Tag Archives: progress in ecology

On Global Science and Local Science

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I suggest that the field of ecology is fragmenting into two large visions of the science which for the sake of simplicity I will call Global Science and Local Science. This fragmentation is not entirely new, and some history might be in order.

Local Science deals with local problems, and while it aspires to develop conclusions that apply to a broader area than the small study area, it has always been tied to useful answers for practical questions. Are predators the major control of caribou declines in northern Canada? Can rats on islands reduce ground-nesting birds to extinction? Does phosphate limit primary production in temperate lakes? Historically Local Science has arisen from the practical problems of pest control and wildlife and fisheries management with a strong focus on understanding how populations and communities work and how humans might solve the ecological problems they have largely produced (Kingsland 2005). The focus of Local Science was always on a set of few species that were key to the problem being studied. As more and more wisdom accumulated on local problems, ecologists turned to broadening the scope of enquiry, asking for example if solutions discovered in Minnesota might also be useful in England or vice versa. Consequently, Local Science began to be amalgamated into a broader program of Global Science.

Global Science can be defined in several ways. One is purely financial and big dollars; this not what I will discuss here. I want to discuss Global Science in terms of ecological syntheses, and Global Science papers can often be recognized by having dozens to hundreds of authors, all with data to share, and with meta-analysis as the major tool of analysis. Global Science is now in my opinion moving away from the experimental approach that was a triumph of Local Science. The prelude to Global Science was the International Biological Program (IBP) of the 1970s that attempted to produce large-scale systems analyses of communities and ecosystems but had little effect in convincing many ecologists that this was the way to the future. At the time the problem was largely the development of a theory of stability, a property barely visible in most ecological systems.

Global Science depends on describing patterns that occur across large spatial scales. These patterns can be discovered only by having an extensive, reliable set of local studies and this leads to two problems. The first is that there may be too few reliable local studies. This may occur because different ecologists use different methods of measurement, do not use a statistically reliable sampling design, or may be constrained by a lack of funding or time. The second problem is that different areas may show different patterns of the variables under measurement or have confounding causes that are not recognized. The approach through meta-analysis is fraught with the decisions that must be made to include or exclude specific studies. For example, a recent meta-analysis of the global insect decline surveyed 5100 papers and used 166 of them for analysis (van Klink et al. 2020). It is not that the strengths and limitations of meta-analysis have been missed (Gurevitch et al. 2018) but rather the question of whether they are increasing our understanding of the Earth’s ecology. Meta-analyses can be useful in suggesting patterns that require more detailed analyses. In effect they violate many of the rules of conventional science in not having an experimental design, so that they suggest patterns but can be validated only by a repeat of the observations. So, in the best situations meta-analyses lead us back to Local Science. In some situations, meta-analyses lead to no clear understanding at all, as illustrated in the conclusions of Geary et al. (2020) who investigated the response of terrestrial vertebrate predators to fire:

“There were no clear, general responses of predators to fire, nor relationships with geographic area, biome or life-history traits (e.g. body mass, hunting strategy and diet). Responses varied considerably between species.” (page 955)

Note that this study is informative in that it indicates that ecologists have not yet identified the variables that determine the response of predators to fire. In other cases, meta-analysis has been useful in redirecting ecological questions because the current global model does not fit the facts very well (Szuwalski et al. 2015).

The result of this movement within both ecological and conservation science toward Global Science has been a shift in the amount of field work being done. Rios-Saldana et al. (2018) surveyed the conservation literature over the last 35 years and found that fieldwork-based publications decreased by 20% in comparison to a rise of 600% and 800% in modelling and data analysis studies. This conclusion could be interpreted that ecologists now realize that less fieldwork is needed at this time, or perhaps the opposite. 

In an overview of ecological science David Currie (2019) described an approach to understanding how progress in ecology has differed from that in the physical sciences. He suggests that the physical sciences focused on a set of properties of nature whose variation they analyzed. They developed ‘laws’ Like Newton’s laws or motion that could be tested in simple or complex systems. By contrast ecology has developed largely by asking how processes like competition or predation work, and not by asking questions about the properties of natural systems, which is what interests the general public trying to solve problems in conservation or pest or fisheries management. Currie (2019) summarized his approach as follows:

“Successful disciplines identify specific goals and measure progress toward those goals. Predictive accuracy of properties of nature is a measure of that progress in ecology. Predictive accuracy is the objective evidence of understanding. It is the most useful tool that science can offer society.” (page 18)

Many of these same questions underlay the critical appraisal of ecology by Peters (1991).

There is no one approach to ecological science, but we need to continue to ask what progress is being made with every approach. These are key questions for the future of ecological research, and they are worthy of much more discussion because they determine what students will be taught and what kinds of research will be favoured for funding in the future.

Currie, D.J. (2019). Where Newton might have taken ecology. Global Ecology and Biogeography 28, 18-27. doi: 10.1111/geb.12842.

Geary, W.L., Doherty, T.S., Nimmo, D.G., Tulloch, A.I.T., and Ritchie, E.G. (2020). Predator responses to fire: A global systematic review and meta-analysis. Journal of Animal Ecology 89, 955-971. doi: 10.1111/1365-2656.13153.

Gurevitch, J., Koricheva, J., Nakagawa, S., and Stewart, G. (2018). Meta-analysis and the science of research synthesis. Nature 555, 175-182. doi: 10.1038/nature25753.

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

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

Ríos-Saldaña, C. Antonio, Delibes-Mateos, Miguel, and Ferreira, Catarina C. (2018). Are fieldwork studies being relegated to second place in conservation science? Global Ecology and Conservation 14: e00389. doi: 10.1016/j.gecco.2018.e00389.

Szuwalski, C.S., Vert-Pre, K.A., Punt, A.E., Branch, T.A., and Hilborn, R. (2015). Examining common assumptions about recruitment: a meta-analysis of recruitment dynamics for worldwide marine fisheries. Fish and Fisheries 16, 633-648. doi: 10.1111/faf.12083.

van Klink, R., Bowler, D.E., Gongalsky, K.B., Swengel, A.B., Gentile, A. and Chase, J.M. (2020). Meta-analysis reveals declines in terrestrial but increases in freshwater insect abundances. Science 368, 417-420. doi: 10.1126/science.aax9931.

On Biodiversity Science

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With David Attenborough and all the amazing picture books on biodiversity there can be few people in the world who have not been alerted to the array of beautiful and interesting species on Earth. Until recently the subject of biodiversity, known to First Nations since long, long ago, had not entered the western world of automobiles, industry, farming, fishing, music, theatres, and movies. Biodiversity is now greatly appreciated by most people, but perhaps more as entertainment for western societies and more for subsistence food in less wealthy parts of our world.

There are many different measures of ‘biodiversity’ and when discussing how we should protect biodiversity we should be careful about exactly how this word is being used. The number of different species in an area is one simple measure of biodiversity. But often the types of organisms being considered are less well defined. Forest ecologists attempt to protect forest biodiversity, but logging companies are more concerned only with trees and tree size for commercial use. Bird watchers are concerned with birds and have developed much citizen science in counting birds. Mushroom connoisseurs may worry about what edible mushrooms will be available this summer. But in many cases biodiversity scientists recognize that the community of organisms and the ecosystem that contains them would be a more appropriate unit of analysis. But as the number of species in an ecosystem increases, the complexity of the ecosystem becomes unmanageable. A single ecosystem may have hundreds to thousands of species, and we are in the infant stage of trying to determine how to study these biological systems.

One result is that, given that there are perhaps 10 million species on Earth and only perhaps 10,000 biologists who study biodiversity, where do we begin? The first and most popular way to answer this question is to pick a single species and concentrate on understanding its ecology. This makes are researcher’s life fairly simple. If elephants in Africa are under threat, find out all about the ecology of elephants. If a particular butterfly in England is very rare, try to find out why and how to protect them. This kind of research is very valuable for conservation because it provides a detailed background for understanding the requirements of each species. But the single species approaches lead into at least two quagmires. First, all species exist in a web of other species and understanding this web greatly expands the problem. It is possible in many cases to decipher the effects other species have on our elephants or butterflies, but this requires many more scientists to assist in analysing the species’ food chain, its diseases, its predators and parasites, and that is only a start. The second quagmire is that one of the general rules of ecology is that most species on Earth are rare, and few are common. So that we must concentrate our person-power on the common species because they are easier to find and study. But it is often the rare species that are of conservation concern, and so we should focus on them rather than the common species. In particular, given that only about 10% of the species on Earth have been described scientifically, we may often be assigned a species that does not have any information on its food habits or habitat requirements, its distribution, and how its abundance might be changing over time, a lifetime research program.

The result of this general overview is that the mantra of our day – Protect Biodiversity – begins as a compelling slogan and ends in enormous scientific complexity. As such it falls into the category of slogans like ‘Reduce Poverty’ and ‘Peace on Earth’, something we can all agree on, but the devil is in the details of how to achieve that particular goal.

One way to avoid all these pitfalls has been to jump over the problems of individual species and analyse communities of species or entire ecosystems. The result of this approach is to boil down all the species in the community to a number that estimates “biodiversity” and then use that number in relating ‘biodiversity’ to community attributes like ‘productivity’ or ‘stability’. This approach leads to testing hypotheses like ‘Higher biodiversity leads to greater stability’. There are serious problems with this approach if it is used to test any such hypothesis. First, biodiversity in this example must be rigorously defined as well as stability. The fact that higher biodiversity of butterflies in a particular region is associated with a more stable abundance of these butterflies over time is worthy of note but not of generalization to global communities or ecosystems. And as in all ecological studies we do not know if this is a generalization applicable to all butterfly populations everywhere until many more studies have been done.

A second problem is that this community or ecosystem approach to address ecological questions about biodiversity is not very useful in promoting conservation which boils down to particular species in particular environments. It should force us back to looking at the population ecology of species that are of conservation concern. It is population ecologists who must push forward the main goals of the conservation of the Earth’s biota, as Caughley (1994) recognized long ago.

The practical goals of conservation have always been local, and this constraint is mostly ignored in papers that demand some global research priorities and global ecological rules. The broad problem is that the conservation of biodiversity is a gigantic scientific and political problem that is currently underfunded and in its scientific infancy. At the present too much biodiversity research is short-term and not structured in a comprehensive framework that identifies critical problems and concentrates research efforts on these problems (Nichols et al. 2019, Sutherland et al. 2018). One more important issue for a seminar discussion group. 

Caughley, G. (1994). Directions in conservation biology. Journal of Animal Ecology 63, 215-244. doi: 10.2307/5542

Nichols, J.D., Kendall, W.L., and Boomer, G.S. (2019). Accumulating evidence in ecology: Once is not enough. Ecology and Evolution 9, 13991-14004. doi: 10.1002/ece3.5836.

Sutherland, W.J., Butchart, Stuart H.M., Connor, B., Culshaw, C., Dicks, L.V., et al. (2018). A 2018 Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity. Trends in Ecology & Evolution 33, 47-58. doi: 10.1016/j.tree.2017.11.006.

A Poem on the State of Agriculture in 1935

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After listening to me rant about the state of modern agriculture in the Anthropocene, a colleague in Australia sent me this poem by C.J. Dennis (1876 – 1938) written long before most of us were born. I reprint it here as a reminder that many of our ecological problems are not new, that we have perhaps made progress on some but that in many areas Dennis’s poem about agriculture could have been published today. A powerful poem that in a classroom discussion might lead us to second thoughts that we now live in the best of all possible worlds. Vale C.J. Dennis.

C.J. Dennis in the Herald in 1935 in Australia
THE SPOILERS

“Because overstocking and continuous grazing have denuded the land of vegetation and removed all resistance to wind and flood, it has now been suddenly realised that erosion in the Western districts of N.S.W. has reduced thousands of acres to little better than desert. A descendant of the original black inhabitants of this country might regard this as just retribution.

Ye are the Great White People, masters and lords of the earth,
Spreading your stern dominion over the world’s wide girth.
Here, where my fathers hunted since Time’s primordial morn,
To our land’s sweet, fecund places, you came with your kine and corn.
Mouthing your creed of Culture to cover a baser creed,
Your talk was of White Man’s magic, but your secret god was Greed.
And now that your generations to the second, the third have run,
White Man, what of my country?  Answer, what have you done?

Now the God of my Simple People was a simple, kindly God,
Meting his treasure wisely that sprang from this generous sod,
With never a beast too many and never a beast too few,
Thro’ the lean years and the fruitful, he held the balance true.
Then the White Lords came in their glory; and their cry was: “More!  Yet more!”
And to make them rich for a season they filched Earth’s age-old store,
And they hunted my Simple People — hunters of yester-year —
And they drove us into the desert — while they wrought fresh deserts here.

They ravaged the verdant uplands and spoiled wealth ages old,
Laid waste with their pumps and sluices for a gunny-bag of gold;
They raided the primal forests and the kind, rain-bringing trees
That poured wealth over the lowlands thro’ countless centuries;
They fed their kine on the grasslands, crowding them over the land,
Till blade and root in the lean years gave place to hungry sand.
Then, warned too late of their folly, the White Lords grew afraid,
And they cried to their great god Science; but Science could not aid.

This have you done to our country, lords of the air and the seas,
This to the hoarded riches of countless centuries —
Life-yielding loam, uncovered, unsheltered in the drought,
In the floods your hand unbridled, to the age-old sea drifts out.
You have sold man’s one true birthright for a White Man’s holiday,
And the smothering sands drift over where once green fields turn grey —
Filched by the White Man’s folly to pamper the White Lords’ vice;
And leave to your sons a desert where you found a paradise.”

Herald, 6 December 1935, page 6

http://www.middlemiss.org/lit/authors/denniscj/newspapers/herald/1935/works/spoilers.html

Ecological Science: Monitoring vs. Stamp Collecting

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Ecology as a science is deeply divided by two views of the natural world. First is the view that we need to monitor changes in the distribution and abundance of the biota and try to explain why these changes are occurring through experiments. The second view is that we need to understand ecosystems as complex systems, and this can be done only by models with a tenuous link to data. It is worth discussing the strengths and weaknesses of each of these views of our science.

The first view could be described as the here-and-now approach, studies of how the populations, communities, and ecosystems are changing in all the biomes on Earth. It is clearly impossible to do this properly because of a lack of funding and person-power. Because of this impossibility we change our focus to short-term studies of populations, species, or communities and try to grasp what is happening in the time scale of our lifetime. This had led to a literature of confusing short-term studies of problems that are long-term. Experiments must be short term because of funding. Any long-term studies such of those highlighted in textbooks are woefully inadequate to support the conclusions reached. Why is this? It is the baffling complexity of even the simplest ecological community. The number of species involved is too large to study all of them, so we concentrate on the more abundant species, assuming all the rare species are of little consequence. This has led to a further division within the monitoring community between conservation ecologists who worry about the extinction of larger, dominant species and those that worry about the loss of rare species.

The first approach is further compromised by climate change and human exploitation of the Earth. You could invest in the study of a grassland ecosystem for 15 years only to find it turned into a subdivision of houses in year 16. We try to draw conclusions in this hypothetical case by the data of the 15 years of study. But if physiological ecologists and climate change models are even approximately correct, the structure of similar grassland ecosystems will change due to rainfall and temperature shifts associated with greenhouse gases. Our only recourse is to hope that evolution of physiological tolerances will change fast enough to rescue our species of interest. But there is no way to know this without further empirical studies that monitor climate and the details of physiological ecology. And we talk now about understanding only single species and are back to the complexity problem of species interactions in communities.

The second approach is to leap over all this complexity as stamp-collecting and concentrate on the larger issues. Are our ecological communities resilient to climate change and species invasions? Part of this approach comes from paleoecology and questions of what has happened during the last 10,000 or one million years. But the details that emerge from paleoecology are very large scale, very interesting but perhaps not a good guide to our future under climate change. If a forward-looking forestry company wishes to make sure it has 100-year-old trees to harvest in 100 years’ time, what species should they plant now in central Canada? Or if a desert community in Chile is to be protected in a national park, what should the management plan involve? These kinds of questions are much harder to answer than simpler ones like how many dingoes will we have in central Australia next year.

Long-term experiments could bridge the gap between these two approaches to ecological understanding, but this would mean proper funding and person-power support for numerous experiments that would have a lifetime of 25 to 100 years or more. This will never happen until we recognize that the Earth is more important than our GDP, and that economics is the king of the sciences.

Where does all this lead ecological scientists? Both approaches have been important to pursue in what has been the first 100 years of ecological studies and they will continue to be important as our ecological understanding improves. We need good experimental science on a small scale and good broad thinking on long time scales with extensive studies of everything from coral reefs to the Alaskan tundra. We need to make use of the insights of behavioural ecology and physiological ecology in reaching our tentative conclusions. And if anyone tells you what will happen in your lifetime in all our forests and all the biodiversity on Earth, you should be very careful to ask for strong evidence before you commit to a future scenario.

Beller, E.E., McClenachan, L., Zavaleta, E.S., and Larsen, L.G. (2020). Past forward: Recommendations from historical ecology for ecosystem management. Global Ecology and Conservation 21, e00836. doi: 10.1016/j.gecco.2019.e00836.

Bro-Jørgensen, J., Franks, D.W., and Meise, K. (2019). Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation. Philosophical Transactions of the Royal Society, B.  Biological Sciences 374: 20190008.  doi: 10.1098/rstb.2019.0008.

Lidicker, W.Z. (2020). A Scientist’s Warning to humanity on human population growth. Global Ecology and Conservation 24, e01232. doi: 10.1016/j.gecco.2020.e01232.

McGowan, D. W., Goldstein, E. D., and Zador, S. (2020). Spatial and temporal dynamics of Pacific capelin Mallotus catervarius in the Gulf of Alaska: implications for ecosystem-based fisheries management. Marine Ecology. Progress Series 637, 117-140. doi: 10.3354/meps13211.

Tsujimoto, M., Kajikawa, Y., and Matsumoto, Y. (2018). A review of the ecosystem concept — Towards coherent ecosystem design. Technological Forecasting & Social Change 136, 49-58. doi: 10.1016/j.techfore.2017.06.032.

Wolfe, Kennedy, Kenyon, Tania M., and Mumby, Peter J. (2021). The biology and ecology of coral rubble and implications for the future of coral reefs. Coral Reefs 40, 1769-1806. doi: 10.1007/s00338-021-02185-9.

Yu, Zicheng, Loisel, J., Brosseau, D.P., Beilman, D.W., and Hunt, S.J. (2010). Global peatland dynamics since the Last Glacial Maximum. Geophysical Research Letters 37, L13402. doi: 10.1029/2010GL043584.

Why Ecology Fails to Prosper

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The general science of Ecology has changed dramatically during the last 60 years and my perception is that at present it is failing its critical role in developing science for the good of the Earth. I ask here if this pessimistic view is correct, why that might be, and if it is possible to change our trajectory. Every science must focus on major problems and these problems are too often lost as time progresses. The causes of these changes are rarely due to the competence of the scientists involved and more typically are found in the social milieu.  

The most obvious problem is science funding. You will appreciate that some sciences are funded very extravagantly and others very poorly. It is a decision of most societies that the sciences of medicine, economics and law are the kings of the hill. More funding probably flows to medical science than to all the other sciences combined. You can argue that this is what should occur, since humans are the most dominant and most important species in the Earth’s ecosystems. The confound here is the ethical one – are the poor of the world to be helped or not? Such a question seems outrageous, but just look at the distribution of Covid vaccines at different countries around the world. Economics is a strange bedfellow of medicine in the apparent view of society and its governments. The result is that there are more economists in the world today than non-medical scientists. We will not change this in our day.

The sciences that are most highly regarded are those that achieve two goals: first, rapid developments that improve our wealth, economic, and social goals, and second, developments that enable Earth as a planet to be exploited for human welfare. The physical sciences and engineering permit us to travel quickly, to fight wars against our enemies, and as a spinoff provide us with better automobiles and kitchen appliances. Geology helps us to find oil, iron ore, and lithium while it maps the Earth to help us understand its history. Zoology and Botany are different. They are supported strongly when they interface with the medical sciences and agriculture at a very practical level but otherwise are low in the funding order.

Ecology differs in that it proposes to understand how the populations of animals and plants, the biological communities, and ecosystems operate and what forces cause these to change. The first problem that arises with this mandate it that ecological understanding requires time frames that exceed human lifespans. So, ecology faces the same problem as geology but is not easily able to be useful in telling us where to build dams, where to mine gold and coal. We face an impossible barrier. To describe the biota of the Earth with its millions of species will occupy us for hundreds of years, assuming the funding is there. To understand why communities and ecosystems change will require an equal time span. But since ecological elements are driven in many ways by weather, climate change forces us to analyse an ever-changing network of species interactions.  

A consequence of this dilemma for ecologists is that they must study how humans are destroying the Earth and suggest a resolution of these problems. We are squeezed between our original objective of understanding how ecological interactions structure our world and serious immediate problems. An introduced pest is killing our trees – do something about this. Deer populations are too high so fix that. Fisheries are in difficulty, manage that. Some iconic species are declining in abundance, so citizens push to have more funding for biodiversity conservation. These are all short-term problems, while the need for ecological understanding is almost entirely long term. This takes us back to funding. For the past 30 or more years governments around the world have been reducing funding for ecological investigations. Government biologists have not increased in number given the urgent problems of the day. University funding of ecological sciences and ecological faculty members has declined partly because ecologists do not increase economic growth. Private funding has not come to the rescue because it is largely directed to social and economic issues, partly because of the feeling that it is the government’s job to deal with long-term issues in research.

The only solution is for ecologists to work together on important large-scale ecological problems with minimal funding. But this is impossible within the university system in which teaching is a focus and research can only be short-term. Attempts to address the large-scale ecological issues have resulted in many publications that use meta-analyses to resolve ecological questions. I doubt that these have achieved the resolution of ecological issues that we need (e.g. Geary et al. 2020).

What can we do about this relatively gloomy situation? One suggestion is to continue as we are, addressing short-term questions with limited funding. The advantage of this approach is that it allows individuals freedom from group constraints. One disadvantage is that two studies of the same problem may not be comparable unless the methods used were the same (e.g. Christie et al. 2019). The argument that climate change is happening so everything will change, and the past will not be relevant to the present is an argument of a broad uncoordinated approach to ecological issues.

Another approach can be to identify the critical ecological questions that we need answered now. Few have been brave enough to attempt this (Sutherland et al. 2010, 2013, 2018) for the broad area of conservation biology. An attempt to judge how much progress had been made on the issues listed in these three papers would be profitable in order to determine if this approach is useful in coordinating research programs. We might hope that ecological discord would be reduced if critical ecological questions were attacked with a consistent experimental design.

This discussion of ecology fits under the ‘empirical ecological studies’ framework of Fulton et al. (2019), and the expansive belief that theoretical models and system models will drive ecology into a successful science is illustrated in this recent review (O’Connor et al. 2020) and the accompanying articles. My concern is that these approaches have gotten us very little ahead in understanding ecological systems to date, and that until empirical ecological studies are increased in scope, duration, and precision we will not know whether models and systems analysis are leading us to a better understanding of the Earth’s ecosystems and the drivers of change or not. There is much left to be done.  

Christie, A.P.et al. (2019). Simple study designs in ecology produce inaccurate estimates of biodiversity responses Journal of Applied Ecology 56, 2742-2754. doi: 10.1111/1365-2664.13499.

Fulton, E.A.et al. (2019). Where the ecological gaps remain, a modelers’ perspective. Frontiers in Ecology and Evolution 7. doi: 10.3389/fevo.2019.00424.

Geary, W.L., et al. (2020). Predator responses to fire: A global systematic review and meta-analysis. Journal of Animal Ecology 89, 955-971. doi: 10.1111/1365-2656.13153.

O’Connor, M.I.et al. (2020). Editorial: Unifying ecology Across scales: Progress, challenges and opportunities. Frontiers in Ecology and Evolution 8, 610459. doi: 10.3389/fevo.2020.610459.

Sutherland, W.J. et al. (2010). A horizon scan of global conservation issues for 2010. Trends in Ecology & Evolution 25, 1-7. doi: 10.1016/j.tree.2009.10.003.

Sutherland, W.J. et al. (2013). Identification of 100 fundamental ecological questions. Journal of Ecology 101, 58-67. doi: 10.1111/1365-2745.12025.

Sutherland, W.J et al. (2018). A 2018 Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity. Trends in Ecology & Evolution 33, 47-58. doi: 10.1016/j.tree.2017.11.006.

On Questionable Research Practices

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Ecologists and evolutionary biologists are tarred and feathered along with many scientists who are guilty of questionable research practices. So says this article in “The Conservation” on the web:
https://theconversation.com/our-survey-found-questionable-research-practices-by-ecologists-and-biologists-heres-what-that-means-94421?utm_source=twitter&utm_medium=twitterbutton

Read this article if you have time but here is the essence of what they state:

“Cherry picking or hiding results, excluding data to meet statistical thresholds and presenting unexpected findings as though they were predicted all along – these are just some of the “questionable research practices” implicated in the replication crisis psychology and medicine have faced over the last half a decade or so.

“We recently surveyed more than 800 ecologists and evolutionary biologists and found high rates of many of these practices. We believe this to be first documentation of these behaviours in these fields of science.

“Our pre-print results have certain shock value, and their release attracted a lot of attention on social media.

  • 64% of surveyed researchers reported they had at least once failed to report results because they were not statistically significant (cherry picking)
  • 42% had collected more data after inspecting whether results were statistically significant (a form of “p hacking”)
  • 51% reported an unexpected finding as though it had been hypothesised from the start (known as “HARKing”, or Hypothesising After Results are Known).”

It is worth looking at these claims a bit more analytically. First, the fact that more than 800 ecologists and evolutionary biologists were surveyed tells you nothing about the precision of these results unless you can be convinced this is a random sample. Most surveys are non-random and yet are reported as though they are a random, reliable sample.

Failing to report results is common in science for a variety of reasons that have nothing to do with questionable research practices. Many graduate theses contain results that are never published. Does this mean their data are being hidden? Many results are not reported because they did not find an expected result. This sounds awful until you realize that journals often turn down papers because they are not exciting enough, even though the results are completely reliable. Other results are not reported because the investigator realized once the study is complete that it was not carried on long enough, and the money has run out to do more research. One would have to have considerable detail about each study to know whether or not these 64% of researchers were “cherry picking”.

Alas the next problem is more serious. The 42% who are accused of “p-hacking” were possibly just using sequential sampling or using a pilot study to get the statistical parameters to conduct a power analysis. Any study which uses replication in time, a highly desirable attribute of an ecological study, would be vilified by this rule. This complaint echos the statistical advice not to use p-values at all (Ioannidis 2005, Bruns and Ioannidis 2016) and refers back to complaints about inappropriate uses of statistical inference (Armhein et al. 2017, Forstmeier et al. 2017). The appropriate solution to this problem is to have a defined experimental design with specified hypotheses and predictions rather than an open ended observational study.

The third problem about unexpected findings hits at an important aspect of science, the uncovering of interesting and important new results. It is an important point and was warned about long ago by Medewar (1963) and emphasized recently by Forstmeier et al. (2017). The general solution should be that novel results in science must be considered tentative until they can be replicated, so that science becomes a self-correcting process. But the temptation to emphasize a new result is hard to restrain in the era of difficult job searches and media attention to novelty. Perhaps the message is that you should read any “unexpected findings” in Science and Nature with a degree of skepticism.

The cited article published in “The Conversation” goes on to discuss some possible interpretations of what these survey results mean. And the authors lean over backwards to indicate that these survey results do not mean that we should not trust the conclusions of science, which unfortunately is exactly what some aspects of the public media have emphasized. Distrust of science can be a justification for rejecting climate change data and rejecting the value of immunizations against diseases. In an era of declining trust in science, these kinds of trivial surveys have shock value but are of little use to scientists trying to sort out the details about how ecological and evolutionary systems operate.

A significant source of these concerns flows from the literature that focuses on medical fads and ‘breakthroughs’ that are announced every day by the media searching for ‘news’ (e.g. “eat butter”, “do not eat butter”). The result is almost a comical model of how good scientists really operate. An essential assumption of science is that scientific results are not written in stone but are always subject to additional testing and modification or rejection. But one result is that we get a parody of science that says “you can’t trust anything you read” (e.g. Ashcroft 2017). Perhaps we just need to repeat to ourselves to be critical, that good science is evidence-based, and then remember George Bernard Shaw’s comment:

Success does not consist in never making mistakes but in never making the same one a second time.

Amrhein, V., Korner-Nievergelt, F., and Roth, T. 2017. The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research. PeerJ  5: e3544. doi: 10.7717/peerj.3544.

Ashcroft, A. 2017. The politics of research-Or why you can’t trust anything you read, including this article! Psychotherapy and Politics International 15(3): e1425. doi: 10.1002/ppi.1425.

Bruns, S.B., and Ioannidis, J.P.A. 2016. p-Curve and p-Hacking in observational research. PLoS ONE 11(2): e0149144. doi: 10.1371/journal.pone.0149144.

Forstmeier, W., Wagenmakers, E.-J., and Parker, T.H. 2017. Detecting and avoiding likely false-positive findings – a practical guide. Biological Reviews 92(4): 1941-1968. doi: 10.1111/brv.12315.

Ioannidis, J.P.A. 2005. Why most published research findings are false. PLOS Medicine 2(8): e124. doi: 10.1371/journal.pmed.0020124.

Medawar, P.B. 1963. Is the scientific paper a fraud? Pp. 228-233 in The Threat and the Glory. Edited by P.B. Medawar. Harper Collins, New York. pp. 228-233. ISBN 978-0-06-039112-6

Three Approaches to Ecology

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I ask the question here why ecology is not appreciated as a science at a time when it is critical to the survival of the existing world. So the first question we need to answer is if this premise is correct. I offer only one example. A university zoology department has recently produced a discussion paper on its plans for faculty recruitment over the next 15 years. This document does not include the word “ecology” in any of its forward planning. Now it is probably not unusual for biology or zoology departments in major universities to downplay ecology when there is so much excitement in molecular biology, but it is an indicator that ecology is not a good place to put your money and reputation as you await a Nobel Prize. So if we can accept the initial premise that ecology is not appreciated, we might ask why this situation exists, a point raised long ago by O’Connor (2000). Here are a few thoughts on the matter.

There are three broad approaches to the science of ecology – theoretical ecology, empirical ecology, and applied ecology. These three areas of ecology rarely talk to each other, although one might hope that they could in future evolve into a seamless thread of science.

Theoretical ecology deals with the mathematical world that has too often only a tangential concern with ecological problems. It has its own journals and a whole set of elegant discussions that have few connections to the real world. It is most useful for exploring what might be if we make certain mathematical assumptions. It is without question the most prestigious part of the broad science of ecology, partly because it involves elegant mathematics and partly because it does not get involved in all the complexities of real-world ecological systems. It is the physics of ecology. As such it carries on in its own world and tends to be ignored by most of those working in the other two broad areas of ecology.

Empirical ecology has set itself the task of understanding how the natural world works at the level of individuals, populations, communities and ecosystems. In its pure form it does not care about solving practical ecological or environmental problems, but its practitioners assume probably correctly that the information they provide will in fact be useful now or in the future. It seeks generality but rarely finds it because all individuals and species differ in how they play the ecological game of survival. If it has a mantra, it is “the devil is in the details”. The problem is the details of empirical ecology are boring to politicians, business people, and to much of the television generation now operating with a 7 second or 140 character limit on concentration.

Applied ecology is where the action is now, and if you wish to be relevant and topical you should be an applied ecologist, whether a conservation biologist, a forester, or an agricultural scientist. The mantra of applied ecologists is to do no harm to the environment while solving real world problems. Applied ecologists are forced to put the human imprint into empirical ecology, so they are very much concerned with declining populations and extinctions of plants and animals. The main but not the sole impact of humans is on climate change, so much of applied ecology traces back to the impacts of climate change on ecosystems, all added to by the increasing human population with its rising expectations. But applied ecologists are always behind the environmental problems of the day because the issues multiply faster than possible solutions can be evaluated. This ought to make for high employment for applied ecologists but in fact the opposite seems to be happening because governments too often avoid long-term problems beyond their 4-year mandate. If you do not agree, think climate change.

So, the consequence is that we have three independent worlds out there. Applied ecologists are too busy to apply the successful paradigms of empirical ecology to their problems because they are under strict time limits by their line managers who need to suggest immediate action on problems. They must therefore fire off solutions like golf balls in all directions, hoping that some might actually help solve problems. Empirical ecologists may not be helpful for applied ecologists if they are overwhelmed by the details of their particular system of study and are constrained by the ‘publish or perish’ mentality of the granting agencies.

Finally, we lay on top all this a lack of funding in the environmental sciences for investigating and solving both immediate and long-term ecological problems. And I am back to my favourite quote in the ecological literature:

“Humans, including ecologists, have a peculiar fascination with attempting to correct one ecological mistake with another, rather than removing the source of the problem.” (Schindler 1997).

What can we do about this? Three things. Pressure our politicians to increase funding on long-term environmental problems. This will provide the person-power to find and test solutions to our known problems. Vote with your ballot and your feet to improve sustainability. And whether you are young or old strive to do no harm to the Earth. And if all this is too difficult, take some practical advice not to buy a house in Miami Beach, or any house near the beach. Do something for the environment every day.

 

O’Connor, R.J. (2000) Why ecology lags behind biology. The Scientist 14(20):35. (October 16, 2000).

Schindler, D.W. (1997) Liming to restore acidified lakes and streams: a typical approach to restoring damaged ecosystems? Restoration Ecology 5:1-6

 

On Ecological Predictions

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The gold standard of ecological studies is the understanding of a particular ecological issue or system and the ability to predict the operation of that system in the future. A simple example is the masting of trees (Pearse et al. 2016). Mast seeding is synchronous and highly variable seed production among years by a population of perennial plants. One ecological question is what environmental drivers cause these masting years and what factors can be used to predict mast years. Weather cues and plant resource states presumably interact to determine mast years. The question I wish to raise here, given this widely observed natural history event, is how good our predictive models can be on a spatial and temporal scale.

On a spatial scale masting events can be widespread or localized, and this provides some cues to the important weather variables that might be important. Assuming we can derive weather models for prediction, we face two often unknown constraints – space and time. If we can derive a weather model for trees in New Zealand, will it also apply to trees in Australia or California? Or on a more constrained geographical view, if it applied on the South Island of New Zealand will it also apply on the North Island? At the other extreme, must we derive models for every population of particular plants in different areas, so that predictability is spatially limited? We hope not and work on the assumption of more spatial generality than what we can measure on our particular small study areas.

The temporal stability of our explanations is now particularly worrisome because of climate change. If we have a good model of masting for a particular tree species in 2017, will it still be working in 2030, 2050 or 2100? A physicist would never ask such a question since a “scientific law” is independent of time. But biology in general and ecology in particular is not time independent both because of evolution and now in particular because of changing climate. But we have not faced up to whether or not we must check our “ecological laws” over and over again as the environment changes, and if we have to do this what must the time scale of rechecking be? Perhaps this question can be answered by determining the speed of potential evolutionary change in species groups. If virus diseases can evolve quickly in terms of months or years, we must be eternally vigilant to consider if the flu virus of 2017 is going to be the same as that of 2016. We should not stop virus research and say that we have sorted out some universal model that will become an equivalent of the laws of physics.

The consequences of these simple observations are not simple. One consequence is the implication that monitoring is an essential ecological activity. But in most ecological funding agencies monitoring is thought to be unscientific, not leading to progress, and more stamp collecting. So we have to establish that, like the Weather Bureau every country supports, we must have an equivalent ecological monitoring bureau. We do have these bureaus for some ecological systems that make money, like marine fisheries, but most other ecosystems are left in limbo with little or no funding on the generalized assumption that “mother or father nature will take care of itself” or expressed more elegantly by a cabinet minister who must be nameless, “there is no need for more forestry research, as we know everything we need to know already”. The urge by politicians to cut research funding lives too much in environmental research.

But ecologists are not just ‘stamp collectors’ as some might think. We need to develop generality but at a time scale and a spatial scale that is reliable and useful for the resolution of the problem that gave rise to the research. Typically for ecological issues this time scale would be 10-25 years, and a rule of thumb might be for 10 generations of the organisms being studied. For many of our questions an annual scale might be most useful, but for long-lived plants and animals we must be thinking of decades or even centuries. Some practical examples from Pacifici et al. (2013): If you study field voles (Microtus spp.) typically you can complete your studies of 10 generations in 3.5 years (on average). If you study red squirrels (Tamiasciurus hudsonicus), the same 10 generations will cost you 39 years, and if red foxes (Vulpes vulpes) 58 years. If wildebeest (Connochaetes taurinus) in the Serengeti, 10 generations will take you 80 years, and if you prefer red kangaroos (Macropus rufus) it will take about 90 years. All these estimates are very approximate but they give you an idea of what the time scale of a long-term study might be. Except for the rodent example, all these study durations are nearly impossible to achieve, and the question for ecologists is this: Should we be concerned about these time scales, or should we scale everything to the human research time scale?

The spatial scale has expanded greatly for ecologists with the advent of radio transmitters and the possibility of satellite tracking. These technological advances allow many conservation questions regarding bird migration to be investigated (e.g. Oppel et al. 2015). But no matter what the spatial scale of interest in a research or management program, variation among individuals and sites must be analyzed by means of the replication of measurements or manipulations at several sites. The spatial scale is dictated by the question under investigation, and the issue of fragmentation has focused attention on the importance of spatial movements both for ecological and evolutionary questions (Betts et al. 2014).

And the major question remains: can we construct an adequate theory of ecology from a series of short-term, small area or small container studies?

Betts, M.G., Fahrig, L., Hadley, A.S., Halstead, K.E., Bowman, J., Robinson, W.D., Wiens, J.A. & Lindenmayer, D.B. (2014) A species-centered approach for uncovering generalities in organism responses to habitat loss and fragmentation. Ecography, 37, 517-527. doi: 10.1111/ecog.00740

Oppel, S., Dobrev, V., Arkumarev, V., Saravia, V., Bounas, A., Kret, E., Velevski, M., Stoychev, S. & Nikolov, S.C. (2015) High juvenile mortality during migration in a declining population of a long-distance migratory raptor. Ibis, 157, 545-557. doi: 10.1111/ibi.12258

Pacifici, M., Santini, L., Di Marco, M., Baisero, D., Francucci, L., Grottolo Marasini, G., Visconti, P. & Rondinini, C. (2013) Database on generation length of mammals. Nature Conservation, 5, 87-94. doi: 10.3897/natureconservation.5.5734

Pearse, I.S., Koenig, W.D. & Kelly, D. (2016) Mechanisms of mast seeding: resources, weather, cues, and selection. New Phytologist, 212 (3), 546-562. doi: 10.1111/nph.14114

Ecological Alternative Facts

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It has become necessary to revise my recent ecological thinking about the principles of ecology along the lines now required in the New World Order. I list here the thirteen cardinal principles of the new ecology 2017:

  1. Population growth is unlimited and is no longer subject to regulation.
  2. Communities undergo succession to the final equilibrium state of the 1%.
  3. Communities and ecosystems are resilient to any and all disturbances and operate best when challenged most strongly, for example with oil spills.
  4. Resources are never limiting under any conditions for the 1% and heavy exploitation helps them to trickle down readily to assist the other 99%.
  5. Overexploiting populations is good for the global ecosystem because it gets rid of the species that are wimps.
  6. Mixing of faunas and floras have been shown over the last 300 years to contribute to the increasing ecological health of Earth.
  7. Recycling is unnecessary in view of recent advances in mining technology.
  8. Carbon dioxide is a valuable resource for plants and we must increase its contribution to atmospheric chemistry.
  9. Climate change is common and advantageous since it occurs from night to day, and has always been with us for many millions of years.
  10. Evolution maximizes wisdom and foresight, especially in mammals.
  11. Conservation of less fit species is an affront to alternative natural laws that were recognized during the 18th century and are now mathematically defined in the new synthetic theory of economic and ecological fitness.
  12. Scientific experiments are no longer necessary because we have computers and technological superiority.
  13. Truth in science is no longer necessary and must be balanced against equally valid post-truth beliefs.

The old ecology, now superseded, was illustrated in Krebs (2016), and is already out of date. Recommendations for other alternative ecological facts will be welcome. Please use the comments.

Krebs, C.J. (2016) Why Ecology Matters. University of Chicago Press, Chicago. 208 pp.

Technology Can Lead Us Astray

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Our iPhones teach us very subtly to have great faith in technology. This leads the public at large to think that technology will solve large issues like greenhouse gases and climate change. But for scientists we should remember that technology must be looked at very carefully when it tells us we have a shortcut to ecological measurement and understanding. For the past 35 years satellite data has been available to calculate an index of greening for vegetation from large landscapes. The available index is called NDVI, normalized difference vegetation index, and is calculated as a ratio of near infrared light to red light reflected from the vegetation being surveyed. I am suspicious that NDVI measurements tell ecologists anything that is useful for the understanding of vegetation dynamics and ecosystem stability. Probably this is because I am focused on local scale events and landscapes of hundreds of km2 and in particular what is happening in the forest understory. The key to one’s evaluation of these satellite technologies most certainly lies in the questions under investigation.

A whole array of different satellites have been used to measure NDVI and since the more recent satellites have different precision and slightly different physical characteristics, there is some problem of comparing results from different satellites in different years if one wishes to study long-term trends (Guay et al. 2014). It is assumed that NDVI measurements can be translated into aboveground net primary production and can be used to start to answer ecological questions about seasonal and annual changes in primary production and to address general issues about the impact of rising CO2 levels on ecosystems.

All inferences about changes in primary production on a broad scale hinge on the reliability of NDVI as an accurate measure of net primary production. Much has been written about the use of NDVI measures and the need for ground truthing. Community ecologists may be concerned about specific components of the vegetation rather than an overall green index, and the question arises whether NDVI measures in a forest community are able to capture changes in both the trees and the understory, or for that matter in the ground vegetation. For overall carbon capture estimates, a greenness index may be accurate enough, but if one wishes to determine whether deciduous trees are replacing evergreen trees, NDVI may not be very useful.

How can we best validate satellite based estimates of primary productivity? To do this on a landscape scale we need to have large areas with ground truthing. Field crops are one potential source of such data. Kang et al. (2016) used crops to quantify the relationship between remotely sensed leaf-area index and other satellite measures such as NDVI. The relationships are clear in a broad sense but highly variable in particular, so that the ability to predict crop yields from satellite data at local levels is subject to considerable error. Johnson (2016, Fig. 6, p. 75) found the same problem with crops such as barley and cotton (see sample data set below). So there is good news and bad news from these kinds of analyses. The good news is that we can have extensive global coverage of trends in vegetation parameters and crop production, but the bad news is that at the local level this information may not be helpful for studies that require high precision for example in local values of net primary production. Simply to assume that satellite measures are accurate measures of ecological variables like net aboveground primary production is too optimistic at present, and work continues on possible improvements.

Many of the critical questions about community changes associated with climate change cannot in my opinion be answered by remote sensing unless there is a much higher correlation of ground-based research that is concurrent with satellite imagery. We must look critically at the available data. Blanco et al. (2016) for example compared NDVI estimates from MODIS satellite data with primary production monitored on the ground in harvested plots in western Argentina. The regression between NDVI and estimated primary production had R2 values of 0.35 for the overall annual values and 0.54 for the data restricted to the peak of annual growth. Whether this is a satisfactory statistical association is up to plant ecologists to decide. I think it is not, and the substitution of p values for the utility of such relationships is poor ecology. Many more of these kind of studies need to be carried out.

The advent of using drones for very detailed spectral data on local study areas will open new opportunities to derive estimates of primary production. For the present I think we should be aware that NDVI and its associated measures of ‘greenness’ from satellites may not be a very reliable measure for local or landscape values of net primary production. Perhaps it is time to move back to the field and away from the computer to find out what is happening to global plant growth.

Blanco, L.J., Paruelo, J.M., Oesterheld, M., and Biurrun, F.N. 2016. Spatial and temporal patterns of herbaceous primary production in semi-arid shrublands: a remote sensing approach. Journal of Vegetation Science 27(4): 716-727. doi: 10.1111/jvs.12398.

Guay, K.C., Beck, P.S.A., Berner, L.T., Goetz, S.J., Baccini, A., and Buermann, W. 2014. Vegetation productivity patterns at high northern latitudes: a multi-sensor satellite data assessment. Global Change Biology 20(10): 3147-3158. doi: 10.1111/gcb.12647.

Johnson, D.M. 2016. A comprehensive assessment of the correlations between field crop yields and commonly used MODIS products. International Journal of Applied Earth Observation and Geoinformation 52(1): 65-81. doi: 10.1016/j.jag.2016.05.010.

Kang, Y., Ozdogan, M., Zipper, S.C., Roman, M.O., and Walker, J. 2016. How universal Is the relationship between remotely sensed vegetation Indices and crop leaf area Index? A global assessment. Remote Sensing 2016 8(7): 597 (591-529). doi: 10.3390/rs8070597.

Cotton yield vs NDVI Index