Spud dud, as agricultural industry potato paper gets pulled a decade after publication

plantphyscoverPlant Physiology, the official journal of the American Society of Plant Biologists, has retracted a 2004 article by a team of ag industry researchers, including a former husband-wife duo, for what could be misconduct by the husband.

The retraction notice is vague enough, however, that we’re not entirely sure what went wrong, and no one wants to help us confirm — or even attempt to disprove — our inferences.

The article, “Crop Improvement through Modification of the Plant’s Own Genome,” appeared in 2004 and has been cited 85 times since, according to Thomson Scientific’s Web of Knowledge.  It was written by Caius Rommens and colleagues at  J.R. Simplot, a privately-held agribusiness firm which makes everything from “flame-roasted fruits and vegetables” to golf-course turf products (It’s a dessert topping AND a floor wax!) and which supplies McDonald’s with half of its french fries, according to this article in Forbes.

Its list of authors was capped by the former husband-wife team of Caius Rommens and Kathy Swords, both of whom have left Simplot.

According to the abstract:

Plant genetic engineering has, until now, relied on the incorporation of foreign DNA into plant genomes. Public concern about the extent to which transgenic crops differ from their traditionally bred counterparts has resulted in molecular strategies and gene choices that limit, but not eliminate, the introduction of foreign DNA. Here, we demonstrate that a plant-derived (P-) DNA fragment can be used to replace the universally employed Agrobacterium transfer (T-) DNA. Marker-free P-DNAs are transferred to plant cell nuclei together with conventional T-DNAs carrying a selectable marker gene. By subsequently linking a positive selection for temporary marker gene expression to a negative selection against marker gene integration, 29% of derived regeneration events contain P-DNA insertions but lack any copies of the T-DNA. Further refinements are accomplished by employing Ω-mutated virD2 and isopentenyl transferase cytokinin genes to impair T-DNA integration and select against backbone integration, respectively. The presented methods are used to produce hundreds of marker-free and backbone-free potato (Solanum tuberosum) plants displaying reduced expression of a tuber-specific polyphenol oxidase gene in potato. The modified plants represent the first example of genetically engineered plants that only contain native DNA.

Except, that wasn’t true. As the retraction notice suggests, Rommens, who at one point was director of research and development for Simplot, and appears to be an expert in the properties of ring fries, made stuff up:

This article has been retracted at the request of the authors. Retraction is based on three inaccurate statements of facts that are associated with a plant-derived transfer DNA. Two of the inaccuracies were described on p. 422 (first paragraph of the “Results” section): the plant-derived transfer DNA was not isolated from pooled wild potato (Solanum tuberosum) DNA but, instead, from DNA of the commercial potato var Ranger Russet, and its sequence was not confirmed by inverse PCR. Furthermore, the sequences of the left and right border-like regions shown in Figure 1B reflect transfer DNA-like primer sequences and are not present in the Ranger Russet genome. The corresponding author, Caius M. Rommens, takes responsibility for the inaccuracies and sincerely apologizes to the readers, reviewers, and editors of Plant Physiology.

Rommens’ Linkedin page lists him as being the “founding member” of an outfit called Nightshade LLC, a year-old company based in Boise. But we can’t find anything online about the firm beyond this placeholder website. An email to the contact provided went unreturned.

We also tried unsuccessfully to reach Swords, a past director of business development at Simplot. The company, with Swords listed as the inventor, was awarded a patent in 2004 for

a method for identifying and isolating native plant nucleic acid sequences that may function as T-DNAs or T-DNA border-like sequences, effecting the transfer of one polynucleotide into another polynucleotide. The present invention also provides a modified tuber, such as a genetically modified mature tuber, that comprises at least one trait that is not exhibited by a non-modified tuber of the same species.

We wonder if that’s related to the now-retracted paper. Rommens and Swords appear on other patents, too, when they worked at Monsanto.

Doug Cole, a spokesperson for Simplot, would not answer questions about Rommens or Swords, including whether Rommens was terminated as a result of the problems with the article or whether any patents might be affected by the retraction. (Swords left the company in 2009, according to her Linkedin page). He also refused to comment when we asked him whether misconduct was at play, which we figured would have been a good opportunity for him to have defended the integrity of the work. However, Cole did say that:

Any incorrect research was specific to that one publication.

Except, that’s not quite true, either.

According to Mike Blatt, editor of Plant Physiology, the journal will be issuing has issued a correction for a 2005 paper by Rommens et al

which is affected to the extent that it refers in passing to the retracted paper. An erratum has been prepared in this case. My reading of this second paper, and that of one of my colleagues, is that a retraction was not justified on the basis of the information available to us.

Here’s the correction for Rommens C.M., Bougri O., Yan H., Humara J.M., Owen J., Swords K., and Ye J., “Plant-Derived Transfer DNAs,” a paper that has been cited 22 times:

The border sequences of St01 and the vector pSIM108 described in this article’s findings were based on data from an article by Rommens et al. (Rommens CM, Bougri O, Yan H, Humara JM, Owen J, Swords K, Ye J [2004] Crop improvement through modification of the plant’s own genome. Plant Physiol 135: 421–431), which has been retracted. Specifically, these sequences, which were presented in this and the preceding article as intragenic, reflect transfer DNA-like primer sequences that are synthetic and not present in the potato (Solanum tuberosum) genome.

Blatt shed a little more light on the case. He told us Rommens contacted the journal in January — the month his Linkedin page indicates he left Simplot — with a draft of the retraction notice, and that the editors made “minor amendments” to the text.

Blatt, however, did said he felt the retraction notice said all it needed to say:

The background leading to the retraction is clearly stated in the retraction text, which indicates that incorrect reporting on several accounts was at issue.

We’ll agree to disagree on that point.

8 thoughts on “Spud dud, as agricultural industry potato paper gets pulled a decade after publication”

    1. Not much. PPOs cause the potato equivalent of scabbing and clotting when the skin is cut. In the presence of oxygen, PPOs oxidize tyrosine, beginning a cascade of reactions which eventually create a brown, dry, cross-linked melanin covering which prevents access by bacteria and insects. But browning and melanin “scabs” are unaesthetic and interfere with mechanical french-fry production. The various PPO genes (it’s a family of related genes) can be deactivated by splicing in other DNA. Agrobacterium plasmids (to make a very long story short) can do this, but some people are squeamish about eating stuff which incorporates bacterial DNA. Rommens et al. reported that they could use Agrobacterium plasmids plus brute-force methods to create potatoes with low PPO activity, in which the deactivating insertions contained potato DNA, rather than bacterial DNA. As it turned out, they had not done so.

      Any consumers who (a) place a high value on the racial purity of their food, but also (b) demand fast-food fried potato products, will be disappointed. Fast food producers who may have planned to promote their fried potato products based on genetic purity will also be disappointed. Some food scientists have probably found they have wasted time and resources trying to duplicate the methods of Rommens et al. I can’t think of any other implications off-hand.

      1. Now I know why my potatoes darken after I have peeled them. Never the bits submerged in water, so I did suspect oxygen to have something to do with it.
        The “racial purity” claim sounds like a marketing ploy, though.

  1. “but some people are squeamish about eating stuff which incorporates bacterial DNA.”

    Which they then eat with their fingers….

  2. “Any consumers who (a) place a high value on the racial purity of their food, but also (b) demand fast-food fried potato products”
    (a) and (b) are completely contradictory. If you like craft food products, you may be interested in the racial purity (and yes, the cheese make from the milk of cows on the S side of mountain X is different from the “same” cheese made with cows spending the summer on the E side of mountain Y), simply because of the greater variety of tastes. You will have no interest in fast food and will generally avoid touching it.
    Note craft foods generally have even more microorganisms (often alive) and their DNA than fast food made from GM sources.
    Moreover, as Toby White states, more microorganism cells than Homo ones.

  3. Would it make sense to retract a paper as a way to attract more attention to it, or, if it is already well entrenched in your h-core, to draw attention to the retraction (are retractions citable?

Leave a Reply to chirality Cancel reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.