Tag Archives: progress in ecology

On Journal Referees

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I have been an editor of enough ecological journals to know the problems of referees first hand. The start is to try to find a referee for a particular paper. I would guess now that more than two-thirds of scientists asked to referee a potential paper say they do not have time. This leads to another question of why no one has any time to do anything, but that is a digression. If one is fortunate you get 2 or 3 good referees.

The next problem comes when the reviews of the paper come back. Besides dealing with the timing of return of the reviews, there are four rules which ought to be enforced on all referees. First, review the potential paper as it is. Do not write a review saying this is what you should have written- that is not your job. Second, if the paper is good enough, be positive in making suggestions for improvement. If it is not good enough in your opinion, try to say so politely and suggest alternate journals. Perhaps the authors are aiming for a journal that is too prestigious. Third, do not say in so many words that the author should cite the following 4 papers of mine…. And fourth, do not make ad hominem attacks on the authors. If you do not like people from Texas, this is not the place to take it out on the particular authors who happen to live there.

Given the reviews, the managing editor for the paper ought to make a judgment. Some reviews do not follow the four rules above. A good editor discards these and puts a black mark on the file of that particular reviewer. I would not submit a referee’s review to the authors if it violated any of the above 4 rules. I have known and respected editors who operated this way in the past.

The difficulty now is that ecological journals are overrun. This is driven in part by the desire to maximize the number of papers one publishes in order to get a job, and in part by journals not wanting to publish longer papers. Journals do not either have the funding or the desire to grow in relation to the number of users. This typically means that papers are sent out for reviews with a note attached saying that we have to reject 80% or so of papers regardless of how good they are, a rather depressing order from above. When this level of automatic rejection is reached, the editor in chief has the power to reject any kinds of papers not in favour at the moment. I like models so let’s publish lots of model papers. Or I like data so let’s publish only a few model papers.

One reason journals are overrun is that many of the papers published in our best ecology journals are discussions of what we ought to be doing. They may be well written but they add nothing to the wisdom of our age if they simply repeat what has been in standard textbooks for the last 30 years. In days gone by, many of these papers I think might have been given as a review seminar, possibly at a meeting, but no one would have thought that they were worthy of publication. Clearly the editors of some of our journals think it is more important to talk about what to do rather than to do it.

I think without any empirical data that the quality of reviews of manuscripts has deteriorated as the number of papers published has increased. I often have to translate reviews for young scientists who are devastated by some casual remark in a review. “Forget that nonsense, deal with this point as it is important, ignore this insult to your supervisor, go have a nice glass of red wine and relax, ……”. One learns how to deal with poor reviews.

I have been reading Bertram Murray’s book “What Were They Thinking? Is Population Ecology a Science?” (2011), unfortunately published after he died in 2010. It is a long diatribe about reviews of some of his papers and it would be instructive for any young ecologist to read it. You can appreciate why Murray had trouble with some editors just from the subtitle of his book, “Is Population Ecology a Science?” It illustrates very well that even established ecologists have difficulty dealing with reviews they think are not fair. In defense of Murray, he was able to get many of his papers published, and he cites these in this book. One will not come away from this reading with much respect for ornithology journals.

I think if you can get one good, thoughtful review of your manuscript you should be delighted. And if you are rejected from your favourite journal, try another one. The walls of academia could be papered with letters of rejection for our most eminent ecologists, so you are in the company of good people.

Meanwhile if you are asked to referee a paper, do a good job and try to obey the four rules. Truth and justice do not always win out in any endeavour if you are trying to get a paper published. At least if you are a referee you can try to avoid these issues.

Barto, E. Kathryn, and Matthias C. Rillig. 2012. “Dissemination biases in ecology: effect sizes matter more than quality.” Oikos 121 (2):228-235. doi: 10.1111/j.1600-0706.2011.19401.x.

Ioannidis, John P. A. 2005. “Why most published research findings are false.” PLoS Medicine 2 (8):e124.

Medawar, P.B. 1963. “Is the scientific paper a fraud?” In The Threat and the Glory, edited by P.B. Medawar, 228-233. New York: Harper Collins.

Merrill, E. 2014. “Should we be publishing more null results?” Journal of Wildlife Management 78 (4):569-570. doi: 10.1002/jwmg.715.

Murray, Bertram G., Jr. 2011. What Were They Thinking? Is Population Ecology a Science? Infinity Publishing. 310 pp. ISBN 9780741463937

 

Some Reflections on Evo-Eco

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Some ecologists study evolutionary processes and we call them evolutionary ecologists. They have their own journals and are a thriving field of science. Other ecologists study populations, communities, and ecosystems in ecological time and do not in general concern themselves with evolutionary changes.The question is should they? Evo-Eco is a search for evolutionary changes that have a decisive impact on observable ecological changes like that of a collapsing bird population.

There are two schools of thought. The first is that evo-eco is very important and the changes that ecologists are trying to understand are partly caused by ecological mechanisms like predation and competition but are also associated with genetic changes that affect survival and reproduction. Consequently an ecologist studying the declining bird population should study both genetics and ecology. The second school of thought is that evo-eco is rarely of any importance in causing ecological changes, so that we can more or less ignore genetics if we wish to understand why this bird population is disappearing.

A practical problem immediately rears its head. To be safe we should all follow evo-eco in case genetics is involved in dynamics. But given the number of problems that ecologists face, the number of scientists available to analyse them, and the research dollars available it is rare to have the time, energy or money to take the comprehensive route. Conservation ecologists are perhaps the most tightly squeezed of all ecologists because they have no time to spare. Environmental managers request answers about what to do, and the immediate causes of conservation problems are (as everyone knows) habitat loss, introduced pests and diseases, and pollution.

The consequence of all this is that the two schools of thought drift apart. I cannot foresee any easy way to solve this issue. Progress in evolutionary ecology is often very slow and knowing the past rarely gives us much insight into predicting the human-affected future. Progress in conventional ecology is faster but our understanding is based on short-term studies of unknown generality for future events. Both schools of thought race along with mathematical models that may or may not tell us anything about the real world, but are conceptually elegant and in a pinch might be called progress if we had time to test them adequately.

The most useful evo-eco approach has been to look at human-caused selection via fishing for large sized fish or hunting for Dall sheep with the largest horns. The overuse of antibiotics for human sickness and as prophylactics for our farm animals is another classic case in which to understand the ecological dynamics we need to know the evolutionary changes that we humans have caused. These are clear cases in which genetic insights can teach us very much.

I end with a story from my past. In the 1950s, nearly 70 years ago now, Dennis Chitty working at Oxford on population fluctuations in small grassland rodents considered that he could reject most of the conventional explanations for animal population changes, and he suggested that individuals might change in quality with population density. This change he thought might involve genetic selection for traits that were favourable only in high density populations that reappeared every 3-4 years. So in some strange sense he was one of the earliest evo-eco ecologists. The result was that he was nearly laughed out of Oxford by the geneticists in control. The great evolutionary geneticist E.B. Ford told Chitty he was completely mad to think that short term selection was possible on a scale to impact population dynamics. Genetic changes took dozens to hundreds of years at the best of time. There were of course in the 1950s only the most primitive of genetic methods available for mammals that all look the same in their coat colour, and the idea that changes in animal behaviour involving territoriality might cause genetic shifts on a short-term period gradually lost favour. Few now think that Chitty was right in being evo-eco, but in some sense he was ahead of his time in thinking that natural selection might operate quickly in field populations. Given the many physiological and behavioural changes that can occur phenotypically in mammals, most subsequent work on grassland rodents has become buried in mechanisms that do not change because of genetic selection.

When we try to sort out whether to be concerned about evo-eco, we must strike a compromise between what the exact question is that we are trying to investigate, and how we can best construct a decision tree that can operate in real time with results that are useful for the research question. Not every ecological problem can be solved by sequencing the study organism.

Chitty, D. 1960. Population processes in the vole and their relevance to general theory. Canadian Journal of Zoology 38:99-113.

On Important Questions in Ecology

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There is a most interesting paper that you should read about the important questions in ecology:

Sutherland, W.J. et al. (2013) Identification of 100 fundamental ecological questions. Journal of Ecology, 101, 58-67.

This paper represents the views of 388 ecologists who culled through all of the 754 questions submitted and vetted in a two day workshop in London in April 2012. There are many thesis topics highlighted in this list and it gives a good overview of what many ecologists think is important. But there are some problems with this approach that you might wish to consider after you read this paper.

We can begin with a relatively trivial point. The title indicates that it will discuss ‘fundamental’ questions in ecology but the Summary changes this to ‘important’ questions. To be sure the authors recognize that what we now think is ‘important’ may be judged in the future to be less than important, so in a sense they recognize this problem. ‘Important’ is not an operational word in science, and consequently it is always a focus for endless argument. But let us not get involved with semantics and look at the actual 100 questions.

As I read the paper I was reminded of the discussion in Peters (1991, p. 13) who had the audacity to point out that academic ecologists thrived on unanswerable questions. In particular Peters (1991) focused on ‘why’ questions as being high on the list of unanswerable ones, and it is good to see that there are only 2 questions out of 100 that have a ‘why’ in them. Most of the questions posed are ‘how’ questions (about 65 instances) and ‘what’ questions (about 52 instances).

In framing questions in any science there is a fine line in the continuum of very broad questions that define an agenda and at the other extreme to very specific questions about one species or community. With very broad questions there will never be a clear point at which we can say that we have answered that question so we can move on. With very specific questions we can answer them experimentally and move on. So where do we cut the cake of questions? Most of these 100 questions are very broad and so they both illuminate and frustrate me because they cannot be answered without making them more specific.

Let me go over just one example. Question 11 What are the evolutionary and ecological mechanisms that govern species’ range margins? First, we might note that this question goes back at least 138 years to Alfred Wallace (1876, The Geographical Distribution of Animals), and has been repeated in many ecology textbooks ever since. There are few organisms for which it has been answered and very much speculation about it. At the moment the ecological mechanism in favour is ‘climate’. This is a question that can be answered ecologically only for particular species, and cannot be answered in real (human) time for the evolutionary mechanisms. Consequently it is an area rife for correlational ecology whose conclusions could possibly be tested in a hundred years if not longer. All of these problems should not stand in the way of doing studies on range margins, and there are many hundreds of papers that attest to this conclusion. My question is when will we know that we have answered this question, and my answer is never. We can in some cases use paleoecology to get at these issues, and then extrapolate that the future will be like the past, a most dubious assumption. My concern is that if we have not answered this question in 138 years, what is the hope that we will answer it now?

It is good to be optimistic about the future development of ecological science. Perhaps I have picked a poor example from the list of 100 questions, and my concern is that in this case at least this is not a question that I would suggest to a new PhD student. Still I am glad to have this list set out so clearly and perhaps the next step would be to write a synthesis paper on each of the 100 topics and discuss how much progress has been made on that particular issue, and what exactly we might do to answer the question more rapidly. How can we avoid in ecology what Cox (2007) called a “yawning abyss of vacuous generalities”?

Cox, D. R. (2007) Applied statistics: A review. Annals of Applied Statistics, 1, 1-16.

Peters, R. H. (1991) A Critique for Ecology, Cambridge University Press, Cambridge, England.

Sutherland, W. J., Freckleton, R. P., Godfray, H. C. J., Beissinger, S. R., Benton, T., Cameron, D. D., Carmel, Y., Coomes, D. A., Coulson, T., Emmerson, M. C., Hails, R. S., Hays, G. C., Hodgson, D. J., Hutchings, M. J., Johnson, D., Jones, J. P. G., Keeling, M. J., Kokko, H., Kunin, W. E. & Lambin, X. (2013) Identification of 100 fundamental ecological questions. Journal of Ecology, 101, 58-67.

On House Mouse Outbreaks in Australia

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It occurred to me after some recent discussions that the problem of house mouse outbreaks in Australia is almost a paradigm for modern ecological science. A brief synopsis. At irregular intervals house mice (an introduced pest) reach high densities in the wheat growing areas of eastern and southern Australia, and cause serious damage to wheat, barley, oats, and sunflower crops. There are two approaches to this applied problem.

The ecological approach is to understand why these outbreaks occur and why for many years (2-9 years) between outbreaks, hardly a mouse can be found. This approach has been highly successful led by a series of excellent Australian ecologists over the last 40 years. The key limitation is food, combined with social interactions, and the food supply is driven by rain at critical times of the year to provide seeds for the mice. There are no competitors for house mice, and there are a few insignificant predators, overwhelmed by the mouse’s high reproductive rate. These ecological facts are clearly known, and the job now is to build the best predictive models to help the farmers anticipate when the outbreak is coming. There are still important ecological questions to be studied, to be sure, but the broad outline of the ecological play is well described.

The management approach is much simpler because farmers can control house mice with poison, primarily zinc phosphide, and for them the question is when to poison, and secondarily (over time and with more research) can we develop better poisons so there are few non-target problems. Poisoning costs time and money so good farmers wish to minimize these costs.

The long-term issues get lost in this situation, a model of the way the world operates now with ecological and environmental problems. Questions about sustainability multiply in any system dependent on poisons for a solution. Will the target organisms become resistant so the poison does not work? Many examples exist of this already. Are there any long-term problems with soil organisms, or non-target species? No research yet on these issues, and perhaps they are more serious with herbicide applications in agriculture. And while predators do not control house mice during outbreaks, they do eat many of them and this food pulse may have implications for the wider ecosystem. We focus on farming and forget the wider ecosystem which has no dollars attached to it.

Ecologists recognize that these issues are not the farmers’ fault, but we raise the question of who worries about the long-term future of this system, and the answers to these long-term questions. The government is rushing to get out of long-term ecological and agricultural research and we leave problems that do not have immediacy.

Consequently we become short-sighted as a society. Long-term research becomes 1-3 years and not the 50-100 years that ecologists would support. And consequently applied ecologists bounce from one problem to the next under the paradigm that, no matter what we do, science will come up with a technological fix. There should be a better way. To go back to our house mice, we might ask (for example) if we implement no-till agriculture, what will be the consequences for house mouse survival and future outbreaks? The practical minister of agriculture will respond that we have no time or money for such research, so we lurch along, managing the world in an ad-hoc manner. There should be a better way. But meanwhile we must follow the money.

10 Limitations on Progress in Ecology

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Ecological science moves along slowly in its mission to understand how the Earth’s populations, communities, and ecosystems operate within the constraints of human impacts on the Biosphere. The question of the day is can we identify the factors currently limiting the rate of progress so that at least in principle we could speed up progress in our science. Here is my list.

1. A shortage of ecologists or more properly jobs for ecologists. In particular a scarcity of government agencies employing ecologists in secure jobs to work on stable, long-term environmental projects that are beyond the scope of university scientists. Many young ecologists of high quality are stalled in positions that are beneath their talents. We are in a situation similar to having highly trained medical doctors being used as hospital janitors. This is a massive failure on many fronts, regional and national, political and scientific. Many governments around the world think economists and lawyers are key while environmental scientists are superfluous.

2. The lack of proper funding from both government, private companies and private individuals. This is typified by the continual downsizing of government scientists working on natural resource problems – fisheries, wildlife, park management – and continuing political interference with scientific objectives. Private companies too often rely on taxpayers to fund their environmental investigations and do not view them as a part of their business model. Private citizens give money to medical research rather than to environmental programs largely based on the belief that of all the life on Earth, only the human component is important.

3. The deficiency of taxonomic expertise to define clearly the species that inhabit the Earth. The estimates vary but perhaps only 10% of the total biota can be given a Latin name and morphological description, leaving out for the moment all the bacteria and viruses. Equate this with having a batch of various shaped coins in your pocket with only a few of them giving the denomination. This problem has been identified for years with little action.

4. Given adequate taxonomy, the lack of adequate natural history data on most of the biota. This activity, so critical for all ecological science, was called “stamp collecting” and thus condemned to the lowest point on the scientific totem pole. The consequence of this is that we try to understand the Earth with data only on butterflies, some birds, and some large mammals.

5. A failure of ecologists to map out the critical questions facing natural populations, communities, and ecosystems on Earth. The roadmap of ecology is littered with wrecks of ideas once pushed to explain nearly everything, and we need a more nuanced map of what is a critical issue. There are a considerable number of fractures within the ecological discipline about what needs to be done, if people and money were available. This fosters the culture of I win = you lose in competition for money and jobs.

6. The confusion of mathematical models with reality. There is a strong disconnect between models and data that persists. Models rapidly proliferate, data are slow to accumulate, so we try to paper over the fragility of our understanding with mathematical wizardry, trying to be like physicists. Connecting model predictions with empirical data studies would go a long way to righting this problem but it is a tall order in a world that confuses the number of publications and h scores with important contributions.

7 The fact that too many ecologists do not adopt the scientific method of investigation, to carry out experiments with multiple alternative hypotheses with clear predictions. Arguments continue endlessly based on words (‘concepts’) that are so vaguely defined as to be meaningless operationally. If you need an example, think ‘stability’ or ‘diversity’. These vague words are then herded into pseudo-hypotheses to doubly confound the confusion over what the critical questions in ecology really are.

8. The need for ecologists to work in stable groups. Serious ecological problems demand expertise in many scientific specialities, and we need better mechanisms to foster and maintain such groups. The assessment of scientists on the basis of individual work is long out of date, the Nobel Prize is an anachronism, and we need strong groups concentrating on important issues for long term studies. At the moment many groups exist to do meta-analyses and fewer to do science.

9. Placing the technological horse in front of the ecological cart. Ecology like many sciences is often led by technology rather than by questions. The current DNA bandwagon is one example, but we should not get so confused to think that that most important questions in ecology are those that use the most technology. Jumping from one technological bandwagon to the next is a good recipe for minimizing progress.

10. The fractionation of ecology into subdisciplines and the assumption that the only important research work has been done since 2000. Aquatic ecologists do not talk to terrestrial ecologists, microbial ecologists live in their own special world, and avian ecologists do not talk to insect ecologists. The result is that the existing literature is too often wasted by investigators who have no idea that question XX has already been answered either in another subdiscipline or in existing literature from 50 years ago.

Not all of these limitations apply to every ecologist, and at best I would view them as a set of guideposts that need to be considered as we move further into the 21st century.

Krebs, C. J. 2006. Ecology after 100 years: progress and pseudo-progress. New Zealand Journal of Ecology 30:3-11.

Majer, J. D. 2012. Critical times: How has ecological research responded over the past 35 years? Austral Ecology 37:149-152.

Sutherland, W. J. et al. 2010. A horizon scan of global conservation issues for 2010. Trends in Ecology & Evolution 25:1-7.