Vesper Flights: a book review and reflection

Vesper Flights by Helen Macdonald

I have been waiting eagerly for a copy of Vesper Flights by Helen Macdonald. If you have read my review of her H is for Hawk, you will understand why. Early reviews of the new book were also positive – “powerful essays,” said The Guardian; “soul-stirring,” said USA Today; “a beautiful and generous book,” said npr. The Goodreads community gave it 4.2 out of 5.

I was fortunate enough to get a copy of Vesper Flights for Christmas. It is a collection of 41 essays, and Helen Macdonald writes “I hope that this book works a little like a Wunderkammer. It is full of strange things and it is concerned with the quality of wonder.” Many of the essays have an autobiographical component. Several moved me to tears.

A Wunderkammer painted by Domenico Remps around 1695 (click images in this review to zoom)

The essays in the collection are:

1. Nests – a reflection on bird’s nests
2. Nothing Like a Pig – coming face-to-face with a wild boar
3. Inspector Calls – a beautifully written and touching account of an autistic boy meeting a parrot
4. Field Guides – a visit to Australia, and praise for field guides

The hairpin banksia gets a mention in essay #4

5. Tekels Park – reminiscences of a childhood spent among nature in Tekels Park
6. High-Rise – a wonderful account of the surprising amount of life that can be found in the night-time sky
7. The Human Flock – about migration
8. The Student’s Tale – about a refugee
9. Ants – about nuptial flights in ants

A winged queen ant (photo credit)

10. Symptomatic – about migraines and impending doom
11. Sex, Death, Mushrooms – “Many toxic fungi closely resemble edible ones, and differentiating each from each requires careful examination, dogged determination and often the inspection of spores stained and measured under a microscope slide.”
12. Winter Woods – walking through woods in the winter
13. Eclipse – an eclipse is an emotional experience
14. In Her Orbit – with Nathalie Cabrol in the Atacama Desert, site of the now-defunct Carrera Solar Atacama (this chapter is based on a New York Times article)

San Pedro de Atacama, Chile (photo credit)

15. Hares
16. Lost, But Catching Up
17. Swan Upping – swan upping on the Thames as social commentary
18. Nestboxes – are they for the birds, for us, or both?
19. Deer in the Headlights – this essay highlights the problem of deer-vehicle collisions (the UK gets about 1 per thousand people per year); Australia has a kangaroo-vehicle collision problem of similar magnitude, but that issue is perhaps viewed a little differently
20. The Falcon and the Tower – about urban peregrine falcons, specifically in Dublin (see also this short documentary film)

The towers of the decommissioned Poolbeg Generating Station in Dublin, with a magnification of the western (leftmost) tower. These towers, around 207 m high, are home to the peregrine falcons described in essay #20 (photo credit)

21. Vesper Flights – the central and title essay, based on a New York Times article, is about swifts
22. In Spight of Prisons – all about glow-worms, Lampyris noctiluca
23. Sun Birds and Cashmere Spheres – golden orioles and bearded reedlings
24. The Observatory – “a swan had come towards me and offered me strange
    companionship at a time when I thought loneliness was all I could feel.”
25. Wicken – Wicken and other fens, which I imagine inspired the home of Puddleglum in the Narnia stories

A hide at Wicken Fen (photo credit)

26. Storm
27. Murmurations – “Words to accompany Sarah Wood’s 2015 film Murmuration x 10”
28. A Cuckoo in the House – about cuckoos and the man who inspired the character ‘M.’ Yes, that ‘M.’
29. The Arrow-Stork – the arrow-stork and the study of bird & animal migration
30. Ashes – on tree diseases
31. A Handful of Corn – as a famous song says: “Come feed the little birds, show them you care, and you’ll be glad if you do; their young ones are hungry, their nests are so bare, all it takes is tuppence from you.”

32. Berries
33. Cherry Stones
34. Birds, Tabled – a fascinating exploration of the morality of bird-watching versus bird-keeping and the class conflicts involved (a number of reviewers online have taken issue with this chapter, specifically)
35. Hiding
36. Eulogy
37. Rescue – a beautiful account of bird rescue and wildlife rehabilitation
38. Goats
39. Dispatches from the Valleys – a heavily autobiographical chapter, raising all kinds of spiritual questions (but not really answering them)
40. The Numinous Ordinary – “I kept trying to find the right words to describe certain experiences and failing. My secular lexicon didn’t capture what they were like. You’ve probably had such experiences yourself – times in which the world stutters, turns and fills with unexpected meaning.”
41. What Animals Taught Me – “When I was a child I’d assumed animals were just like me. Later I thought I could escape myself by pretending I was an animal. Both were founded on the same mistake. For the deepest lesson animals have taught me is how easily and unconsciously we see other lives as mirrors of our own.”

Not surprisingly, about half the chapters in this book are about birds, in some way or other:

At its best, this book is as good as the superb H is for Hawk, but is not consistently so (indeed, it scarcely could be). While some of the chapters are truly wonderful, others have a moralistic tone that I thought was a little more heavy-handed than it needed to be, and which became a little repetitive after a while. In the last chapter Helen Macdonald offers a corrective: “These days I take emotional solace from knowing that animals are not like me, that their lives are not about us at all.” Or, as C.S. Lewis once put it:

“Come out, look back, and then you will see … this astonishing cataract of bears, babies, and bananas: this immoderate deluge of atoms, orchids, oranges, cancers, canaries, fleas, gases, tornadoes and toads. How could you ever have thought this was the ultimate reality? How could you ever have thought that it was merely a stage-set for the moral drama of men and women? She is herself. Offer her neither worship nor contempt. Meet her and know her. If we are immortal, and if she is doomed (as the scientists tell us) to run down and die, we shall miss this half-shy and half-flamboyant creature, this ogress, this hoyden, this incorrigible fairy, this dumb witch.”

Helen Macdonald has a genuine talent for showing the reader what she saw, and the reader of a book like this will feel appropriate things in that situation. Perhaps the more moralistic tone is the inevitable, and possibly appropriate, nature of an essay written for a newspaper or magazine. The fact that this book is a collection of such essays would then explain why it feels a little repetitive at times.

My recommendation: buy this book, but only read a few chapters each week. And think about them.

Vesper Flights by Helen Macdonald: 4 stars

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Dune by Frank Herbert: a book review

Dune by Frank Herbert (1965)

I recently re-read the classic 1965 novel Dune by Frank Herbert. This is Frank Herbert’s best book, and one of the best science fiction novels ever written. It won the Hugo Award in 1966 (jointly with Roger Zelazny’s This Immortal) and won the inaugural Nebula Award. It became a quite terrible 1984 film and a somewhat better miniseries.

Parts of the novel are reminiscent of the work of Cordwainer Smith, notably the idea of a desert planet producing spice, and the idea that navigating a faster-than-light ship requires a guild of unusual navigators who can see into the future. However, most of the novel was so original that it became a huge hit when it first appeared. Themes that are particularly notable are those of planetary ecology, intergalactic politics, and unusual human skills.

I have always been moved by Herbert’s idea of a symbolic ecological language that can “arm the mind to manipulate an entire landscape” (Appendix 1), and the idea of making ecological literacy a key part of education:

“At a chalkboard against the far wall stood a woman in a yellow wraparound, a projecto-stylus in one hand. The board was filled with designs – circles, wedges and curves, snake tracks and squares, flowing arcs split by parallel lines. The woman pointed to the designs one after the other as fast as she could move the stylus, and the children chanted in rhythm with her moving hand.
Paul listened, hearing the voices grow dimmer behind as he moved deeper into the sietch with Harah.
‘Tree,’ the children chanted. ‘Tree, grass, dune, wind, mountain, hill, fire, lightning, rock, rocks, dust, sand, heat, shelter, heat, full, winter, cold, empty, erosion, summer, cavern, day, tension, moon, night, caprock, sandtide, slope, planting, binder. …’” (Chapter 22)

The unusual ecology of the desert planet Arrakis encourages us, of course, to think more deeply about our own planet (and Arrakis was apparently inspired by the Oregon Dunes here on Earth).

Also fascinating is the idea that the human race has turned away from computers and the Internet, and gone back to training human minds to remember, calculate, and think:

“‘Once men turned their thinking over to machines in the hope that this would set them free. But that only permitted other men with machines to enslave them.’
‘Thou shalt not make a machine in the likeness of a man’s mind,’ Paul quoted. […]
‘The Great Revolt took away a crutch,’ she said. ‘It forced human minds to develop. Schools were started to train human talents.’” (Chapter 1)

The most obvious theme, and the source of the novel’s action, is the galaxy-wide intrigue between the noble House Corrino, House Atreides, and House Harkonnen; the resulting warfare between them; and the resistance of the desert Fremen to occupation (inspired by Lawrence of Arabia):

“Paul took two deep breaths. ‘She said a thing.’ He closed his eyes, calling up the words, and when he spoke his voice unconsciously took on some of the old woman’s tone: ‘ “You, Paul Atreides, descendant of kings, son of a Duke, you must learn to rule. It’s something none of your ancestors learned”.’ Paul opened his eyes, said: ‘That made me angry and I said my father rules an entire planet. And she said, “He’s losing it.” And I said my father was getting a richer planet. And she said. “He’ll lose that one, too.” And I wanted to run and warn my father, but she said he’d already been warned – by you, by Mother, by many people.’” (Chapter 2)

Goodreads rates this classic science fiction novel 4.2. I’m giving it 4½ stars (but be aware that the sequels are not nearly as good).

Dune by Frank Herbert: 4½ stars

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MODSIM Conference, Day 1

I am attending the MODSIM International Congress on Modelling and Simulation in Hobart, Tasmania. It promises to be another great event.

I spoke today on “Sampling bias and implicit knowledge in ecological niche modelling.” Out of the many interesting talks I listened to, one that stands out is “The Waroona fire: extreme fire behaviour and simulations with a coupled fire-atmosphere model” by Mika Peace. It introduced me to “pyrocumulonimbus clouds,” and some of the complex weather–fire interactions in severe bushfires. This is certainly a phenomenon that needs to be better understood.

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Ecological literacy and Frank Herbert’s Dune, half a century on

Dune by Frank Herbert

The year 1965 saw the appearance of what has been called “the first planetary ecology novel on a grand scale.” Frank Herbert’s Dune explored a plethora of interesting themes, notably that of ecology. The novel speaks of “… teaching [the children] ecological literacy, creating a new language with symbols that arm the mind to manipulate an entire landscape, its climate, seasonal limits, and finally to break through all ideas of force into the dazzling awareness of order.”

The use of food webs, like the one for waterbirds of Chesapeake Bay above, was fairly standard by 1965, and Herbert seems to be hinting at a graphical language for ecology going beyond that. Exactly what he was referring to is unclear.

But are we teaching the kind of ecological literacy Herbert refers to? A 2013 survey indicated that, out of 145 US tertiary institutions ranked for “Ecology and Evolutionary Biology” and “Integrative Biology,” only 47% taught a course in ecosystem ecology or biogeochemistry, and only 22% of the courses included field experiences. A 1993 survey of UK secondary teaching (A-levels and GCSE) showed that students only studied a median of 2 or 3 different habitats:

So how many children actually understand, say, trophic cascades in the wolf–elk ecosystem? How many adults, for that matter? The evidence suggests that it’s not very many, judging by the resistance to sensible management of National Parks. If we do not wish to recreate the desert planet Arrakis, we might like to work on that.

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Ecological networks and the Australian dingo

I’m excited at the publication of a joint paper on network ecology, with a focus on the Australian dingo: “Trophic cascades in 3D: Network analysis reveals how apex predators structure ecosystems” (by Arian D. Wallach, Anthony H. Dekker, Miguel Lurgi, Jose M. Montoya, Damien A. Fordham & Euan G. Ritchie, and appearing in Methods in Ecology and Evolution).

Associated with this publication is an animation I put together for the paper showing how the ecological network changes if the role of the dingo as apex predator is weakened. I’m grateful to my ecologist co-authors at the opportunity to contribute my mathematical skills to such an interesting project.

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The Blue Mountains Water Skink

The endangered Blue Mountains Water Skink, Eulamprus leuraensis (photo: “Sarshag7”)

I have previously mentioned my interest in ecological niche modelling and amphibians. The cute little skink above, native to the Blue Mountains near Sydney, is sadly endangered. The black circles in the map below show online occurrence records for the skink. These range in altitude from approximately 530 to 1,170 m.

The blue area shows a predicted potential range for the species, based on MaxEnt modelling using those occurrence records and BioClim climate data. The model does not take into account the skink’s need for sedge and shrub swamps with permanently wet boggy soils – there are readily available online land cover datasets, but these have insufficient spatial resolution to identify the 30 or so swamps in which the skink is found. The predicted potential range for the skink is consequently very much exaggerated, and covers 1,320 sq km, of which 63% falls within national parks or other protected areas. Hopefully that is enough to stop this beautiful amphibian from becoming extinct, although it continues to face threats from urban sprawl, feral cats, and vegetation changes.

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Ecological Niche Modelling and Frogs

Predicted suitable range (in blue) of frogs from the Leptolalax applebyi group in Vietnam, Cambodia, and Laos (modified from Rowley et al. 2015). The vertical colour scale shows elevation in metres. Frog images are by Jodi Rowley.

I was very excited to have the opportunity to collaborate recently with AMRI at the Australian Museum on a paper about frogs, which has just appeared in PLOS ONE: Undiagnosed Cryptic Diversity in Small, Microendemic Frogs (Leptolalax) from the Central Highlands of Vietnam (Jodi J. L. Rowley, Dao T. A. Tran, Greta J. Frankham, Anthony H. Dekker, Duong T. T. Le, Truong Q. Nguyen, Vinh Q. Dau, Huy D. Hoang). My main contribution to the work was in ecological niche modelling – see the map above.

The Leptolalax applebyi group discussed in the paper hides a number of similar-looking but distinct species of frogs, often restricted to small geographic areas (DNA and acoustic evidence can be used to distinguish them). Ecological niche modelling using climatic and terrain data produced the above map of areas predicted to be suitable for these frogs. Unfortunately, as of a 2008 satellite study, only 55% of this suitable area (in blue on the map) was covered by the broadleaf evergreen forest which these frogs need. The resultant habitat loss may therefore have already led to the extinction of frog species which we will never know about. Less than a third of the remaining area has government protection, so further habitat loss is, sadly, a strong possibility.

The example of the Leptolalax applebyi group underscores the need both to strengthen conservation efforts around the world, and to put more effort into describing the world’s species diversity, so that we know what needs protecting! Losing a species (like the passenger pigeon or the gastric-brooding frog) is tragic, but sadder still is losing species without even realising that they existed.

Some beautiful photographs

Today, some pretty pictures from recent photographic competitions. First, the European Geosciences Union Photo Contest 2014. “Erosion Spider” by John Clemens was one of the winning entries:

Second, the BioMedCentral Ecology Image Competition. “A sticky snack for mice” by Petra Wester was the overall winner:

Finally, the Neuro Bureau Brain Art Competition 2014. “Heart of the Brain” by Chris Steele (MPI Leipzig) won the Best Visualization of Probabilistic Connectivity category:

All images used under Creative Commons license (CC BY-NC-ND, CC BY, and CC BY-NC-SA respectively). Click images to zoom and/or read more about the photographs.

Best Scientific Visualizations of 2013

Wired is listing their “Best Scientific Visualizations of 2013.”

Included on their list is the interesting network diagram below, from the paper “Parasites Affect Food Web Structure Primarily through Increased Diversity and Complexity” by Jennifer Dunne et al. (PLoS Biology, Vol. 11, No. 6, June 2013) – a paper which I have previously mentioned.

Integrating NetLogo and Java: #3

My previous two posts (one and two) described a simple NetLogo example integrated with a NetLogo Java extension, where the Java code implemented a diffusion process on the “patches,” as shown above. As presented, the example used two NetLogo loops to copy data between the DiffusionGrid object and the patches:

  ask patches [
    set value (random-float 9.9)
    diffusion:set-grid-cell grid pxcor pycor value
    set-patch-color
  ]
  
  ...
  
  ask patches [
    set value (diffusion:get-grid-cell grid pxcor pycor)
    set-patch-color
  ]

It is also possible to carry out these loops in Java, but doing so requires delving deeper into poorly documented parts of the extensions API. We introduce two new commands which interact directly with the patches from Java. However, these require knowing that the value variable of a patch is number 5 in the variable list. This fact may be subject to change (if it is not listed first, or if other predefined patch variables are defined).

  ask patches [
    set value (random-float 9.9)
    set-patch-color
  ]
  diffusion:copy-patches-to-grid grid patches
  
  ...
  
  diffusion:copy-grid-to-patches grid patches
  ask patches [
    set-patch-color
  ]

This version runs in about 3.5 milliseconds per iteration step in “fast” mode (compared to 5.8 milliseconds per iteration step for the previous version, and 41.8 milliseconds per iteration step for a pure NetLogo version). It exploits some more advanced features of the NetLogo Java API:

The Java code behind our modified example consists of two classes implementing copy-patches-to-grid and copy-grid-to-patches. Direct patch interaction is shown in green. In red is a Java iteration over the supplied “agentset” of patches:

class SetGridFromPatches extends DefaultCommand {
  public Syntax getSyntax() {
    return Syntax.commandSyntax(new int[] {Syntax.WildcardType(), Syntax.AgentsetType()});
  }
  
  public void perform(Argument args[], Context context) throws ExtensionException, LogoException {
    Object g = args[0].get();
    if (g instanceof DiffusionGrid) {
      DiffusionGrid dg = (DiffusionGrid) g;
      AgentSet aset = args[1].getAgentSet(); 
      for (Agent a : aset.agents()) {
        if (a instanceof Patch) {
          Patch p = (Patch) a;
          int x = p.pxcor();
          int y = p.pycor();
          Object v = p.getVariable(5);
          if (v instanceof Double) dg.setValue (x, y, ((Double) v).doubleValue ());
          else throw new ExtensionException("Did not find numeric patch variable in slot " + 5);
        } else throw new ExtensionException("Non-patch agents passed into copy-patches-to-grid") ;
      }
    } else throw new ExtensionException(g + " is not a DiffusionGrid") ;
  }
}

class SetPatchesFromGrid extends DefaultCommand {
  public Syntax getSyntax() {
    return Syntax.commandSyntax(new int[] {Syntax.WildcardType(), Syntax.AgentsetType()});
  }
  
  public void perform(Argument args[], Context context) throws ExtensionException, LogoException {
    Object g = args[0].get();
    if (g instanceof DiffusionGrid) {
      DiffusionGrid dg = (DiffusionGrid) g;
      AgentSet aset = args[1].getAgentSet(); 
      for (Agent a : aset.agents()) {
        if (a instanceof Patch) {
          Patch p = (Patch) a;
          int x = p.pxcor();
          int y = p.pycor();
          double v = dg.getValue (x, y);
          try {
            p.setVariable(5, new Double (v));
          } catch (AgentException e) {
            throw new ExtensionException("Could not set variable in slot " + 5 + " because of " + e);
          }
        } else throw new ExtensionException("Non-patch agents passed into copy-grid-to-patches") ;
      }
    } else throw new ExtensionException(g + " is not a DiffusionGrid") ;
  }
}

Even closer integration than this is possible; but with greater chances of being impacted by changes to the NetLogo code, or changes in how NetLogo works. The level of integration described here is probably all that is needed, in most cases. For those interested, the complete Java file is here (with all files also at Modeling Commons).

The source code for the standard GIS extension shows how more closely integrated Java can be written.