Dangers of forcing regressions through the origin

17 10 2017

correlationsI had an interesting ‘discussion’ on Twitter yesterday that convinced me the topic would make a useful post. The specific example has nothing whatsoever to do with conservation, but it serves as a valuable statistical lesson for all concerned about demonstrating adequate evidence before jumping to conclusions.

The data in question were used in a correlation between national gun ownership (guns per capita) and gun-related deaths and injuries (total deaths and injuries from guns per 100,000 people) (the third figure in the article). As you might intuitively expect, the author concluded that there was a positive correlation between gun-related deaths and injuries, and gun ownership:

image-20160307-30436-2rzo6k

__

Now, if you’re an empirical skeptic like me, there was something fishy about that fitted trend line. So, I replotted the data (available here) using Plot Digitizer (if you haven’t yet discovered this wonderful tool for lifting data out of figures, you would be wise to get it now), and ran a little analysis of my own in R:

Rplot01

Just doing a little 2-parameter linear model (y ~ α + βx) in R on these log-log data (which means, it’s assumed to be a power relationship), shows that there’s no relationship at all — the intercept is 1.3565 (± 0.3814) in log space (i.e., 101.3565 = 22.72), and there’s no evidence for a non-zero slope (in fact, the estimated slope is negative at -0.1411, but it has no support). See R code here.

Now, the author pointed out what appears to be a rather intuitive requirement for this analysis — you should not have a positive number of gun-related deaths/injuries if there are no guns in the population; in other words, the relationship should be forced to go through the origin (xy = 0, 0). You can easily do this in R by using the lm function and setting the relationship to y ~ 0 + x; see code here). Read the rest of this entry »





Massive yet grossly underestimated global costs of invasive insects

4 10 2016
Portrait of a red imported fire ant, Solenopsis invicta. This species arrived to the southeastern United States from South America in the 1930s. Specimen from Brackenridge Field Laboratory, Austin, Texas, USA. Public domain image by Alex Wild, produced by the University of Texas "Insects Unlocked" program.

Portrait of a red imported fire ant Solenopsis invicta. This species arrived to the southeastern USA from South America in the 1930s. Specimen from Brackenridge Field Laboratory, Austin, Texas, USA. Public domain image by Alex Wild, produced by the University of Texas “Insects Unlocked” program.

As many of you already know, I spent a good deal of time in France last year basking in the hospitality of Franck Courchamp and his vibrant Systematic Ecology & Evolution lab at Université Paris-Sud. Of course, I had a wonderful time and was sad to leave in the end, but now I have some hard evidence that I wasn’t just eating cheese and visiting castles. I was actually doing some pretty cool science too.

Financed by BNP-Paribas and Agence Nationale de Recherche, the project InvaCost was designed to look at the global impact of invasive insects, including projections of range dynamics under climate change and shifting trade patterns. The first of hopefully many papers is now out.

Just published in Nature Communications, I am proud that many months of hard work by a brilliant team of ecologists, epidemiologists and economists has culminated in this article entitled Massive yet grossly underestimated costs of invasive insects, which in my opinion is  the first robust analysis of its kind. Despite some previous attempts at estimating the global costs of invasive species1-4 (which have been largely exposed as guesswork and fantasy5-10), our paper rigorously treats the economic cost estimates and categorises them into ‘reproducible’ and ‘irreproducible’ categories.

Lymantria

Gypsy moth (Lymantria dispar) adult. Dimitri Geystor (France)

What we found was sobering. If we look at just ‘goods and services’ affected by invasive insects, the annual global costs run at about US$70 billion. These include agricultural, forestry and infrastructure damages, as well as many of the direct costs of clean-up and eradication, and the indirect costs of prevention. When you examine that number a little more closely and only include the ‘reproducible’ studies, the total annual costs dip to about US$25 billion, meaning that almost 65% of the costs recorded are without any real empirical support. Scary, especially considering how much credence people put on previously published global ‘estimates’ (for example, see some citation statistics here).

Coptotermes_formosanus

Formosan subterranean termite Coptotermes formosanus by Scott Bauer, US Department of Agriculture, Agricultural Research Service

There’s a great example to illustrate this. If you take it at face value, the most expensive invasive insect in the world is the Formosan subterranean termite Coptotermes formosanus estimated at US$30.2 billion/yr globally. However, that irreproducible estimate is based on a single non-sourced value of US$2.2 billion per year for the USA, a personal communication supporting a ratio of 1:4 of control:repair costs in a single US city (New Orleans), and an unvalidated assumption that the US costs represent 50% of the global total.

Read the rest of this entry »





Ice Age? No. Abrupt warmings and hunting together polished off Holarctic megafauna

24 07 2015
Oh shit oh shit oh shit ...

Oh shit oh shit oh shit …

Did ice ages cause the Pleistocene megafauna to go extinct? Contrary to popular opinion, no, they didn’t. But climate change did have something to do with them, only it was global warming events instead.

Just out today in Science, our long-time-coming (9 years in total if you count the time from the original idea to today) paper ‘Abrupt warmings drove Late Pleistocene Holarctic megafaunal turnover‘ demonstrates for the first time that abrupt warming periods over the last 60,000 years were at least partially responsible for the collapse of the megafauna in Eurasia and North America.

You might recall that I’ve been a bit sceptical of claims that climate changes had much to do with megafauna extinctions during the Late Pleistocene and early Holocene, mainly because of the overwhelming evidence that humans had a big part to play in their demise (surprise, surprise). What I’ve rejected though isn’t so much that climate had nothing to do with the extinctions; rather, I took issue with claims that climate change was the dominant driver. I’ve also had problems with blanket claims that it was ‘always this’ or ‘always that’, when the complexity of biogeography and community dynamics means that it was most assuredly more complicated than most people think.

I’m happy to say that our latest paper indeed demonstrates the complexity of megafauna extinctions, and that it took a heap of fairly complex datasets and analyses to demonstrate. Not only were the data varied – the combination of scientists involved was just as eclectic, with ancient DNA specialists, palaeo-climatologists and ecological modellers (including yours truly) assembled to make sense of the complicated story that the data ultimately revealed. Read the rest of this entry »





Demonising the hellbender

19 09 2014
Not 'Hellraiser', FFS - 'hellbender'

Not ‘Hellraiser’, FFS – ‘hellbender’

Here’s one by my new PhD student, Leah Collett:

I have never heard of the hellbender before. “Brilliant name”, I thought. Then I saw it mentioned again a few days later, in company with honey badgers and blue-footed boobies, in a recent article on why we need to see nature as useless in order to ‘save’ it.

So what is it? The hellbender is a species of salamander found in eastern North America, the only species of its genus it turns out, and one of only three left in its family (Cryptobranchidae – ‘hidden gills’). It is assessed as Near Threatened with possible extinction in the near future by the IUCN Red List. Along with the, sadly all too often, habitat degradation it is suffering due to it being highly sensitive to environmental change, it is still believed to be poisonous and that it will kill other fish and their eggs with this poison. In this day and age, some people will kill these salamanders when they come across them when they are out fishing, due to inaccurate held beliefs. I think I found it more incredible that this still occurs in a country where people have quick access to research and information denouncing such a myth.

This wonderful document on the biology and ecology of the hellbenders includes a section titled ‘Man and Hellbenders’ and highlights the likely culprit for starting the ‘hellbenders are poisonous – kill them all’ campaign:

“Dr N. Bayard Green (1971) related how a former editor of the Pocahontas Times (Pocahontas, West Virginia) in 1926 continually tried to vilify the hellbender as a destroyer of game fish and their eggs. Throughout West Virginia many sportsmen’s groups attempted to eradicate many of the so-called enemies of fish and game.”

(I could not read the original paper of Dr Green’s, although it might be available in the collections section). Read the rest of this entry »





Eye on the taiga

24 03 2014

boreal damageDun! Dun, dun, dun! Dun, dun, dun! Dun, dun, daaaaah!

I’ve waited nearly two years to do that, with possibly our best title yet for a peer-reviewed paper: Eye on the taiga: removing global policy impediments to safeguard the boreal forest (recently published online in Conservation Letters).

Of course, the paper has nothing to do with cheesy Eighties music, underdog boxers or even tigers, but it does highlight an important oversight in world carbon politics. The boreal forest (also known as taiga from the Russian) spans much of the land mass of the Northern Hemisphere and represents approximately one quarter of the entire planet’s forests. As a result, this massive forest contains more than 35% of all terrestrially bound carbon (below and above ground). One doesn’t require much more information to come to the conclusion that this massive second lung of the planet (considering the Amazon the first lung) is a vital component of the world’s carbon cycle, and temperate biodiversity.

The boreal forest has been largely expanding since the retreat of the glaciers following the Last Glacial Maximum about 20,000 years ago, which means that its slow progression northward has produced a net carbon sink (i.e., it takes up more atmospheric carbon that it releases from decomposition). However, recent evidence suggests that due to a combination of increased deforestation, fire from both human encroachment and climate change, mass outbreaks of tree-killing insects and permafrost melting, the boreal forest is tipping towards becoming a net carbon source (i.e., emitting more carbon into the atmosphere than it takes up from photosynthesis). This is not a good thing for the world’s carbon cycle, because it means yet another positive feedback that will exacerbate the rapid warming of the planet. Read the rest of this entry »





Native invaders divide loyalties

7 09 2012

California sea lion at Bonneville fish ladder. Credit: U.S. National Oceanic and Atmospheric Administration

As if to mimic the weirder and weirder weather human-caused climate disruption is cooking up for us, related science stories seem to come in floods and droughts. Yes, research trends become fashionable too (imagine a science fashion show? – but I digress…).

Only yesterday, the ABC published an opinion piece on the controversies surrounding which species we call ‘native’ and ‘invasive’ (based on a recent paper published in Global Ecology and Biogeography), and in June this year, Salvador Herrando-Pérez wrote a great little article on the topic entitled “The invader’s double edge“.

Then today, I received a request to publish a guest post here on ConservationBytes.com from Lauren Kuehne, a research scientist in Julian Olden‘s lab at the University of Washington in Seattle. The topic? Why, the controversies surrounding invasive species, of course! Lauren’s following article demonstrates yet again that it’s not that simple.

A drawback to the attention garnered by high-profile invasive species is the tendency to infer that every non-native species is bad news, the inverse assumption being that all native species must be ‘good’. While this storyline works well for Hollywood films and faerie tales, in ecology the truth is rarely that simple. A new review article in the September issue of Frontiers in Ecology and the Environment, describes the challenges and heartbreaks when native species run amok in the sense of having negative ecological impacts we typically associate with non-native species. Examples in the paper range from unchecked expansions of juniper trees in sagebrush ecosystems with wildfire suppression, to overgrazing by elk (wapiti) released from predation following the removal of wolves and mountain lions. Read the rest of this entry »





You’re not even remotely concerned enough

31 08 2012

I’ve just returned from a 6-week trip to the United States and I am now dealing with the intensity of things left undone for so long [sigh]. But that trip was interesting for many reasons. First, and as I’ve already posted, I finished a book with Paul Ehrlich that will be out sometime early in 2013 (but I won’t deal with that here). I also attended an interesting, if slightly confusing, conference on ecosystem services. And finally, I had the pleasure of meeting Tony Barnosky in person, and we decided that we should definitely collaborate on a few things.

Another thing that struck me – and this happens no matter how often I visit the U.S., is just how completely insane that country’s politics are. The extremist, libertarian, plutotheocratic bullshit spewed by the far right to the detriment of the very people who support them is enough to make you vomit. And this startling and thoroughly backward world-view is now starting to penetrate more and more into Australian society and politics. From an environmental perspective, it’s a continuation of a downhill slide that started with Reagan’s destruction of environmentalism in the U.S., and Joh Bjelke-Petersen‘s war on the environment in Australia, and will only continue to get worse.

Of course, the main victim of reason in all these polemic politics is that we are doing next to nothing to mitigate horrendous climate disruption. Only yesterday, George Monbiot was lamenting (nay, pleading) that our governments are doing practically nil to avoid what can only be described as the greatest threat to our way of life since the World War II – in fact, the War and its associated holocaust is small bikkies compared to what awaits us.

And this is the most stressing part – even people who choose to use their brains and accept that we have an immense, global problem on our hands generally are not even remotely concerned enough. Read the rest of this entry »





Degraded States of Ausmerica

20 08 2012

You might remember that I’ve been in California for several weeks now. The principal reason for my visit was to finish a book that Paul Ehrlich and I started last year. So, without the major distractions of everyday university life, I’ve spent much of my time lately at Stanford University in a little office next to Paul’s trying to finish (I also attended a conference in Portland, Oregon).

Yesterday, we wrote the last few paragraphs. A giant gorilla has now lumbered its way off my back.

So. What is the book about, you might ask? I can’t give away too many details, but I will give a few teasers. The book is called, at least for now, ‘Oz & US’, which is a bit of a play of words. In the book we contrast the environmental histories, current state of affairs, and likely futures of our respective nations. It’s written in a popular style so that non-specialists can learn a little something about how bad the environment has become in our two countries.

At first glance, one might wonder why we chose to contrast the U.S. and Australia – they are quite different beasts, indeed. Their histories are immensely different, from the aboriginal populations, through to European colonisation (timing and drivers), biological (including agricultural) productivities, carrying capacities, population sizes and politics. But these differences belie too many convergences in the environmental states of each nation – we now both have increasingly degraded environments, we have both pushed the boundaries of our carrying capacities, and our environmental politics are in a shambles. In other words, despite having started with completely different conditions, our toll on nature’s life-support systems is now remarkably similar.

And anyone who knows Paul and me will appreciate that the book is completely irreverent. We have taken off the gloves in preparation for a bare-knuckle fight with the plutocrats and theocrats now threatening the lives of our grandchildren. We pull no punches here. Read the rest of this entry »





Get boreal

7 06 2012

I’ve been a little quiet this last week because I’ve had to travel to the other side of the planet for what turned out to be a very interesting and scientifically lucrative workshop. After travelling 31 hours from Adelaide to Umeå in northern Sweden, I wondered to myself if it was going to be worth it for a 2.5-day workshop on a little island (Norrbyskär) in the Baltic Sea (which, as it turned out, didn’t have internet access).

The answer is a categorical ‘yes’!

Many of you know that I’ve dabbled in boreal forest conservation in the past, but I could never claim any real expertise in the area. Hence it came as something of a shock when Jon Moen of Umeå University asked me to attend a specialist workshop focused loosely on making the plight and importance of the boreal forest more widely acknowledged. I dragged my feet initially, but Jon convinced me that I could add something to the mix.

It was a small workshop, but well-represented by all boreal countries save Norway (i.e., we had Russians, Swedes, Finns, Canadians and Americans – this Australian was indeed the odd one out). We also had a wide array of expertise, from carbon accountants, political scientists, political economists, native cultures experts, ecologists to foresters. Our mandate – justify why we should pay more attention to this globally important region.

Just how important is the boreal forest? We managed to unearth some little-appreciated facts: Read the rest of this entry »





Mega-meta-model manager

24 07 2010

As Barry Brook just mentioned over at BraveNewClimate.com, I’ll be travelling with him and several of our lab to Chicago tomorrow to work on some new aspects of linked climate, disease, meta-population, demographic and vegetation modelling. Barry has this to say, so I won’t bother re-inventing the wheel:

… working for a week with Dr Robert LacyProf Resit Akcakaya and collaborators, on integrating spatial-demographic ecological models with climate change forecasts, and implementing multi-species projections (with the aim of improving estimates of extinction risk and provide better ranking of management and adaptation options). This work builds on a major research theme at the global ecology lab, and consequently, a whole bunch of my team are going with me — Prof Corey Bradshaw (lab co-director), my postdocs Dr Damien FordhamDr Mike Watts and Dr Thomas Prowse and Corey’s and my ex-postdoc, Dr Clive McMahon. This builds on earlier work that Corey and I had been pursuing, which he described on ConservationBytes last year.

The ‘mega-meta-model manager’ part is a clever piece of control-centre software that integrates these disparate ecological, climate and disease dynamic inputs. Should be some good papers coming out of the work soon.

Of course, I’ll continue to blog over the coming week. I’m not looking forward to the 30-hour travel tomorrow to Chicago, but it should be fun and productive once I get there.

CJA Bradshaw

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Who are the world’s biggest environmental reprobates?

5 05 2010

Everyone is a at least a little competitive, and when it comes to international relations, there could be no higher incentive for trying to do better than your neighbours than a bit of nationalism (just think of the Olympics).

We rank the world’s countries for pretty much everything, relative wealth, health, governance quality and even happiness. There are also many, many different types of ‘environmental’ indices ranking countries. Some attempt to get at that nebulous concept of ‘sustainability’, some incorporate human health indices, and other are just plain black box (see Böhringer et al. 2007 for a review).

With that in mind, we have just published a robust (i.e., to missing data, choices for thresholds, etc.), readily quantifiable (data available for most countries) and objective (no arbitrary weighting systems) index of a country’s relative environmental impact that focuses ONLY on environment (i.e., not human health or economic indicators) – something no other metric does. We also looked at indices relative to opportunity – that is, looking at how much each country has degraded relative to what it had to start with.

We used the following metrics to create a combined environmental impact rank: natural forest loss, habitat conversion, fisheries and other marine captures, fertiliser use, water pollution, carbon emissions from land-use change and threatened species.

The paper, entitled Evaluating the relative environmental impact of countries was just published in the open-access journal PLoS One with my colleagues Navjot Sodhi of the National University of Singapore (NUS) and Xingli Giam, formerly of NUS but now at Princeton University in the USA.

So who were the worst? Relative to resource availability (i.e,. how much forest area, coastline, water, arable land, species, etc. each country has), the proportional environmental impact ranked (from worst) the following ten countries:

  1. Singapore
  2. Korea
  3. Qatar
  4. Kuwait
  5. Japan
  6. Thailand
  7. Bahrain
  8. Malaysia
  9. Philippines
  10. Netherlands

When considering just the absolute impact (i.e., not controlling for resource availability), the worst ten were:

  1. Brazil
  2. USA
  3. China
  4. Indonesia
  5. Japan
  6. Mexico
  7. India
  8. Russia
  9. Australia
  10. Peru

Interestingly (and quite unexpectedly), the authors’ home countries (Singapore, Australia, USA) were in either the worst ten proportional or absolute ranks. Embarrassing, really (for a full list of all countries, see supporting information). Read the rest of this entry »





Fragmen borealis: degradation of the world’s last great forest

12 08 2009
© energyportal.eu

© energyportal.eu

I have the dubious pleasure today of introducing a recently published paper of ours that was at the same time both intellectually stimulating and demoralising to write. I will make no apologies for becoming emotionally involved in the scientific issues about which my colleagues and I write (as long as I can maintain with absolute sincerity that the data used and conclusions drawn are as objectively presented as I am capable), and this paper probably epitomises that stance more than most I’ve written during my career.

The topic is especially important to me because of its subtle, yet potentially disastrous consequences for biodiversity and climate change. It’s also a personal issue because it’s happening in a place I used to (many, many years ago) call home.

Despite comprising about a third of the world’s entire forested area and harbouring some of the lowest human densities anywhere, the great boreal forest that stretches across Alaska, Canada, Scandinavia and a huge chunk of Russia is under severe threat.

Surprised that we’re not talking about tropical deforestation for once? Surprised that so-called ‘developed’ nations are pilfering the last great carbon sink and biodiversity haven left on the planet? If you have read any of the posts on this blog, you probably shouldn’t be.

The paper today appeared online in Trends in Ecology and Evolution and is entitled Urgent preservation of boreal carbon stocks and biodiversity (by CJA Bradshaw, IG Warkentin & NS Sodhi). It’s essentially a review of the status of the boreal forest from a biodiversity perspective, and includes a detailed assessment of the degree of its fragmentation, species threat, climate- and human-influenced disturbance regime, and its carbon sequestration/emission status. I’ll summarise some of the main findings below:

borealfire

© NASA

  • Russia contains ~53 % of the boreal forest, followed by Canada (25 %), USA (18 %, mostly in Alaska), Sweden (2 %) and Finland and Norway (~1 % each); there are small areas of boreal forest in northern China and Mongolia.
  • Fire is the main driver of change in the boreal forest. Although clearing for logging and mining abounds, it pales in comparison to the massive driver that is fire.
  • There is evidence that climate change is increasing the frequency and possibly extent of fires in the boreal zone. That said, most fires are started by humans, and this is particularly the case in the largest expanse in Russia (in Russia alone, 7.5 and 14.5 million hectares burnt in 2002 and 2003, respectively).
  • While few countries report an overall change in boreal forest extent, the degree of fragmentation and ‘quality’ is declining – only about 40 % of the total forested area is considered ‘intact’ (defined here as areas ≥ 500 km2, internally undivided by things such as roads, and with linear dimensions ≥ 10 km).
  • Russian boreal forest is the most degraded and least ‘intact’, and has suffered the greatest decline in the last few decades compared to other boreal countries.
  • Boreal countries have only < 10 % of their forests protected from wood exploitation, except Sweden where it’s about 20 %.
  • There are over 20000 species described in the boreal forest – a number much less than that estimated for tropical forests even of much smaller size.
  • 94 % of the 348 IUCN Red Listed boreal species are considered to be threatened with extinction, but other estimates from local assessments compiled together in 2000 (the United Nations’ Temperate and Boreal Forest Resources Assessment) place the percentages of threatened species up to 46 % for some taxa in some countries (e.g., mosses in Sweden). The latter assessment placed the Fennoscandian countries as having the highest proportions of at-risk taxa (ferns, mosses, lichens, vascular plants, butterflies, birds, mammals and ‘other vertebrates’), with Sweden having the highest proportion in almost all categories.
  • Boreal forest ecosystems contain about 30 % of the terrestrial carbon stored on Earth (~ 550 Gigatonnes).
  • © BC Ministry For Range/L. Maclaughlan

    Warmer temperatures have predisposed coniferous forest in western Canada to a severe outbreak of mountain pine beetle (Dendroctonus ponderosae) extending over > 13 M ha. © BC Ministry For Range/L. Maclaughlan

  • Mass insect outbreaks killing millions of trees across the entire boreal region are on the rise.
  • Although considered in the past as a global carbon sink, recent disturbances (e.g., increasing fire and insect outbreak) and refinements of measurement mean that much of the area is probably a carbon source (at least, temporarily).
  • A single insect outbreak in western Canada earlier this decade thought to be the direct result of a warming planet contributed more carbon to the atmosphere than all of that country’s transport industry and fire-caused release combined.
  • Current timber harvest management is inadequately prepared to emulate natural fire regimes and account for shifting fire patterns with climate change.
  • No amount of timber management can offset the damage done by increasing fire – we must manage fire better to have any chance of saving the boreal forest as a carbon sink and biodiversity haven.

Those include the main take-home messages. I invite you to read the paper in full and contact us (the authors) if you have any questions.

CJA Bradshaw

Full reference: Bradshaw, CJA, IG Warkentin, NS Sodhi. 2009. Urgent preservation of boreal carbon stocks and biodiversity. Trends in Ecology and Evolution DOI: 10.1016/j.tree.2009.03.019

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