Category Archives: General Ecology

What Do We Need to Know About Covid-19?

2 Replies

We are currently in a chaotic mess about how to come out of the covid-19 pandemic with minimal casualties and grace. Why should this be? We have had enough examples of pandemics within the last century or two to have some ideas about what will work and what will not, but it would appear that this information is not being used effectively. Part of this can be explained away by the actions of political figures who are incompetent beyond belief, but this is not the only cause of the problem. We have many first-class epidemiologists and modellers around the world working on plans for dealing with covid-19 but there is less coordinated planning than would seem desirable. Perhaps the lack of coordination is highly desirable. We now have experimental situations that any field ecologist would be ecstatic about – cruise ships that are closed systems of potential infections in replicate, states and provinces that practice self-distancing at 1.5 to 2 m and others that ignore this infringement on their liberty or because of poverty do not have the luxury of having enough spacious accommodation to self-distance. Why with all these measurements, good intentions, and data from testing for the virus and antibodies is the picture on what best to do still so cloudy? Given the operational suggestions of social distancing at 2 m, avoiding crowds, washing hands frequently, what ideas need testing to make life less forced? Here are my challenges for some evidence-based questions to answer:

  • Is all covid transmission people to people, and not via door nobs, handrails, and counter tops so that all the cleaning is a waste of resources, time and money? But does cleaning reduce other infections so that it has a net benefit to society?
  • Distance works, but exactly what distance 1m. 1.5 m, 2m? And note 2 m ≠ 6 feet.
  • Are school kids basically immune so that schools should not be closed if teachers can be kept covid free and tested? If we can keep students and teachers safe, it is a colossal waste of resources to close schools, colleges, and universities and pretend that on-line teaching will educate properly (in spite of the clever on-line methods being developed).
  • Given that old people can be protected from covid-19 and given distancing precautions, it is not clear that the mortality from covid-19 for those aged 15 to 60 is much different from the annual flu that runs around year after year. If covid-19 is indeed 5x as toxic as ordinary flu and persists like ordinary flu, how much are we willing as a society to completely reorganize to keep old people safe?
  • Is relying on a vaccine to restore normal life dangerous? Do strategies that are partially effective need further discussion for a Plan B? We may find ourselves in the same situation we have currently with the normal flu virus, partial immunity but not complete and many people refusing vaccinations.
  • Does asymptomatic transmission of covid-19 actually occur, or is it more likely due to poor testing methods and poor patient memory?
  • How much of the covid-19 mortality is ‘natural selection’, how much bad luck, how much is not being self isolated after being warned, how much is the prevailing belief that we can do anything and the doctors will save us?

In my opinion, having 50 or 200 research groups working on covid-19 vaccines when malaria, diphtheria, and TB ravages the poor of the world is more “rich white people are all that matter”. If we wish to put all these resources into one virus, we should provide an equal effort for the poor among us so that our promise is not only “bring covid-19 under control” but rather “bring poverty under control”.

On Ecological Models and the Coronavirus

Leave a reply

We are caught up now in a coronavirus pandemic with an unknown end point. There is a great deal now available about COVID-19, and I want to concentrate on the models of this pandemic that currently fill our media channels. In particular I want to use the current situation to reflect on the role of mathematical models in helping to solve ecological problems and make predictions of future trends. To oversimplify greatly, the scientific world is aligned along an axis from those supporting simple models to those tied up in complex multifactor models. To make this specific, the simple epidemic model approach provides us with a coronavirus model that has three classes of actors – susceptible, infected, and recovered individuals, and one key parameter, the relative infection rate of one person to another. If you as an infected person pass on the disease to more than one additional person, the pandemic will grow. If you pass the disease on to less than one person (on average), the pandemic will collapse. Social distancing will flip us into the favourable state of declining infections. There is a similar sort of model in ecology for predator-prey interactions, called the Lotka-Volterra model, in which one predator eating one prey species will change the population size of both depending on the rate of killing of the predator and the rate of reproduction of the prey.

So far so good. We can all have an intuitive understanding of such simple models, but of course the critics rise up in horror with the cry that “the devil is in the details”. And indeed this is also a universal truth. All humans are not equally affected by COVID-19. Older people do poorly, young children appear to be little bothered by the virus. All prey individuals in nature are also not equally susceptible to being caught by a predator. Young prey may not run as fast as adults, poorly fed prey in winter may run more slowly than well fed animals. The consequences of this ‘inequality’ is what leads to the need for an increasing investment in scientific research. We can pretend the world is simple and the virus will just “go away”, and a simple view of predation that “larger animals eat smaller animals” could fail to recognize that a small predator might drive a dinosaur species extinct if the small predator eats only the eggs of the prey and avoids the big adults. The world is complicated, and that is what makes it both interesting to many and infuriating to some who demand simplicity.

One of the purposes of a mathematical model is to allow predictions of coming events, and we hear much of this with the COVID-19 models currently in circulation. A simple principle is “all models are wrong’ but this must be matched with the corollary that in general “the simpler the model the more likely it is to provide poor forecasts. But there is a corollary that might be called the “Carl Walters’ Law” that there is some optimal level of complexity for a good result, and too much complexity is also a recipe for poor projections. The difficulty is that we can often only find this optimal point after the fact, so that we learn by doing. This does not sit well with politicians and business-people who demand “PRECISE PRECISION PROMPTLY!” 

These uncertainties reflect on to our current decision making in the coronavirus pandemic, in issues to fight climate change, and in the conservation of threatened species and ecosystems. Our models, our scientific understanding, and our decisions are never perfect or complete, and as we see so clearly with COVID-19 the science in particular can be pushed but cannot be rushed, even when money is not limiting. The combination of planning, judgement and knowledge that we call wisdom may come more slowly than we wish. Meanwhile there are many details that need investigation.  

Adam, D. (2020) Modelling the Pandemic: The simulations driving the world’s response to COVID-19. Nature, 580, 316-318. Doi: 10.1038/d41586-020-01003-6 

Neher, R.A., Dyrdak, R., Druelle, V., Hodcroft, E.B. & Albert, J. (2020) Potential impact of seasonal forcing on a SARS-CoV-2 pandemic. Swiss Medical Weekly 150, w20224. Doi: 10.4414/smw.2020.20224.

Xu, B., Cai, J., He, D., Chowell, G. & Xu, B. (2020) Mechanistic modelling of multiple waves in an influenza epidemic or pandemic. Journal of Theoretical Biology, 486, 110070. Doi: 10.1016/j.jtbi.2019.110070.

On Rice and Climate Change

Leave a reply

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 Declining Bird Populations

2 Replies

The conservation literature and the media are alive with cries of declining bird populations around the world (Rosenberg et al. 2019). Birds are well liked by people, and an important part of our environment so they garner a lot of attention when the cry goes out that all is not well. The problems from a scientific perspective is what evidence is required to “cry wolf’. There are many different opinions on what data provide reliable evidence. There is a splendid critique of the Rosenberg et al paper by Brian McGill that you should read::
https://dynamicecology.wordpress.com/2019/09/20/did-north-america-really-lose-3-billion-birds-what-does-it-mean/

My object here is to add a comment from the viewpoint of population ecology. It might be useful for bird ecologists to have a brief overview of what ecological evidence is required to decide that a bird population or a bird species or a whole group of birds is threatened or endangered. One simple way to make this decision is with a verbal flow chart and I offer here one example of how to proceed.

  1. Get accurate and precise data on the populations of interest. If you claim a population is declining or endangered, you need to define the population and know its abundance over a reasonable time period.

Note that this is already a nearly impossible demand. For birds that are continuously resident it is possible to census them well. Let me guess that continuous residency occurs in at most 5% or fewer of the birds of the world. The other birds we would like to protect are global or local migrants or move unpredictably in search of food resources, so it is difficult to define a population and determine if the population as a whole is rising or falling. Compounding all this are the truly rare bird species that are difficult to census like all rare species. Dorey and Walker (2018) examine these concerns for Canada.

The next problem is what is a reasonable time period for the census data. The Committee on the Status of Endangered Wildlife in Canada (COSEWIC) gives 10 years or 3 generations, whichever is longer (see web link below). So now we need to know the generation time of the species of concern. We can make a guess at generation time but let us stick with 10 years for the moment. For how many bird species in Canada do we have 10 years of accurate population estimates?

  • Next, we need to determine the causes of the decline if we wish to instigate management actions. Populations decline because of a falling reproductive rate, increasing death rate, or higher emigration rates. There are very few birds for which we have 10 years of diagnosis for the causes of changes in these vital rates. Strong conclusions should not rest on weak data.

The absence of much of these required data force conservation biologists to guess about what is driving numbers down, knowing only that population numbers are falling. Typically, many things are happening over the 10 years of assessment – climate is changing, habitats are being lost or gained, invasive species are spreading, new toxic chemical are being used for pest control, diseases are appearing, the list is long. We have little time or money to determine the critical limiting factors. We can only make a guess.

  • At this stage we must specify an action plan to recommend management actions for the recovery of the declining bird population. Management actions are limited. We cannot in the short term alter climate. Regulating toxic chemical use in agriculture takes years. In a few cases we can set aside more habitat as a generalized solution for all declining birds. We have difficulty controlling invasive species, and some invasive species might be native species expanding their geographic range (e.g. Bodine and Capaldi 2017, Thibault et al. 2018).

Conservation ecologists are now up against the wall because all management actions that are recommended will cost money and will face potential opposition from some people. Success is not guaranteed because most of the data available are inadequate. Medical doctors face the same problem with rare diseases and uncertain treatments when deciding how to treat patients with no certainty of success.

In my opinion the data on which the present concern over bird losses is too poor to justify the hyper-publicity about declining birds. I realize most conservation biologists will disagree but that is why I think we need to lift our game by having a more rigorous set of data rules for categories of concern in conservation. A more balanced tone of concern may be more useful in gathering public support for management efforts. Stanton et al. (2018) provide a good example for farmland birds. Overuse of the word ‘extinction’ is counterproductive in my opinion. Trying to provide better data is highly desirable so that conservation papers do not always end with the statement ‘but detailed mechanistic studies are lacking’. Pleas for declining populations ought to be balanced by recommendations for solutions to the problem. Local solutions are most useful, global solutions are critical in the long run but given current global governance are too much fairy tales.

Bodine, E.N. and Capaldi, A. (2017). Can culling Barred Owls save a declining Northern Spotted Owl population? Natural Resource Modeling 30, e12131. doi: 10.1111/nrm.12131.

Dorey, K. and Walker, T.R. (2018). Limitations of threatened species lists in Canada: A federal and provincial perspective. Biological Conservation 217, 259-268. doi: 10.1016/j.biocon.2017.11.018.

Rosenberg, K.V., et al. (2019). Decline of the North American avifauna. Science 366, 120-124. doi: 10.1126/science.aaw1313.

Stanton, R.L., Morrissey, C.A., and Clark, R.G. (2018). Analysis of trends and agricultural drivers of farmland bird declines in North America: A review. Agriculture, Ecosystems & Environment 254, 244-254. doi: 10.1016/j.agee.2017.11.028.

Thibault, M., et al. (2018). The invasive Red-vented bulbul (Pycnonotus cafer) outcompetes native birds in a tropical biodiversity hotspot. PLoS ONE 13, e0192249. doi: 10.1371/journal.pone.0192249.

http://cosewic.ca/index.php/en-ca/assessment-process/wildlife-species-assessment-process-categories-guidelines/quantitative-criteria

On Fires in Australia

2 Replies

The fires of Australia in their summer 2019-20 are in the news constantly, partly because the media survive on death and destruction and partly because to date we have never seen a whole continent burn up. It is hardly a ‘Welcome to the Anthropocene”  kind of event to celebrate, and the northern media display the fires as nearly all news of the Southern Hemisphere is treated, something unusual, often bad, but of no general importance to the real world of the Northern Hemisphere.

What do we hear from a cacophony of public opinion?

“Nothing unusual. We have always had fires in the past. Why in 1863…..”
“Nothing to do with climate change. Climate has always been changing….(see point 1)
“Main cause had been Green Policies. If we had more forestry, there would have been many fewer trees to burn….”
“Inadequate controlled burning because of the Greens’ policies….(see point 3)
“Why doesn’t the Government do something about this?”
“Fortunately these fires are a rare event and not likely to occur again…….

In reply an ecologist might offer these facts:

  1. Much research by plant geographers and ecologists have shown how many plant communities are dominated by fire. The boreal forest is one, the chaparral of Southern California is another, the grasslands of Africa and the Great Plains of the USA are yet more.
  2. By preventing fire in these communities over time the fuel load builds up so that, should there be a subsequent fire, the fire severity would be very high.
  3. By building houses, towns, and cities in these plant communities fire danger increases, and an active plan of fire management must be implemented. Most of these plans are effective for normal fires but for extreme conditions no fire management plan is effective.
  4. Climate change is now producing extreme conditions that were once very rare but are now commonly achieved. With no rainfall, high winds, and temperatures over 40-45ºC fires cannot be contained. Severe fires generate their own weather that accelerates fire spread with embers being blown kilometers ahead of the active fire front.
  5. The long-term plan to have controlled patch burns to relieve these fire conditions are impossible to implement because they require no wind, low temperatures, and considerable person-power to prevent controlled burns getting away from containment lines should the weather change.

Since a sizeable fraction of dangerous fires are deliberately set by humans, methods to detect and prevent this behaviour could help in some cases. Infrastructure such as power lines could be upgraded to reduce the likelihood of falling power poles and lines shorting out. All this will cost money, and the less the fire frequency, the fewer the people willing to pay more taxes to reduce public risk. Some serious thinking is needed now because Australia 2020 is just the start of a century of fire, drought, floods, and high winds. We do not need the politicians of 2050 telling us “why didn’t someone warn us?

There is a very large literature on fire in human landscapes (e.g. Gibbons et al. 2012), and I include only a few references here. They illustrate that the landscape effects of fire are multiple and area specific. Much more field research is needed, and landscape ecology has a vital role to play in understanding and managing the interface of humans and fire.

Badia, A. et al. (2019). Wildfires in the wildland-urban interface in Catalonia: Vulnerability analysis based on land use and land cover change. Science of The Total Environment 673, 184-196. doi: 10.1016/j.scitotenv.2019.04.012.

Gibbons, P, et. al. (2012) Land management practices associated with house loss in wildfires. PLoS ONE 7(1): e29212. https://doi.org/10.1371/journal.pone.0029212

Gustafsson, L. et al. (2019). Rapid ecological response and intensified knowledge accumulation following a north European mega-fire. Scandinavian Journal of Forest Research 34, 234-253. doi: 10.1080/02827581.2019.1603323.

Minor, J. and Boyce, G.A. (2018). Smokey Bear and the pyropolitics of United States forest governance. Political Geography 62, 79-93. doi: 10.1016/j.polgeo.2017.10.005.

Ramage, B.S., O’Hara, K.L., and Caldwell, B.T. (2010). The role of fire in the competitive dynamics of coast redwood forests. Ecosphere 1(6), art20. doi: 10.1890/ES10-00134.1.

On Progress in Ecology

Leave a reply

We are in ecology continually discussing what progress we are making in answering the central questions of our science. For this reason, it is sometimes interesting to compare our situation with that of economics, the queen of the social sciences, where the same argument also continues. A review by David Graeber (2019) in the New York Review of Books contains some comments about the ‘theoretical war’ in economics that might apply to some ecology subdisciplines. In it he discusses the arguments in social science between two divergent views of economics, that of the school of Keynesians and that of the now dominant Neoclassical School led by Frederich Hayek and later by Milton Friedman and many others of the Chicago School. John Maynard Keynes threw down a challenge illustrated in this quote from Graeber (2019):

“In other words, ‘(Keynes)’ assumed that the ground was always shifting under the analysts’ feet; the object of any social science was inherently unstable. Max Weber, for similar reasons, argued that it would never be possible for social scientists to come up with anything remotely like the laws of physics, because by the time they had come anywhere near to gathering enough information, society itself, and what analysts felt was important to know about it, would have changed so much that the information would be irrelevant. (p. 57)”

Precise quantitative predictions could be provided by simplified economic models, the Chicago School argued in rebutting Keynes. Graeber (2019) comments:

“Surely there’s nothing wrong with creating simplified models. Arguably, this is how any science of human affairs has to proceed. But an empirical science then goes on to test those models against what people actually do, and adjust them accordingly. This is precisely what economists did not do. Instead, they discovered that, if one encased those models in mathematical formulae completely impenetrable to the noninitiate, it would be possible to create a universe in which those premises could never be refuted. (“All actors are engaged in the maximization of utility. What is utility? Whatever it is that an actor appears to be maximizing.”) The mathematical equations allowed economists to plausibly claim theirs was the only branch of social theory that had advanced to anything like a predictive science.  (p. 57)”

In ecology the major divergence between schools of thought promoting progress have never been quite this distinct. Shades of complaint are evident in the writings of Peters (1991) and a burst of comment after that ranged from optimism (e.g. Bibby 2003) to more support for Peter’s critique (Underwood et al. 2000, Graham and Dayton 2002). Interest at this time seems to have waned in favour of very specific topics for review. If you check the Web of Science for the last 5 years for “progress” and “ecology” you will find reviews of root microbes, remote sensing of the carbon cycle, reintroduction of fishes in Canada and a host of very important reviews of small parts of the broad nature of ecology. As Kingsland (2004, 2005) recognized, ecology is an integrating science that brings together data from diverse fields of study. If this is correct, it is not surprising that ecologists differ in answering questions about progress in ecology. We should stick to small specific problems on which we can make detailed studies, measurements, and experiments to increase understanding of the causes of the original problem.

One of the most thoughtful papers on progress in ecology was that of Graham and Dayton (2002) who made an important point about progress in ecology:

“We believe that many consequences of ecological advancement will be obstacles to future progress. Here we briefly discuss just a few: (1) ecological specialization; (2) erasure of history; and (3) expansion of the literature. These problems are interconnected and have the potential to divert researchers and hinder ecological breakthroughs.” (p. 1486)

My question to all ecologists is whether or not we agree with this ‘prediction’ from 2002. There is no question in my judgement that ecology is much more specialized now, that history is erased in spite of search engines like the Web of Science and that the ecology literature is booming so rapidly that it feeds back to ecological specialization. There is no clear solution to these problems. The fact that ecology is integrative has developed into a belief that anyone with a little training in ecological science can call themselves an ecologist and pontificate about the problems of our day. This element of ‘fake news’ is not confined to ecology and we can counter it only by calling out errors propagated by politicians and others who continue to confuse truth in science with their uneducated beliefs.

Bibby, C.J. (2003). Fifty years of Bird Study. Bird Study 50, 194-210. Doi: 10.1080/00063650309461314.

Graham, M.H. and Dayton, P.K. (2002). On the evolution of ecological ideas: paradigms and scientific progress. Ecology 83, 1481-1489. Doi: 10.1890/0012-9658(2002)083[1481:OTEOEI]2.0.CO;2.

Graeber, D. (2019). Against Economics. New York Review of Books 66, 52-58. December 5, 2019.

Kingsland, S. (2004). Conveying the intellectual challenge of ecology: an historical perspective. Frontiers in Ecology and the Environment 2, 367-374. Doi: 10.1890/1540-9295(2004)002[0367:CTICOE]2.0.CO;2.

Kingsland, S.E. (2005) The Evolution of American Ecology, 1890-2000. Johns Hopkins University Press: Baltimore. 313 pp. ISBN 0801881714

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

Underwood, A.J., Chapman, M.G., and Connell, S.D. (2000). Observations in ecology: you can’t make progress on processes without understanding the patterns. Journal of Experimental Marine Biology and Ecology 250, 97-115. Doi: 10.1016/S0022-0981(00)00181-7.

On Christmas Holiday Wishes

Leave a reply

We are all supposed to make some wishes over the Holiday Season, no matter what our age or occupation. So, this blog is in that holiday spirit with the constraint that I will write about ecology, rather than the whole world, to keep it short and specific. So, here are my 12 wishes for improving the science of ecology in 2020:

  1. When you start your thesis or study, write down in 50 words or less what is the problem, what are the possible solutions to this problem, and what can we do about it.
  2. Take this statement and convert it to a 7 second sound bite that points out clearly for the person on the street or the head of the Research Council why this is an important use of the foundation’s or taxpayers’ money.
  3. Read the literature that is available on your topic of study even if it was published in the last century.
  4. When writing your report, thesis, or paper on your research, prepare an abstract or summary that follows the old rules of stating clearly WHO, WHAT, WHEN, WHERE, WHY, and HOW. Spend much time on this step, since many of your readers will only be able to read this far. 
  5. Make tables and graphs that are clear and to the point. Define the points or histograms on a graph.
  6. Define all three- and four-letter acronyms. Not everyone will know what RSE or SECR means.
  7. Remember the cardinal rule of data presentation that if your data are an estimate of some value, you should provide the confidence limits or credible intervals of your data.
  8. Above all be truthful and modest in your conclusions. If your evidence points in one direction but is weak, say so. If the support of your evidence is strong, say so. But do not say that this is the first time anyone has ever suggested your conclusions.
  9. In the discussion of your results, give some space to suggesting what limits apply to your conclusions. Do your statements apply only to brown trout, or to all trout, or to all freshwater fish? Are your conclusions limited to one biogeographic zone, or one plant community, or to one small national park?  
  10. The key point at the end of your report should be what next? You or others will take up your challenges, and since you have worked hard and thought much about the ecological problems you have faced, you should be the best person to suggest some future directions for research.
  11. Once your have completed your report or paper, go back and read again all the literature that is available on your topic of study and review it critically.
  12. Finish your report or paper, keeping in mind the old adage, the perfect is the enemy of the good. It is quite impossible in science to be perfect. Better good than perfect.

And as you dive into any kind of biological research, it is useful to read about some of the controversies that you may run into as you write your papers or reports, particularly in the statistical treatment of biological data (Hardwicke and Ioannidis 2019, Ioannidis 2019). The statistical controversy over p-values has been a hot issue for several years and you will likely run into it sooner or later (Ioannidis 2019a, Siontis and Ioannidis 2018). The important point you should remember is that ecologists are scientists and our view of the value of our research work is the antithesis of Shakespeare’s Macbeth:

“Life’s but a walking shadow, a poor player that struts and frets his hour upon the stage, and then is heard no more. It is a tale told by an idiot, full of sound and fury,
signifying nothing.” (Act 5, Scene 5)

This is because our scientific work is valuable for conserving life on Earth, and so it must be carried out to a high and improving standard. It will be there as a contribution to knowledge and available for a long time. It may be useful now, or in one year, or perhaps in 10 or 100 years as an important contribution to solving ecological problems. So, we should strive for the best.

Hardwicke, T.E. and Ioannidis, J.P.A. (2019). Petitions in scientific argumentation: Dissecting the request to retire statistical significance. European Journal of Clinical Investigation 49, e13162.  doi: 10.1111/eci.13162.

Ioannidis, J.P.A. (2019). Options for publishing research without any P-values. European Heart Journal 40, 2555-2556. doi: 10.1093/eurheartj/ehz556.

Ioannidis, J.P.A. (2019a Ioannidis). What have we (not) learnt from millions of scientific papers with P values? American Statistician 73, 20-25. doi: 10.1080/00031305.2018.1447512.

Siontis, K.C. and Ioannidis, J.P.A. (2018). Replication, duplication, and waste in a quarter million systematic reviews and meta-analyses. Circulation: Cardiovascular Quality and Outcomes 11, e005212. doi: 10.1161/CIRCOUTCOMES.118.005212.

On Salmon Hatcheries as an Ecological Paradigm

Leave a reply

The West Coast of North America hosts 5 species of Pacific salmon that are an invaluable fishery resource and at least in theory a resource that is completely sustainable. The management of these fisheries provides a useful case study in how humans currently approach major resources, the mistakes they make, and how attempts to fix mistakes can lead to even further mistakes.

Salmon have been a major resource utilized by the First Nations of the Pacific Coast after the glaciers melted some 10-12,000 years ago. Salmon are anadromous fish, living in the ocean and spawning in fresh water. Their populations fluctuate from year to year but until the 1900s they were essentially considered an inexhaustible resource and thus became a target for exploitation. The buildup of salmon fisheries during the last 100 years coincided with an increase in environmental damage to freshwater spawning grounds. Dams on rivers cut migration routes to spawning grounds, pollution arising from mining, and erosion from forestry and agriculture all began to cut into spawning habitat and subsequently the available catch for the fishery. Salmon catches began to decline and in the late 1800s hatcheries began to be built both to restore fish stocks that were threatened and to increase the abundance of desirable fish like salmon (Naish et al 2007).

The simple model of salmon hatcheries was that the abundance of juvenile fish was the main factor limiting the adult population, so that adding more juveniles to wild juveniles moving out into the ocean would be profitable. This view of the world I call the “Farmer Paradigm” and if you are a dairy farmer with 4 cows that produce X milk, if you add 4 more cows to your farm, you now get 2X milk and thus more profit. But it became apparent with fish hatcheries that adding more juvenile fish did not necessarily increase the resulting fish catch. Some simple reasons might be that more juveniles were eaten by the predators waiting at the mouth of the river or stream, so that predation on juvenile fish was limiting. Alternatively, perhaps the ocean only had a given amount of food for juvenile growth, so that adding too many juveniles induced starvation deaths. Other explanations involving disease transmission could also be invoked.

Whatever the mechanism, it became clear that hatcheries for salmon sometimes worked and sometimes did not work to increase the productivity of the fishery. The Farmer Paradigm had to add a footnote to say “its complicated”. One complication noted early on was the possibility that natural selection in hatcheries was not equivalent to natural selection in wild populations. If hatchery fish were replacing wild fish in any population, the genetic changes involved could work in two directions by either making the entire population more fit or less fit, more productive or less. Much depends on what traits are selected for in hatcheries. In one example for sockeye salmon in Washington State, hatcheries appear to have selected for earlier spawning, so that wild sockeye in one river system return to spawn later than hatchery raised sockeye raised in the same river (Tillotson et al. 2019). Since in general juveniles from early spawners have poorer survival, climate change could favour earlier breeding and thereby reduce the overall productivity of the sockeye population in the river system. We are far from knowing the long-term selection that is occurring in hatcheries, and what it means for future populations of salmon (Cline et al. 2019, Stevenson et al. 2019).

Hatcheries are popular with the public because they indicate the government is doing something to assist fishers and hatcheries should increase and maintain fisheries production for species we love to eat. Consequently, there is a social signal that might be suppressed in data that might suggest a particular hatchery was in fact harming the fishery for a particular river or lake system. If someone wishes to do an economic analysis of the costs and benefits of a hatchery, one runs up against the standard simple belief that more juvenile fish equals higher fishery production. When Amoroso et al. (2017) tried to evaluate for pink salmon in Alaska whether hatcheries were an economic benefit or a loss, their best analysis suggested that recent increases in pink salmon productivity were higher in areas of Alaska with no hatcheries, compared with those with hatcheries. Since different river populations of pink salmon mix in their oceanic phase, it is difficult to obtain a clear experimental signal of hatchery success or failure. The immediate and the longer-term unintended consequences of hatcheries require further study. The assumption that every hatchery is an ecological and social good cannot be presumed.  

Salmon hatcheries are for me an ecological paradigm because they illustrate the management sequence: unlimited abundance → overharvesting → collapse of resource → find a technological fix → misdiagnosed problem → failure of technological fix → better diagnosis of the problem → competing socio-economic objectives → failure to act → collapse of the resource. This need not be the case, and we need to do better (Bendriem et al. 2019).

Amoroso, R.O. et al. (2017). Measuring the net biological impact of fisheries enhancement: Pink salmon hatcheries can increase yield, but with apparent costs to wild populations. Canadian Journal of Fisheries and Aquatic Sciences 74, 1233-1242. doi: 10.1139/cjfas-2016-0334.

Bendriem, N. et al. (2019). A review of the fate of southern British Columbia coho salmon over time. Fisheries Research 218, 10-21. doi: 10.1016/j.fishres.2019.04.002.

Cline, T.J. et al. (2019). Effects of warming climate and competition in the ocean for life-histories of Pacific salmon. Nature Ecology & Evolution 3, 935-942. doi: 10.1038/s41559-019-0901-7.

Naish, K.A. et al. (2007). An evaluation of the effects of conservation and fishery enhancement hatcheries on wild populations of salmon. Advances in Marine Biology 53, 61-194. doi: 10.1016/S0065-2881(07)53002-6.

Stevenson, C.F. et al. (2019). The influence of smolt age on freshwater and early marine behavior and survival of migrating juvenile sockeye salmon. Transactions of the American Fisheries Society 148, 636-651. doi: 10.1002/tafs.10156.

Tillotson, M.D. et al. (2019). Artificial selection on reproductive timing in hatchery salmon drives a phenological shift and potential maladaptation to climate change. Evolutionary Applications 12, 1344-1359. doi: 10.1111/eva.12730.

Do We Need Commissioners for the Environment?

Canada has just gone through an election, the USA will next year, and elections are a recurring news item everywhere. In our Canadian election we were spared any news on the state of the environment, and the dominant theme of the election was jobs, the economy, oil, gas, and a bit on climate change. The simplest theme was climate change, and yes, we are all in favour of stopping it so long as we do not need to do anything about it that would cost money or change our lifestyles. Meanwhile the fires of California and Australia and elsewhere carry on, generating another news cycle of crazy comments about the state of the environment.

Is there a better way? How can we get governments of the world to consider that the environment is worthy of some discussion? There is, and New Zealand has led the way in one direction. New Zealand has a Parliamentary Commissioner for the Environment, an independent Officer of Parliament, whose job it is to provide Members of Parliament with independent advice on matters that may have impacts on the environment. The Office is independent of the government of the day and the Prime Minister, and consequently can “tell it like it is”. A few quotations for the 2019 report give the flavour of this recent New Zealand report:

“If there is one thing that stands out from [our] reports, it is the extent of what we don’t know about what’s going on with our environment.  

“…the blind spots in our environmental reporting system don’t represent conscious choices to collect data or undertake research in some fields rather than others. Rather, they represent the unplanned consequences of a myriad choices over decades. Ours has been a passive system that has harvested whatever data is there and done the best it can to navigate what’s missing.

“In some ways, the most important recommendations in this report are those that relate to the prioritising and gathering of data in a consistent way. Despite attempts over more than two decades, no agreement has ever been reached on a set of core environmental indicators. This has to happen. Consistent and authoritative time series coupled with improved spatial coverage are essential if we are to detect trends. Only then will we be able to judge confidently whether we are making progress or going backwards – and get a handle on whether costly interventions are having an effect.

https://www.pce.parliament.nz/publications/focusing-aotearoa-new-zealand-s-environmental-reporting-system

This report is full of ecological wisdom and would be a useful starting point for many countries. Canada has (to my knowledge) no Environmental Commissioner and although various provinces and cities provide State of the Environment Reports, they are largely based on inadequate data. In some cases, like commercial fisheries, Parliaments or Congress have mandated annual reports, provided the secure funding, and retained independence of the relevant director and staff. In many cases there is far too much bickering between jurisdictions, use of inadequate methods of data collecting, long time periods between sampling, and no indication that the national interest has been taken into account.

Most Western countries have National Academies or Royal Societies which provide some scientific advice, sometimes requested, sometimes not. But these scientific publications are typically on very specific topics like smoking and lung cancer, vaccine protection, or automobile safety requirements. We can see this problem most clearly in the current climate emergency. The Intergovernmental Panel on Climate Change (IPCC) of the United Nations provides excellent reports on the climate emergency but no government is required to listen to their recommendations or to implement them. So, we have local problems, regional problems and global problems, and we need the political structures to address environmental problems at all these levels. New Zealand has provided a way forward, and here is another quote from the 2019 report that ecologists should echo:

Given that many of the environmental problems we face have been decades in the making and that for nearly 30 years we have [made] specific reference to cumulative effects that arise over time…it is astonishing that we have so little data on trends over time.

….it takes time to assemble time series. If we start collecting data today, it may be a decade or more before we can confidently judge whether the issue being monitored is getting better or worse. Every year that we delay the collection of data in an area identified as a significant gap, we commit New Zealand to flying blind in that area. …..A lack of time series in respect of some environmental pressure points could be costing us dearly in terms of poorly designed policies or irreversible damage.

One example may be enough. Caribou herds in southern Canada are threatened with extinction (Hebblewhite 2017, DeMars et al. 2019). Here is one example of counts on one caribou herd in southern Canada:

2009 = 2093 caribou
2012 = 1003
2019 = 185

It would be difficult to manage the conservation of any species of animal or plant that has such limited monitoring data. We can and must do better. We can start by dragging state of the environment reports out of the control of political parties by demanding to have in every country Commissioners of the Environment that are fully funded but independent of political influence. As long as the vision of elected governments is limited to 3 years, environmental decay will continue, out of sight, out of mind.

There is of course no reason that elected governments need follow the advice of any independent commission, so this recommendation is not a panacea for environmental issues. If citizens have independent information however, they can choose to use it and demand action.

DeMars, C.A.et al. (2019). Moose, caribou, and fire: have we got it right yet? Canadian Journal of Zoology 97, 866-879. doi: 10.1139/cjz-2018-0319.

Hebblewhite, M. (2017). Billion dollar boreal woodland caribou and the biodiversity impacts of the global oil and gas industry. Biological Conservation 206, 102-111. doi: 10.1016/j.biocon.2016.12.014.

The Central Predicament of Ecological Science

Leave a reply

Ecology like all the hard sciences aims to find generalizations that are eternally true. Just as physicists assume that the universal law of gravitation will still be valid 10,000 years from now, so do ecologists assume that we can find laws or generalizations for populations and ecosystems that will be valid into the future. But the reality for ecological science is quite different. If the laws of ecology depend on the climate being stable, soil development being ongoing, evolution being optimized, and extinction being slow in human-generation time, we are in serious trouble.

Paleoecology is an important subdiscipline of ecology because, like human history, we need to understand the past. But the generalizations of paleoecology may be of little use to understand the future changes the Earth faces for one major reason – human disturbance of both climate and landscapes. Climates are changing due to rising greenhouse gases that have a long half-life. Land and water are being appropriated by a rising human population that is very slow to stabilize, so natural habitats are continually lost. There is little hope in the absence of an Apocalypse that these forces will alleviate during the next 200 years. Given these changes in the Anthropocene where does ecology sit and what can we do about it?

If climate is a major driver of ecological systems, as Andrewartha and Birch (1954) argued (to the scorn of the Northern Hemisphere ecologists of the time), the rules of the past will not necessarily apply to a future in which climate is changing. Plant succession, that slow and orderly process we now use to predict future communities, will change in speed and direction under the influence of climatic shifts and the introduction of new plant species, plant pests, and diseases that we have little control over. Technological optimists in agriculture and forestry assume that by genetic manipulations and proper artificial selection we can outwit climate change and solve pest problems, and we can only hope that they are successful. Understanding all these changes in slow-moving ecosystems depends on climate models that are accurate in projecting future climate changes. Success to date has been limited because of both questionable biology and poor statistical procedures in climate models (Frank 2019; Kumarathunge et al. 2019; Yates et al. 2018).

If prediction is the key to ecological understanding, as Houlahan et al. (2017) have cogently argued, we are in a quandary if the models that provide predictions wander with time to become less predictive. Yates et al. (2018) have provided an excellent review of the challenges of making good models for ecological prediction. As such their review is either encouraging – ‘here are the challenges in bold type’ – or terribly depressing – ‘where are the long-term, precise data for predictive model evaluation?’ My colleagues and I have spent 47 years trying to provide reliable data on one small part of the boreal forest ecosystem, and the models we have developed to predict changes in this ecosystem are probably still too imprecise to use for management. Additional years of observations produce some ecosystem states that have been predictable but other changes that we have never seen before over this time frame of nearly 50 years.

In contrast to the optimism of Yates et al. (2018), Houlahan et al. (2017) state that:

“Ecology, with a few exceptions, has abandoned prediction and therefore the ability to demonstrate understanding. Here we address how this has inhibited progress in ecology and explore how a renewed focus on prediction would benefit ecologists. The lack of emphasis on prediction has resulted in a discipline that tests qualitative, imprecise hypotheses with little concern for whether the results are generalizable beyond where and when the data were collected.  (page 1)

I see this difference in views as a dilemma because despite much talk, there is little money or interest in the field work that would deliver reliable data for models in order to test their accuracy in predictions at small and large scales. An example this year is the failure of the expected large salmon runs to the British Columbia fishery, with model failure partly due to the lack of monitoring in the North Pacific (https://globalnews.ca/news/5802595/bc-salmon-stocks-plunge/; https://www.citynews1130.com/2019/09/09/worst-year-for-salmon/ , and in contrast with Alaska runs: https://www.adn.com/business-economy/2019/07/25/bristol-bay-sockeye-harvest-blowing-away-forecast-once-again/ ). Whatever the cause of the failure of B.C. salmon runs in 2019, the lack of precision in models of a large commercial fishery that has been studied for at least 65 yeas is not a vote of confidence in our current ecological modelling.

Andrewartha, H.G. and Birch, L.C. (1954) ‘The Distribution and Abundance of Animals.’ University of Chicago Press: Chicago. 782 pp.

Frank, P. (2019). Propagation of error and the reliability of global air temperature projections. Frontiers in Earth Science 7, 223. doi: 10.3389/feart.2019.00223.

Houlahan, J.E., McKinney, S.T., Anderson, T.M., and McGill, B.J. (2017). The priority of prediction in ecological understanding. Oikos 126, 1-7. doi: 10.1111/oik.03726.

Kumarathunge, D.P., Medlyn, B.E., Drake, J.E., Tjoelker, M.G., Aspinwall, M.J., et al. (2019). Acclimation and adaptation components of the temperature dependence of plant photosynthesis at the global scale. New Phytologist 222, 768-784. doi: 10.1111/nph.15668.

Yates, K.L., Bouchet, P.J., Caley, M.J., Mengersen, K., Randin, C.F., Parnell, S., Fielding, A.H., Bamford, A.J., et al. (2018). Outstanding challenges in the transferability of ecological models. Trends in Ecology & Evolution 33, 790-802. doi: 10.1016/j.tree.2018.08.001.