There are so many tools, techniques, communication platforms and methods out there for ecologists that it can be hard to keep track of them all. Whether it be LaTeX, Linux, or Twitter, someone has probably suggested that your research life will improve if you use their favourite tool.
Online science has allowed fantastic networking and information exchange. However, one side effect of the increased usage of social media can be the feeling that you can’t keep up. The phrase ‘Fear of Missing Out’ in social psychology was coined to describe the anxiety arising from looking at social media and fearing that you have chosen how to spend our time poorly. But this can extend to academic working life too – that nagging fear that your colleagues are doing cooler things (going to more conferences, using more cutting edge techniques, publishing more papers) than you. It can be disconcerting to see that there’s a cool R package you know nothing about, or to receive yet another invite to a work-based social media platform you’ve never heard of.
There are people who are the early adopters and the technological trendsetters; people who derive their success from their methodological/technological skill sets. These people are fantastic, since they provide the examples for others in the field to follow. But for most researchers, it is practical to recognize that knowing every new technique and tool doesn’t promise success.
Graduate students may suffer this fear of falling behind most intensely, given how closely it relates to imposter syndrome and the general skills gap that grad students have to overcome. But I’d argue for most students, that balance is key. Otherwise it can be a slippery slope: maybe you learn R, then find that people recommend knitR and R Markdown, then you learn Shiny to show your results beautifully, then someone suggests things would be faster in a lower level language – and maybe months have gone by. That’s not necessarily bad, intellectual freedom and self-teaching are some of the best parts of graduate school, and if you are going to learn a bunch of new techniques, that is the perfect time. But aficionados will make arguments for everything from Python, Linux, Emacs (apparently the one true operating system), Github, to LaTeX/BibTeX, etc, etc. And every one of these is a useful tool, but maybe not always a necessary tool.
Researchers can never learn everything, and some things will fall out of fashion as quickly as they arose. Sure, it is less than ideal to be a researcher who hasn’t learned a new approach since the advent of SAS. But we need to balance necessity (is it fundamental to my research?), the time investment, and the utility of these skills for future endeavours (e.g. if you are applying for a data analyst job after grad school, learning a few languages might be smart - but if you will rarely use it again, perhaps it is not so important). The danger for many students is that either the time investment in learning a less-than-fundamental tool is very high, or else they learn a number of tools but never master any of them. This isn't to say you can shirk on quantitative skills - on the contrary, having those skills is far more important than mastering any specific program or language. I can think of fantastic ecologists who don’t know what Twitter is, who still use SAS, who have never learned R, and who produce brilliant work. The questions, the ideas, and the knowledge matter too, after all.
(*I should note that I'm a quantitative/theoretical ecologist, and I think every ecologist should have a strong quantitative education! Just that you can do that using lots of different methods and doing it well should always be the first priority.)
Monday, August 3, 2015
Friday, July 17, 2015
The first null model war in ecology didn't prevent the second one*
The most exciting advances in science often
involve scientific conflict and debate. These can be friendly and cordial
exchanges, or they can be acrimonious and personal. Scientists often wed
themselves to their ideas and can be quite reluctant to admit that their
precious idea was wrong. Students in ecology often learn about some of these
classic debates (Clements v. Gleason; Diamond v. Simberloff and Connor), but
often other debates fade from our collective memory. Scientific debates are important things to study, they tell
us about how scientists function, how they communicate, but more importantly by
studying them we are less likely to repeat them! Take for example the debate
over species per genus ratios, which happened twice, first in the 1920s, then
again in the 1940s. The second debate happened in ignorance of the first, with
the same solution being offered!
To understand the importance of testing
species-genus ratios we can start with a prediction from Darwin:
As species of the same genus have
usually, though by no means invariably, some similarity in habits and
constitution, and always in structure, the struggle will generally be more
severe between species of the same genus, when they come into competition with
each other, than between species of distinct genera (Darwin 1859)
To test this hypotheses, the Swiss
botanist, Paul Jaccard (1901) created a ‘generic coefficient’ to describe biogeographical
patterns and to measure the effects of competition on diversity. The generic
coefficient was a form of the species-genus ratio (S/G), calculated as G/S x
100, and he interpreted a low S/G ratio (or high coefficient) to mean that
competition between close relatives was high, and a high ratio (low
coefficient) meant that there was a high diversity of ‘ecological conditions’
supporting closely related species in slightly different habitats (Jaccard 1922). At the same time as Jaccard was working on his generic coefficient,
the Finnish botanist, Alvar Palmgren, compiled S/G patterns across the Aland
Islands and inferred the low S/G values on distant islands to reflect random
chance (Palmgren 1921). Over several years, Jaccard and Palmgren had a heated exchange in
the literature (across different journals and languages!) about interpreting
S/G ratios (e.g., Jaccard 1922, Palmgren 1925). Palmgren’s contention was that the S/G ratios he observed were
related to the number of species occurring on the islands –an argument which
later work vindicates. A few years after their exchange, another Swiss
scientist, Arthur Maillefer, showed that Jaccard’s interpretation was not
supported by statistical inference (Maillefer 1928, 1929). Maillefer created what is likely one of the first null model in
ecology (Jarvinen 1982). He calculated the expected relationship between Jaccard’s generic
coefficient and species richness from ‘chance’ communities that were randomly
assembled (Fig. 1 –curve II). Maillefer rightly concluded that since the
number of genera increase at a slower rate than richness, the ratio between the
two couldn’t be independent of richness.
This example is especially poignant because
it foreshadowed another debate 20 years later –and not just in terms of using a
null expectation, but that S/G ratios cannot be understood without comparison
to the appropriate null. Elton (1946) examined an impressive set of studies to show that small
assemblages tended to have low S/G ratios, which he thought indicated
competitive interactions. Mirroring the earlier debate, Williams (1947), showed that S/G ratios were not independent of richness and that
inferences about competition can only be supported if observed S/G values
differed from expected null values. However, the error of inferring competition
from S/G ratios without comparing them to null expectations continued into the
1960s (Grant 1966, Moreau 1966), until Dan Simberloff (1970) showed, unambiguously, that, independent of any ecological
mechanism, lower S/G are expected on islands with fewer species. Because he
compared observationed values to null expectations, Simberloff was able to show
that assemblages actually tended to have higher S/G ratios than one would
expect by chance (Simberloff 1970). So not only is competition not supported, but the available
evidence indicated that perhaps there were more closely related species
on islands, which Simberloff took to mean that close relatives prefer the same
environments (Simberloff 1970).
Darwin, C. 1859. The origin of the species by means of
natural selection. Murray, London.
Elton, C. S. 1946. Competition and the
Structure of Ecological Communities. Journal of Animal Ecology 15:54-68.
Grant, P. R. 1966. Ecological Compatibility
of Bird Species on Islands. The American Naturalist 100:451-462.
Jaccard, P. 1901. Etude comparative de la
distribution florale dans une portion des Alpes et du Jura. Bulletin de la
Societe Vaudoise des Sciences Naturelle 37:547-579.
Jaccard, P. 1922. La chorologie selective
et sa signification pour la sociologie vegetale. Memoires de la Societe
Vaudoise des Sciences Naturelle 2:81-107.
Jarvinen, O. 1982. Species-To-Genus Ratios
in Biogeography: A Historical Note. Journal of Biogeography 9:363-370.
Maillefer, A. 1928. Les courbes de Willis:
Repar- tition des especes dans les genres de diff6rente etendue. Bulletin de la
Societe Vaudoise des Sciences Naturelle 56:617-631.
Maillefer, A. 1929. Le Coefficient
générique de P. Jaccard et sa signification. Memoires de la Societe Vaudoise
des Sciences Naturelle 3:9-183.
Moreau, R. E. 1966. The bird faunas of
Africa and its islands. Academic Press, New York, NY.
Palmgren, A. 1921. Die Entfernung als
pflanzengeographischer faktor. Series Acta Societatis pro Fauna et Flora
Fennica 49:1-113.
Palmgren, A. 1925. Die Artenzahl als
pflanzengeographischer Charakter sowie der Zufall und die säkulare Landhebung
als pflanzengeographischer Faktoren. Ein pflanzengeographische Entwurf, basiert
auf Material aus dem åländischen Schärenarchipel. Acta Botanica Fennica 1:1-143.
Simberloff, D. S. 1970. Taxonomic Diversity
of Island Biotas. Evolution 24:23-47.
Williams, C. B. 1947. The Generic Relations
of Species in Small Ecological Communities. Journal of Animal Ecology 16:11-18.
*This text has been modified from a forthcoming book on ecophylogenetics authored by Cadotte and Davies and published by Princeton University Press
Wednesday, July 8, 2015
Taking stock of exotic species in the new wild: Acknowledging the good and the bad.*
Are exotics good or bad? They are neither. They just are. But some exotics cause harm and impede certain priorities, and debates about exotics often ignore reality.
Book review: Fred Pearce. 2015. The New Wild:
Why Invasive Species Will Be Nature’s Salvation. Beacon Press
There has been much soul-searching in invasion biology, with
attacks, and subsequent rebuttals, on the very nature of why we study, manage
and attempt prevent the spread of exotic species (Davis et al. 2011) (Alyokhin 2011, Lockwood et al. 2011, Simberloff 2011).
What is needed at this juncture is a thoughtful and balanced perspective on the
nature of the discipline of biological invasion. Unfortunately, the book “The
New Wild” authored by Fred Pearce, is not that balanced treatment. What is
presented in this book is a very one-sided view, where counter-evidence to the
thesis that exotics will save nature is most often overlooked, straw men are
erected to aid in this goal, and the positions of working ecologists and
conservation biologists are represented as simplistic, anachronistic or just
plain incorrect.
What Pearce has written is a book-long argument about why
exotics shouldn’t be feared, but rather embraced as a partial solution to
anthropogenic land use change. I do not wish to undermine the reality that
exotics can play important roles in urban landscapes, or that some ecologists
and conservation biologists do indeed harbour suspicions of exotics and subscribe
to unrealistic notions of purely native landscapes. Exotic policy is at the
confluence of culture, science, economics and politics, and this is why the
science is so valuable (Sandiford et al. 2014). For Pearce, the truth of
what most ecologists do and think seems like an inconvenient reality. There are a number of pervasive, frustrating
problems with Pearce’s book, where bad arguments, logical flaws and empirical
slight-of-hand obfuscate issues that desperately need honest and reflective
treatment.
A monoculture of the exotic plant Vincetoxicum rossicum that spans open and understory habitats near Toronto, Canada (photo by M. Cadotte). This is a species that interferes with other management goals and needs to be actively managed. |
There are major problems with ‘The New Wild’ and these
include:
1) A premise
built on a non sequitur and wishful thinking. The general premise of the
book, that exotics represent a way out of our environmental doldrums, is
myopic. Pearce’s reasoning seems to be that he has conflated “the world is not
pristine and restoration is difficult…” with the alternative being that exotics
are positive and “we should bring them on”. Certainly we can question exotic
control efficacy, costs and conservation goals, but that does not mean that
exotics are necessarily the solution.
2)
Underrepresenting
the observed effects of some invasive non-indigenous species. Pearce’s book
is not balanced. The perceived benefits of exotics in this ‘New Wild’ are extolled while dismissing
some of the problems that invasive ones might cause. He says that exotics
typically “die out or settle down and become model eco-citizens” (p. xii). But
there is a third outcome that Pearce ignores –they move in and become unruly
neighbours. When he must acknowledge extinctions, he minimizes their
importance. For example when discussing Hawaiian bird extinctions: “The are only 71 known extinctions” (p. 12
–italics mine), or with California: “But only
30 native species are known to have become extinct as a result [of exotics]”
(p. 64 –italics mine).
He also implies throughout the
book that exotics increase diversity because “Aliens may find new jobs to do or
share jobs with natives.” (p. 113). The available evidence strongly suggests
that the numbers of species inhabiting communities has not increased over time (Vellend et al. 2013, Dornelas et al. 2014).
Which on the surface seems like a good thing, except that many communities are
now comprised of 20-35% exotics. This means that there have been losers.
Vellend and colleagues (2013) show that the largest impact on native species
diversity has been the presence of exotics. So, they do not necessarily find
new jobs, but rather outcompete some natives.
3)
Conservation
biologists and ecologists in the crosshairs. Pearce continually lauds those
like-minded, outspoken advocates of exotics while belittling ecologists and
conservation biologists who don’t agree with him. His disrespect for the
process of science comes in two forms. First, he seldom considers evidence or
presents opinions counter to his thesis. He gives a partial reason about this
bias; he says that ecologists (except for those few brave pioneering souls)
ignore novel ecosystems and the functional contributions of exotics (for
example on p. 13). This is demonstrably false (see next section). Pearce has
little affection for conservation biologists and mainstream ecologists. Both
groups are disparaged and dismissed throughout the book. Conservation
biologists get a particularly rough ride, and he never acknowledges the
difficulty of their task of balancing multiple priorities: extinction vs.
ecosystem function, habitat preservation vs. socioeconomic wellbeing, etc. For
example, Pearce states: “Conservation scientists are mostly blind to nature
outside of what they think of as pristine habitats and routinely ignore its
value” –again a demonstrably false assertion.
In a particularly galling
example, Pearce resorts to ‘guilt by association’ as an ad hominem attack to undermine the validity of opposing views. He
links conservation with eugenics: “Many conservationists of the first half of
the twentieth century were prominent proponents of eugenics” (p. 141). It would
be equally valid to state that most journalists were proponents of eugenics in
the first half of the twentieth century. Pearce, being a journalist, should see
this as a specious argument at best.
Ecologists share in this odd and
unfair derision. “Ecologists are tying themselves in knots because they refuse
to recognize that these novel, hybrid ecosystems are desirable habitats for
anything.” (p. 156). Unfortunately for Pearce, there are more than 4000 papers
on ‘novel ecosystems’.
4)
Misrepresenting
modern ecology and conservation.
Pearce attacks ecological science throughout the book and as an example Pearce
makes observations about the role of disturbance and refusal to acknowledge this
by ecologists “intent on preserving their own vision of balanced nature” (p.
144). However, disturbance has been a central component of community ecology
for the past five decades. Because of this balance-of-nature view, Pearce says
ecologists are not studying degraded, disturbed or recovering systems. For
example, with secondary forests, he says: “Yet the blinkered thinking persists.
Degraded forests and forests in recovery are almost everywhere under-researched
and undervalued.” (p. 157). Yet there are almost 9,500 papers on secondary
forests –highlighting the ecological interest in these widespread systems.
There are numerous such examples.
5)
A
black and white, either-or dichotomy. What
Pearce provides is a series of stark dichotomies with little room for subtle
distinction. He ties resilience and ecosystem wellbeing to the arrival of exotics,
without adequately assessing the drawbacks: “Nature’s resilience is
increasingly expressed in the strength and colonizing abilities of alien
species …we need to stand back and applaud” (p. xii).
Invariably in ecology, debates over ‘either/or’
dichotomies end up with the realization that these dichotomies are endpoints of
a continuum. This is exactly the case with exotics. Are they bad or good? The
answer is neither. They just are. Some exotics species provide economic
opportunity, ecosystem services and help meet other management goals. Some
exotics cause harm and impede certain priorities. Modern management needs to
be, and in many cases is, cognizant of these realities.
Alyokhin, A. 2011. Non-natives: put biodiversity at
risk. Nature 475:36-36.
Davis, M. A., M. K. Chew, R. J. Hobbs, A.
E. Lugo, J. J. Ewel, G. J. Vermeij, J. H. Brown, M. L. Rosenzweig, M. R.
Gardener, and S. P. Carroll. 2011. Don't judge species on their origins. Nature
474:153-154.
Dornelas, M., N. J. Gotelli, B. McGill, H.
Shimadzu, F. Moyes, C. Sievers, and A. E. Magurran. 2014. Assemblage Time
Series Reveal Biodiversity Change but Not Systematic Loss. Science 344:296-299.
Lockwood, J. L., M. F. Hoopes, and M. P.
Marchetti. 2011. Non-natives: plusses of invasion ecology. Nature 475:36-36.
Sandiford, G., R. P. Keller, and M.
Cadotte. 2014. Final Thoughts: Nature and Human Nature. Invasive Species in a
Globalized World: Ecological, Social, and Legal Perspectives on Policy:381.
Simberloff, D. 2011. Non-natives: 141
scientists object. Nature 475:36-36.
Vellend, M., L. Baeten, I. H. Myers-Smith,
S. C. Elmendorf, R. Beauséjour, C. D. Brown, P. De Frenne, K. Verheyen, and S.
Wipf. 2013. Global meta-analysis reveals no net change in local-scale plant
biodiversity over time. Proceedings of the National Academy of Sciences 110:19456-19459.
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