Monthly Archives: January 2017

Spiral Sunday #19 – a fragment of shell

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Whenever I take a walk on a beach or in the countryside I’m liable to pick up interesting bits of shell, stone, sea glass or wood to take home as a memento of the visit.  Doesn’t always work, though, as I forget where I found this fragment of shell!  I have a feeling that it was on Tenerife.  I love the way the sea has rounded the sharp edges and a piece of stone has forced its way into the opening, a perfect sculpture in miniature as today’s Spiral Sunday contribution.

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The road to degradation: is “naming all the species” achievable or even desirable?

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In 2013 Mark Costello, Robert May and Nigel Stork published a review paper in the journal Science called “Can We Name Earth’s Species Before They Go Extinct?”  It’s a paper that I discuss with my students in their final year Biodiversity and Conservation module, and it always generates a lot of interest, and it’s has been well cited since it first appeared (143 citations* to date according to Web of Science).  There was an interesting response by Mora et al., with a riposte by Costello et al., but overall the original paper has been rather influential in framing some discussions about taxonomic effort and description of species, and the idea that we can “name everything” with additional resources.  At the end of the review Costello and colleagues answered their own question by stating: “We believe that with modestly increased effort in taxonomy and conservation, most species could be discovered and protected from extinction” [my emphasis].

Is their optimism justified?  Can “most species be discovered”?  And what are the implications for how we go about “discovering” these species that are unknown to science?

In my professional life I’ve been fortunate enough to carry out field work with some great colleagues in some wonderful parts of the world, including tropical rainforest and savannah in Guyana and Gabon, mountain scrub in the High Andes of Peru, seasonal dry forest in Australia, montane grasslands in South Africa, Namibian desert, and Brazilian cerrado and Atlantic rainforest.  All of these were sites where non-biologists would rarely venture: off the beaten track and (usually**) away from the typical tourist haunts.  It would be tempting to describe these places as “remote” but really they were not, because they all shared something in common: accessibility.  We were able to reach these sites by traveling along roads, of variable quality, usually in four-wheel drive vehicles.  The roads were often not in good condition, and frequently not metaled, but they were roads nonetheless.

It’s sometimes said that if one were to map the geographical coordinates of plant specimens stored in herbariums such as the one at Kew, you would end up with a road map of the world.  That’s because collecting biological specimens, or carrying out field work, requires us to be able to gain access to an area.  And accessibility usually means roads, unless one is working on the coast or along a river or lake, or have lots and lots of funding to allow teams to be helicoptered into an area (which is rare, but makes for exciting television).  Therefore most collecting of biological specimens is done in areas not far from roads.

So, any initiative that intends to “name all the species” in a particular group is going to require access to the remotest parts of the planet, areas that currently have no roads running through them.

There are still areas of the world that we can consider “remote” and “wilderness”, areas that are more than 100km from the nearest road – as a study published at the end of 2016 demonstrated.  But these are often found in the most biologically rich parts of the planet, for example tropical rainforest and mountainous areas, where we wouldn’t necessarily want to put roads to make them accessible to taxonomists (or even ecologists).  That’s because where roads go, people go, and accessibility to an area is usually followed by exploitation and degradation: illegal hunting, logging, mining, poaching of specimens for sale, etc. etc.

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Now, don’t get me wrong, taxonomy is absolutely vital to the conservation of the earth’s biodiversity.  It also underpins much ecological, bio-molecular and agricultural research and technology.  But the trade off for taxonomists is that they must gather their specimens and data from accessible areas, and that often means roads, and roads mean degradation.

The impetus for this post came from Twitter where a taxonomist highlighted the very good work done by the Virtual Institute of Spider Taxonomy Research (VINT) and described it as an “initiative to discover all spider species of the world in 30 years”.  Interestingly I can’t find that aspiration on the VINT website, but if it exists I’m not sure it’s achievable for spiders or any other diverse group of species, without being able to access parts of the world that are best left un-degraded.  Again, this is particularly true of the tropics where species can have very limited distributions.  A number of years ago an Australian botanist told me about how he was only able to collect some epiphytic Hoya specimens in Papua New Guinea by going into areas of rainforest that had been illegally logged, removing the plants from crowns of the felled trees, with no little risk to his own safety if the loggers had spotted him.  Some of those species might have remained undescribed if the area had not been opened up by a road prior to deforestation.  That would have been a loss for Hoya taxonomy, but surely positive for conservation.

Can “most species be discovered”?  Is this even a desirable thing?  I used to think so, because of the oft-stated view that we can’t conserve what we don’t know.  Now I’m not so sure, for reasons I hope I’ve articulated.  But as always I’d welcome your comments and criticisms.

 

*Including one in the conference: Annual Forum on Grumpy Scientists: the Ecological Conscience of a Nation:Royal Zoological Society, Sydney, Australia.  I’d have liked to have been a fly on the wall at that meeting!

**Usually, but not always: I have a few papers where some or all data collection was done in and around back-packers hostels, hotels, and tourist lodges.  Hey, you take your opportunities where you find them in this game!

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Spiral Sunday #18 – fossils from Glasgow

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Spiral Sunday this week is brought to you by Fergus Chadwick, and is (in his words) a “spiral of spirals”: a spiral display of spiral ammonite fossils at the Kelvin Grove Museum in Glasgow.  Thanks for the photo Fergus!

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When did plastic plants become acceptable?

Plants are important.  Really, really important.  They play important roles in society and in the nature that supports our societies: plants feed us; they are a source of many pharmaceuticals; they produce oxygen and store up carbon dioxide; they can remove pollutants from city atmospheres; and they are the foundation for much of the world’s ecological functioning.  In addition they inspire poets, artists, musicians, and have huge cultural significance, as well as bringing beauty and biodiversity to even the most urban of environments. Plants positively add to our quality of life, and make us happy, whether we are aware of it or not.

OK, there’s a bit of personal bias going on here: I’ve always loved studying and growing plants, they are a huge part of my life.  But the basic facts of what I laid out in that opening paragraph are correct: plants matter.  So I find it troubling that there seems to be a recent trend in using artificial (mainly plastic) plants indoors and in outside “gardens”.  When did this happen?  When did plastic plants become acceptable?

It first struck me that there had been a recent shift in how we view plastic plants back in the summer when I visited the newly refurbished main restaurant at the university’s Park Campus.  The refurb was very nicely done and there’s a big display about how much of the university’s waste we are recycling, and there’s lots of greenery about the place – except that most of it is plastic.

Then in November we visited my son Patrick in Lancaster.  We stayed a night in a nice hotel in the city centre, in a room that led out into a private courtyard – full of plastic plants.  There was a plastic lawn, a plastic palm, even plastic ivy.  Ivy!  One of the easiest plants in the world to grow – why would you need to make it out of plastic?!  It makes itself perfectly well which you can see if you peep over the wall at the back of the courtyard:

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Then the following week I was in London at the Wellcome Trust to take part in a project review panel.  The Wellcome’s building near Euston Station is wonderful, really striking on the inside, full of light and life.  I was initially please to see an avenue of fig trees in large containers arrayed along the centre of the main concourse:

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But when I looked closely I realised that although the trunks and branches were real, these were not living plants: the leaves are artificial, made from wire and synthetic material.  So someone has gone to the trouble of growing real fig trees only to dismember them and festoon them with faux foliage.  Please, no one tell Mike Shanahan!

I’m really surprised at the Wellcome Trust, an organisation I have a lot of respect for;  we know that real plants have a positive effect on psychology and health, though I very much doubt that the same can be said for artificial ones.  In their defence the Wellcome Trust building does have some real plants scattered about the place, but they missed a huge opportunity in not using real figs here.  Even that cathedral to capitalism that is the Milton Keynes shopping centre uses real plants in most of its displays, including some lovely tree ferns:

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And splendid palms:

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Finally, insult was added to injury as we entered the New Year.  As I mentioned in my Spiral Sunday post a couple of weeks ago, we bought a wreath as a Christmas decoration and I took it apart to compost and recycle at the start of the year.  What I hadn’t noticed when we bought it was that half of the holly berries were plastic:

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This was hugely ironic given our recent study of how insects boost the value of holly by pollinating the female flowers that produce the berries!

All of this is more than just snobbery on my part.  Yes, you can argue that plastic plants are a bit naff and can never take the place of the “real” thing.  But my main concern here is an environmental one: plastic plants require resources (usually oil-based polymers and energy) to make.  And I doubt very much whether they are recycled very often.  Yes, real plants also cost resources to grow (though that can be minimised depending on how they are grown).  But they also provide a range of benefits and, at the end of their life, they can be composted.  Not something I can do with my plastic holly berries.  Not only that, but I suspect that most (all?) of the plastic plants that are sold are manufactured in the Far East.  Using British- or Europe-grown real plants would cut down on the carbon-miles required and support more local horticultural industries.

Early in 2017 Andrew Lucas at Swansea University, on Twitter, described what he thought was the most depressing tweet of 2017 so far:  “Transform your garden today: buy Artificial Grass from ExpressGrass. Cut to your size for easy DIY installation”.

Agreed, hugely depressing, but we can do something about it: stop buying fake plants.  Perhaps we need a Campaign for Real Plants?  Its theme tune could be Radiohead’s Fake Plastic Trees:

Her green plastic watering can
For her fake Chinese rubber plant
In the fake plastic earth
That she bought from a rubber man
In a town full of rubber plans
To get rid of itself…..

……It wears me out

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Filed under Biodiversity, Biodiversity and culture, Ecosystem services, Gardens, Personal biodiversity, Pollination, University of Northampton, Urban biodiversity

Spiral Sunday #17 – sculpted hair from Louisiana

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This week’s Spiral Sunday features a close-up of  hair sculpted in marble, taken during the visit to Copenhagen’s Louisiana Museum of Modern Art I mentioned in Spiral Sunday 5. Sadly I forgot to note down the name of the artist, but I do like the way s/he has depicted the hair as deeply carved, close-set spirals.

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Research seminar: Dr Hazel Chapman – “Conservation ecology of West Africa’s montane forest habitats – seed dispersers and their substitutes”

We start the new term with a guest speaker from New Zealand – Dr Hazel Chapman – who is coming to give a research seminar this Friday at 1pm in Newton NW205, University of Northampton, Avenue Campus. Here’s the details:
 
Conservation ecology of West Africa’s montane forest habitats – seed dispersers and their substitutes.
 
The Nigerian Montane Forest Project (NMFP) is a conservation and biodiversity research program founded on a field station located on the Nigeria-Cameroon border. Run out of the University of Canterbury, New Zealand, the Project is aimed at understanding the ecology of Nigeria’s montane forest fragments for informed management of this fragile ecosystem. The research focus is predominantly plant-animal mutualisms and forest restoration. This talk will introduce the NMFP and present research aimed at understanding how seed dispersal processes are changing in response to forest fragmentation and hunting.
 
Hazel Chapman is an Associate Professor at the University of Canterbury (UC) NZ, where she lectures in evolutionary ecology. Hazel’s research focus is tropical forest conservation and she is the Founder and Director of the NMFP. Since 2004, the Project has seen a stream of international and Nigerian postgraduate students enrolled at UC doing their field research in Nigeria. In addition the NMFP trains undergraduate Nigerian students in conservation biology, and works with local schools and the community. The Project is run almost entirely by the local community. It is home to a 20ha Smithsonian CTFS Forest Geo Plot.
 
All welcome.

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Spiral Sunday #16 – Christmas is over

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Yesterday we took down the Christmas decorations that have festooned the house this year.  Whilst I was taking apart the wreath we’d hung on the door I noticed for the first time that the bow had a lovely spiral design.  I thought it would make a nice Spiral Sunday for this year, and we’ll re-use it next year.

More on that wreath later in the week….

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What’s the point of the h-index? UPDATED

UPDATE: I’ve increased the sample size of EEB scientists I used in the analysis.

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Over at the Dynamic Ecology blog yesterday, Jeremy Fox posted an interesting analysis of which metrics correlate with the chances of early career researchers in ecology and evolutionary biology (EEB) gaining an interview for an academic post in North America.   Spoiler alert: none of them correlate, except the number of job applications you submit.

These metrics include number of papers published, number of first author papers, number of large (>$100,000) grants held, number of years post-doc, and h-index.  Nada, zilch, nothing, nowt is significantly correlated.  Which is good: as Jeremy (and the stream of commenters) discuss, it means that interview panels are looking roundly at individuals and what they can offer a university department, and not relying on (sometimes dubious) metrics.

Which brings us to the h-index….  Jeremy linked to an old post of mine called “How does a scientist’s h-index change over time?“, a piece that was far and away my most viewed post last year (and second-most viewed post in 2015).  This suggests that there’s still a huge “appetite” for the h-index, in terms of understanding what it is and how it can/should (or cannot/should not) be used.  Even before the Dynamic Ecology post came out I was planning to update it and give examples where I think it might be useful, so this seems like a good time to do that.

Opinions on the h-index vary hugely.  Some of the links in my original post were to writings by scientists who really like the idea of being able to use it to track the academic impact of an individual (or at least some measure of it).  Others despise it, and indeed all academic metrics, as pernicious and potentially dangerous to science – see David Colquhoun’s video on this topic, for instance.

I’m somewhere in the middle – I recognise the weaknesses of the h-index, but I also think that it’s measuring something, even if the something that it’s measuring may not be directly translatable into a measure of “quality” or “impact”, and especially not “employability” or “worthy of promotion” (and I would certainly never countenance using the h-index as a the sole measure of the latter two).

So when is the h-index useful?  Well one use is as a personal tracker of one’s own standing or contribution within a field, assessing the trajectory of a career, and perhaps gauging when it’s time to apply for promotion (at least in the UK system which is a less transparent process than in North America, or at least that’s my impression).  To illustrate this I’ve collated the h-indexes and years since first publication for 72 EEB scientists using Google Scholar (GS).  I used GS rather than Web of Science (WoS) as, although GS is less conservative, WoS seems to be becoming noticeably less accurate; for example it’s recently assigned to me chapters on which I was not an author but which are included in a book that I co-edited.  Another advantage of GS, of course, is that it’s publicly available and not pay walled.

It’s long been known that a scientist’s h-index should increase over their professional lives, and indeed that’s what we find if we plot number of years since first publication against an individual’s h-index:

h-index-graph

It’s a fairly strong correlation, though with a lot of scatter (something Jeremy noted in his blog) and it suggests that EEB scholars accrue their h-index  at a rate of about 1.6 papers per year, on average, though with a big range (0.3 to 4.2 papers per year).  One (albeit fanciful*) way to think about this graph is that it’s analogous to a Hertzsprung–Russell (HR) diagram in astronomy, where, as they age, stars shift position predictably on a plot of colour versus magnitude.  In a similar way, as EEB scientists age professionally, their position on this plot moves in ways that may be predictable from their scientific output.

There’s a lot of structure in HR diagrams, including the famous Main Sequence, where most stars lie, as well as stellar evolutionary tracks for Giants, Super Giants, White Dwarfs, etc.  In this modest sample I think we’re starting to see similar structure, with individuals lying far above or below the “h-index Main Sequence”, indicating that they are accruing greater or fewer citations than might be expected.  UPDATE:  In particular, three individuals who are “Super Giants” (to use the astronomical terminology) and lie far above the Main Sequence.  Carlos Herrera makes an interesting point in the comments (below) about self-selection in GS which could mean that there are far fewer people with low h-indexes represented than we might expect.

One of the things that could be explored using these type of data is exactly why it is that this is happening: is it a question of where they are based, or their nationality, or where they publish, their sub-field, or what?  One easy analysis to do is to assess whether there is a difference between female and male scientists, as follows:

h-index-graph-mf

Previous research has suggested that women on average receive fewer citations for their papers than men (see this 2013 study in Nature for instance) and this graph gives some support to that idea, though I’ve not formally tested the difference between the two lines. What is also interesting is that the R-squared values are identical, indicating as much variation in female as male career trajectories, at least as measured in this way.

UPDATE:  These additional data suggest that the h-indexes of male and female researchers diverge over time, and that most of the difference is for mid to late career scientists.  It’s unclear to me why this might be the case, but we could speculate about factors such as career breaks to have children.  Note that I struggled to find female EEB scientists with an h-index larger than about 80 – if I’ve missed any please let me know.

The data set I used for this analysis is certainly not random and contains a lot of people I know personally or by reputation, so a larger, more systematic analysis could come to some rather different conclusions.  However I thought this was an interesting starting point and if anyone else wants to play with the data, you can download the anonymised spreadsheet here.

 

*I’m not at all convinced about this analogy myself and am happy for anyone to explain to me why it’s a very poor one 🙂  UPDATE:  Though Stephen Heard seems to like it.

 

 

 

 

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Should scientists accept funding from agro-chemical companies? The devil’s in the details

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The relationship between use of pesticides (particularly neonicotinoids) and the decline of pollinators is one that I’ve touched on a few times in this blog – see for example:  Bees and pesticides – a major new study just publishedButterflies and pesticides – a new study and a smoking gun; and Pesticides and pollinators: some new studies and contrasting conclusions.  It’s an important and controversial topic that’s unlikely to go away any time soon.  In an article in the New York Times, journalist Danny Hakim has given that particular pot a further stir by discussing Scientists Loved and Loathed by an Agrochemical Giant.

Although it’s been online since New Year’s Eve, the first I heard about the article was when an American colleague sent me a link this morning (the day it appeared in the printed version) and asked me if I had any thoughts and comments about one of the scientists featured – James Cresswell of the University of Exeter.  I’ve known and respected James for over 20 years and I think his contribution to this article provides a brave and open answer to the question I pose in the title of this post: should scientists accept funding from agro-chemical companies?

Please do read that article, it’s fascinating, if not entirely objective in its own right.  The tone and focus of the piece is best summed up by the one-sentence summary at the start, which incorporates a quote from Dave Goulson (University of Sussex):  “With corporate funding of research, “there’s no scientist who comes out of this unscathed””.  In fact that quote is taken rather out of context because Dave’s point was about perceptions of motives and biases, rather than actual corruption of the science and scientists concerned.

Having said that, the article does present a prima facie case that some scientists (though I emphasise not James himself) are playing fast-and-loose with the evidence related to pesticides and GM crops.

Back to perceptions.  Industry funding of university-led scientific research is incredibly common, far more common than the public probably realises.  There are three reasons for that.  First of all, universities are where many subject experts are based, of course.  Secondly, scientific research is expensive: it requires staff, facilities, equipment, funding for overheads, etc.  University researchers are therefore always hunting for money to enable them to carry out research (which in turn is linked to promotion success, career development, and so forth).  Thirdly, external income is an important performance indicator for universities and their constituent departments: James himself is quoted as saying “I was pressured enormously by my university to take that money”, a sentence that will resonate with many UK researchers.

In general the public’s perception (as far as I can tell) is that most of that research is not being corrupted by the industry funding that is attached to it.  In my own faculty at the University of Northampton, for instance, my colleagues have obtained industry funding for research and consultancy work in areas such as product design, lift engineering, materials science, leather processing, computer networks, app development, and so forth.  All controversy-free.

In much of the environmental sector that’s also the case: we’ve had funding from a large water utilities company to write a report on habitat management strategies for reducing rabbit densities close to water bodies, and one of my current research students is being funded by a solar farm company.  Likewise colleagues have been funded by wastes management companies to advise and research in that field.  None of this has generated any negative perceptions, with the possible exception of some aspects of wastes management where issues such as “waste-to-energy” remain controversial.

In other areas of environmental research, however, there have always been accusations of bias levelled at university researchers who are perceived to be industry shills, especially if they are not seen to be toeing a particular line.  I’m deliberately using that word – shill – because it’s something I was accused of being during a heated social media discussion of causes of pollinator declines.  A commenter claimed that I was an “industry shill” for daring to suggest that this was a complex topic, and that there were no easy answers to why (some) pollinators are declining, but that neonicotinoid pesticides were not the only cause.  “Which chemical company is funding your research?” she aggressively demanded to know.  I think I convinced her that I was not (and never have been) funded by chemical companies.  But it raised an interesting question: would I ever accept funding from such companies, if it was offered?

The simple answer is that I don’t know.  It depends what the money was for and what strings were attached in terms of non-disclosure, ownership of data, etc.  As the title of this post states, the devil’s in the details.  I know quite a number of researchers in my field who have had funding from Syngenta, Bayer, and other agro-chemical companies.  Some of these are colleagues with whom I have published research papers.  In general I have no reason to believe that the research conducted by any of these colleagues has been corrupted by their association with the funders.  However in one instance I had a disagreement with a colleague who was not (in my opinion) objective in how they wished to frame part of a paper’s discussion and who may (in my opinion) have been influenced by their association with a particular funder.  In the end this didn’t change the conclusions of the research (which was not itself industry funded) but it did make me pause to consider these subtle biases, which I’m sure could affect anyone*.  Again, perceptions are key here.

Money for the kind of research that’s done by colleagues and myself is always, always going to be in short supply and competitively pursued, and failure to obtain it will always be much more common than success.  Unless funding to address important ecological research questions from government (i.e. taxpayer money) and charities vastly increases, industry will be there to fund research in its own interests, and the perception of scientific bias will remain, whether or not it actually exists.

 

*I’m not prepared to say more about this particular example so please don’t ask.

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Filed under Bees, Biodiversity, Honey bees, Neonicotinoids, University of Northampton

Waxwings in Northants

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This afternoon I spent a very pleasant couple of hours watching a flock of 14 waxwings (Bombycilla garrulus) a beautiful and enigmatic bird  that I’ve mentioned before on this blog.  This flock has been hanging around the village of Roade just outside Northampton since the 29th December, feeding on a crop of rowan berries (Sorbus aucuparia var.) and amusing the locals.  As usual they were very confiding and unperturbed by neither traffic nor twitchers (which at one point, I was told, numbered around 40 people).  Feeding with the waxwings were a couple of blackbirds that may well have travelled down from the far north with them.  Here’s a few pictures:

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