OpenPlantPathology Interview — Embrace open science to advance your career

You have a strong presence in social media, together with other prominent plant pathologists, advocating for more open and transparent science and data sharing. Tell us a bit about your background and when you realized that open science and data sharing were important to furthering science

I think I have always been tuned to new technologies and tools. I’m also aware of the importance of science communication and networking. Therefore, it’s perhaps no surprise that I quickly became hooked to Twitter and related social media tools such as Twitter has become an integral part of my daily routine. I use it primarily to broadcast, gather new information and interact with a wide range of people beyond my immediate colleagues. I love that incessant flow of information we get through Twitter. In some ways, I’m addicted to knowledge and social interactions, and Twitter is my drug.

Why tweet?
Open science — a new paradigm in science communication.

How do you compare the overall field of plant pathology to others in relation to the level of adoption of open science practices? Is there any kind of formal education and training that graduate schools/advisors should be more proactive to educate the new generation of scientists, or is this a matter of individual efforts?

I want to start by saying that OPP is an absolutely amazing initiative that stands out from the conservative stance of many of our plant pathologist colleagues. My experience is that plant pathologists tend to be too slow in embracing the cultural changes that are sweeping the biological sciences. For example, a few months ago I participated in a workshop on response to new plant disease outbreaks and some participants argued against open science approaches. There was even opposition to the simple concept of sharing data and biomaterial with experts. Remarkably, our biomedical colleagues manage to do just fine.

Rapid and systematic genome sequencing and publishing of plant pathogens is yet to become a reality.
Get your institution to sign DORA! And then hold them accountable to DORA principles.

You are among several scientists who strongly voice against the current scholarly publishing practices. You have even refused to review and submit articles for some journals because of the publisher. What is your advice for young scientists who expect recognition publishing in Nature/Cell/Science (NCS) journals?

Indeed, it’s well established that scientific publishing is broken at several levels. But the onus shouldn’t be on early career scientists to fix the system, although they can create momentum and enable cultural changes by lobbying for DORA principles, embracing preprints and various other open science initiatives. My advice to early career scientists is to be fully aware that publishing is important. This is our main currency in science. I’m not arguing against that. But to be a successful scientist, it is critical to have a full set of skills.

Work on your weaknesses, don’t neglect them.

As a part of your objections to the current publishing practices you strongly support preprints. What advice do you give for getting started with using preprints?

Preprints are central to the open science philosophy. I really wish to see more preprints in bioRxiv from the plant path community. This is a tremendous way to get your work out there and share it with others much earlier than is traditionally the case [See ASAPBIO Preprint FAQ]. It also relieves the stress associated with waiting for reviews and the tedious revision process. After all, the paper is already out there, so what if the final version takes a few more weeks. It’s liberating to post a preprint just when you finish writing up the paper.

Embrace preprints!

What do you see as the most significant outcome from your work as a result of using open science practices?

One amazing anecdote is that when we went public with the sequences from the wheat blast outbreak in Bangladesh, there was only one (ONE!) genome sequence available of a wheat blast isolate. Obviously, we couldn’t do much in interpreting the Bangladeshi sequences based on a single genome. However, it turned out that several labs had unpublished genome sequences of wheat blast isolates sitting in their computers. Within days, there was over 20 genome sequences available. That goes to show the importance of sharing data and also coming up with processes where depositing datasets is recognized as a scholarly contribution just like any other activity.


Finally, the Open Plant Pathology community welcomes not only pathologists, but anyone who works in the field and wish to stay connected with other researchers to learn and share knowledge and contribute to promote open science and reproducible research. Surely, it does not fit everyone’s needs given the focus of OPP on more computational aspects and use of free open source software (FOSS). What are the areas and target audience that you think might benefit most from participating and taking leadership in this community?

SK: Open science can impact several areas of plant pathology beyond computational biology. One example would be the reporting of new disease outbreaks and the first response to these outbreaks. Think of how basic the ProMED-mail platform is. I think this is the only centralized online platform that rapidly reports new plant disease outbreaks. We should have something akin to a global extension platform with plant pathologists openly contributing advice and analyses on how to respond to these outbreaks. It’s shocking to me that the most common word on ProMED-mail is “undiagnosed”.

Wordcloud summary of Global Plant Diseases registered in Promed. Credit: Ksenia Krasileva.



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Biologist; passionate about science, plant pathogens, genomics, and evolution; loves travel, food, and sports; nomad and hunter-gatherer.