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Natural Products

Scooped, I Suppose the Word Is

Via Retraction Watch, here’s a situation that I don’t recall seeing before: a group at Foshan University in China published a paper in the journal Natural Product Research on the crystal structure of aspergicine. Here’s the original abstract in PubMed – their work prompted them to revise their previously published structure of a related alkaloid, aspergicin, which the group had first reported in 2011. These compounds are produced by an Aspergillus marine fungus that lives in mangrove swamps – and so far, this sounds like perfectly typical natural products work.

Unfortunately, it turns out that aspergicine itself was already a known compound, only it was known under the name “Circumdatin B”. It had been reported in 2008 by a group in Japan, in a J. Org. Chem. paper where, by golly, X-ray crystallography was used to determine the structure. Now, I can certainly imagine rediscovering a natural product without realizing it at first. And in this case, since the structure was at first wrongly assigned by the group from Foshan, a structure search through the literature wouldn’t have turned it up.

But after you’ve gone to the trouble of getting an X-ray structure and revised your first proposal, you don’t run that one through the literature search engines again? And you don’t check to see if that structure is already in the X-ray databases? Being scooped in a race to discovery is one thing; finding out that your compound’s structure was reported almost ten years ago is quite another. And another point: you don’t go back on principle and read all the literature on the isolated alkaloids from your exact species of Aspergillus to see if those publications might possibly have any bearing on your own work?

This latest paper has now been retracted, as it should be, so the scientific record has been pulled back into line on this topic. But how did things get to this state? Admittedly, the name and structure of a particular fungal product from the mangrove swamps is probably not such a big deal, but (A) natural products have a way of being either totally obscure or wildly important all of a sudden and (B), in the larger scheme, this is no way to do research on anything, from swamp fungi on up.

27 comments on “Scooped, I Suppose the Word Is”

  1. Andy says:

    Concentrated gains and diffuse losses: it’s in the interest of everyone involved to appear to have performed some good science and have it recognised through a paper. The scientists, the department, the university and the funding body all benefit, with no malicious intent at whatsoever.
    Sadly of course, the losses are borne by the entire scientific community, but the individual ‘cost’ is incredibly small.

  2. Anon2 says:

    Often called the “tragedy of commons”, this problem seems to be everywhere in modern life.

  3. Anon says:

    What is the difference between this paper and 10 different total synthesis papers for the same natural product?

    1. Derek Lowe says:

      In terms of utility? The different approaches (in theory) have different points to make about synthesis, so there’s that. And at least the different syntheses acknowledge that others have worked on the molecule before. This would be like a synthesis of some compound that’s already been made, with a claim that it was a first. Embarrassing.

    2. Natural chemist says:

      Because the syntheses are “different” (your words!)

    3. Dtfbpy says:

      Ask the same questions about all the worthless methods papers gracing the pages of JACS or SCIENCE. If you just republish decades old reactions with a titillating new word you invented (mellatioredox) then you can declare a major advance 🎉

  4. Isidore says:

    When I was in graduate school, eons ago, I learned how to carry out a proper literature search. Are the younger scientists able to so this, or is Google their first and last resource?

    1. NJBiologist says:

      Academic research* seems to have gotten to a place where if you’re not moving forward, you’re going backward. One of the casualties of this is thoughtful literature review, particularly in a debugging mode where one might catch this sort of thing.

      * I’m basing my comments on friends in US institutions; I have no insight into the pressures these authors are under.

    2. KevinH says:

      Nah, we run a couple of keywords through PubMed, too.

  5. me says:

    Eh, I don’t mind this one. Things slip through eventually.

  6. Anon says:

    About the statement, “But how did things get to this state?” Shall I say, a greed to get published as fast as you can. The fact is these days people ignore the works of previous people, self-referencing and I can go on and on. To their credit, it was retracted.

  7. Christophe Verlinde says:

    Nearly 40 years ago a friend of mine who was in grad school published “Novel synthesis of … “. A month later he received a letter from down under. The letter writer said “nihil novum sub sole”. He was a former grad student of Derek Barton who had published the same synthesis more than 20 years earlier.

    1. Dave says:

      Savage af…

  8. MoMo says:

    Is it greed, avarice or lack of sophisticated literature searching? Ye Gods! they don’t even have Google access in China let alone Scifinder accounts. How barbaric! Its a canary in coal mine for the American Pharma industry.

    But the real blame goes to the journal for its stellar reviewer panel. You get what you pay for.

    1. W says:

      appropriately, the note on Retraction Watch is titled “Doesn’t anyone do a literature review any more?”. It’s bad enough sloppy work happens by the authors, be it for plain laziness or to boost their publication record or whatever, but how can something like that get through the review process, if a simple reference search should have made it obvious ?
      To the community, losing an article is but a drop in the ocean; the questions it raises about the publication process are more painful.

  9. eeee4 says:

    One of the aglains was reisolated and given a new name many year later. I forget which. Pretty sure I saw at least one other instance of this, too. There’s a lot of poor quality papers in isolation chemistry.

  10. Imaging guy says:

    I don’t think this paper should have been retracted. Currently we are talking about reproducibility crisis in science. As one paper says, “within a culture that pressures scientists to produce rather than discover, the outcome is a biased and impoverished science in which most published results are either unconfirmed genuine discoveries or unchallenged fallacies”. In order to solve this problem, we have to replicate studies and to do so you have to allocate resources. There is no other way. For example, “Reproducibility Project: Cancer Biology” tried to reproduce some papers published in high impact journals (1). Here, you can’t accuse them of wasting resources. What they do in that project is they first publish “a registered report” where they discuss how they are going to replicate a study. The original authors and others can give suggestions at this stage. Later they do the replication studies and finally publish papers which include the meta-analysis of original and replication studies in the discussion section. In current case the authors did not know a paper had already been published. So, they were working with free minds which was even better. Therefore, they should be allowed to publish a correction where they report a meta-analysis of the original paper and their findings.
    https://elifesciences.org/collections/9b1e83d1/reproducibility-project-cancer-biology

    1. skeptical says:

      You make an excellent point. It doesn’t make any sense to force the retraction of this paper at the same time that we’re trying to encourage replication studies.

      On the other hand, the journal may feel that the authors led them astray, and retraction is a way to discipline them.

    2. Ian Malone says:

      Yes, the only shortcoming here is the failure at the second juncture to re-revise the literature and spot the new result had been found previously (as opposed to the original one which hadn’t). That and an obsession with priority causing a published report re-discovering earlier work to be pulled. Not being a chemist I have no idea whether the reviewers should have picked it up or not, but the paper addressing the misidentification is still a valid correction to the authors’ previous work and would have thought that was publishable after corrections to correctly cite the earlier discovery. As others have said, it’s unsurprising people talk about a reproducibility crisis.

      (And yet, the infamous “A mathematical model for the determination of total area under glucose tolerance and other metabolic curves.” has never been pulled and continues to receive new citations.)

  11. Natural chemist says:

    This is totally the reviewers’ fault. I might add, as a natural product chemist, that I’ve never even heard of this journal.

  12. MTK says:

    I’m not that bothered by this TBH, assuming that this was a honest mistake due to sloppiness, which seems to be the case since issuing a correction followed by a retraction would be really bad if you’re trying to somehow fake or take credit for something you don’t deserve. The authors won’t make this mistake again. It’s embarrassing, but it’s not like it sent an entire field or multiple groups chasing down something that didn’t exist or was fabricated.

  13. Scott says:

    Given that the researchers retracted the paper, seems more like an honest mistake than malice.

    My guess is that they honestly didn’t see the need to re-run their search for previous papers specifically looking at the X-ray crystal structures when they’d already run at least two other searches on other details.

  14. Nick K says:

    This time at least we’re talking about an honest mistake, not fraud.

    1. Isidore says:

      It’s not fraud, but the “honest mistake” was due either to laziness or, more likely, to inability, due to lack of knowledge, to conduct a proper literature search. Either should be source of embarrassment for a scientist.

  15. Ursa Major says:

    Should this paper have been retracted? Now the scientific record still has the name aspergicin attached to a structure that has perhaps never existed, and it doesn’t record that the compound isolated as aspergicin is actually the same as that named circumdatin B. That’s important information which wouldn’t have rendered their revised structure unpublishable.

    Instead, should not a correction have been published saying “Since publication of this paper, it has come to our attention that this structure has previously been described as circumdatin B in [reference]”?

  16. Anonymous says:

    The authors having failed to do a search, competent referees should have caught this. But a lot of junk gets past referees. (Many such papers have been discussed in Pipeline.) I also see it as wasted funding AND funding denied to a more competent group to study a more important problem.

    ScienceMag IT: Please remove the avatar from this post. I never used an avatar as Anonymous and it creates confusion. Just leave the white on grey silhouette. Thank you.

  17. A Nonny Mouse says:

    Ha, reminds me of my Phd; we could not figure out why opposite isomers of a natural product series were being formed (according to the literature). This lead to a hunt for the original X-ray samples which had been done at the university many years before. These were found covered in bird droppings in a loft storage space. The original X-ray picture was also found.

    A new X-ray revealed that the original determination had been correct, but the picture had simply been read and published in reverse!

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