Sunday, January 21, 2018

I can't steal (text) from myself, can I??? (hint: your text might not be yours anymore)

So, a journal policy issue came up for me this week. I've anonymized the details, so I can discuss the big-picture conceptual issues.

We had an author of a paper who recycled big chunks of the methods from his/her past paper(s). Same data (analyzed in new ways), so same methods, so why rewrite the whole thing. As a result, more than 1/4 of the whole paper was recycled text. We pointed this out.

The author responded that big long-term data studies are often the subject of multiple publications, that all rely on the same data set and hence the same methods to collect the data.  This is actually quite a common issue in biology, and not at all unique to datasets like the one in this maanuscript. Moreover, even new datasets can be obtained through the same methods as previous papers, such as when I use the same molecular genetics protocol to obtain DNA sequence data, albeit for different biological specimens. So, this is indeed a recurrent subject of angst and confusion.

So, why the policy barring extended re-use of one’s own text?


Cyanide and Happiness Self Plagiarism
(cartoon by Cyanide and Happiness)

Before answering that, I want to point out that very modest re-use, a sentence here or there, or sentence fragments, is common and does not typically raise any red flags (as long as the text is one’s own). What we are concerned with here is extensive re-use of very large blocks of text. Many journals have software that automatically scans for re-use of text available on the web. iThenticate scores are often 5% to 10% repeated text, and this is often driven by citations in the paper, which are by necessity repeated.


The fundamental reason for this policy has to do with copyright law.  If you hold the copyright to the previously published text, or if it is not copyrighted, then there is no official legal problem. For instance, your grant proposal contains lovely introductory and methods text, and is not copyrighted. You may re-use chunks of it for a submission.


But, authors rarely retain unfettered copyright to their published work. Chances are, that previously published paper is copyrighted and the copyright probably belongs to the publisher. So, even though you authored a previous methods section, you need to get permission from the publisher of the previous paper (or whoever holds its copyrights), to re-use large chunks of text.  So, this isn’t our journal’s arbitrary editorial policy that we can change at a whim. It is our obligation to follow copyright law.  There is a caveat here: there is the option for “fair-use” in citation, but this usually applies to small stretches of text, not extensive quotation. And, to qualify as fair-use under the law the quoted text must be clearly denoted as a quotation (e.g., surrounded by quotation marks), with attribution to the original soure.

Given that we do not have legal flexibility here, what is an author to do? 


First, one can subtly rephrase the original text. This is what most of us do when we submit repetitive methods sections; we reorganize sentences, substitute synonyms when possible, and generally make the text a non-exact copy. That’s usually not too hard to do.  

Second, one can actually place the methods section in question in quotes, with attribution to your previous work. That’s atypical in our field (I’ve never ever seen it done). But, it is legal though it will raise eyebrows. 

Third, you can shorten your methods and refer readers to the methods section of the prior paper. This is commonly done, though reviewers (and readers) sometimes get annoyed that not everything is written down in one place. But really, we all implicitly build our methods on the backs of past papers (I don’t, for example, re-derive a proof for an ANOVA or regression, each time I use statistics), so it’s not unreasonable to do this third option.

For more on this topic, there are a wide variety of online resources commenting on this issue. You are clearly not the first to ponder this subject, given the extensive list of readings available on “self-plagiarism”. Reading these sources reiterates for me that our journal’s policy is legally necessary and typical within the natural sciences. Here are a few sources:


Moskovitz, 2016. Self-plagiarism, text recycling, and science education. Bioscience 66: 5-6
https://doi.org/10.1093/biosci/biv160


Garfinkel, 2015, A fresh look at self-plagiarism. American Association for the Advancement of Science
https://www.aaas.org/news/fresh-look-self-plagiarism


Culley TM. 2014. APPS’s stance on self-plagiarism: Just say no. Applications in Plant Sciences 2(7): 1400055 (doi: http://dx.doi.org/10.3732/apps.1400055).


Roig M. ND. 2013. Avoiding plagiarism, self-plagiarism, and other questionable writing practices: A guide to ethical writing. U.S. Department of Health and Human Services, Office of Research Integrity. http://ori.hhs.gov/sites/default/files/plagiarism.pdf


COPE (Committee on Publication Ethics). 2009. Case 09-21: Self plagiarism. http://publicationethics.org/case/self-plagiarism


Gnanavel, 2015. Self-plagiarism: the latest ethical dilemma in biomedical research. Indian Journal of Psychological Medicine (I include this to show this is not just a US issue)


Here's the perspective from iThenticate, the software company that checks for plagiarism generally (granted, they have some financial interest in this issue): http://turnitin.com/en_us/resources/blog/421-general/2554-is-recycling-your-own-work-plagiarism

And here are a few others for good measure:
http://blog.apastyle.org/apastyle/2016/05/avoiding-plagiarism.htmlhttps://www.insidehighered.com/views/2010/12/03/zirkelhttps://ori.hhs.gov/avoiding-plagiarism-self-plagiarism-and-other-questionable-writing-practices-guide-ethical-writing


There is a counter-argument here, of course. Quite a few people on twitter and elsewhere have responded that they feel this rule and tradition is misled.  Some just seem to feel it is unjust that authors don't have the right to reuse their own text whenever they want. Some expressed frustration at the waste of time required to rephrase text to say the same thing. The author of the manuscript in question was dissatisfied by my narrow explanation of the rule. My saying "its the law" does not explain the rationale behind this. Laws can be changed. But this is broader than just the law; it is also an academic norm. People trying to push this boundary will meet with more resistance from their academic peers, than from lawyers.
Image result for self-plagiarism


UPDATE:
I've been pleased to see that this post has generated some serious conversations on twitter (and perhaps elsewhere). Some quite critical of my post. I want to respond by making a few things clear:

1) I am not a lawyer. My statements above about legality are my understanding from discussions with people in journal publishing (also not lawyers, but better informed than I). I also based my comments on the various links above.

2) I don't actually seriously endorse all of the solutions listed above. For instance, the block quote of methods, was meant in jest (I ignored the number one rule in online writing: irony does not translate well to text). For instance, Lenny Teytelman took me to task (https://www.protocols.io/groups/protocolsio/news/is-reproducible-reporting-of-research-methods-in-conflict) for suggesting this option. Lenny also disliked my statement that you can cite a prior methods section of another paper. I totally agree with Lenny that this can lead to chains of poorly detailed methods that undermine our goal of reproducibility. I noted that this chain of citing other methods is common (it is), and annoying (it is). He correctly points out that it can also lead to ambiguity. To be clear, I was listing these two options for sake of completeness, not endorsement.

3) Lenny also disliked my more serious comment: rephrase. He said this undermines precision. I disagree. This is done all the time, slightly modifying bits of prose in ways that is not "artificially changing method details", just changing the words and sentence structures used to describe them in ways that are truly synonymous. If there's really only one way to say something, then by all means say it the same way. I just doubt that's often true.

Friday, January 5, 2018

Adding sheep to the mountain

With much help from Marc-Antoine Poirier, Département de biologie, Université de Sherbrooke

When I teach wildlife management, I start by saying that wildlife got along very nicely, thank you, long before people wanted to manage it.  As with most of conservation biology, wildlife management usually involves minimizing the negative impacts of people.  That often includes remnant populations that are so small that their chances of persistence are tiny.  Enter wildlife management, through translocations.

Translocations are very popular: they make it look like you're doing something.  You can take pictures of animals being released! But do they work, and are they justified? Supplementations are appropriate when population recovery appears limited by genetic factors, or simply by small numbers.  If habitat is available and the population is not limited by disease, predation, poaching or other persisting threats, then if you release additional animals you should increase genetic variability, diminish the risk of inbreeding and see a faster increase in numbers. A well-known and apparently successful recent example is the supplementation of 'Florida panthers' with 'Texas cougars' (sometime we'll need a blog about local names of the same animal...).  Another case that is much discussed and may or may not happen is the supplementation of the last 1-2 wolves left in Isle Royale National Park.

Supplementations are not risk-free. They could break local adaptations or introduce pathogens.  When remaining numbers are very low, however, inbreeding becomes nearly inevitable and transplants are a reasonable option, provided a suitable source population exists.

But what happens after the photo-op is over and transplanted animals are left to their own devices? Few studies have examined the social integration of individuals.  In many species, social integration is essential, for example to ensure that transplanted individuals learn the location of seasonal food sources or integrate groups to participate in antipredator vigilance.  We took advantage of a supplementation of the Ram Mountain population of bighorn sheep to explore this topic.

First, a bit of history.  Bighorn sheep at Ram Mountain have been monitored since 1971.  After several years of experimental ewe removals, the population was allowed to increase and more than doubled, from 105 in 1980 to 232 in 1991.  It then began to decline. Perhaps overly confident that density-dependence is all that matters with ungulate populations, in 1997 we removed 14 of 83 ewes, expecting a positive response in population growth.  Little did we know...  Partly because of cougar predation, the population plummeted, from 189 in 1996 to 40 in 2002. It then stagnated for 5 years, and inbreeding limited lamb survival. The cougar predation episode ended in 2000.  To attempt a demographic and genetic rescue, we transplanted 12 adult sheep in 2005, from an abundant source population about 130 km to the north-west. Near-total failure: only 1 of 6 ewes and 2 of 6 rams remained to reproduce, the others disappeared.  The ones that remained were young, so we thought age may be a factor in transplant success. We tried again: in March 2007 we released 12 yearlings.  Partial success: 2 ewes and 3 rams reproduced on Ram Mountain, but not until 3 years later. Things started to look good: genes from the transplanted sheep spread in the population and lambs with 'introduced' genes seemed to have better survival than 'resident' lambs. The population increased to 74 by 2012. Then, a setback: another cougar started preying on sheep, 10 of 28 adult ewes disappeared over a year, and by 2014 we were back to 46 sheep. A cougar was shot during the hunting season and predation appeared to stop, so in 2015 we conducted a third transplant.  By then, the source population had had a few years of poor recruitment and did not include many young sheep, so we could not be too choosy.  Our colleagues in the field caught 9 sheep: one male yearling and 8 ewes aged 1 to 3 years.  They were flown to Ram Mountain in March and April, and we observed them from late May to late September that year and the following year.

Initially, the 'new' sheep were mostly on their own and spent a lot of time alert.  They seemed to avoid the residents, as confirmed by social network analyses. So much for the idea that all sheep are equal and just follow each other.  This was not good, as we had just published results suggesting that sociality increases fitness: there are reasons why sheep behave like sheep!  As the summer progressed, the transplanted sheep spent more time with the residents, but both residents and transplants spent more time alert when in 'mixed' groups, appearing nervous about each other.  The transplanted sheep also received three times more aggressive behaviors, mostly horn butts, than residents of the same age.  Slow social integration appeared to have negative consequences: transplanted sheep gained 20% less mass during the summer than residents of the same age.  That was possibly because they were recovering from the stress of capture and transplant, but we suspect that the difficult social integration and lack of local knowledge about where to forage also played a role.

One year later, the transplanted sheep seemed fully integrated in the local population and their mass gain was similar to that of residents.  They all survived to 2017, when 6 of the 8 ewes produced lambs, contributing to a population increase of 27% from 2016, the highest we have ever seen and close to the theoretical maximum for the species. 

So, what did we learn?  Social integration is important, and genetic rescue is possible but not easy.  The population of 88 sheep in September 2017 is more than double what it was in 2006, but considering that we moved 33 sheep over 10 years, this does not look like a resounding conservation success. Less than half of transplanted sheep contributed genes to the Ram Mountain population. Eleven were still on Ram Mountain in September 2017.  Yet, projections based on vital rates from the last 14 years suggest that without the transplant the population had a high risk of extinction. The transplant was justified, but it was not cheap: it required helicopters and help from wildlife biologists, veterinarians and volunteers.  It was only possible through the initiative and support of Alberta Fish & Wildlife biologists and the Alberta Section of the Wild Sheep Society, hunter-conservationists that contributed both financially and logistically to this exercise.

Ours is not the first well-documented genetic and demographic rescue of a bighorn sheep population: a similar successful experiment was undertaken by Jack Hogg at the National Bison Range in Montana.  Similarly to what we found at Ram Mountain, Jack had documented inbreeding and loss of genetic diversity, while habitat availability and predation did not appear to be limiting factors.  Transplants are expensive and involve risks. They should not be used unless the need is well documented and the chance of success substantial.



The social network of bighorn sheep females and yearling rams at Ram Mountain. Period 1 is from late May to July 2015, period 2 is from August to late September 2015.  Periods 3 and 4 are at the same dates for 2016.  Translocated sheep are yellow, the orange symbols are 9 resident sheep of the same sex-age class as the transplants and grey symbols are other resident sheep.  Circles are females, squares are yearling males.  From Poirier and Festa-Bianchet 2018.


Wooden crates containing bighorn sheep are flown to Ram Mountain, Alberta, April 2015. Photo credit Jon Jorgenson.



 The photo op!  Transplanted sheep released near the sheep trap, April 2015.  All nine sheep released in 2015 were still on the mountain in September 2017.  Photo credit Jon Jorgenson.

Tuesday, January 2, 2018

Should we cite mean people?

The recent #MeToo movement brought to light that some great artists and authors and broadcasters and producers (and others in every sphere of life) were simply despicable people. Like many others, I began to struggle with whether or not I could still watch, like, and admire their work. Shakespeare in Love was one of my favorite movies – but how can I now look at it the same way knowing how Harvey Weinstein treated Gwenth Paltrow and others working on that and his other movies. The opinion of many observers was that we should separate the work of a person from the personality of a person, thus enjoying Shakespeare in Love while detesting the man (one of them anyway) who made it. Others, however, felt that to continue to laud the work of such a horrible person is akin to not punishing that person. With movies, I think it makes a lot of sense to take the first tack, simply because any given movie is the work of many people – and to downgrade that movie for the sins of one contributor is also punishment to the many other people who contributed that movie.

But what about in science? My first impression is that, really, most people in science – at least in my field – are quite nice, helpful, and giving. They generally want to improve the science and advance the careers of those around them – even at some expense to themselves. However, like any sphere of life, truly despicable people exist in science. Fortunately, some of these people have been outed before and after the #MeToo movement – and I hope this trend continues to reveal and punish truly dangerous, predatory, and lascivious scientists.

However, I am here also thinking of “despicable people” in a more general “jerk” sense to include those who are simply mean to others, such as their students, collaborators, field crew, or even competitors. Such meanness can be in-your-face overt insults or degradation or it can be subtle behind-the-scenes (or behind the screen of anonymous peer-review) maneuvering to reject grants or papers of competitors. When we have knowledge of which people out there are jerks, how should we treat their science? Should we read it in discussion groups? Should we invite them for seminars? Should we cite their work? Should we continue to laud them? If these people weren’t influential, then it would perhaps be a much simpler matter, but some them have published exceptional and influential 
studies.

Perhaps, we have less of a conundrum here than in the case of enterprises like movies, where many other people are involved. That is, perhaps we should feel comfortable about punishing (or at least not rewarding) a person by downgrading their science. For instance, I see no reason to invite, for a symposium or key note or even departmental seminar, someone who is a jerk. Also, if a choice exists between citing several different papers, I would happily cite those by nice people over those by known jerks. (Of course, it is sometimes impossible to avoid citing some papers by jerks.)

Yet is more complicated than that. First, jerkiness is in the eye of the beholder. I have met some people who think that a given scientist is the nicest and most helpful person they know, while other people will swear up-and-down that the same person is mean and vindictive. Second, some people might be nice to your face but mean behind the scenes – and this is hard to know. For instance, many people spend time trying to guess who the mean reviewers of their papers or grants were, and then spend years hating that person – even without actual confirmation that their guess was correct. Third, any given paper often has multiple authors and it would not be right to punish other authors of that paper for the sins of one of them. Fourth, meanness is, in part, an interaction between people, such that a given person can very nice to some people but very mean to others.

In the end, perhaps the best approach is to simply not go out of our way to laud people who we know are jerks. Let’s just ignore them whenever we can.



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1. If you are a student, and a professor is being a jerk to you, or engaging in inappropriate behavior toward you or others, then you should definitely report it to the appropriate office in your university – typically the ombudsperson.

2. I am not attempting to name any jerks – you know who they are. Or do you? Some years ago, I was at a reception and talking to an older professor who – unsolicited – starting telling me how downright awful was a (now long dead) man who is universally lauded as one of the most important contributors to the environmental movement.

3. I acknowledge that some people - hopefully not too many - likely think that I am a jerk.

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