content (the "proteome") of a cell or a tissue sample. Virtually all scientists reading this journal are familiar with evolutionary theory, but the journal itself is not a forum for discussion of evolution. No one would expect a paper on creationism to appear here.

The paper submitted by Warda and Han was a review paper about mitochondria. The mitochondrion is an organelle contained within the cells of most multicellular life, including plants and animals. Mitochondria are often referred to as the "energy factories" of the cell, because they produce adenosine triphosphate, ATP, which is the source of much of the chemical energy that a cell uses. Of course, mitochondria do not "make" energy — they merely help to convert energy from food into another form of energy that the body can use.

Review papers are different from other scientific papers: rather than describing novel experiments and results, they review and summarize the work of others on a particular topic. Reviews do not normally contain new conclusions, but once in a while a review paper might distill many related findings into a broader result than any of the individual papers discussed in the review. The Warda and Han paper professed to be a summary of how proteins in the cell interact with the mitochondrial genome. Fair enough. It turned out, though, that Warda and Han are creationists, and their "review" was a stealth attempt to get their creationist claims into the peer-reviewed literature. This report describes what they did and how they got caught.

The paper and the "mighty creator"

Like many journals, Proteomics releases papers on-line before the official publication appears. In early February 2008, I was alerted by Andrew MacArthur, an evolutionary biologist, that there was a new paper in Proteomics that gave a "mighty creator" credit for designing the mitochondrion. The paper was titled "Mitochondria, the missing link between body and soul: Proteomic prospective evidence." Much of the paper reads like any review paper, with considerable technical detail and 239 references to the literature. However, the paper had four major red flags that the journal's reviewers and editors should have caught before accepting it for publication:
The title
The abstract
The creationist claim
The conclusions
The title. Scientific papers do not talk about the "soul", and although this could be just a clever metaphorical usage of that word, the title should raise suspicions that the paper contains something other than science.

The abstract. The very first paragraph of most papers is the abstract, a short summary of the main results. Warda and Han write that their review includes "novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative."

First of all, novel evidence does not belong in a review, so the reviewers should have been on the alert when they saw that. But more important, this claim should be quite startling to any evolutionary biologist. The endosymbiotic hypothesis proposes that the mitochondria found in many organisms today are the remnants of an ancient bacterium that was engulfed by an early, single-celled ancestor of eukaryotes about two billion years ago. This hypothesis dates back many decades (see http://en.wikipedia.org/wiki/Endosymbiotic_theory) and has been gaining support since the 1960s; for example, see the papers by Kurland and Andersson (2000) and Gray and others (2001). The sequencing of the mitochondrial genomes of many animals and plants has greatly strengthened the endosymbiotic hypothesis. So what do Warda and Han have to offer as an alternative? The abstract does not say.

The creationist claim. The paper reviews the literature in a rather dry fashion until page 8, in a section titled "Mitochondrial integrated function disproves endosymbiotic hypothesis of mitochondrial evolution." In this section, Warda and Han do some funny things. First, they cite a number of references that have nothing to do with the findings in this section. Then they offer up the statement that attracted the most attention from the blogosphere:
Alternatively, instead of sinking into a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption. ... More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life.
Aside from the fact that this sentence is so badly written as to be nearly incomprehensible, the phrase "mighty creator" sticks out like a sore thumb. Boiled down to its essence, Warda and Han are saying "God did it."

The conclusion. Does the article contain any more creationist assertions? After the "mighty creator" section, it just jumps back into review mode and continues like that almost until the end — until the very last paragraph. There, Warda and Han had one more surprise. They concluded that "many controversial questions still need to be answered, e.g., how signaling molecules ... precisely translocate from or to mitochondria in a matter of milliseconds while crossing a huge ocean of soluble and insoluble barriers." Perhaps this is a legitimate question, but then they wrote: "we still need to know the secret behind this disciplined organized wisdom. We realize so far that mitochondria could be the link between the body and this preserved wisdom of the soul devoted to guaranteeing life." This is simply nonsense — the mitochondria are linked to the "wisdom of the soul"? It is gibberish, and nothing in the article supported it, but somehow it slipped past the reviewers.

The plagiarism is uncovered

Thanks to the rapid action of the blogosphere, and four blogs in particular, this paper came to the attention of many scientists before the print version appeared. I first blogged on the paper on February 7, 2008 (http://genefinding.blogspot.com/2008/02/stealth-attempt-to-sneak-creationism.html). Attila Cordas (http://pimm.wordpress.com/2008/01/29/http://pimm.wordpress.com/2008/01/29/can-you-tell-a-good-article-from-a-bad-article-based-on-the-abstract-and-the-title/) and Lars Juhl Jensen (http://larsjuhljensen.wordpress.com/2008/02/10/commentary-neither-buried-nor-treasure) also blogged about it. PZ Myers mentioned it a day before I did on his widely-read Pharyngula blog (http://scienceblogs.com/pharyngula/2008/02/a_baffling_failure_of_peer_rev.php), and within a matter of hours a commenter named Sili asked, "has anyone yet checked to see whether this might be plagiarized?" The disjointed style was the first clue — much of the article appears technically competent, although the writing style varies, and the creationist claims are written very poorly. Within a few more hours, the first evidence of plagiarism was uncovered: an entire paragraph copied verbatim from another article.

From there, the evidence quickly snowballed. Within a few days there were dozens of examples, and it appeared that the majority of the text was simply copied wholesale from other sources. John MacDonald, a professor at the University of Delaware, compiled many of these into a document (http://udel.edu/~mcdonald/wardahan.pdf) showing that Warda and Han stole much of their article from six different articles plus a scientific website. The examples fill eight pages. In all cases, Warda and Han copied text word-for-word without attribution.

Plagiarism is a gross violation of scientific ethics. From the journal's point of view, it represents another problem: copyright violation. Because the text was taken without attribution and without permission, the authors were violating the copyright of the original authors. Ironically, the discovery of plagiarism by the bloggers gave Proteomics an easy out: because of the plagiarism, editor-in-chief Michael Dunn insisted that Warda and Han retract the paper.

The article was removed from the journal website, which now says only that the retraction is "due [to] a substantial overlap of the content of this article with previously published articles in other journals." Further adding to the irony, the article remains the fourth most highly-accessed article for the journal in the past year, no doubt because of the controversy.

The authors

Mohamad Warda and Jin Han submitted the article from Inje University in Korea, a relatively new university that as yet has little international stature for scientific research. Han has published multiple scientific articles in respectable journals; Warda was apparently working as Han's student or postdoc, and now lists his address as Cairo University in Egypt. Warda and Han had published together previously, including at least one paper in the journal Proteomics. The authors were contacted directly by James Randerson of The Guardian, who reported the incident on his blog (http://www.guardian.co.uk/science/blog/2008/feb/13/thankstocjv5040forputting). Only Warda responded, and his response makes it clear that (a) he is a creationist, and (b) he cannot write English well. In an e-mail quoted by Randerson, Warda wrote:
The problem is that we described in very clear and definite way the disciplined nature that takes part inside our cells. We supported our meaning with define proteomics evidences that cry in front of scientists that the mitochondria is not evolved from other prokaryotes. They want to destroy us because we say the truth; only the truth.
And in response to a question about plagiarism, he wrote "I not burrow [sic] any sentences from others," despite the obvious evidence that he borrowed voluminously.

PZ Myers was able to get a response (see http://scienceblogs.com/pharyngula/2008/02/one_author_responds.php) from Jin Han, who explained that:
I found the serious mistakes in the paper during the process of edits, which I confused between the early drafts and the latest versions: I did not check the use of the sentences in the references (more than 200 references). Finally I made serious error to make the final version. In order to rectify an error, I requested to retract the paper to the editorial office of Proteomics.
Myers pointed out, correctly, that this response does not really explain anything: not the creationist claims, nor the bizarre title, and certainly not the extensive plagiarism.

Clearly, based on their efforts to sneak false creationist claims past reviewers, Warda and Han are dishonest scientists whose work should be viewed with great skepticism in the future. Their extensive plagiarism is a second offense, and that alone would disqualify them from work in most legitimate scientific laboratories. In the United States, plagiarism is one of the few activities that can (and has, in some cases) lead to the firing of a tenured professor. Warda and Han should at a minimum be censured by their universities, but thus far there is no evidence that any action was taken.

The editor's response

I contacted the editor-in-chief of Proteomics, Michael Dunn, to find out more about what happened. Many scientists have speculated publicly that the peer review process went seriously wrong for this paper. Dunn assured me that the paper was reviewed by two "well-respected and highly competent reviewers" both of whom recommended minor revisions. For some reason, though, "neither picked up the references to creationism, nor did they recognize that sections of the text were plagiarized," according to Dunn. It is not too surprising that the reviewers missed the plagiarism, but the title and abstract should have raised huge red flags warning the reviewers that this article had questionable science. I have to conclude that the reviewers were very sloppy, incompetent, or both; at the very least they were inattentive in this case, despite the editor's claims to the contrary. And Dunn himself is not without responsibility in this case: he must have seen the reference to "the soul" in the article's title, and he should have been more pro-active. His failure to make any public statement about the creationist claims in the article also raises questions about the leadership at the journal.

Conclusion

This entire episode points out a weakness in scientific peer review that creationists and other pseudoscience proponents may try to exploit again. We only caught this attempted fraud thanks to the diligence of bloggers: the journal itself had already missed it. What is perhaps more troubling is the fact that the journal relied solely on the plagiarism to force the retraction: if not for that, the article might have been published despite its unsubstantiated creationist claims. I asked Dunn specifically about this issue, but he declined to comment. The Warda and Han paper demonstrates a new strategy that proponents of creationism might attempt again, and perhaps next time they will not be so foolish as to plagiarize their text. We can only hope that the publicity surrounding this incident will alert both reviewers and editors of scientific journals to be on the lookout for "stealth" creationist claims in the future.

References

Gray MW, Burger G, Lang BF. 2001. The origin and early evolution of mitochondria. Genome Biology 2 (6): reviews1018.1–1018.5. Available on-line at http://genomebiology.com/2001/2/6/REVIEWS/1018.

Kurland CG, Andersson SG. 2001. Origin and evolution of the mitochondrial proteome. Microbiology and Molecular Biology Reviews 64 (4): 786–820.

About the Author(s): 
Steven L Salzberg
Center for Bioinformatics and Computational Biology
3125 Biomolecular Sciences Building #296
University of Maryland
College Park MD 20742
salzberg@umd.edu

Steven L Salzberg is the Director of the Center for Bioinformatics and Computational Biology and the Horvitz Professor of Computer Science at the University of Maryland, College Park. Before switching to bioinformatics and genomics, his research focused on machine learning and its research applications. Salzberg and his research team develop computational gene finders and systems for large-scale genome sequence alignment and assembly, including the open-source genome assembler AMOS. In addition to his software systems, Salzberg has contributed analyses to many genome sequencing projects, using computational methods to analyze genome duplications, rearrangements, and other evolutionary phenomena in a wide range of organisms, including the first large-scale genomics study of the human and avian influenza A viruses. Salzberg has authored or co-authored two books and over 150 publications in leading scientific journals. He is a Fellow of the American Association for the Advancement of Science (AAAS) and a member of the Board of Scientific Counselors of the National Center for Biotechnology Information at the National Institutes of Health.