Monthly Archives: August 2015

On Sequencing the Entire Biosphere

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There is an eternal war going on in science which rests on the simple question of “What should we fund?” If you are at a cocktail party and want to set up a storm of argument you should ask this question. There may be general agreement among many scientists that we should reduce funding on guns and wars and increase funding on alleviating poverty. But then the going gets tough. It is easier to restrict our discussion to science. There is a clear hierarchy in science funding favouring the physical sciences that can make money and the medical sciences that keep us alive until 150 years of age. But now let’s go down to biology.

The major rift in biology is between funding blue sky research and practical research. In the discussions about funding, protagonists often confound these two categories by saying that blue sky research will lead us to practical research and nirvana. We can accept salesmanship to a degree. The current bandwagon in Canada is to barcode all of life on earth, at a cost of perhaps $2 billion but probably much more. Or we can sequence everything we can get our hands on with the implicit promise that it will help us understand these organisms better or solve practical problems in conservation and management. But all of this is driven by what we can do technically, so it is machine driven, not necessarily thought driven. So if you want another heated discussion among ecologists, ask them how they would spend $2 billion for research in ecology.

We sequence because we can. Fifty years ago I heard a lecture by Richard Lewontin in which he asked what we would know if we had a telephone book with all the genetic sequences of all the organisms on earth. He concluded, as I remember, that we would know nothing unless we had a purely ‘genetic-determinism’ view of life. There is more to life than amino acid sequences perhaps.

No one I know thinks that current ecological changes are driven by genetics, but perhaps I do not know the right people. So for example, if we sequence the genomes of all the top predators on earth (Estes et al. 2011, Ripple et al. 2014), would we know anything about their importance in community and ecosystem dynamics? Probably not. But still we are told that if in New Zealand we sequence the common wasp genome we will find new ways to control this insect pest. Perhaps an equally important area would be funding to understand their biology in New Zealand, and the threats and threatening processes in an ecosystem context.

We are back to the starting question about the allocation of resources within biology. Perhaps we cycle endlessly in science funding in search of the Promised Land. In a recent paper Richards (2015) makes the argument that genome sequencing is the key to biology and thus the Promised Land:

“The unifying theme of biology is evolutionary conservation of the gene set and the resultant proteins that make up the biochemical and structural networks of cells and organisms throughout the tree of life.”

“The absence of these genome references is not just slowing research into specific questions; it is precluding a complete description of the molecular underpinnings of biology necessary for a true understanding of life on our planet.” (p. 414)

There seems little room in all this for ecological thought or ecological viewpoints. It is implicit to me that these arguments for genome sequencing have as a background assumption that ecological research is rather useless for achieving biological understanding or for solving any of the problems we currently face in conservation or management. Richards (2015) makes the point himself in saying:

“While the author is fond of ‘stamp collecting’, there are many good reasons to expand the reference sequences that underlie biological research (Table 2).”

The table he refers to in his paper has not a single item on ecological research, except that this approach will achieve “Acceleration of total biological research output”. It remains to be seen whether this view will achieve much more than stamp collecting and a massive confusion of correlation with causation. It requires a great leap of faith that this approach through genome sequencing can help to solve practical ecological problems.

Richards, S. (2015) It’s more than stamp collecting: how genome sequencing can unify biological research. Trends in Genetics, 31, 411-421.

Estes, J.A., et al. (2011) Trophic downgrading of Planet Earth. Science, 333, 301-306.

Ripple, W.J., et al. (2014) Status and ecological effects of the world’s largest carnivores. Science, 343, 1241484.

On the Use of “Density-dependent” in the Ecological Literature

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The words ‘density-dependent’ or ‘density dependence’ appear very frequently in the ecological literature, and I write this blog in a plea to never use these words unless you have a very strong definition attached to them. If you have a spare day, count how many times these words appear in a single recent issue of Ecology or the Journal of Animal Ecology and you will get a dose of my dismay. In the Web of Science a search for these words in a general ecology context gives about 1300 papers using these words since 2010, or approximately 1 paper per day.

There is an extensive literature on what density dependence means. In the modeling world, the definition is simple and can be found in every introductory ecology textbook. But it is the usage of the words ‘density-dependence’ in the real world that I want to discuss in this blog.

The concept can be quite meaningless, as Murray (1982) pointed out so many years ago. At its most modest extreme, it only says that, sooner or later, something happens when a population gets too large. Everyone could agree with that simple definition. But if you want to understand or manage population changes, you will need something much more specific. More specific might mean to plot a regression of some demographic variable with population density on the X axis. As Don Strong (1986) pointed out long ago a more typical result is density-vagueness. So if and when you write about a density-dependent relationship, at least determine how well the data fit a straight or curved line, and if the correlation coefficient is 0.3 or less you should get concerned that density has little to do with your demographic variable. If you wish to understand population dynamics, you will need to understand mechanisms and population density is not a mechanism.

Often the term density-dependent is used as a shorthand to indicate that some measured variable such as the amount of item X in the diet is related to population density. In most of these cases it is more appropriate to say that item X is statistically related to population density, and avoid all the baggage associated with the original term. Too often statements are made about mortality process X being ‘inversely density dependent’ or ‘directly density dependent’ with no data that supports such a strong conclusion.

So if there is a simple message here it is only that when you write ‘density-dependent’ in your manuscript, see if is related to the population regulation concept or if it is a simple statistical statement that is better described in simple statistical language. In both cases evaluate the strength of the evidence.

Ecology is plagued with imprecise words that can mean almost anything if they are not specified clearly, so statements about ‘biodiversity’, ‘ecosystems’, ‘resilience’, ‘diversity’, ‘metapopulations’, and ‘competition’ are fine to use so long as you indicate exactly what the operational meaning of the word entails. ‘Density-dependence’ is one of these slippery words best avoided unless you have some clear mechanism or process in mind.

Murray, B.G., Jr. (1982) On the meaning of density dependence. Oecologia, 53, 370-373.

Strong, D.R. (1986) Density-vague population change. Trends in Ecology and Evolution, 1, 39-42.

Was the Chitty Hypothesis of Population Regulation a ‘Big Idea’ in Ecology and was it successful?

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Jeremy Fox in his ‘Dynamic Ecology’ Blog has raised the eternal question of what have been the big ideas in ecology and were they successful, and this has stimulated me to write about the Chitty Hypothesis and its history since 1952. I will write this from my personal observations which can be faulty, and I will not bother to put in many references since this is a blog and not a formal paper.

In 1952 when Dennis Chitty at Oxford finished his thesis on vole cycles in Wales, he was considered a relatively young heretic because he did not see any evidence in favour of the two dominant paradigms of population dynamics – that populations rose and fell because of food shortage or predation. David Lack vetoed the publication of his Ph.D. paper because he did not agree with Chitty’s findings (Lack believed that food supplies explained all population changes). His 1952 thesis paper was published only because of the intervention of Peter Medawar. Chitty could see no evidence of these two factors in his vole populations and he began to suspect that social factors were involved in population cycles. He tested Jack Christian’s ideas that social stress was a possible cause, since it was well known that some rodents were territorial and highly aggressive, but stress as measured by adrenal gland size did not fit the population trends very well. He then began to suspect that there might be genetic changes in fluctuating vole populations, and that population processes that occurred in voles and lemmings may occur in a wide variety of species, not just in the relatively small group of rodent species, which everyone could ignore as a special case of no generality. This culminated in his 1960 paper in the Canadian Journal of Zoology. This paper stimulated many field ecologists to begin experiments on population regulation in small mammals.

Chitty’s early work contained a ‘big idea’ that population dynamics and population genetics might have something to contribute to each other, and that one could not assume that every individual had equal properties. These ideas of course were not just his, and Bill Wellington had many of the same ideas in studying tent caterpillar population fluctuations. When Chitty suggested these ideas during the late 1950s he was told by several eminent geneticists who must remain nameless that his ideas were impossible, and that ecologists should stay out of genetics because the speed of natural selection was so slow that nothing could be achieved in ecological time. Clearly thinking has now changed on this general idea.

So if one could recognize these early beginnings as a ‘big idea’ it might be stated simply as ‘study individual behaviour, physiology, and genetics to understand population changes’, and it was instrumental in adding another page to the many discussions of population changes that had previously mostly included only predators, food supplies, and potentially disease. All this happened before the rise of behavioural ecology in the 1970s.

I leave others to judge the longer term effects of Chitty’s early suggestions. At present the evidence is largely against any rapid genetic changes in fluctuating populations of mammals and birds, and maternal effects now seem a strong candidate for non-genetic inheritance of traits that affect fitness in a variety of vertebrate species. And in a turn of fate, stress seems to be a strong candidate for at least some maternal effects, and we are back to the early ideas of Jack Christian and Hans Selye of the 1940s, but with greatly improved techniques of measurement of stress in field populations.

Dennis Chitty was a stickler for field experiments in ecology, a trend now long established, and he made many predictions from his ideas, often rejected later but always leading to more insights of what might be happening in field populations. He was a champion of discussing mechanisms of population change, and found little use for the dominant paradigm of the density dependent regulation of populations. Was he successful? I think so, from my biased viewpoint. I note he had less recognition in his lifetime than he deserved because he offended the powers that be. For example, he was never elected to the Royal Society, a victim of the insularity and politics of British science. But that is another story.

Chitty, D. (1952) Mortality among voles (Microtus agrestis) at Lake Vyrnwy, Montgomeryshire in 1936-9. Philosophical Transactions of the Royal Society of London, 236, 505-552.

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