Category Archives: History of science

Travelling July: a pilgrimage to the tomb of Sir Richard Francis and Lady Isabel Burton

The blog has been very quiet during June and July as it’s been quite a couple of months! At the very end of June the sale of our house was completed. Since then Karin and I have been staying with family and friends, doing some house-sitting and living in Air BnBs as we completed work commitments, and traveled around the country seeing people, prior to our departure to Denmark.

During a trip to London last week we managed to squeeze in a side trip to a place that I have longed to visit for over 30 years: the tomb of Captain Sir Richard Francis Burton and his wife Lady Isabel Burton. As I recounted in a post a few years ago, Burton’s life and exploits have long been a subject of fascination for me – see: Sex and drugs and the source of the Nile.

The couple’s burial place is in Mortlake – check out the Burtonia website for details. The mausoleum, designed by Lady Isabel, is in the form of an Arabian tent, and features both Christian and Islamic imagery – very fitting for a man who converted to Islam and was given Catholic last rights on his death bed at the insistence of his wife.

An unusual feature of the tomb is that there is a set of steel steps leading to a glass window at the rear, through which one can view the devoted couple’s coffins and grave goods. It’s a poignant and touching experience. Below are some photographs that we took on the day.

Get a 30% discount if you pre-order my new book Pollinators & Pollination: Nature and Society

PollinatorsandPollination-frontcover

In the next few months my new book Pollinators & Pollination: Nature and Society will be published.  As you can imagine, I’m very excited! The book is currently available to pre-order: you can find full details here at the Pelagic Publishing website.  If you do pre-order it you can claim a 30% discount by using the pre-publication offer code POLLINATOR.

As with my blog, the book is aimed at a very broad audience including the interested public, gardeners, conservationists, and scientists working in the various sub-fields of pollinator and pollination research. The chapter titles are as follows:

Preface and Acknowledgements
1. The importance of pollinators and pollination
2. More than just bees: the diversity of pollinators
3. To be a flower
4. Fidelity and promiscuity in Darwin’s entangled bank
5. The evolution of pollination strategies
6. A matter of time: from daily cycles to climate change
7. Agricultural perspectives
8. Urban environments
9. The significance of gardens
10. Shifting fates of pollinators
11. New bees on the block
12. Managing, restoring and connecting habitats
13. The politics of pollination
14. Studying pollinators and pollination
References
Index

 

 

What exactly is a “pollination system”?

Pollination systems

This is a post I’ve been meaning to write for some time, but have never got round to.  What’s catalysed me is an email this morning from Casper van der Kooi asking me about how I define the term “pollination system”, as he’d had some discussions about its use with his colleagues in The Netherlands.

“Pollination system” is one of those terms that seems to mean different things to different people. The way I use it, and I think the way we meant it in the 1996 paper Generalization in pollination systems and why it matters, is that the pollination system = floral phenotype + pollinators.  That is to say, the colour, shape, size, odour, rewards, etc. produced by a flower (or an inflorescence functioning as a single reproductive unit) plus the animals that effectively transfer pollen.

To me this is distinct from a “pollination syndrome” which refers only to the floral phenotype, or “pollinator guild/functional group” which refers only to the flower visitors.  However I have seen “pollination syndrome” used to include floral phenotype + pollinators.  But to my mind they are distinct things.

I have also seen other authors use “pollination system” to mean the community of plants and pollinators in an area, or as analogous to the breeding system, but neither of those are the way that I use it.  I decided to look at the history of the term on Web of Science and the earliest use on there is a paper by Levin & Berube (1972): Phlox and Colias – efficiency of a pollination system.  There were a few other papers from the same decade and all were using pollination system in the way I described above, i.e. floral phenotype + pollinators.

To look for earlier usage of pollination system I searched the Google Ngram Viewer; as you can see in the image above, I found examples of the term back as far as the 1940s in which the pollination system of grasses is referred to as being “cross pollination” (i.e. what we would now refer to as the breeding system).  There’s also texts from the 1950s referring to artificial wind pollination of date palms as a “helicopter pollination system”.

Does it matter how “pollination system” is used, or that it varies in meaning according to the author?  Probably not as long as the meaning is defined in the text.  Ecology is replete with terminology that has slightly different usage according to the researcher (“biodiversity” being an obvious example) and I don’t get a sense that this has held back the field.  Or is that too optimistic a conclusion?  Do you use the term in a different way to me?  As always, your comments are welcomed.

A short history of ecology doctorates in the UK

UK ecology doctorates

Doctorate-level research qualifications (DSc, PhD, DPhil, etc.) do not have an especially long history, although as academics we take them for granted as the usual gateway drug qualification to professional research.  In the UK the first research doctorates were awarded only towards the end of the 19th century and took some time to become fully established in the university landscape.  The British Library’s EThOS site provides a searchable database of doctorates awarded by UK institutions.  Although it’s not complete, the 500,000 records it holds provides a fascinating resource for anyone curious about the history of doctoral education and in research trends in their own discipline.

I thought it would be interesting to look at the history of UK ecology doctorates and, using “ecology” as a search term discovered the following:

  • The earliest record for an ecology doctorate (actually a DSc) was for “An ecological survey of Natal: the Pietermaritzburg district” by J.W. Bews, awarded by the University of Edinburgh in 1912.
  • As far as I can tell from the names (which often give only the initials) the first woman to be awarded an ecology PhD was Mary Seaton for “A floristical and ecological survey of West Lothian” in 1927, again at the University of Edinburgh.
  • As you can see from the graph above, for the first half of the 20th century the number of ecology doctorates averaged only one or two a year, and in many years none were awarded.
  • From about 1950 onward there begins a steep rise in the number of awards.  I was expecting that this rise would be broadly exponential, in line with the widening of access to higher education and the increasing rate of scientific discovery.  However there are some interesting peaks and troughs in the observed pattern.
  •  The first bulge occurs in the early- to mid-1980s, with a second bulge from the mid-1990s until the early 2000s.  It would be interesting to speculate on what had caused those.
  • However it’s from 2010 onward that the really steep rise in ecology doctorates occurs: in the decade from 2010 to 2019 (which I have not graphed as the year has not yet ended) 3833 doctorates were awarded.  That compares to 4820 for the previous c. 100 years.
  • However, one must be careful about assigning any given thesis to the field of ecology as the word is increasingly used outside of the subject, e.g. in a thesis entitled “Understanding extra-judicial responses to young people’s offending : out of court disposals and ‘diversion’ in social context” (University of Bedfordshire 2019).
  • Possibly balancing that latter bias is the trend of using the word “biodiversity” rather than ecology; there are at least 700 such theses.  Some of these will be taxonomic rather than ecological, but by no means all.
  • I wonder whether we reached a peak in ecology doctorates in 2016 (when 506 were awarded).  As of June 2019 only 92 have been awarded so the downward trend seen in the last couple of years may be continuing.

There is no doubt much more that could be discovered by someone with an interest in the history of science and the time to dig further into the topic.  If anyone wants a copy of the raw data, drop me an email and I will happily send it.

When did the flowering plants evolve? Two new studies come to different conclusions

2019-04-23 17.42.40.jpg

The angiosperms (flowering plants) are far and away the most diverse group of plants ever to have evolved.  There are an estimated 350,000 to 370,000 species, more than all other groups of plants (ferns, conifers, cycads, mosses, etc.) combined, living and extinct.  The origin of the flowering plants was termed an “abominable mystery” by Charles Darwin – or perhaps it wasn’t: see this essay by Prof. Richard Buggs for an alternative view of what Darwin was describing, and this paper by Prof. William Friedman giving a different interpretation.

These disagreements about what Darwin meant are as nothing compared to disagreements about when the flowering plants actually evolved and how we interpret fossils and evidence from molecular phylogenies.  Two new studies illustrate this point: they use some of the same information to come to completely different conclusions.  I’ve copied the details and abstracts below, with links to the originals, and emphasised the areas of disagreement in bold text.  And I’m going to leave it at that; I don’t have a horse in this race and I have no idea which (if either) is correct.

There are, however, profound implications for understanding when and how relationships between flowering plants and their pollinators evolved, as I noted in my recent review of pollinator diversity.  If the much earlier, Triassic origin of the angiosperms is correct then perhaps the earliest flowering plants did not co-opt pollinators that were already servicing gymnosperms.  Perhaps the relationships between plants and pollinators originated with the (Triassic) angiosperms and the gymnosperms subsequently evolved to exploit this.  My feeling is that only more, better fossils will provide definitive answers.

Here’s the details of the studies:

Coiro et al. (2019) How deep is the conflict between molecular and fossil evidence on the age of angiosperms? New Phytologist

Abstract: The timing of the origin of angiosperms is a hotly debated topic in plant evolution. Molecular dating analyses that consistently retrieve pre‐Cretaceous ages for crown‐group angiosperms have eroded confidence in the fossil record, which indicates a radiation and possibly also origin in the Early Cretaceous. Here, we evaluate paleobotanical evidence on the age of the angiosperms, showing how fossils provide crucial data for clarifying the situation. Pollen floras document a Northern Gondwanan appearance of monosulcate angiosperms in the Valanginian and subsequent poleward spread of monosulcates and tricolpate eudicots, accelerating in the Albian. The sequence of pollen types agrees with molecular phylogenetic inferences on the course of pollen evolution, but it conflicts strongly with Triassic and early Jurassic molecular ages, and the discrepancy is difficult to explain by geographic or taphonomic biases. Critical scrutiny shows that supposed pre‐Cretaceous angiosperms either represent other plant groups or lack features that might confidently assign them to the angiosperms. However, the record may allow the Late Jurassic existence of ecologically restricted angiosperms, like those seen in the basal ANITA grade. Finally, we examine recently recognized biases in molecular dating and argue that a thoughtful integration of fossil and molecular evidence could help resolve these conflicts.

 

Li et al. (2019) Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants

Abstract: Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the ‘Jurassic angiosperm gap’. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.

 

Celebrating Conrad Gesner Day 2017 (and Spiral Sunday #27)!

Gessner house Zurich March 2008 018

Happy Conrad Gesner Day!  Who is he, you may ask?  And why does he have a day?  Conrad Gesner (sometimes spelled Konrad Gessner) was a Swiss naturalist and polymath, born on this day (26th March) in 1516; he lived much of his life in Zurich, where he died on 13 December 1565.  Gesner was an extremely important figure in Renaissance science and scholarship, and when I visited Zurich in 2008 to give a seminar at the university, a tour of the old town revealed a number of references to the great man, including the memorial stone above.

Gesner’s Historia animalium (“History of Animals”)  is considered one of the founding texts of modern zoology, and for that reason he is memorialised in the name Gesneria Hübner, 1825; this is a genus of moths in the family Crambidae.

However Gesner was also a botanist and wrote a couple of books on the subject, though his Historia plantarum was not published until two centuries after his death.  To celebrate Gesner’s botanical achievements Linnaeus erected the genus Gesneria L. for a group of flowering plants.  Sounds odd to have the same name for two very different types of organism, but this cross-kingdom duplication of genera is allowable under the various codes of taxonomic nomenclature.

Gesneria in turn is the type genus for the family Gesneriaceae.  It’s quite a big family (about 3,450 species in 152 genera) and is ecologically important in the tropics and subtropics, where species may be pollinated by insects and birds, and are often epiphytic on trees.  It’s not a particularly economically important family, though a number of genera are widely grown as ornamentals, and there are specialist gesneriad growers and collectors.  The more familiar plants include those mainstays of Mothering Sunday (which by coincidence is also today) African Violets (Saintpaulia), Cape Primroses (Streptocarpus) and gloxinias (Gloxinia):

Gloxinias 20170325_105735

As I was looking through my photographs from the trip to Zurich in 2008 I spotted the following image of some wrought ironwork from the old city which may well be contemporary with Gesner.  This seems a fitting way to celebrate both the great man and this week’s Spiral Sunday:

Spirals in Zurich March 2008 119.png Happy Birthday Dr Gesner!

Dispelling the myth that orchid species usually only have a single pollinator

Orchids at Kew 2014-02-24 15.30.32

The idea that members of the plant family Orchidaceae (the orchids) “typically have exclusive relationships with their pollinators“, such that each orchid has only one pollinator, is a persistent one.  Recently I’ve encountered it on horticultural websites (follow that last link), in grant proposals, and on Wikipedia.

The problem is that it’s not true: it’s a myth that is perpetuated by people (often botanists or horticulturalists) who may know a lot about orchids but don’t know as much as they think they know about pollination ecology.

Orchids certainly have some fascinating and often quite intricate floral mechanisms to ensure pollination, but these have not necessarily evolved to attract and exploit just one species of pollinator.  Even in the case of sexually deceptive orchids that fool their (male) pollinating insects into believing that they are mating with a female of the same species, it is sometimes the case that more than one insect species is involved.  For example, in the well studied genus Ophrysflowers are pollinated by a narrow taxonomic range of pollinators, from a single species to up to five closely related species“.  As the authors of that last paper state, this is not the same as the mythological “extreme case of one orchid/one pollinator”.

Likewise different species of orchid bees may pollinate the same orchid flowers as they visit to collect scent compounds; for example in the Brazilian species Dichaea pendula, species from at least two different bee genera act as pollinators (Nunes et al. 2016).

The fact that “one orchid/one pollinator” is a myth is not new knowledge, it’s been widely discussed in the pollination ecology literature for decades.  For example, in our 1996 paper “Generalization in Pollination Systems, and Why it Matters” we showed data from the late 19th/early 20th centuries that clearly indicated a range of specialization in European orchids (follow that link and look at  Figure 3B).  Even earlier than this, in his 1992 paper “Trends in the pollination ecology of the Orchidaceae: evolution and systematics” Raymond Tremblay showed that only about 62% of species for which he could find data had a single pollinator, and that this varied considerably between different subfamilies of Orchidaceae, with some subfamilies being more specialized than others.

More recently, in a chapter in the 2006 book I co-edited with Nick Waser entitled “Geographical Variation in Diversity and Specificity of Pollination Systems” Steve Johnson, Andrew Hingston and myself looked at data from southern African compared to North American and European orchids; here’s the figure from that assessment:

 

Ollerton et al Figure 7 - JPEG

Orchids  are more specialized in southern Africa compared to Europe and North America (as are a number of other plant groups including the asclepiads, which we’re comparing them with here).  But even in southern Africa, only about 65% of the orchids studied have a single pollinator species.  It’s worth pointing out, though, that many of the species included in this analysis, and in Raymond Tremblay’s paper, have been studied only at single sites and often in single years, meaning that we have no idea if there is any spatio-temporal variation in the pollinators a particular orchid species exploits.

Why does this myth persist?  I think it’s for the same reason that myths are retold from generation to generation: they are great stories that fascinate the teller and the audience.  Indeed, orchids are very special plants with some amazing floral and vegetative adaptations, fascinating relationships with fungi, and incredible diversity.  But we don’t have to mythologise their relationships with their pollinators to try to make orchids more special than they already are.

Honey bee or honeybee; bumblebee or bumble bee?

screen-shot-2017-02-28-at-10-18-20

Language is fascinating, particularly the way in which it changes over time to incorporate new words, or old words used differently.  In science this has important implications for understanding: semantics matter.  With this in mind I’ve been curious about the alternative ways in which authors write the informal names of species.  Scientific names (Genus species)  should be fairly stable in their spelling and presentation (though not always, especially in the older literature); but “common” names of species vary widely geographically and temporally.

Here’s an example using Google’s Ngram Viewer which is a useful tool for tracking changes in word use over time.  Different authors currently use the terms “honey bee” and “honeybee”, sometimes in the same publication.  But as the image above shows. historical analysis suggests that “honey bee” is the more traditional term, and that “honeybee” only came into common usage from the start of the 20th century, and by the late 1920s had taken over “honey bee”.

Likewise “bumblebee” and “bumble bee”; despite “bumble bee” having a much earlier usage, “bumblebee” has dominated since the late 19th century:

screen-shot-2017-02-28-at-10-16-51It’s interesting to speculate about what might have caused these shifts in use, and it’s possible that in these examples it was the publication of especially influential books that used one term over another and influenced subsequent writers.  Could make a good project for a student studying how use of language varies in different time periods.

For my own part I tend to prefer “honey bee” and “bumblebee”, but I can’t precisely articulate why; perhaps it’s because in Europe we talk about “the honey bee” as a single species (Apis mellifera) but not “the bumblebee” because there is usually more than one co-occurring Bombus species in a particular area.  Do others have a particular preference?

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

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

——————————————————-

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.

 

 

 

 

Elsevier successfully patents a common peer review process

As reported yesterday on Mike Taylor’s Sauropod Vertebra blog, who in turn picked up the story from the sec.uno site, at the end of August the giant publisher Elsevier successfully patented what they see as a unique form of peer review: waterfall (or cascading as it’s long been known) peer review. This is described as “the transfer of submitted articles from one journal to another journal” owned by the same publisher.  And there’s nothing new about it, it’s been accepted practice for a number of publishers for years now.

If you want to look at the original U.S. patent, here’s a link to it.

I don’t often re-work the content of others’ blogs, but his is exceptional: the motivation for Elsevier’s actions seem dubious at best and it’s worth clicking through and reading those pieces in detail.  What is Elsevier thinking?

The timing of this one story is also interesting.  It’s as if the Gods of Publishing had actually read my last post about peer-reviewed versus non-peer-reviewed publishing, and decided to have some fun with us mere mortals…..