Monthly Archives: March 2014

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.

Open Letter from a Scientist to a Bureaucrat

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Let us assume for the moment that I am a scientist who has worked in a government research organization for 25 years under a series of bureaucrats. I have just retired and the object of this letter is to tell a bureaucrat what is good and what is bad about the bureaucratic government system. If you work in a perfect government system, perhaps you do not need to read further.

Dear Sir/Madam:

I would like to offer you some free advice that comes from a scientist who has worked in government for many years. This is presumptuous to be sure in light of our relative positions, but I feel you might benefit from some notes from the trenches.

First, science should never be organized in a top-down manner. We ecologists know about trophic cascades and the consequences it has for the lower trophic levels. You should not tell us what to do because you know nothing about the subject matter of the science, in this case ecology. I note especially that an MBA does not confer infinite wisdom on science matters. So I suggest you consider organizing things bottom-up. Your job is to provide scientists with the technical support, the funding, and the facilities to do their work. I note that this does not preclude you providing us with general areas of science in which we are expected to do our research. If our general position is to study the effectiveness of pollination in California crops, you should not tolerate us going to Africa to study elephant ecology. We appreciate that the government has at least some general ideas of what is critical to study. If they do not, it would be advisable to gather a group of scientists to discuss what the critical problems are in a particular area of science. Scientists do not work in closed rooms and do have a general understanding of what is happening in their field.

Second, do not muzzle us about anything scientific. We do not work for you or for the current government but we do work for the people of Canada or Australia or whatever country, and our mandate is to speak out on scientific questions, to provide evidence based policy guidance and to educate the public when errors are promulgated by people who know nothing about what they speak. This could well include government ministers who are known at least on occasion to utter complete nonsense. Our job is not to support the government’s policies of the day but to provide evidence about scientific questions. In general we scientists do not see government ministers crying out that they know more about brain surgery than trained doctors, so we think the same attitude ought to be taken toward ecologists.

Third, ask your scientists about the time frame of their scientific studies. Most bureaucrats seem to think that, since the world was created in 7 days, scientific work ought to take no more than a year or two or perhaps three. We would like to tell you that many, perhaps most, important ecological questions involve a time frame of 10 years or more, and some require continuous funding and support for periods in excess of 50 years. You apparently did not ask medical scientists to stop working on cancer or malaria after 3 years or even 50 years, so we are uncertain why ecologists should be kept to short time frames for their research. Ecological research is perhaps the most difficult of all the sciences, so if we do not find answers in a few years it is not because we are not working hard enough.

Finally, ask your scientists to publish in national and international journals because that is the corner stone for judging scientific progress. We do not mind having rules about rates of publication. And as a spur please fund your scientists to go to scientific meetings to present their results to the scientific world. And have them communicate to the public what they are doing and what they have found. After all the public pays, so why should they not hear about what has come of their tax dollars.

Your job, in a nutshell, is to support your scientists not to hinder them, to encourage their work, and to speak to the higher levels of government about why funding science is important. And to (at least on occasion) protest about government policies that are not based on scientific evidence. If you are successful in all of this, the people of your country will be the better for it. On the other hand, you may be headed for early retirement if you follow my advice.

I wish you success.

Sincerely yours,

A.B.C. Jones PhD, DSc, FRS, FAA
Retired

Two Visions of Ecological Research

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Let us assume for the moment that the goal of scientific ecology is to understand the reasons for changes in the distribution and abundance of animals, plants, and microbes. If you do not think this is our main agenda, perhaps you should not read further.

The conventional, old paradigm to achieve this goal is to obtain a good description of the natural history of the organisms of interest in a population or community, define the food web they operate within, and then determine by observations or manipulations the parameters that limit its distribution and abundance. This can be difficult to achieve in rich food webs with many species, and in systems in which the species are not yet taxonomically described, and particularly in microbe communities. Consequently a prerequisite of this paradigm is to have good taxonomy and to be able to recognize species X versus species Y. A whole variety of techniques can be used for this taxonomy, including morphology (the traditional approach) and genetics. Using this approach ecologists over the past 90 years have made much progress in deriving some tentative explanations for the changes that occur in populations and communities. If there has been a problem with this approach, it is largely because of disagreements about what data are sufficient to test hypothesis X, and whether the results of manipulation Y are convincing. A great deal of the accumulated data obtained with this approach has been useful to fisheries management, wildlife management, pest control, and agricultural production.

The new metagenomics paradigm, to use one label, suggests that this old approach is not getting us anywhere fast enough for microbial communities, and we need to forget most of this nonsense and get into sequencing, particularly for microbial communities. New improvements in the speed of doing this work makes it feasible. The question I wish to address here is not the validity or the great improvements in genetic analysis, but rather whether or not this approach can replace the conventional old paradigm. I appreciate that if we grab a sample of mud, water, or the bugs in an insect trap and grind it all up, and run it through these amazing sequencing machines, we get a very great amount of data. We then might try to associate some of these kinds of data with particular ‘species’ and this may well work in groups for which the morphological species are well described. But what do we do about the undescribed sequences? We know that microbial diversity is much higher than what we can currently culture in the laboratory. We can make rules about what to call unknown unit A, unknown unit B, and so on. That is fine, but now what? We are in some sense back where Linnaeus was in 1753 in giving names to plants.

Now comes the difficult bit. Do we just take the metagenomics approach and tack it on to the conventional approach, using unknown A, unknown B, etc. instead of Pseudomonas flavescens or Bacillus licheniformis? We cannot get very far this way because the first thing we need to decide is does unknown A a primary producer or unknown B a decomposer of complex organic molecules? So perhaps this leads us to invent a whole new taxonomy to replace the old one. But perhaps we will go another way to say we will answer questions with the new system like is this pond ecosystem changing in response to global warming or nutrient additions? We can describe many system shifts in DNA-terminology but will we have any knowledge of what they mean or how management might change these trends? We could work all this out in the long term I presume. So I guess my confusion is largely exactly which set of hypotheses are you going to test with the new metagenomics paradigm? I can see a great deal of alpha-descriptive information being captured but I am not sure where to go from there. My challenge to the developers of the new paradigm is to list a set of problems in the Earth’s ecosystems for which this new paradigm could provide better answers more quickly than the old approach.

Microbial ecology is certainly much more difficult to carry out than traditional ecology on macroscopic animals and plants. As such it should be able to use new technology that can improve understanding of the structure and function of microbe communities. All new advances in technology are helpful for solving some ecological problems and should be so used. The suggestion that the conventional approach is out of date should certainly be entertained but in the last 70 years the development of air photos, of radio telemetry, of satellite imagery, of electrophoresis, of simplified chemical analyses, of automated weather stations, and the new possibilities of genetic analysis have been most valuable to solving ecological questions for many of our larger species. But in every case, at every step we should be more careful to ask exactly what questions the new technology can answer. Piling up terabytes of data is not science and could in fact hinder science. We do not wish to validate the Rutherford prediction that our ecological science is “stamp collecting”.

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.

Should All Ecologists Become Social Scientists or Politicians?

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Two items this week have stirred me to write about the state of ecology. The first was a talk by an eminent biologist, who must remain nameless, about how scientists should operate. All very good, we should be evidence-based, open to falsification of hypotheses, and we should work as best we can to counter media misinformation. He/she talked about the future of biology in optimistic terms and in the entire one hour talk the word ‘biodiversity’ occurred once and the word ‘environment’ once. So my conclusion was that to this eminent biologist ecology was not on the radar as anything very important. We should be principally concerned about improving the health and wealth of humanity, and increasing economic growth.

This got me to thinking about why ecology falls at the bottom of the totem pole of science so that even though we work hard to understand the functioning of nature, ecologists seem to have value only to ourselves rather than to society. Perhaps society as a whole appreciates us for light entertainment about birds and bees, but when ecologists investigate problems and offer solutions they seem to be sidelined rapidly. Perhaps this is because taking care of the biosphere will cost money, and while we happily spend money on cars and new airplanes and guns, we can afford little for the natural world. One possible explanation for this is that many people and most politicians believe that “Mother Nature will take care of herself” at no financial cost.

If this is even partly correct, we need to change society’s view. There are several ways to do this, perhaps most importantly via education, but a more direct way is for ecologists to become social scientists and perhaps politicians. My experience with this recommendation is not terribly good. Social scientists have in my experience accomplished little for all their work on the human foibles of our time. Perhaps going into politics would be useful for our science if anyone wishes to cross that Rubicon, but there are few role models that we can put up.

So we continue in a political world where few ecologists sit in high places to challenge the modern paradigm of economic growth fuelled by non-renewable resources, and many of our national leaders see no human footprint on climatic warming. Short-term thinking is one element of this puzzle for we ecologists who take a longer view of life on Earth, but it must really rankle our paleo-ecologists who take a very long term look at changes in the Earth’s environment.

The second item this week that has encapsulated all of this was the announcement from a developed country that a new institute with over 1000 scientists was to be set up to study molecular biology for the improvement of human health. Now this is a noble cause that I do not wish to cast aspersions on, but it occurred to me that this was possibly a number greater than the total number of ecologists working in Canada or Australia or New Zealand. The numbers are hard to document, but I have not seen anything like this kind of announcement for a new institute that would address any of our many ecological problems. There is money for many things but very little for ecology.

None of this is terribly new but I am puzzled why this is the case. We live in a world of inequality in which the rich squander the wealth of the Earth while the future of the planet seems of little concern. Luckily ecologists are a happy lot once they get a job because they can work in the laboratory or in the field on interesting problems and issues (if they can get the money). And to quote the latest Nature (March 13, 2014, p. 140) “If ecologists want to produce work useful to conservation, they might do better to spend their days sitting quietly in ecosystems with waterproof notebooks and hand lenses, writing everything down.” That will cost little money fortunately.

Why I am Bored with Biodiversity and Ecosystem Services

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Ecosystem services have become the flavour of the month and already it seems tired and bland.  “Biodiversity must be preserved for its ecosystem services” but making the tie between diversity and services has been elusive and will continue to be so. A body of literature has accumulated on the results of small-scale experiments in which plant diversity is manipulated and some service, let’s say productivity, is monitored. In some cases a relationship is found − more species more productivity; but not always. A rancher who wants to increase the productivity of her rangeland would be more inclined to plant to a monoculture of a highly productive grass. For example the introduced species, Crested Wheat Grass (Agropyron cristatum), was widely used in British Columbia in the early 20th century. Cheat grass (Bromus tectorum), another exotic species (if we are talking about North America) is expanding into rangeland and while it might increase the diversity, it reduces the productivity for forage.

Recently Mark Vellend (TREE 29(3): 138, March 2014) reviewed a book by Donald Maier, “What’s so Good about Biodiversity? A Call for Better Reasoning about Nature’s Value. “(Springer 2012). The take home message of this book is that the biodiversity−ecosystem services rationale for protecting biodiversity does not always hold and more species does not necessarily translate into more food or less disease.  It is time to get rid of platitudes and to confront our biases in a critical manner when it comes to biodiversity.

Further to this topic, in December 2013 the first meeting was held of the budding International Panel on Biodiversity and Ecosystem Services. It will focus on the following topics:

1) Task force on capacity building
2) Task force on indigenous and local knowledge systems
3) Task force on knowledge and data
4) Development of a guide to the production and integration of assessments from and across all levels
5) Assessment on pollination and pollinators associated with food production
6) Methodological assessment on scenario analysis and modeling of biodiversity and ecosystem services
7)  Methodological assessment on the conceptualization of values of biodiversity and nature’s benefits to people
8) Development of a catalogue of policy support tools and methodologies and providing guidance on how further development of such tools and methodologies could be promoted and catalyzed

Given the involvement of 115 countries it will be interesting to track the success of this panel.  Note that pollination and pollinators are identified as a specific ecosystem service. Critical experimental ecologists should be involved if this panel is to be productive in a meaningful way and, if not on the panel, they should track its progress and comment accordingly. Stay tuned for further updates.