Friday, May 27, 2016

How to deal with poor science?

Publishing research articles is the bedrock of science. Knowledge advances through testing hypotheses, and the only way such advances are communicated to the broader community of scientists is by writing up the results in a report and sending it to a peer-reviewed journal. The assumption is that papers passing through this review filter report robust and solid science.

Of course this is not always the case. Many papers include questionable methodology and data, or are poorly analyzed. And a small minority actually fabricate or misrepresent data. As Retraction Watch often reminds us, we need to be vigilant against bad science creeping into the published literature.

Why should we care about bad science? Erroneous results or incorrect conclusions in scientific papers can lead other researchers astray and result in bad policy. Take for example the well-flogged Andrew Wakefield, a since discredited researcher who published a paper linking autism to vaccines. The paper is so flawed that it does not stand up to basic scrutiny and was rightly retracted (though how it could have passed through peer review is an astounding mystery). However, this incredibly bad science invigorated an anti-vaccine movement in Europe and North America that is responsible for the re-emergence of childhood diseases that should have been eradicated. This bad science is responsible for hundreds of deaths.

From Huffington Post 

Of course most bad science will not result in death. But bad articles waste time and money if researchers go down blind alleys or work to rebut papers. The important thing is that there are avenues available to researchers to question and criticize published work. Now days this usually means that papers are criticized through two channels. First is through blogs (and other social media). Researchers can communicate their concerns and opinion about a paper to the audience that reads their blog or through social media shares. A classic example was the blog post by Rosie Redfield criticizing a paper published in Science that claimed to have discovered bacteria that used arsenic as a food source.

However, there are a few problems with this avenue. First is that it is not clear that the correct audience is being targeted. For example, if you normally blog about your cat, and your blog followers are fellow cat lovers, then a seemingly random post about a bad paper will likely fall on deaf ears. Secondly, the authors of the original paper may not see your critique and do not have a fair opportunity to rebut your claims. Finally, your criticism is not peer-reviewed and so flaws or misunderstandings in your writing are less likely to be caught.

Unlike the relatively new blog medium, the second option is as old as scientific publication –writing a commentary that is published in the same journal (and often with an opportunity for the authors of the original article to respond). These commentaries are usually reviewed and target the correct audience, namely the scientific community that reads the journal. However, some journals do not have a commentary section and so this avenue is not available to researchers.

Caroline and I experienced this recently when we enquired about the possibility to write a commentary on an article was published and that contained flawed analyses. The Editor responded that they do not publish commentaries on their papers! I am an Editor-in-Chief and I routinely deal with letters sent to me that criticize papers we publish. This is important part of the scientific process. We investigate all claims of error or wrongdoing and if their concerns appear valid, and do not meet the threshold for a retraction, we invite them to write a commentary (and invite the original authors to write a response). This option is so critical to science that it cannot be overstated. Bad science needs to be criticized and the broader community of scientists should to feel like they have opportunities to check and critique publications.

I could perceive that there are many reasons why a journal might not bother with commentaries –to save page space for articles, they’re seen as petty squabbles, etc. but I would argue that scientific journals have important responsibilities to the research community and one of them must be to hold the papers they publish accountable and allow for sound and reasoned criticism of potentially flawed papers.

Looking over the author guidelines of the 40 main ecology and evolution journals (and apologies if I missed statements -author guidelines can be very verbose), only 24 had a clear statement about publishing commentaries on previously published papers. While they all had differing names for these commentary type articles, they all clearly spelled out that there was a set of guidelines to publish a critique of an article and how they handle it. I call these 'Group A' journals. The Group A journals hold peer critique after publication as an important part of their publishing philosophy and should be seen as having a higher ethical standard.

Next are the 'Group B' journals. These five journals had unclear statements about publishing commentaries of previously published papers, but they appeared to have article types that could be used for commentary and critique. It could very well be that these journals do welcome critiques of papers, but they need to clearly state this.

The final class, 'Group C' journals did not have any clear statements about welcoming commentaries or critiques. These 11 journals might accept critiques, but they did not say so. Further, there was no indication of an article type that would allow commentary on previously published material. If these journals do not allow commentary, I would argue that they should re-evaluate their publishing philosophy. A journal that did away with peer-review would be rightly ostracized and seen as not a fully scientific journal and I believe that post publication criticism is just as essential as peer review.

I highlight the differences in journals not to shame specific journals, but rather highlight that we need a set of universal standards to guide all journals. Most journals now adhere to a set of standards for data accessibility and competing interest statements, and I think that they should also feel pressured into accepting a standardized set of protocols to deal with post-publication criticism. 

Wednesday, May 25, 2016

Thoughts on successful postdoc-ing

Unlike grad school, postdoc positions start and end without much fanfare. If grad students are apprentices, postdocs are the journeymen/women of the trade. (Wikipedia defines journeymen as… “considered competent and authorized to work in that field as a fully qualified employee… [but] they are not yet able to work as a self-employed master craftsman.”) Though short compared to a PhD, postdoc jobs are an important stepping stone towards a 'real' job, be that another postdoc, or a position inside or outside of academia. There’s less advice out there about being successful as a postdoc, and often you are on your own to figure things out. I’m finishing a first postdoc this week, and moving on to a second one, and while I think the last 2 years worked out well, they took their own, unexpected path. Some of this is good advice that I was given, some comes from experience or observation, some I even manage to follow :-) *

Choose carefully. If you have some choice, be strategic in choosing a postdoc job. Decide what the position is going to accomplish for you: that may be expanding your skill set, such as by learning a new experimental system or additional analytical techniques; improving your current skills by working with an expert; being involved in high profile research; or being in a certain locale for various reasons. Beware projects too far from your current skill set – the risk is that the learning curve may be so steep that you will be barely competent at the end, and have little to show for your time. Of course, you might decide to use a postdoc to pursue interdisciplinary work, or move away from your dissertation work, in which case this is a risk worth taking.

Because postdocs are short, it may seem as though having a good fit with your supervisor is less important. Don’t assume that your new supervisor be broadly similar in approach to your previous supervisor (or an improvement). Mismatched expectations between supervisors and postdocs seem pretty common and it’s important to get an understanding of what your role is beforehand. The variation in expectations from supervisor to supervisor is huge - from those that require time sheets and expect strict hours, to those that give you total autonomy. Does your supervisor see postdocs as colleagues? 9-5 employees? Advanced students? Lab managers? Talk to friends, colleagues, and students. This may depend on the source of funding as well - will you be working on a specific existing project with specific timelines (common in the US where many postdocs are funded off of NSF grants), or are you funded by a fellowship and therefore more independent?

Get to know your neighbours. Once you’ve chosen and started your postdoc, the most important thing to do is to establish connections in your lab and department immediately. I cannot emphasize this enough. Don’t wait to settle in, or get on top of some papers, or hope people in the hallway will introduce themselves. Postdoc positions are short, and in many departments postdocs are isolated, not students but not really faculty. This can lead to feelings of disconnection, loneliness, and frustration. Seek out the other postdocs - join or organize postdoc social events, go to lab meetings and journal clubs, get the department to maintain an active postdoc email list. Not only will this give you a sense of belonging, but now you have people to talk to (and sometimes rant to), with whom to navigate administrative issues, and potential collaborators. Postdocs are an invaluable resource for job applications as well: they usually have the most up-to-date experience on the job market, and can provide great feedback on job applications and practice job talks. For example, the postdocs in my current department built an exhaustive list of potential questions asked during academic interviews, and shared interview horror stories over drinks.

Mental health and life balance. Postdocs don’t get the kinder, gentler approach sometimes given to grad students and people expect you to stand on your own. This can reignite imposter syndrome. There is no easy solution to this, but some combination of taking care of yourself, working on that mythical thick skin, and highlighting the positive events in your life can help.

Time management continues to become more important, at least for me. More than in grad school, you have to actively decide how much work you want to be doing. There is always something that you *could* be working on, so start scheduling when things will get done based on priority, energy, etc, is important. In addition, people start inviting you to things or asking for you input on projects. Learn to say no. Be strategic about your time management – it’s flattering to wanted, but time is limited and not all invitations are of equal value towards your specific goals.

Practice professional networking. On the other hand, don’t say no to everything: networking and the opportunities it creates are very helpful. Focus on the professional areas that are of interest to you, but consider joining and being active in ESA sections (including the Early Career section) or other relevant organizations; organize workshops or symposia at conferences; host invited speakers. If your department hosts an external seminar series, take advantage (nicely!) of the revolving cast of scientists. They are a great way to make connections with people whose work you admire, and even speakers you have less in common with are great practice for networking skills. From experience, if you have breakfast with a different visiting speaker every week, you will quickly improve your description of your research and your ability to keep a conversation going (also, you will become an expert on your city’s breakfast places). These are helpful skills to have for faculty interviews, for talking to the media and press, even for telling your family what you do.

Take initiative. You are your own advocate now. If you wish you could learn something, or be invited to a working group, or get teaching experience, look into making it happen yourself. This may include organizing working groups (many provide competitive funding, for example, iDiv/sDiv, CIEE (Canada), the new NCEAS, SESYNC), applying for small grants and other project funding on your own, recruiting undergraduates and mentoring them, organizing or co-teaching courses.

Similarly, don’t stop learning new things. Inertia gets higher the less time you have, and it can be hard find the time to pick up the next skill.

Focus on publishing (if you are interested in academic jobs)– this may be obvious, but publishing is more important than ever as a postdoc. You need to show that you are independently able to produce work after leaving your PhD lab. This counters the ‘maybe they just had a good supervisor’ concern. It can be hard to find time to work on both current and past projects, but try to. From experience (and illustrated by the periodic emails from my PhD supervisor), the longer your dissertation chapters sit around, the less likely they are to ever be published…

Know what your dream job is, and apply for it if you see it. Be willing to move on if something better comes up. Postdocs usually have to think in the short-term, because most funding is in 1-2 year increments. So keep an eye on new sources of funding/positions. Make decisions based on your needs (be they career-related, family-related, whatever): it’s easy to feel guilty moving on from one unfinished position to another, but the reality is that postdocs are temporary and fleeting.

I was told to start applying for jobs as early as I felt reasonably qualified. The logic was that the best practice for job interviews is doing actual job interviews, and further, it is better to fail when it doesn’t matter, rather than when it is your dream job.

well, sort of...
*Obviously nothing is one-size-fits all, and this is mostly aimed at people who plan to apply for faculty jobs eventually. Other advice, especially for non-academic tracks, would be welcome in the comments!

Friday, May 6, 2016

What’s so great about Spain? Assessing UNESCO World Heritage inequality.

Some places are more valuable than others. We often regard places as being of high or unique value if they possess high biological diversity, ancient cultural artefacts and structures, or outstanding geological features. These valuable places deserve special recognition and protection. The sad reality is that when we are driven by immediate needs and desires, these special places are lost.

The natural world, and the wonderful diversity of plants and animals, is on the losing end of a long and undiminished conflict with human population growth, development, and resource extraction. We don’t notice it when there is ample natural space, but as nature becomes increasingly relegated to a few remaining places, we place a high value on them.

The same can be said for places with significant cultural value. Ancient temples, villages, and human achievement are too valuable to lose and we often only have a few remnants to connect us to the past.

In either case, natural or cultural, when they’re gone, we lose a part of us. That is because these special places tell us about ourselves; where we come from, how the world shaped us, and what unites all of humanity. Why did the world cry out in a united voice when the Taliban destroyed the Buddhas of Bamiyan in 2001, even though many of those concerned people were not Buddhist? The answer is simple –the expansion of Buddhism out of India along ancient trade routes tells us why many Asian nations share a common religion. They tell us about ourselves, the differences that interest us, and the similarities that bind us. The same can be said about the global outcry over the recent destruction of the ancient city of Palmyra by ISIS.

Before and after photos of the taller of the Buddhas of Bamiyan. Image posted by Carl Montgomery CC BY-SA 3.0.

Similarly, the natural world tells us about ourselves. The natural world has constantly shaped and influenced what it means to be human. Our desires, fears, and how we interact with the natural world are products of our evolution. If I flash a picture of a car to my 500-student ecology class, very few students, if any, screech in fear. But if I flash a photo of a hissing cobra or close-up of a spider, invariably a bunch of students squirm, gasp, or scream. Rationally, this is an odd response, since cars are the leading cause of death and injury in many western countries. Snakes and spiders kill very few people in Canada.

These special places deserve recognition and protection, and that is what the UNESCO World Heritage designation is meant to achieve. To get this designation for a site requires that countries nominate ones that represent unique and globally significant contributions to world heritage, and are adequately protected to ensure the long-term existence of these sites.  World Heritage sites are amazing places. They represent the gems of our global shared heritage. They need to be protected in perpetuity and should be accessible to all people. Though some I have visited seem like they are loved too much with high visitation rates degrading some elements of Heritage sites.

Examples of UNESCO World Heritage sites. A) The Great Wall of China. B) The Gaoligong Mountains, part of the Three Parallel Rivers of Yunnan. C) Angkor Wat in Cambodia. D) An example of a site that may be too loved -Lijiang in Yunnan. All photos by Shirley Lo-Cadotte and posted on our family travel blog -All The Pretty Places.

UNESCO World Heritage sites should also be representative. What I mean by this is that they should be designated regardless of national borders. Heritage sites are found on all continents across most countries –though a number of politically unstable countries (e.g., Liberia, Somalia, etc.) do not possess Heritage sites, likely because they lack the organization or resources to undertake the designation application process, and they lack the governance to ensure a site is adequately protected. But there are substantial differences in the number of World Heritage sites across nations[1]. Some countries, because of inherent priorities, national pride, resources or expertise, are better able to identify and persuade UNESCO that a particular place deserves designation.

The distribution of the number of UNESCO World Heritage sites across countries and the top ten.

Why do we see such disparity in the number of World Heritage sites -where many countries have few sites, and a few countries have many sites? This is a difficult question to answer, and to do so I took an empirical approach. I combined data on the number of sites per country with Gross Domestic Product (GDP)[2], country size[3], and country population size[4]. I then ran simple statistical analyses to figure out what predicts the number of Heritage sites, and identified those countries that are greatly over-represented by Heritage sites, and those that are very under-represented. A couple things to note, the best statistical models included variables that were all log-transformed, I excluded the World Heritage sites that spanned more than one country, and I did not include countries that did not have any Heritage sites. The data and R code have been posted to Figshare and are freely available.

All three of GDP, area, and population size predicted the number of World Heritage sites. It is important to note that these three country measures are not strongly correlated with one another (only moderately so). So, larger, richer and more populous countries had more World Heritage sites. This makes sense –big countries should contain more unique sites due to random chance and more populous countries tend to have longer historical presence of organized states, and so should possess more cultural relics (especially China). GDP is more difficult to assign a reason, but high GDP countries should have robust national parks or other bureaucratic structures that assess and protect important sites, making them easier to document and justify for UNESCO.  GDP is quite interesting, because it is the single best measure for predicting the number of Heritage sites, better than population size and area. Further, neither country density (population/area) nor productivity (GDP/population) are strong predictors of the number of Heritage sites.

The relationships between the number of World Heritage sites and GDP, area, and population. Note that the axes are all log-transformed.

While these relationships make sense, it is also clear that countries are not all close to the main regression line and some countries are well above the line –meaning they have more Heritage sites than predicted; as well as some below the line and thus having fewer sites. When I combine the different measures in different combinations and look for the best single statistical explanation for the number of World Heritage sites, I find that the combination including GDP and population size, and their interaction (meaning that population size is more important for high GDP countries) is the best. For aficionados, this model explains about 65% of the variation in the number of Heritage sites.

Now, we can identify those countries that are over or under represented by UNESCO World Heritage sites according to how far above or below countries are from the predicted line (technically, looking at statistical residuals).

The deviation of countries from the predicted relationship between the number of sites and GDP and population (and their interaction). The top 5 over-represented and under-represented countries are highlighted.

The top five over-represented countries are all European, which means that given their GDP and population size, these countries have more World Heritage sites than expected. At the other extreme, countries under-represented come from more diverse regions including Africa, the Middle East and Southeast Asia.

An interesting comparison to think about is Germany and Indonesia. Germany has more World Heritage sites than expected (residual = +0.61) and is a moderately sized, high GDP country. Let me say, I like Germany, I’ve been there a half a dozen times, and it has beautiful landscapes and great culture. However, does it deserve so much more World Heritage recognition than Indonesia, which has fewer sites than expected (residual = -0.63)? Indonesia has spectacular landscapes and immense biodiversity and great cultural diversity and history. To put it in perspective, Germany has 35 World Heritage sites and Indonesia has just 8.

To answer the question in the title of this post: what’s so great about Spain? Well, it not only has beautiful and diverse natural landscapes and cultural history, but it appears to have the infrastructure in place to identify and protect these sites. It's place at the top of UNESCOs relative (to GDP and population) ranking of the number of World Heritage sites means that Spain's natural and cultural wonders are in good hands. However, for the countries at the other end of the spectrum, having relatively few World Heritage sites probably is not a reflection of these countries being uninteresting, or that they have little to offer the world, rather it is something more alarming. These places lack the financial capacity or national will to fully recognize those places that are of value to the whole world. The problem is that the globally important heritage that does exist in these places is at risk of being lost. These under-represented countries serve as a call to the whole world to help countries not just identify and protect heritage sites but to aid these countries with infrastructure and human well-being that empowers them to prioritize their natural and cultural heritage.

Wednesday, May 4, 2016

The future of community phylogenetics

Community phylogenetics has received plenty of criticism over the last ten years (e.g. Mayfield and Levine, 2010; Gerhold et al. 2015). Much of the criticism is tied to concerns about pattern-based inference, the use of proxy variables, and untested assumptions. These issues are hardly unique to community phylogenetics, and I think that few ideas are solely ''good or solely 'bad'. They are useful in moulding our thinking as ecologists and inspiring new directions of thought. Many influential ideas in ecology have bobbled in confidence through time, but remain valuable nonetheless [e.g. interspecific competition, character displacement (Schoener 1982; Strong 1979)]. But still, it can be hard to see exactly how to use phylogenetic distances to inform community-level analyses in a rigorous way. Fortunately, there is research showing exactly this. The key, to me at least, to avoid treating a phylogeny as just another matrix to analyze, but to consider and test the mechanisms that might link the outcome of millions of years of evolution to community-level interactions.

A couple of potential approaches to move forward questions about community phylogenetics are discussed below. The first is to consider the mechanisms behind the pattern-inference analyses and ask whether assumptions hold.

1) Phylogenies and traits - testing assumptions about proxy value
As you know, if you have read the introductory paragraph of many community phylogenetic papers, Charles Darwin was the first to highlight that two closely related species might have different interactions than two distantly related species. People have tested this hypothesis in many ways in various systems, with mixed results. The most important directions forward is to make explicit the assumptions behind such ideas and experimentally test them. I.e. Do phylogenetic distances/divergence between species capture trait and ultimately ecological divergence between species?

From Kelly et al. 2015 Fig 1b.
Because evolutionary divergence should relate to feature divergence (sensu Faith), the most direct question to ask is how functionally important trait differences increase with increasing phylogenetic distances. For example, Kelly et al. (2014) found that “close relatives share more features than distant relatives but beyond a certain threshold increasingly more distant relatives are not more divergent in phenotype”, although in a limited test based only on patristic distances. This suggests that at short distances, phylogenetic distances may be a reasonable proxy for feature divergence, but that the relationship is not useful for making predictions about distant relatives.

Phylogenies and coexistence/competition. Ecological questions about communities may not be interested in traits alone. The key assumption behind many early analyses was that closely related species shared more similar *niches*, and so competed more strongly than distantly related species. Thus the question is one step removed from trait evolution, asking instead how phylogenetic divergence correlates into fitness differences or interaction strength. Not surprisingly, current papers suggest there is a fairly mixed, less predictable relationship between phylogenetic relatedness and competitive outcomes.

Recent findings have varied from “Stabilising niche differences were unrelated to phylogenetic distance, while species’ average fitness showed phylogenetic structure” (California grassland plants, Godoy et al. 2014); to, there is no signal in fitness or niche differences (algae species, Narwani et al. 2013); to, when species are sympatric, both stabilizing and fitness differences increase with phylogenetic distance (mediterranean annual plants; Germain et al. 2016). Given constraints, tradeoffs and convergence of strategies, it is really not surprising that the idea of simply inferring the importance of competition from patterns along a phylogenetic tree is not generally possible (Kraft et al. 2015; blogpost).

2) Phylogenies and the regional species pool
Really more interesting than testing for proxy value is to think about the mechanisms that tie evolution and community dynamics together. A key role for evolution in questions about community ecology is to ask what we can learn about the regional species pool—from which local communities are assembled. What information about the history of the lineages in a regional species pool informs the composition of local composition?

The character of the regional species pool is determined in part by the evolutionary history of the region, and this can in turn greatly constrain the evolutionary history of the community (Bartish et al. 2010). The abundance of past habitat types may alter the species pool, while certain communities may act as 'museums' harbouring particular clades. For example, Bartish et al. 2016 found that the lineages represented in different habitat types in a region differ in the evolutionary history they represent, with communities in dry habitats disproportionately including lineages from dry epochs and similar for wet habitats. Here, considering the phylogeny provides insight into the evolutionary component of an ecological idea like 'environmental filtering'.

Similarly, species pools are formed by both ecological processes (dispersal and constraints on dispersal) and evolutionary ones (extinctions, speciation in situ), and one suggestion is that appropriate null models for communities may need to consider both ecological and evolutionary processes (Pigot and Etienne, 2015).
Invasive species also should be considered in the context of evolution and ecology. Gallien et al. 2016 found that “currently invasive species belong to lineages that were particularly successful at colonizing new regions in the past.”

I think using phylogenies in this way is philosophically in line with ideas like Robert Ricklef's 'regional community' concept. The recognition is that a single time scale may be limiting in terms of understanding ecological communities.

  1. Mayfield, Margaret M., and Jonathan M. Levine. "Opposing effects of competitive exclusion on the phylogenetic structure of communities." Ecology letters 13.9 (2010): 1085-1093.
  2. Gerhold, Pille, et al. "Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)." Functional Ecology 29.5 (2015): 600-614.
  3. Schoener, Thomas W. "The controversy over interspecific competition: despite spirited criticism, competition continues to occupy a major domain in ecological thought." American Scientist 70.6 (1982): 586-595. 
  4. Strong Jr, Donald R., Lee Ann Szyska, and Daniel S. Simberloff. "Test of community-wide character displacement against null hypotheses." Evolution(1979): 897-913. 
  5. Kelly, Steven, Richard Grenyer, and Robert W. Scotland. "Phylogenetic trees do not reliably predict feature diversity." Diversity and distributions 20.5 (2014): 600-612.
  6. Godoy, Oscar, Nathan JB Kraft, and Jonathan M. Levine. "Phylogenetic relatedness and the determinants of competitive outcomes." Ecology Letters17.7 (2014): 836-844.
  7. Narwani, Anita, et al. "Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae." Ecology Letters 16.11 (2013): 1373-1381.
  8. Rachel M. Germain, Jason T. Weir, Benjamin Gilbert. Species coexistence: macroevolutionary relationships and the contingency of historical interactions. Proc. R. Soc. B 2016 283 20160047
  9. Nathan J. B. Kraft, Oscar Godoy, and Jonathan M. Levine. Plant functional traits and the multidimensional nature of species coexistence. 2015. PNAS.
  10. Bartish, Igor V., et al. "Species pools along contemporary environmental gradients represent different levels of diversification." Journal of Biogeography 37.12 (2010): 2317-2331.
  11. IV Bartish, WA Ozinga, MI Bartish, GW Wamelink, SM Hennekens. 2016. Different habitats within a region contain evolutionary heritage from different epochs depending on the abiotic environment. Global Ecology and Biogeography
  12. Pigot, Alex L., and Rampal S. Etienne. "A new dynamic null model for phylogenetic community structure." Ecology letters 18.2 (2015): 153-163.
  13. Gallien, L., Saladin, B., Boucher, F. C., Richardson, D. M. and Zimmermann, N. E. (2016), Does the legacy of historical biogeography shape current invasiveness in pines?. New Phytol, 209: 1096–1105.