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On Critical Evaluation in Ecology

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Science proceeds by “conjecture-and-refutation” if we agree with Karl Popper (1963). There is a rich literature on science in general and ecological science in particular that is well worth a series of graduate discussions even if it is pre-2000 ancient history (Peters 1991, Weiner 1995, Woodward and Goodstein 1996). But I wish to focus on a current problem that I think is hindering ecological progress. I propose that ecological journals at this time are focusing their publications on papers that present apparent progress and are shedding papers that are critical of apparent progress. Or in Popper’s words, they focus on publishing ‘conjecture’ and avoid ‘refutation’. The most important aspect of this issue involves wildlife management and conservation issues. The human side of this issue may involve personal criticism and on occasion the loss of a job or promotion. The issue arises in part because of a confusion between the critique of ideas or data and the interpretation that all critiques are personal. So, the first principle of this discussion is that I discuss here only critiques of ideas or data.

There are many simple reasons for critiques of experimental design and data gathering. Are the treatments replicated, are the estimates of data variables reliable and sufficient, are proxy variables good or poor? Have the studies been carried out long enough? All these critiques can be summarized under the umbrella of measurement reliability. There are many examples we can use to illustrate these ideas. Are bird populations declining across the globe or locally? Are fisheries overharvesting particular species? Can we use climate change as a universal explanation of all changes in wildlife populations? Are survey methods for population changes across very large areas reliable? The problem is tied into the need for good or bad news that must be filtered to the news media or social media with high impact but little reliability. 

The problem at the level of science is the temptation to extrapolate beyond the limits of the available data. Now we come to the critical issue – how do our scientific journals respond to critical reviews of papers already published? My concern is that in the present time journals do not wish to receive or accept manuscripts that are critical of previously published papers. These decisions are no doubt confidential for journal publishers. There is perhaps some justification for this rejection policy, given that in the few cases where critiques are published on existing papers, the citation score of the original paper may greatly exceed that of the critique. So, conjecture pays, refutation does not.

Journals are flooded with papers and for the better journals I would expect at least a 60-80% rejection rate. For Science the rejection rate is 94%, for Nature 92%, and for the Journal of Animal Ecology 85% of submitted manuscripts are rejected. Consequently, the suggestion that they reserve space for ‘refutation’ is too negative to their publication model. There is little I can suggest if one in caught in this dilemma except to try another less premium journal, and remember that web searches find papers easily no matter where published. If you need inspiration, you can follow Peters (1991) and write a book critique and suffer the brickbats from the establishment (e.g. Nature 354: 444, 12 December 1991).

But if you are upset about a particular paper or series of papers, remember critiques are valuable but follow these rules for a critique:

  1. Keep it short, 5 typed pages should be near maximal length.
  2. Raise a set of major points. Do not try to cover everything.
  3. Summarize briefly the key points you are in agreement with, so they are not confounded in the discussion.
  4. Discuss what studies might distinguish hypothesis A vs B, or A+B vs C.
  5. Discuss what better methods of measurement might be used if funding is available.
  6. Never attack individuals or research groups. The discussion is about ideas, results, and inferences.

Decisions to accept some management actions may have to be taken immediately and journal editors must take that into consideration. Prognostication over accepting critiques may be damaging. But all actions must be continually evaluated and changed once the understanding of the problem changes.

There are too many examples to recommend reading about past and present controversies in ecology, so here are only two examples. Dowding et al. (2009) report a comment on suggested methods of controlling introduced pests on Macquarie Island in the Southern Ocean. I was involved in that discussion. A much bigger controversy in Canada involves Southern Mountain caribou populations which are in rapid decline. The proximate explanation for the decline is postulated to be predation by wolves and thus the suggested management action is shooting the wolves. Johnson et al. (2022), Lamb et al. (2022) and Superbie et al. (2022) provide an entre into this literature and the decisions of what to do now and in the future to prevent extinction of these ungulates. The caribou problem is complicated by the interaction of human alteration of landscapes and the natural processes of predation and food availability. Alas nothing is simple.

All these ecological dilemmas are controversial and the important role of criticism involving evaluations of alternative hypotheses are the only way forward for ecologists involved in controversies. In my opinion most ecological journals are not doing their part is publishing critiques of the conventional wisdom.

Dowding, J.E., Murphy, E.C., Springer, K., Peacock, A.J. & Krebs, C.J. (2009) Cats, rabbits, Myxoma virus, and vegetation on Macquarie Island: a comment on Bergstrom et al. (2009). Journal of Applied Ecology, 46, 1129-1132. doi: 10.1111/j.1365-2664.2009.01690.x.

Johnson, C.J., Ray, J.C. & St-Laurent, M.-H. (2022) Efficacy and ethics of intensive predator management to save endangered caribou. Conservation Science and Practice, 4: e12729. doi: 10.1111/csp2.12729.

Lamb, C.T., Willson, R., Richter, C., Owens-Beek, N., Napoleon, J., Muir, B., McNay, R.S., Lavis, E., Hebblewhite, M., Giguere, L., Dokkie, T., Boutin, S. & Ford, A.T. (2022) Indigenous-led conservation: Pathways to recovery for the nearly extirpated Klinse-Za mountain caribou. Ecological Applications 32 (5): e2581. doi: 10.1002/eap.2581.

Peters, R.H. (1991) A Critique for Ecology. Cambridge University Press, Cambridge, England. 366 pp. ISBN:0521400171.

Popper, K.R. (1963) Conjectures and Refutations: The Growth of Scientific Knowledge. Routledge and Kegan Paul, London. 412 pp. ISBN-13: 978-0415285940.

Superbie, C., Stewart, K.M., Regan, C.E., Johnstone, J.F. & McLoughlin, P.D. (2022) Northern boreal caribou conservation should focus on anthropogenic disturbance, not disturbance-mediated apparent competition. Biological Conservation, 265, 109426. doi: 10.1016/j.biocon.2021.109426.

Weiner, J. (1995) On the practice of ecology. Journal of Ecology, 83, 153-158.

Woodward, J. & Goodstein, D. (1996) Conduct, misconduct and the structure of science. American Scientist, 84, 479-490.

On Administration and Scientific Progress

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After talking and listening to my colleagues and friends who are still employed, I have the urge to try to quantify the utility of administrative meetings to scientific progress. I begin with a very simple model of what this relationship might look like.

The Neutral Model suggests that scientific progress is independent from the number of meetings that are focused on the scientific problem at hand. This is most likely the preferred model of administrators. The Optimistic Model suggests that scientific progress is positively related to the number of administrative meetings, possibly because the coordination among the members of the scientific team is enhanced. The Pessimistic Model suggests that the reverse is true, and if you as a scientific director wish to slow the progress of your scientific team, you should schedule many meetings all the time, presumably with a long agenda.

It is far from clear which model is appropriate for an ecological scientific team and more research is needed on this topic. Many scientists struggling with measurements and data collection are possibly attracted to the Pessimistic Model because time is the limiting element in their lives and both data and results are what limit progress. On the other hand, scientific administrators are possibly drawn to the Optimistic Model if they believe that meetings are the most important point of scientific progress and time is not the limiting factor, or perhaps they are drawn to the Neutral Model if they assume their scientists will work diligently and achieve the same goals no matter how many meetings are scheduled.

I hesitate to present this model given that the underlying mathematics are relatively simple, plus there are probably more business textbooks that make a detailed analysis of this issue than there are words in this blog. In a more realistic framework, we may have a peaked curve that indicate many meetings early in a project and fewer meetings once things are moving forward smoothly. There is going to be no magic numbers here, and the only purpose of this brief discussion is to think about how much you need to meet to define and deliver a set of objectives for a scientific question.

All my speculations above arose from an old paper (Moss 1978) illustrating these same general principles. Parkinson (1958) framed the law that “Work Expands To Fill The Time Available For Its Completion” and showed one consequence of this was that the fraction of administrators within a public organisation tends to increase irrespective of the amount of external scientific work done by that organisation. Moss (1978) produced these data to illustrate this law for British science data from 1976-77, illustrated in this graph:

Moss (1980) further elaborated on how Parkinson’s Law applied to scientific research organizations and noted that it may apply to many other research organizations. Although it is an old ‘law’ it may still be worth some discussion and consideration today.

Moss, R. (1978). An empirical test of Parkinson’s Law. Nature 273, 184. doi: 10.1038/273184a0.

Moss, R. (1980). Expanding on Parkinson’s Law. Nature 285, 9. doi: 10.1038/285009a0.

On Rice and Climate Change

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After I retired, I was privileged to be able to team-teach a short course in pest management at the International Rice Research Institute at Los Baños in the Philippines. The course was run by Grant Singleton and David Johnson and was taught every second or third year to about 30 young scientists from Southeast Asia who were mostly concerned about rice cultivation, rodent pests and weeds in rice. The course was an eye-opener for me both to the world of rice, the extensive and excellent research going on at IRRI on rice cultivation, and the very bright and enthusiastic young scientists from Southeast Asia, many of which had never traveled outside their home country before taking this course.

Why should we worry about rice? Rice is the staple food of at least 4 billion people on Earth. That is one clear message that defines its importance for humans. When I was revising my ecology textbook some years ago, one of the reviewers complained about all the material on rice in my book and asked why I did not use more North American crops for examples. We should not be this short-sighted. Population growth and food security are now front-page issues on every continent, and scientists at IRRI (established in 1960 and now with more than 1000 staff) continue to do research with the goal of improving the yield of rice varieties and the livelihood of rice farmers around the world. Much of IRRI’s research has involved developing and improving varieties of rice to make them more productive, and our ecological goal in teaching about the ecology of pest management was to suggest ways of reducing losses to rice pests that could range from 15-40% of the total crop (Htwe et al. 2019). But as IRRI scientists realized long ago, the quality of the rice crop is as important as the quantity.

Whither rice cultivation in a world of climate change? Changing temperature and rainfall are key concerns for all crops but nutritional value is another. Zhu et al. (2018) have reviewed the possible effects of rising CO2 on the nutritional value of rice. The answer is not good. At many different sites Zhu et al. (2018) grew 18 varieties of rice in FACE (Free Air CO2 Enriched) experiments and measured the changes in the quality of the rice in protein and vitamin content. Current levels of CO2 are about 410 ppm, and in their experiments, they increased CO2 to 570-590 ppm (the level expected within this century). One graph illustrates their main results:

Folate (vitamin B12) is not shown because it is off the graph at -30.3% decrease.

About 600 million people, primarily in Southeast Asia, consume ≥50% of their per capita dietary energy and/or protein directly from rice (Smith and Myers 2019). The concern is that even small losses of these vitamins in rice caused by higher CO2 could have potentially large impacts on global health, placing tens of millions of people at new risk of deficiencies in one or more of these nutrients. Singer et al. (2019) review the main biotechnological research strategies that are currently underway with the aim of improving photosynthetic efficiency and biomass production/yields in the context of a future of rising CO2. Rising temperatures change the developmental processes of plants and the key for crops is artificial selection for varieties more adapted to warm temperature but for wild plants only relatively slow natural selection is available to achieve the same goals, which may well increase the rate of extinction of our native plants without some intervention (Lippmann et al. 2019).

Another issue that is behind rice cultivation as well as all modern agriculture is soil nutrient conservation. At IRRI they grew several rice varieties for demonstration purposes, cultivating them on rich volcanic soils. One of their treatment plots was a control – no fertilizers were added, and the same unchanged rice variety was used each year. One of the results of these demonstration plots was that the control plot, which we had assumed should be stable and sustainable, was declining in rice production per ha at a rate of 1-2% per year. During the 38-year study (1968-2005) climate was changing, CO2 was increasing, air pollution may have changed, so that soil productivity is only one possible explanation of these declining rice yields. Slow changes in soil fertility are difficult to track and yet vitally important in the long run if we are to have sustainable agriculture under climate change and human population growth. Now it is clear that we not only need to maintain soil fertility in agricultural soils for high productivity but also need to be concerned about high quality of the grains and vegetables being produced in a climate-changing world. We do not live in a constant environment and can no longer assume stability in the quality of our food supplies.

Htwe, Nyo Me, Singleton, G.R. and Johnson, D.E. (2019). Interactions between rodents and weeds in a lowland rice agro-ecosystem: the need for an integrated approach to management. Integrative Zoology 14, 396-409. doi: 10.1111/1749-4877.12395

Lippmann, R. et.al. (2019). Development of wild and cultivated plants under global warming conditions. Current Biology 29, R1326-R1338. doi: 10.1016/j.cub.2019.10.016

Singer, S.D. et al. (2019). Biotechnological strategies for improved photosynthesis in a future of elevated atmospheric CO2. Planta 251, 24. doi: 10.1007/s00425-019-03301-4.

Smith, M.R. and Myers, S.S. (2019). Global health implications of nutrient changes in rice under high atmospheric carbon dioxide. Geohealth 3, 190-200. doi: 10.1029/2019GH000188

Zhu, C. et al. (2018). Carbon dioxide (CO2) levels this century will alter the protein, micronutrients, and vitamin content of rice grains with potential health consequences for the poorest rice-dependent countries. Science Advances 4, eaaq1012. doi: 10.1126/sciadv.aaq1012 

On Political Ecology

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When I give a general lecture now, I typically have to inform the audience that I am talking about scientific ecology not political ecology. What is the difference? Scientific ecology is classical boring science, stating hypotheses, doing experiments or observations to gather the data, testing the idea, and accepting or rejecting it, outlined clearly in many papers (Platt 1963, Wolff and Krebs (2008), and illustrated in this diagram:

Scientific ecology is clearly out-of-date, and no longer ‘cool’ when compared to the new political ecology.

Political ecology is a curious mix of traditional ecology added to the advocacy issue of protecting biodiversity. Political ecology is aimed at convincing society in general and politicians in particular to protect the Earth’s biodiversity. This is a noble cause, and my complaint is only that when we advocate and use scientific ecology in pursuit of a political agenda we should be scientifically rigorous. Yet much of biodiversity science is a mix of belief and evidence, with unsuitable evidence used in support of what is a noble belief. If we believe that the end justifies the means, we would be happy with this. But I am not.

One example will illustrate my frustration with political ecology. Dirzo et al. (2014) in a recent Science paper give an illustration of the effects of removing large animals from an ecosystem. In their Figure 4, page 404, a set of 4 graphs purport to show experimentally what happens when you remove large wildlife species in Kenya, the Kenya Long-term Exclosure Experiment (Young et al. 1997). But this experiment is hopelessly flawed in being carried out on a set of plots of 4 ha, a postage stamp of habitat relative to large mammal movements and ecosystem processes. But the fact that this particular experiment was not properly designed for the questions it is now being used to address is not a problem if this is political ecology rather than scientific ecology. The overall goal of the Dirzo et al. (2014) paper is admirable, but it is achieved by quoting a whole series of questionable extrapolations given in other papers. The counter-argument in conservation biology has always been that we do not have time to do proper research and we must act now. The consequence is the elevation of expert opinion in conservation science to the realm of truth without going through the proper scientific process.

We are left with this prediction from Dirzo et al. (2014):

“Cumulatively, systematic defaunation clearly threatens to fundamentally alter basic ecological functions and is contributing to push us toward global-scale “tipping points” from which we may not be able to return ……. If unchecked, Anthropocene defaunation will become not only a characteristic of the planet’s sixth mass extinction, but also a driver of fundamental global transformations in ecosystem functioning.”

I fear that statements like this are more akin to something like a religion of conservation fundamentalism, while we proclaim to be scientists.

Dirzo, R., Young, H.S., Galetti, M., Ceballos, G., Isaac, N.J.B. & Collen, B. (2014) Defaunation in the Anthropocene. Science, 345, 401-406.

Platt, J.R. (1964) Strong inference. Science, 146, 347-353.

Wolff, J.O. & Krebs, C.J. (2008) Hypothesis testing and the scientific method revisited. Acta Zoologica Sinica, 54, 383-386.

Young, T.P., Okello, B.D., Kinyua, D. & Palmer, T.M. (1997) KLEE: A long‐term multi‐species herbivore exclusion experiment in Laikipia, Kenya. African Journal of Range & Forage Science, 14, 94-102.