on classification [scrapbook]

Darwin, in The Descent of Man

Every naturalist who has had the misfortune to undertake the description of a group of highly varying organisms, has encountered cases (I speak after experience) precisely like that of man; and if of a cautious disposition, he will end by uniting all the forms which graduate into each other as a single species; for he will say to himself that he has no right to give names to objects which he cannot define.

1871, 1st ed. vol 1, p. 226-7

An ethnography of grant review

Over the last couple of weekend lunches I’ve read Michéle Lamont’s  How Professors Think: Inside the Curious World of Academic Judgment. Here’s the (slightly hype-y) blurb from Harvard University Press:

Excellence. Originality. Intelligence. Everyone in academia stresses quality. But what exactly is it, and how do professors identify it? In the academic evaluation system known as “peer review,” highly respected professors pass judgment, usually confidentially, on the work of others. But only those present in the deliberative chambers know exactly what is said. Michèle Lamont observed deliberations for fellowships and research grants, and interviewed panel members at length. In How Professors Think, she reveals what she discovered about this secretive, powerful, peculiar world.

I think “peculiar” is the most apt of the adjectives in that last sentence, because Lamont didn’t really address the interface between the grant-review process and the outcomes – it was more concerned with the processes of deliberation and the construction of norms of quality that go on. A really interesting read, particularly if you are US-based social scientist (the “study population”). I found myself itching to know more about the cultural differences that might occur, between for example the US, the UK, and Europe; or between the social sciences as construed in the book (from economics to English literature) and the behavioural and life sciences (psychology, biological anthropology, biology). But those are interests motivated by my own disciplinary and geographic situation.

I took two things away from the book: the first, Lamont’s message that quality/excellence are a bit ineffable, but that in general people “know it when they see it”, regardless of disciplinary background. The second was that there are two levels of the process that the applicant has no control over: the  mix of people and perspectives on a grant review committee, and the alchemy of how they reach their decisions about what is quality and deserves to be funded and what is not. These seem to be almost completely unpredictable, and would encourage me, if a grant proposal were rejected somewhere or sometime, to resubmit it elsewhere.

The book is very readable, with a great mix of synthetic commentary and verbatim quotes from the reviewer participants. Gave me a real insight into the decision-making criteria used by more interpretive disciplines/individuals, too.

Note: have been travelling and busy, but a return to regular postings next week. Starter for 10 will go monthly from now on, too.

definitions of evolution [scrapbook]

Evolution is not changes in gene frequencies. Genes are part of a network of developmental causes that lead to the manifestation of traits that have general properties in common across individuals while retaining individual differences. Evolution is change in the frequencies of alternative developmental causes that yield variations in developmental trajectories (a phrase that is more cumbersome than ‘‘changes in gene frequencies’’ but nevertheless more correct).

Source: Michel, GF and Tyler, AN. Developing human nature:“Development to” versus “Development from?”. Developmental Psychobiology (2007) vol. 49 (8) pp. 788-799  DOI: 10.1002/dev.20261

Starter for 10: Rod Page

What with the interdisciplinary thing, I know some delightful and interesting people in quite disparate fields. Starter for 10 is a semi-regular (fortnightly) series of peer interviews, with questions both serious and trivial for your edification.

I’m very excited that this week’s interview is with Professor Rod Page, an evolutionary biologist at the University of Glasgow – although see the answer to the second question for what he really does. I met Rod when I was doing my masters on language evolution, and his immensely useful software methods and textbooks made my phylogenetics learning curve much less steep than it could have been! Basically, if it combines computing and evolution, Rod has already thought about it, mashed it up, made it available on iPhylo and Twittered about it before you had your breakfast.

1. In the little space for “occupation” on immigration cards at airports, what do you write?


2. Give me your conference tea-break pitch: ” … and what do you work on?”

I’m interested in joining the dots. It drives me nuts that we have all this information about the phylogeny, geographic distribution, and taxonomy of organisms and we can’t quite seem to bring it all together in one place. Think of it as Google for systematics.

3. What’s your origin story – how did you end up in your field? Was there a defining moment, or person, or something else that steered you?

I ended up in biology because it felt that you could still discover things without requiring lots of money or equipment. For instance, my first paper described a new species of pea crab that I found in Auckland harbour. Then I discovered the joys of programming, which is addictive because you regularly feel like master of the universe … at least for a few seconds. But perhaps the thing which grabbed me most as a graduate student was biogeography. New Zealand in the late 80’s was a hot bed of panbiogeography, with Leon Croizat’s work being rediscovered, and it was an exciting time. The wheels rather came off panbiogeography, but being in New Zealand felt like being in the centre of things.

4. And why are you trying to forget about lice? You say so on your old webpage …

Lice have been good to me, but empirical work is hard! All the tracking down collectors, storing specimens, keeping track of data, difficulties sequencing decent genes, struggling to align what sequences we did get, making sense of ropey trees at the end. Methodology is much more fun, especially for somebody like me who is easily distracted by shiny baubles.

5. Do you have a favourite quirky academic paper? Mine is the one about the homosexual necrophiliac duck.

I don’t have a paper, but the “Chicken chicken chicken” talk is a favourite. I show this to undergraduates in tutorials about how to give talks.

6. Professor-level-question: what three things are strikingly different in your field now from when you first started out?

Dub dub dub (WWW). It’s changed everything. That and large scale sequencing. Put another way, biology has become overwhelmingly digital. Some parts of biology have been quicker to adjust to this than than others. [FJ: *sigh* the revolution is still to come in anthropology and linguistics]

7. For a month, you get to do a job-swap outside of academia. What would you do?

Design book covers.

8. Who’s your favourite fictional scientist?

Isadore Nabi [FJ: I think I will start calling myself an “Intrepid Investigator” too]

9. Too much time, money and intellect has been wasted researching what?

Rather than pick something specific, I worry that there’s a poor correlation between amount of money thrown at a subject and the amount of progress made. Results don’t scale linearly with money. I’m underwhelmed by “big science” approaches in biodiversity.

10. Recommend for me (a) a good pop-science book (b) a good history/philosophy/politics book and (c) a poem.

Book: “Envisioning Information” by Edward Tufte ISBN 978-0961392116 – Perhaps not strictly “pop-science”, but just an awesome book, both visually and intellectually. [FJ: EVERYONE should read Tufte]

Philosophy: “The Gentle Art of Philosophical Polemics” by Joseph Agassi ISBN 978-0912050638 – Fierce criticism as a mark of respect, makes me feel good about saying “well this sucks” all the time. [FJ: This arrived in my pigeonhole today, looking forward to it!]

Poem: Robert Burns Tam o’ Shanter “Nursing her wrath to keep it warm” – glorious line.

Although Rod’s disciplinary interests are firmly within biology, much of what he blogs about at iPhylo has crossover appeal – at the moment he’s reviewing iPad apps for reading scientific articles.

A game from 3000 years ago

I came across this great paper today*:

CONNAUGHTON, S. P., TACHÉ, K., & BURLEY, D. V. (2010). Taupita: A 3000-year-old Shell Game in the Lapita Cultural Complex of TongaJournal of Social Archaeology, 10(1), 118-137. DOI:10.1177/1469605309354400  [link]

Abstract: Recent excavations at the archaeological site of Nukuleka on Tongatapu in the Tongan Archipelago have yielded the largest Lapita collection of perforated Ark (Anadara) shells known to date. In this article, we focus on the unusually large collection of modified Ark shells from Nukuleka in an attempt to unravel the ambiguity that surrounds their functional interpretation. Former interpretations of perforated Anadara as shell net weights may only explain one possible cause of their construction. We proffer, through relational analogy, that we are witnessing a 3000-year-old Lapita shell game.

These shells-with-holes in the 3000-year old archaeological record for Lapita have long been thought of as weighting material for fishing nets. But! The authors describe how during the field season on Tonga the local field assistants would, in their breaks, play a shell-based game (Taupita) – and the “debris” from this game matched that of the so-called net weights. Some lovely experimental archaeology later, and while they can’t discount the idea that the shells were used as net-weights, it’s certainly just as plausible that they were the pieces in a ancestral game resembling Taupita.

From the paper: Left: Playing Taupita Right: Anadara antiquata shells

This is groovy. I often mention in talks that one of the reasons for using phylogenetic methods on cultural and linguistic data is for the purposes of “virtual archaeology” – being able to infer something about social life in the past in the absence of appropriate material culture from archaeology. But there are of course some aspects of human behaviour and social life that combine both of these things: they leave some trace through artifacts, but there are missing pieces of the puzzle in terms of cognition, communication, or other cultural/behavioural aspects that remain outstanding. Games are a really good example – and often overlooked by both anthropologists and archaeologists. In the discussion the authors say:

As a community of archaeological scholars in pursuit of ‘big’ questions and larger anthropological themes, we sometimes lose sight of the day-to-day aspects of a society, including leisure time games which are rarely mentioned (but see Culin,1975; DeBoer,2001). Games are a social mechanism that can provide a unique opportunity to develop a skill, educate, make a tool,and/or potentially create a better understanding of one’s self. Games are also fun and part of the human experience.

Pacific anthropology has pulled its weight here, I think (no pun intended) – from the earliest late 19th century descriptions games were frequently mentioned, and there were detailed descriptions of string figures in a number of classic Pacific ethnographies, many published by the Bishop Museum. Honor Maude’s wonderful book on Nauru comes to mind here. I’d love to see more comparative and historical work on games – let me know if you have suggestions.

*So great I wanted to blog about it straight away, causing me to deviate from the master plan for today … but at least now I won’t go and do unnecessary research for this post all afternoon?

Starter for 10: Disa Sauter

What with the interdisciplinary thing, I know some delightful and interesting people in quite disparate fields. Starter for 10 is a semi-regular (fortnightly) series of peer interviews, with questions both serious and trivial for your edification.

This week’s interview is with Dr Disa Sauter, who works three doors down from me at the Max Planck Institute for Psycholinguistics. Disa and I both did PhDs at UCL in London, but it took us moving to the Netherlands to bump into one another!

1. In the little space for “occupation” on immigration cards at airports, what do you write?
I’m actually a little stumped by this every time – you’d think I’d have decided on a word to summarize what I do by now! So I alternate between researcher, scientist, and psychologist.

2. Give me your conference tea-break pitch: ” … and what do you work on?”

I work on emotions and the ways that we communicate to others how we feel using facial expressions and vocalisations. I’m especially interested in whether emotions and expressions are the same or different depending on people’s cultural backgrounds. [FJ: Disa has done field work with the Himba people in Namibia, and is currently working with a Mayan group in Mexico]

3. What’s your origin story – how did you end up in your field? Was there a defining moment, or person, or something else that steered you?
I was always interested in the human mind, but torn between philosophy of mind and psychology. Having done my final year school project in philosophy, I decided to focus on psychology instead… Doing a PhD on emotions with Sophie Scott at UCL made me want to continue in research for as long as I can.
4. Journalists reckon that scientists “discover” things. Tell me the coolest thing you’ve “discovered” in your career so far.
In a study published earlier this year, me and my colleagues showed that some sounds that we make to express emotions, like growls and sobs, are shared by people with dramatically different cultural backgrounds, suggesting that they are part of the common human heritage. But while quite a few negative emotions were signalled in the same way across the groups, the sounds used to express many positive emotions were different – the exception to this was laughter, which had the same meaning across cultures.
5. I hear you’re Swedish. In the interests of cultural understanding, tell me something about Swedish language or culture that  doesn’t really have an English equivalent.
‘Lagom’ is a Swedish word and concept that doesn’t have a good equivalent in other languages. The best translation I think would be ‘just right’, like for example neither too much nor too little – but it can be applied in pretty much any domain, size, temperature, satiation etc. Unlike ‘perfekt’ (perfect), ‘lagom’ is not particularly celebratory, it’s more a matter-of-fact statement, which is what makes it so Swedish. [FJ: this brilliant word has its own wikipedia entry, it’s so useful]
6. For a month, you get to do a job-swap outside of academia. What would you do?

I’d be an apprentice in the kitchen of a fancy vegetarian restaurant. [FJ: Mmmm, good choice with the transferable skills!]
7. Too much time, money and intellect has been wasted researching what?
The neural correlates of poorly understood and badly operationalized psychological phenomena.
8. Recommend for me (a) a good pop-science book (b) a good history/philosophy/politics book and (c) a poem.
a) Bad Science by Ben Goldacre
c) The Road Not Taken by Robert Frost
9. Who’s your favourite fictional scientist?
Dexter Morgan. [FJ: I am hiding the sharp objects in the canteen]
10. What science-y thing did you do yesterday?
I submitted a paper and started revising another.
Disa’s publications and research interests are listed at her website, including a recent review of positive emotions and how they’re a bit more complex than just “happy”. The media covered her cross-cultural emotion work earlier this year, you can see some of the write-ups here and here.

South Pacific

Pohutukawa flowers on Orewa Beach, New Zealand

I’m watching the BBC series South Pacific on DVD at the moment, and I’m up to the third episode. The series has beautiful cinematography: astonishing ultra-slow-motion footage of waves breaking on Pohnpei was the centrepiece of the first episode, and I’m not going to forget the creepy carnivorous caterpillars in action in Hawaii or the tiger sharks eating the albatross fledglings.

But the series is very much suffering from being “thematic” in the way that many modern museum collections are: without historical or geographic context, a loose set of narratives on a theme is forgettable. Set-pieces become nothing more than passing fancy for the eyes, with only the shocking or unexpected being committed to memory. It’s a great shame – as someone who works on Austronesian cultural diversity and comes from Oceania, it’s always disappointed me that there’s not been a good television series on the natural and cultural history of the Pacific. This series aspires to be that, but it’s a string of anecdotes, lurching from zoology to weather to culture, picking out the amazing (vine-jumping Pentecost Islanders from Vanuatu) and the extreme (freezing Macquarie Island with its penguins and elephant seals), with no contextual background of what the biology of the region is like as a whole, or how the fascinating and complex human settlement history has shaped the social and cultural diversity of today.

Most disappointly, the anthropology has made me cringe. The series is narrated (albeit by the splendid Benedict Cumberbatch) rather than having interviewers or allowing people to speak, and it all comes across as terribly touristic and superficial. Anutans were glowing described as people living in mystical harmony with their tiny atoll environment, and contrasted with those rapacious Rapa Nui who used up all their resources. You would think there was no-one living on Easter Island today, because all we got were atmospheric shots of the moai.

I’m relegating it to the background now and just waiting for the bits about keas. Keas are cool. Here’s one walking up a snowy slope with its beak. Bet you can’t do that.

ARKive video - Kea walking up snowy mountain side - using beak

Starter for 10: Simon Greenhill

What with the interdisciplinary thing, I know some delightful and interesting people in quite disparate fields. Starter for 10 will be a semi-regular (fortnightly) series of peer interviews, with questions both serious and trivial for your edification.
I’m starting off with my friend and colleague Dr Simon Greenhill, from the University of Auckland.
1. In the little space for “occupation” on immigration cards at airports, what do you write?
2. Give me your conference tea-break pitch: ” … and what do you work on?”
I study how languages and cultures evolve using computational methods drawn from evolutionary biology.

3. What’s your origin story – how did you end up in your field? Was there a defining moment, or person, or something else that steered you?

I guess I’d always been interested in languages – I took French, German and Latin at school (the first two reasonably successfully, the latter rather abysmally). At university I intended to get a degree in computer science, but quickly decided I didn’t want to be spending my life doing tech support. At that time I’d discovered how awesome evolutionary biology was and I moved over to biology/psychology and thoroughly enjoyed myself. I ended up taking a course on Evolution, Behavior and Cognition (where a certain young Ms. Jordan was my lab instructor) [FJ notes: Simon is the original skeptic and raised my game!] and I loved every minute of it. I eventually harassed Russell Gray enough so that he had to take me on as a student. It’s all been downhill since there.
4. Journalists reckon that scientists “discover” things. Tell me the coolest thing you’ve “discovered” in your career so far.
In 2009 Russell Gray, Alexei Drummond and I published a paper where we tested different models of Pacific settlement. We showed that the Pacific was settled relatively recently – beginning around 5,200 years ago from Taiwan. The cool thing we discovered there was that we could really nuance our understanding of prehistory by identifying patterns of expansion pulses and settlement pauses, and estimating the timing of these events.
5. What’s the geekiest thing you know how to do?
I cured my addiction to sudoku by writing a program to solve the damn things. [FJ: !!!! ]
6. For a month, you get to do a job-swap outside of academia. What would you do?
Software development.
7. What’s your favourite dinosaur?
You can’t beat Tyrannosaurus rex, although I do have a soft-spot for Opabinia regalis (non-dino, I know).
8. Recommend for me (a) a good pop-science book (b) a good history/philosophy/politics book and (c) a poem.
a) Guns, Germs and Steel by Jared Diamond. It’s not perfect, but epic in scale and full of interesting, and very testable ideas.
b) David Hull’s “Science as a Process: An Evolutionary Account of the Social and Conceptual Development of Science“. This is an excellent account of how modern systematic biology developed in the 1970s-1980s. Hull describes the major players in the field, how their influences rise and fall over time, and the infighting and squabbling that occurred (the debate between phylogeneticists and cladists is infamously vicious). All in all,  the book is a wonderful example of philosophy/history of science. [FJ: This is indeed a marvellous book, full of scientists being totally human]
c) Preludes by T.S. Eliott, but Evolution by Langdon Smith is probably more appropriate for this blog.
9. Who’s your favourite fictional scientist?
10. What science-y thing did you do yesterday?
My two main achievements yesterday were reviewing a paper, and implementing an XML generator for certain BEAST analyses.
You can find out more about Simon’s research and projects at his (rather beautifully designed) website, which has links to the outstanding Austronesian Basic Vocabulary Database. One of his very cool on-the-side projects is HENRY, The Human Evolution News RelaY.

how to have a mini-sabbatical

Around May, I somehow ended up with a whole glut of projects and publications that were in revision, near completion, in draft, or fully designed and just waiting for words on paper. All that each of them needed were some short chunks of time: a day, two or three, or a week. Concentrated, non-disturbed time.
On Darwin's Sandwalk, 2007
I should say that have the fortune, at this stage of my career, to work at a research institute without class teaching or administrative duties, so one would think that it would be easier to have those blocks of time. But distractions expand to fill the available space, and there’s always another seminar, a conference, an interesting chat with a colleague, a discussion about a potential project, time spent with research group members, and I am nothing if not distractable. Eventually it became clear that I had to get hardcore about it or my CV would have nothing but conference talks* with no ensuing publications.
So – a break was required. I blocked out two periods of three weeks in July and August (this is the first week of the second one), with a week in between to catch up and then have a break (it *is* summer). Our institute is pretty quiet in these months, so there’s much less going on in terms of meetings and commitments anyhow. Three weeks seemed to be an acceptable period of time – enough to get into stuff but not more than the psychological barrier of a month. With no funds available for a retreat in the Alps, I just decided notto be at my desk and took a change of scenery approach. Most of the time I’ve worked from home, or in the public or work library, but I also spent five days in Amsterdam house-sitting.
I did make a commitment to go into the office one day a week, which I did because I felt a bit anxious about total selfish abandonment of my colleagues, especially students and research assistants. But this is probably just an inflated sense of my own indispensability, and this second period I’ll go in tomorrow and then probably only if there’s something vital.
So what did I accomplish in #ProjectReadWrite, as I’ve been calling it on Twitter? The first period I picked the low-hanging fruit, but I:
  • Submitted a paper on population size and language change, coauthored with Tom Currie
  • Submitted a paper on comparative cognition with Daniel HaunGiorgio Vallortigara and Nicky Clayton
  • Did the revisions on a paper (my first single-author publication!) on kin-term evolution
  • Did the revisions on a BBS commentary with my group leader, Michael Dunn
  • Read about 15 papers, variously on marriage transfers, semantic change, coalescent theory, and Pacific prehistory
  • Completed a peer-review (my policy: one-out, one-in. I’m now in arrears)
  • Caught up my backlog of journal-content alerts, dumped them all into Google Reader and now feel on top of the literature (as much as one can!)
  • Thought through the theme for a grant proposal
  • Strategised how to pull a bunch of disparate projects together into just two manuscripts
  • And yesterday – I actually consolidated all of my computer files into an organised and navigatable system.
This next period I hope to finish the revisions on one more manuscript (two if I get reviews back), and write the bulk of another. Extra reading for that has made me think I might need to revisit the analyses as well, but it’s all about pushing things forward (and out!), so I’ll be happy just chugging it along.
I’ll post again on my evaluation of how useful this has been at the end of August.
* I am a sucker for the pleasure of designing a conference presentation.