The Atavism

Carnival of Evolution here next week

2012-01-26T09:30:00.000+13:00

Have you blogged about evolution this month? Are you going to? Then let me know about it, because I'm hosting the next iteration of the Carnival of Evolution (last seen at The EEB and flow).

I don't care if it's a post about population genetics, fossils, phylogeny, the history or philosophy of evolutionary biology, a dispatch from the front of the fight against creationism or a really great cartoon you found or drew -submit anything you've written about evolution in the last month using either the auto-magic form or an email to david.winter[at]gmail.com and check in next week to see what the evolutionary arm of the blogosphere has been up to in January.

Sunday Spinelessness - For Ted

2012-01-22T09:34:00.000+13:00

As I said last week, I've just returned from a bit of a summer holiday. I'm not the sort of person who can do absolutely nothing for any length of time, so I tend to find my relaxation in doing things that I wouldn't have a chance to if I was at home.Like riding a mountain bike. As far as I'm concerned, the best place in Dunedin is the top of Sandymount, an eroded volcanic cone that marks the start of the descent from Highcliff down to Portobello when you ride the Otago peninsular*. I could get all lyrical about the feeling of being away from the rest of the world, or the joy of the moment that you roll from the stiff climb into the fast and flowing descent, but thankfully Brian Tuner has already written a poem about my favourite bike ride:

... I push the gear
down a little and the chain
drops onto a small sprocket
and the wheels start to spin
faster, and the air's
like a quick tongue
in my hair as I descend
swinging in wide curves
around the hill...

Training on the Peninsular

When I spend time at my parent's house in the Wairarapa I leave my road bike behind and borrow my dad's old mountain bike to explore some slower, bumpier rides. That's how I ended up, in the middle of a mid-summer day, struggling my way up a crushed limestone path in a small reserve in Masterton. Bike riding is one of the past times that had to give way when my thesis ate all my spare time, so this really was a struggle. Even riding in the lowest gear I could, I soon gave up on the nice "upright" form that helps a rider spin their way up a hill and instead grovelled my way up, shoulders slumped and head down. And that was a good thing, because with my eyes pointing down I spotted a small creature, seeming to hover just above the ground as it zoomed out across the path, .The creature stopped, turned a few degrees, sprinted down the path a little and stopped again. So I stopped, not, of course, because I needed a break from the hill, but because I've read Ted MacRae's blog long enough to recognise the behaviour playing out in front of me.

If you like bugs and you don't read Ted's blog (Beetle's in the Bush) then you really ought to fix that oversight. He's a great photographer and an immensely knowledgeable entomologist, but the thing that really springs from Ted's posts is a love for natural history. Tiger beetles are one of the bits of natural history that Ted loves the most, and its through his photos and posts that I've been introduced to these wonderfully rapacious critters. Tiger beetles live almost everywhere on earth. New Zealand plays hosts to a small radiation (12 species, all arising in the last 10 million years, Pons et al. 2011, doi: 10.1016/j.ympev.2011.02.013s) and, although they aren't particularly rare, I'd never seen one before this day. So I scooted a little closer, and the beetle (raised up from the ground by slender legs, and not actually hovering above it) sprinted a little further. And so it went: scoot. sprint. scoot, sprint, until I got within a metre or so and the beetle added "fly" to its repertoire and disappeared into the long grass.

I was happy just to have at last seen one of our tigers, but I wanted to get a little closer and even see if I could grab a photo of the skittish creature. So that evening I drove out to the reserve and walked along the paths at the top of the hill, hoping to see another beetle zoom into view. A couple of laps of those tracks yielded nothing. If you want to see something interesting the best bet is stop and let the world happen around for you for a little bit, so I stopped. Before long I was watching native (Lasioglossum) bees investigating nesting sites on the ground and then, out of the corner of me eye: Sprint. Stop. Sprint.

Neocicindela tuberculata is the most widespread of our tiger beetles, and an ecological generalist that copes with disturbed habitats as well as beaches, riverbanks and forests. Like tiger beetles everywhere, they are predators that use their bursts of speed to hunt down smaller insects. The harsh light, the beetle's shininess and my lack of photographic skills didn't combine all that favourably, but I did get a few headshots that let you get an idea of what happens to a prey item once a tiger beetle has caught it:

I'm not sure, but I think the protuberance you can see in these photos may be an ovipositor - an organ used for laying eggs. These beetles lays their eggs in burrows, and the larvae that develop in them are every bit as fearsome looking as the elders. Since it seemed like this beetle might in the process of keeping this population going, I decided I should let her get on her way while I could be satisfied with a beetle I'd long wanted to see marked off my "life list". The only problem with being a invertebrate fancier is that makes it another one down, approximately 10 million to go!

* At least it is if you don't find yourself stuck behind a camper van trundling down the skinny road at 20 kph!

Sunday Spinelessness - 2012

2012-01-15T13:11:00.000+13:00

Alright, it's time to break out from the post-thesis/ Christmas holiday / summertime lethargy that this blog, and its writer, have sunk into and get properly started with 2012.

Following tradition*, I'll start the year with further proof that the lol-fauna of science blogs is entirely more diverse than that of any other corner of the internet. A nymph of the New Zealand praying mantis (Orthodera novaezealandiae or whē) eyeing up the photographer from an anemone leaf in my parents' garden (thanks to Rafael maia (@hylopsar) for the idea).

*Well, it's happened twice now.

Sunday Spinelessness - A rare case of secondary spinelessness

2011-12-18T12:11:00.000+13:00

These Sunday posts are about celebrating the spineless multitude - that under-appreciated majority of animal-life that makes it way around the world without the aid of a backbone. We usualy call thsoe creatures "invertebrates", but that name doesn't apply to an actual taxonomic group. These days, taxonomists generally classify organisms based on their shared evolutionary history. So although having a backbone might been the most obvious factor that groups the species in the sub-phylum Vertebrata together, the reason we place fishes, reptiles, amphibians birds and mammals together is the fact they as a group, they are more closely related to each other than any other animals. In fact, the presence of vertebrae in all these groups is one of the reasons we know they are related to each other - since it's much more likely that the modern species each inherited their backbones from a common ancestor than each coming up with the idea on their own. The "invertebrates" are simply all the animal species that don't fall into the group Veterbrata, by they are not a natural group because some of them (like sea-squirts) are much more closely related to vertebrates that other inverts.

Using the evolutionary history of species as a way to classify them leads to some slightly ill-fitting names. The mammalian order Carnivora includes the Panda (an animal that very rarely eats anything other than bamboo) and snakes are still tetrapods even if that name means "four-footed". As far as I know, there is only one species of vertebrate that lacks a backbone and might therefor sneak in to these posts, the New Zealand endemic Cacaopiscus althaea "or chocolate fish":

Ok. So the entire post up until this point was a setup for a terrible 'joke' (and an excuse to shoehorn some "news" into the Sunday post). For those reading from outside New Zealand, a chocolate fish is a marshmallow (Athaea) filled, chocolate (cacao) covered fish (piscus) shaped confectionery, which has somehow become the standard currency for a small job well done. In that spirit, the doctoral office here at Otago gives everyone that actually makes it to the end of the small task of writing and submitting their PhD thesis a chocolate fish. This is my chocolate fish.

I'd write about my thoughts about the PhD process, the struggles of writing and the inevitable dramas of printing the thing, but I'm not sure my thoughts have caught up with me yet. I'm mainly in the "wandering around the house unsure what to do with myself stage" for now. So if you'll excuse me, I'll get back to that.

(repost) Sunday Spinelessness - The origin and extinction of species

2011-12-11T15:27:00.001+13:00

I'm still experiencing a severe spare-time deficiency down here, so, to stop myself from becoming one of those bloggers, here's something I prepared earlier.

I chose this post to recycle with good reason, I'm thrilled to say that an edited version of this will appear in print in The Open Lab 2012 - a collection of some of the best online science writing from the last year. Do check out the other entries that made it the anthology, and the other excellent posts that didn't quite fit into this years collection.

I don't use these pages to write about my own work very much, partly because it's not yet published and partly because I write about that all day as it is. The shortest answer I can provide to the question "what do you do" is "I use genetic tools to study evolution" and I guess that makes me an evolutionary geneticist. You can split the people that work in our field into two groups: there are biologists that are really interested in a group of organisms and have learned some genetics to help their study of them, and there are people who are interested in a particular question and have chosen their study organisms to suit. I'm very much of the second sort, and like most people in that group I've caught myself saying "I'm interested in the questions, not the animals". Paraphrased, that becomes something like, "Oh sure, I study Pacific land snails, but for all I care they're just little bags of genes that help me answer questions". But that's a lie. You can't work on animals without having them effect you. When I started my PhD I had no particular love of snails, but now I'm a complete snail fan-boy and I frequently find myself preaching on the wonders of life as a terrestrial mollusc to people whose only mistake was to ask me what I do for a living. Did you know most slugs retain the remnants of their shells? Or that almost all snail shells coil to the right? Or that mating in many land snail species only proceeds after one snail has stabbed the other with a "love dart"? A couple of weeks ago I was recounting the the sad tale of The Society Islands partulids to someone I'd met three minutes earlier, and today I'm going to tell you that story (though, of course you have an advantage over the first recipient of the story, since you don't have to read this crap)
Believe it or not, land snails are one of the characteristic animals of Pacific Islands. Anak krakatau is so young it's still smoldering, and it has a native land snail species and Rapa nui (Easter Island), which is arguably the most isolated island in the Pacfic, had its own land snail fauna back when it had forests. It's not entirely clear how these unlikely colonists get to islands. Darwin was so interested in the question* he, ever the experimentalist, stuck snails to ducks' feet to see if they'd survive an inter-island journey. Birds have been shown to carry snails great distances, but wind blown leaves are probably a more common mode of conveyance. We might not know exactly how snails get to islands, but we know what happens once they establish themselves. The land snails of the Pacific include some of the most outrageous explosions of diversity in the biological world. Chief among these evolutionary radiations were the partulid snails of The Society Islands (the French Polynesian archipelago that includes Tahiti). Partulids are very elegant tree snails that form part of the land snail fauna across most of Polynesia, in the Societies they made up most of the land snail fauna. In total, the tiny islands had 58 species of these snails with each of the main islands have their own endemic forms.

A plate from Crampton's monograph on the partulids of Moorea

The Society Islands' land snails were a marvel all by themselves, but they were also an extraordinary resource for scientists. The first person to seriously take up their study was the American embryologist and evolutionary biologist Henry Crampton. Crampton was working at the turn of the 20th century, a time in which the mechanisms underlying genetics and evolution were very much up for debate, and he hoped Tahitian and Moorean partulids could help set the story straight. Crampton's monogrpahs are famous (at least among people that spend thier lives thinking about snails) for their detail. He collected and measured over two hundred thousand shells, then calculated summary statistics for each species, each site and each measurement. By hand. To eight decimal places.

Those massive tables (there are more than 100 pages of them in the Moorean monograph) might seem like an old-fashioned, descriptive, way to do biology. But in many ways Crampton was ahead of his time. For one, he was a Darwinist when not every evolutionist was. By the end of the 19th century Darwin had convinced the world of the fact evolution had happened, but relatively few naturalist bought his theory of how evolutionary change happened. The anti-Darwinian theories that prospered during the so called "eclipse of Darwinism" placed very little importance on the variation within species. The orthogenesists and the lamarckians thought evolution had a driving force, pushing species towards perfection. In their scheme variation within a species was deviance from the mainstream of evolution and was quckly stamped out by natural selection (which they didn't deny, they just said it couldn't be a creative force). Similarly, saltationists thought large-scale evolutionary changes occurred in a single generation, and the small changes you see in populations were of no consequence in the grand scheme of evolution. Crampton realised that, in a Darwinian world, variation within populations was the raw material of evolution. He was obsessive about measuring his shells because he knew could use the data he was recording to understand where species came from. In particular, we was able to show that isolated populations of the same species varied from each other. That finding that makes sense in light of Darwin's theory, since species arise from populations evolving away from each other; but is harder to fit into progressive theories of evolution, in which you'd expect different populations of the same species to follow the same trajectory.
Crampton's results influenced people like Dobzhanky, Mayr and Huxley who helped to re-establish Darwinism as the principal theory of evolution in the Modern Evolutionary Synthesis. But Crampton also predicted arguably the most important development in evolutionary theory since the modern synthesis. In the middle of the 20th century evolutionary genetics was defined by a single debate. The "classical" school held that populations in the wild would have almost no genetic variation, because for every gene there would be one 'best' version and every member of the population would have two copies of that gene. Arguing against the classical school, the "balance" school argued that, quite often, there would be no single best gene and organisms would do better having two different versions of the same gene**. The ballancers thought natural selection would keep lots of different versions of maybe 10% of a species' genes. Both schools assumed natural selection was such a pervasive force that selection would dictate the way populations were made up, they just disagreed on what would result from it. Here's the funny thing, they were both spectacularly wrong. When scientists started being able to measure he genetic diversity of populations in the 1960s it became clear almost every single gene had multiple different versions. Now, in the post-genomic age there is a database with 30 million examples of one sort of genetic variant amongst humans.
Faced with the overwhelming variation he recorded in partulid shells, Crampton had argued natural selection didn't have a damn thing to do with it. Snails isolated from each other by a mountain weren't adapting to their local habitat, they just varied with respect to traits that had no influence on their survival. The fact two populations were isolated meant each would follow its own path and two populations could drift apart from each other. Faced with the overwhelming genetic variation coming from studies in the 1960s Motoo Kimura proposed the neurtral theory of molecualr evolution. Kimura's explanation was the same as Crampton's, almost all of the variation we see at genetic level has no bearing on the success or failure or organisms so the frequency of different variants drifts around at random. The neutral theory is at the heart of a lot of modern evolutionary genetics, and Crampton had understood the underlying principle 50 years before we knew we needed it!
At the end of his monograph on the partulids of Moorea, Crampton said he'd got as far as his measurements could take him, and it was time for someone to study their genetics. In took a bit longer than Crampton might have hoped, but in the 1960s two leading geneticists took up the study of his snails. James Murray from Virginia and Bryan Clarke from Nottingham spent almost 20 years working in what they called, in more than one paper, the perfect "museum and laboratory" in which to study the origin of species. Their work helped scientists understand, among other things, how ecology can contribute the formation of new species and what happens to species when they hybridise with others from time to time. Then, in 1984, Murray and Clarke had to write the most heart-breaking scientific paper I've ever read. It's written in the careful prose scientists use to talk to each other, but the message it delivered was devestating:

In an attempt to control the numbers of the giant African snail, Achatina fulica, which is an agricultural pest, a carnivorous snail, Euglandina rosea; has been introduced into Moorea. It is spreading across the island at the rate of about 1.2 km per year, eliminating the endemic Partula. One species is aiready extinct in the wild ; and extrapolating the rate of spread of Euglandina , it is expected that all the remaining taxa (possibly excepting P. exigua) will be eliminated by 1986-1987.

The bad guys: Euglandina on the left, Achatina on the right.

Euglandina rosea is better known as the Rosy Wolf Snail. It senses the mucous trails of other snails, tracks them down and eats them. It's not clear if the wolf snail had any effect on the pest species it was introduced to control, but it had huge impact on the partulids. By the time Murray and Clarke wrote their paper, E. rosea had already done for one species and it was too well established to control. All they could do was watch as human stupidity and molluscan hunger slowly (1.2 km per year) destroyed the species they'd been studying for 20 years and Crampton had dedicated 50 years of his life to. The same slow torture played itself out in Tahiti and then the rest of the Society Islands. Where there were 58 named species, there are now 5 alive in the wild. Crampton's hundreds of pages of tables should have been the starting point from which the evolution of the partulids could have been tracked. Murray and Clarke's natural laboratory should still be open and be taking advantage of a new generation of technologies that might be able to reveal the genetic and genomic changes that occur when a new species arises. Extinction is a natural part of life, and the fate of all species eventually, but when it's driven by human short-sightedness and robs us of not just a wonderful product of nature but a window through which we might have understood nature's working it's very hard to write about.
I should end by saying there is just a tiny scrap of good news in this story. The partulids are no longer an iconic species in the study of evolution, but they have become the pandas of invertebrate conservation. Murray and Clarke were able to get 15 of the species of the islands and into zoos and labs across the Northern Hemisphere. Breeding programs have been succesful, and new lab-based studies come out form time to time. The relict populations back in the Societies don't have nearly the range they used to, but it appears they've held on to most of their original genetic variation. Perhaps, one day, Eulglandina can be taken care of and some of the partulids can have their islands back.

*Darwin had to be interested in dispersal. Before evolution was widely accepted naturalists thought creatures were created for their habitat (the modern creationist notion of a post-flood diaspora explaining the distribution of animals is almost entirely an invention of Seventh Day Adventists, no, really, it is), Darwin's theory did away with special creation but still needed to explain how life came to live everywhere
** A concept similar to "hybrid vigour", in which crosses between relatively unrelated strains/cultivar bring together different genes and do well as a result. You've seen evidence of this phenomenon any time you've eaten yellow and white "honey and pearl" corn. That corn is a hybrid between a white and yellow cultivar and if you count up the kernals you should get close to the 3:1 ratio Mendel preficts for a dihybrid cross.

Some further reading:
Stephen Jay Gould, who was a snail man himself, wrote and essay on Crampton and the Society Island partulids in which made a humanistic argument for the importance conservation. I resisted the urge to re-read it in researching this piece so anything I stole from him I stole sub-consciously!

Gould, S.J., 1994. Unenchanted evening in Eight Little Piggies: Reflections in Natural History

Crampton's monograph on the Mooeran partulids (from which the figures above are taken) is available online

Crampton, H.E., 1932. Studies on the variation, distribution, and evolution of the genusPartula. The species inhabiting Moorea. Carnegie Institution of Washington, 410, 1335.

Finally, the paper in which Clarke and Murray told the world about the demise of their snails:

Clarke, B., Murray, J. & Johnson, M.S., 1984. The extinction of endemic species by a program of biological control. Pacific Science, 38(2), 97-104.

Sunday Spinelessness - Giant weta are amazing... but not the biggest bugs

2011-12-04T11:31:00.001+13:00

I'm probably as big a cheerleader as you'll find for New Zeland's unique and wonderful invertebrates. So, you'd think I'd be happy to see one of our insects make the pages (or the pixels) of the The Daily Mail, The Sun, Boing Boing, The Huffington Post, The Mirror, The Times of India, io9 and damn near every other blog and newspaper in the world. Instead, I've spend the whole time feeling like the grinch that stole the gloss from the headlines.

The story, as it was presented in the tabloids at least, goes that an American tourist traveled to a remote island of the coast of New Zealand where he spent several days searching for a fabled giant bug before finally uncovering the creature and in the process breaking the record for the largest ever insect.

The only problem with the story is that every single detail of it is wrong. The "American tourist" is, in fact, Mark Moffett, former curator of Ants at the Havard Museum of Comparative Zoology turned explorer and a constant feature in National Geographic and in various other media. Little Barrier Island isn't particularly remote; it's two hours boat ride from Auckland, almost always has scientific and conservation workers living on it and even has electricity provided by a solar panels. The insect in this photograph is certainly endangered, but it's apparently not very hard to find on Little Barrier. Most importantly, there is really no way that the insect chomping down on a carrot in this photograph is the largest insect ever recorded.

The creature in question is a Giant Weta, wetapunga ("god of ugly things") in Māori and Deinacrida heteracantha ("mighty locust with differing spines") in Latin. Here in New Zealand, we give the name "weta" to a large and taxonomically diverse group of cricket-like insects. Most weta are relatively small, not much larger than what you might think of as a standard cricket. Even the small species have a way of freaking people out. Cave weta (called "camel crickets" in other countries that have them) often roost in piles of firewood - I don't know how many logs have been dropped on how many toes as a result of long antennae an spindly legs poking out form an armful of wood. Perhaps even worse, ground weta (like the hibernating one I recently disturbed) seek cool and dark roosts for the day time, so frequently sleep inside shoes, much to the alarm of those owners who blindly poke their toes into them and meet resistance.

People that are scared of the smaller weta probably don't want to contemplate the eleven species of giant weta that make up the genus Deinacrida. The body of these species is about 10 cm long, and they have antennae and legs to add to that (they don't as io9 and several other outlets suggested, have a "wingspan", what, with them being flightless). Although the reporting of Moffett's "discovery" has made a lot about this being the biggest ever giant weta, it's been rather short on actual numbers. In fact, the one number that keeps coming up in reports is 71 grams. That's the current record for the heaviest adult insect, and it belongs to a Little Barrier Island Giant Weta, but there is no way the one in this photo can come close to it. In the wild, once weta have mated they move down from the trees in which they live and deposit their eggs deep into soil via that impressive "spike" they carry on their back-end (which is called an ovipositor). However, if you keep giant weta in captivity, unmated and with no access to soil in which to deposit their eggs, they just accumulate egg after egg after egg. The 71 gram behemoth that holds the current record was a captive female, which was retaining eggs and, so, quite unlike anything that would be crawling around trees on Little Barrier. In the wild females with eggs might be able to maintain a weight close to 40 grams. According to people who know, the female pictured with the carrot here isn't particularly big for the Little Barrier species, so there is no reason to think she approaches the record holder.

I feel a little unpatriotic about this, but I also have to point out that even that 71 gram beast isn't the largest insect in the world. Goliath beetles (from the scarab beetle family) and the titan beetle (a long horn beetle) probably both beat the the local contender on this front. The internet is full of claims of adult goliath beetles weighing up to 100 grams, but this appears to be one of those fact-like-objects that are often repeated but have no basis in reality. David M. Williams, who has tried to get to the bottom of the largest insect problem, thinks it might be a result of the the reasonable metric measure "35 grams" entering an imperial brain as "3.5 oz". In fact, it seems adult goliath beetles probably weight in the order of 30-50 grams - quite likely more than the natural range for giant weta. The titan beetle is longer than the goliath, but it's not clear that these beetles are bulky enough to weigh more than the giant scarabs. What is clear however, is that the larvae of goliath beetles leave weta in the shade. These 13 cm long grubs tip the scales at around 80-100 grams. Scientists have yet to find the larvae of titan beetles, but they may well get even bigger. I struggle to see a good reason to restrict the "largest insect" to only adult forms, so I'm afraid the weta will have to lose that crown.

I really do feel awful about being such a downer on this rare occasion of a New Zealand invertebrate getting some exposure in the worlds's press. I trust the poor reporting that came out of the story can be blamed on the tabloids that broke it and the other sources which ran it without doing any checks, and that it's not a case of someone trying to buy themselves a headline by flying into the country and spotting an insect they knew they'd find. Still, it's shame that the stories have been about the bogus "discovery" of this animal, and the claim that it's a record breaker, because there are plenty of good reasons to talk about giant weta. In many ways, these bugs are a prefect example of the wierdness of biology in New Zealand. Our islands are just isolated enough from the rest of the world that, for the most part, invasions from overseas are rare and the bulk of species that live here live nowhere else. Those species that do establish themselves need to adapt to unique conditions and interactions that come with life on our islands, and the results are often very strange indeed. Where else would you end up with the kakapo, a giant flightless parrot in which the males attract mates with a near sub-sonic "boom" that is broadcast up to 5 kilometers from its origin. Giant weta might not be quite as bizarre as the kakapo, but they are a huge flightless cricket that has adapted to life entirely in the trees - that's pretty cool.

The giant weta exemplify another story that is too common in the New Zealand flora and fauna. The weta and the kakapo seem to have developed in a country that was free from large mammalian predators*, and so never needed to evolve ways to escape or fight off such threats. The introduction of mice, rats, stoats, weasels and possums to our naive ecosystems, and the massive habitat losses that came at the same time, have had a disastrous effect on our natural heritage. At least 60 species of vertebrate have become extinct since human settlement, and many more invertebrates will have past unnoticed. There are about 150 kakpo left, and only a few mainland enclaves and offshore islands play host to giant weta. Most of the other weta species are doing better than the giants, but they are still having to deal with predators for which their evolutionary history provides them no counter-measures. It's easy to look at the recent history of life in New Zealand and feel forlorn - I wish I had the chance to see a pair of Huia feeding or find a half-metre long gecko - but with the weta at least we have a chance to help. The giants need to be managed, and that means we need to make sure the Department of Conservation is funded to the extend that it can live up to its name. The main threat to the smaller weta species, at least in suburban settings, are mice and rats. Providing weta with a few roosting sites that are too slim for a mammal to squeeze into in your garden is enough to stack the odds in the insects' favour. The Department of Conservation even has plans that you can use to bulid your own weta motel. And for those that think wetas are just too creepy to help in this way - I'm sure providing them safe lodgings will keep them out of your shoes!

You should check Mike Bok's great post on the biggest insects here and David Williams chapter on the same, discussed above. I'm not going to link to all the news sources that ran with the silly version of this story, by kudos to Alan Boyle at MSNBC and The New Zealand Herald for digging a bit deeper.

*There are two endemic species of bat, one of which is adatpted to feeding on the ground but probably wouldn't take on an adult giant weta. There is also a 20 million year old fossil species of mammal that was probably more distantly related to modern placental mammals than marsupials are. We know precisely nothing about how this mammal, or its relatives made a living in New Zealand but the one that got fossilised was very small.

Kiwis blogging about evolution

2011-11-29T11:51:00.001+13:00

As any regular readers here may have noticed, my plate is pretty full at the moment. All you are likely to read here for the next little while are quick photo-centric posts about bugs and maybe a few results of my recreational statistics (I know, it's an illness really) on the New Zealand election.

So, if you are looking for some meatier posts about evolutionary biology and the like, you might want to know that there are a couple of other New Zealanders out there writing on these topics.

Paul McBride is a PhD student from AUT who blogs at Still Monkeys. Paul works on understanding how the ecological setting of a group's evolution can effect the patterns and rates of change observed in that group. So far, his evolutionary blogging has mostly been about junk DNA and the ways in which we know many of the sequences in genomes serve no particular purpose.

I particularly liked finding out that Susumu Ohno had provided a theoretical argument as to why most of our genome would prove to be useless way back in the 1970s -just as the first genetic sequences were being read in labs. You can add Ohno's insight to Haldane's estimate of the human mutation rate (before we knew what a gene was made of!) and Nei's use of the theory of segregation load to show that most observed genetic changes must occur without the help of natural selection and start to see the wisdom of the elders of population genetics! (Paul also blogs about beer, which suits me, and reminds me to add a post about the science of brewing to my todo list).

Jarrod Cusens is a Masters student, also at AUT, and he blogs at of trees birds and other things. I gather Jarrod's research is at the hub of evolution and ecology - specifically looking at how to some habitats end up playing host to diverse, species-rich assemblages of organisms while others are dominated by a few species.

Jarrod's recent posts include a look at a couple of schools in New Zealand who have given up the (very good) biology curriculum in favour of biblical creationism (including one, I'm said to say, in my turangawaewae), a profile of one of the birds that make the New Zealand spring, the shinning cuckoo, with a bit more of the cuckoo's special brand of parasitism and a whole bunch of quotes.

So, be sure to add Paul and Jarrod to your favourite feed reader, and if you know of any other kiwis bogging about evolution and ecology let met know in the comments.

How did the pollsters go?

2011-11-28T19:18:00.001+13:00

A couple of weeks ago I wrote a post comparing the various polling companies that work in New Zealand, trying to see if there were any systematic biases in the results each company produces. In that post, it wasn't possible to compare each company's estimates to an external standard because, without an election its impossible to know exactly what the population is thinking. On Saturday night we got to know just what the electorate was thinking, and there were a couple of surprises.

So, here's the last estimate of each polling company compared with the results from Saturday night for each of the four parties that made the 5% cut:

The solid line is the election result for each party. Dashed lines are a 95% margin of error for a poll with 1 000 respondents and the given level of support

As you can see, the polls had National too high and New Zealand First too low more or less across the board. It's hard to say any company did better than the others, Roy Morgan got New Zealand First about right and were the closest to National's final result, but they made up for that by over-estimating the Green Party and under-estimating Labour.

So, why did most of the companies get New Zealand First and National wrong? Of course, it's possible that the polling companies had it right, and that people across the nation changed their minds once they had the orange felt-tip pen in their hands. It could also have something to do with who bothered to turn up on Saturday. In the run up to the election, polling companies generally reported around 15% of the electorate were undecided but about 25% didn't vote. So, some of the people who recorded a preference in a poll didn't bother to have that preference recorded in the election. As far as I know, New Zealand polling companies don't ask any questions to determine how likely a respondent is to vote, and ignoring this information could bias their results.

It's not possible to reconstruct the motivations of those people that didn't show up on Saturday, but we can look at some data at a coarser grain. If people that express a preference for New Zealand First were more likely to vote than the electorate at large (and so, not including a 'likely voter' question in polling would lower their estimate in a poll) then you might expect electorates that really pulled for that party to have higher turnout. It's not perfect, but it's all we've got, and it doesn't really fit the story. National actually had stronger support in electorates with high turnout and there isn't much going on with New Zealand First (I estimate about a 0.8% increase in support votes per 1 000 voters, but that's not near to significantly different from no increase):

Percentage turnout is calculated relative to total enrollment for electorate (special votes not yet included)

By the way, that graph, with such poor turnout in the electorates that with the largest proportion of Labour voters, might be depressing viewing for Labour supporters. Indeed, I'm sure they'll want to work on "getting out the vote" in the Māori electorates and South Auckland, but that pattern doesn't explain the erosion of Labour's support in this election. Turnout was low in these electorates in 2008. Here's the support for each party plotted against change in turnout for each electorate (not including special votes):

Sunday Spinelessness - How long 'till they rise up and kill us all?

2011-11-27T20:08:00.001+13:00

The title contains everything i have to say on this video:

Will early returns accurately predict tonight's outcome?

2011-11-26T15:18:00.001+13:00

It's election day.

I'm sure that later this evening we'll be treated to one of the staples of election night coverage, results from early returns delivered with the qualifier that they are unlikely to represent a reliable estimate of the final result.

Part of that reason for that qualifier is the obvious point that any small sample only provides an uncertain estimate what's going on in the population large. That sampling error can be compounded if there is some bias that makes the early-returning booths pull further left or right than the population at large. In New Zealand at least, you'll often here people say the small polling booths that quickly count and report their results are predominantly from rural areas and, so, favor right wing parties compared with larger, urban booths. (The meme that passes among some right-wing folks, that Labour only won the 2005 election because of South Auckland voters is an example of this narrative).

So, I thought I'd see if there was any evidence for that these stories are right. It's easy to get the data from each of the 6 000 or so polling booths used in the 2008 election and munge it together to see if there is a relationship between how red or blue a booth was and how many people voted there (which is a pretty good proxy for how quickly the results will be reported):

If polling booths were unbiased samples of the electorate (they really aren't...), we'd expect all 99% of the dots in these graphs to fall between those dashed lines.

As you can see, at least in 2008, the common wisdom appears to be wrong: the larger polling booths went more toward National and less toward Labour than the rest of the country.

Tonight's early results will certainly only be an indicator of where things will end up, but things won't necessary get better for left-leaning parties as the night goes on.

UPDATE Thanks for a comment from Luis Apiolaza, who suggests a better way of getting the question. These plots show the percent favouring each major party after each polling booth's data is added in order of how many votes were recorded. As you can see, it takes a long time for Natinoal's vote to approach its final number. I wonder if this is in part be an artifact of many small booths in Maori electorates? Of course, polling booths won't necessarily report in order of how many votes were cast in them.

Sunday Spinelessness - Hover fly

2011-11-20T14:21:00.001+13:00

One of these days I'll use these posts to say something substantive and intersting about the nature of life on earth. Today is not that day. Instead, an old photo of the most common pollinators in New Zealand gardens: Melangyna novaezelandiae, the New Zealand Hover Fly:

Sunday Spinelessness - The 95%

2011-11-13T09:04:00.000+13:00

No the least bit original (1,2), but fun, and entirely featuring critters that have appeared here in the last year or so:

Fans of the spineless may want to join the Octopi wall street movement of Facebook.

Polling bias among local pollsters?

2011-11-09T23:06:00.002+13:00

Lew from Kiwipolitco stumbled across an interesting analysis of Australian pollsters, looking at whether the methods employed by particular polling companies might lead to biases in the numbers they produce . As that post notes, it's impossible to tell whether any particular pollster is showing a bias with respect to the real levels of support for each party, because we only find out what the whole population is thinking when we have an election. We can, however, see if a particular polling company is pulling in a different direction than others. Since I've had about all the thesis-editing I can stand for one day, I decided to see if the data I put together for those charts from this morning could tell us anything about polling bias among New Zealand pollsters.

Obviously, the first step is decide on how to find the "average" number against which all polls should be compared. I went with a local regression which just fits a smoothed line through all the points. From there you can measure how far a single estimate is from the smoothed value at the same date*:

Even if all the companies are perfectly sampling the population, we'd expect estimates from single polls to show a good deal of scatter, just because polls are estimates of the population value and come with uncertainty. Indeed, there are dots all over the place in that graph. By collating all those differences between a point and the smoothed lines for the same date we can see if any of the companies are consistently finding higher or lower estimates of a party's support:

And the answer is... sort of. It seems TV3 tends to get National a little higher and Labour a little lower than the rest of the pollsters, and perhaps the Herald goes the other way. I think trying to gain anything more meaningful than that from these results is probably the statistical equivalent of reading tea leaves, but feel free to stare at the graph and confirm your own political biases!

*You should note, this approach introduces biases of its own and you should take these results with several grains of salt. In particular Roy Morgan polls a lot more often than the other companies, so that company's polling will contribute more towards the smoothed line than others, so it's no surprise they show only small biases.

If you are interested in trends in polling bias, I have these differences plotted over time here. As always, I have the raw data here so let me know if you want a csv file to play with.

Election graphics

2011-11-09T10:08:00.000+13:00

As you may have noticed, there is an election around the corner. I'm not about to subject anyone to my political opinions, but I do have an area interest in which I could probably match the most tribal Labour or National supporter for fervent opinion. Bad graphs. Being able to clearly and succinctly display data is a really important scientific skill, and it's one that some of our newspapers have so far failed to develop. Take this chart, which appeared in the Christchurch Press and is apparently showing the break-down of a recent poll (thanks to John Kerr for pointing this out on Stats Chat)

I have no words. I honestly have no idea why there is a third dimension in this chart, or, really what I'm meant to take from any of it. This was so bad I had to have a go at fixing it.

The point of a political poll is to tell which party, along with its idealogical allies, is likely to win a majority of the seats in parliament. Since we are talking about proportions, and there is a real "something" that those proportions add up to, this a rare case in which a pie chart (or its bastard cousin the torus) might make an effective visualisation. Even so, people are generally better and assessing differences between lengths of objects than their area, so I went with a stacked bar chart.

Of course, even MMP isn't a perfectly proportional electoral system, and, especially with the overhang likely caused by the Māori Party winning more electorate seats that their party votes alone would entitle them to, the break-down of seats in parliament won't exactly match the break-down of the party vote. Here's what would happen if these results were mirrored on election day, and Act, Mana and the Māori Party held their electorate seats while the fine people of Ohariu-Belmont remove Peter Dunne, the Member for the anti-1080 lobby.

In this case, if Act were to lose Epsom the next list seat would go to the Green Party. Of course, you shouldn't use a single poll to say anything very meaningful about what a specific result is likely to be. Polls are estimates of what's going on in the population at large, and estimates always come with uncertainty. We can go some way to quantifying that uncertainty but giving each estimate a "margin of error". Using some slightly twisty logic you can say, "we don't know what the support for the National Party really is, but if it was 52.6 %, as our poll suggests, and we did lots of surveys, each of 1000 people, then 95% of the time we'd get a result between 49.5% and 55.7%". It's hard to include that uncertainty in a stacked bar chart, so here's each estimate from that poll, along with its margin of error (the "2nd seat" line is at 1.2%, the point at which a party with an electorate seat would probably get another on the list, the "govern alone" line is 51.6%, the proportion of party votes required to get 62 seats, a majority in a 123 seat parliament*)

If the fairfax poll was the only thing we had to go on, it might give left-leaning folks (like me) some hope that the true value of the National Party support was less than the "govern alone" threshold. Unfortunately, we have a whole series of polls conducted over the course of the year that suggest National's support is pretty close to the point estimate, and there appears to be little trend across those polls (except perhaps the Green party picking up Labour supporters):

That chart munges all the political polls taken this year together, and fits a smooth line between them. But some polls are probably better than others, it's hard to take a truly representative sample of the country, and it's likely that some of the companies running the polls do a better job. So here's the trend across each polling company:

And you can do the same thing looking at each of the smaller parties.

I'm sure there are lots of ways you could improve these charts (let me know if you think of some), but surely they are all more useful than that awful one from The Press?

*It should be pointed out, these thresholds are really indicative rather than absolute. The real cuts with vary depending on how many votes go to parties that don't make the 5% threshold or win an electorate seat and the size of any overhang

The polling data used here is taken from Wikipedia. Contact me if you want a csv file with the dates in an R-friendly format. The stacked bar charts were done manually in Inkscape and all the other plots were done with ggplot then tweaked in Inkscape.

Sunday Spinelessness - A darkling beetle

2011-11-06T20:11:00.000+13:00

Life continues to be busy down here in Dunedin, so this will have to be another Sunday marked by a quick photo-heavy look into the world of the spineless. I don't pretend to be a great photographer, but I do get a lot of pleasure from recording the small creatures I come across. One of the real joys of bug photography is the way even a rank amateur like me can find something that wasn't obvious at first glance. Take this darkling beetle (tenebrionid) I found the other day. An interesting enough beetle...

...but it wasn't until I'd seen the photos that I notice those neat compound eyes, it's as id I'd found a trilobite

in my garden!

Sunday Spinelessness - Om nom nom nom

2011-10-30T14:36:00.000+13:00

I wasn't very happy with the caterpillar photos last week, so I had another go. Still not quite there, but I think I might end up with a nice shot of these guys before they turn into moths:

Sunday Spinelessness - Spike

2011-10-23T16:06:00.001+13:00

Blogging is going to be slow going around here for a little while, in fact, it may just be limited to photographs of bugs from out back garden. Here's one, the absurdly spiky caterpillar of a magpie moth (taken in the glaring sun, sorry):

I can't tell if this is the endemic species Nyctemera annulata, or its cousin from across the Tasmin sea, N. amica. The latter has established itself in New Zealand, and, since the two species are very closely related and can seemingly interbreed quite happily, it seems we may be witnessing the re-amalgamation of previously seperate evolutionary lineages. The philosophical implications of such a process, and what it means for the definition of species or the goals of conservation biology (did you know DoC shoots pied stilts that pair-off with the endemic black stilt?) will have to wait until I have enough time to say something sensible about them. For now, the caterpillars are pretty cool:

Sunday Spinelessness - a weta

2011-10-16T14:25:00.003+13:00

The ground weta we uncovered in the garden this afternoon, which got sick of its photoshoot and decided to round on the photographer

Sunday Spinelessness - The other monster

2011-10-09T13:15:00.000+13:00

I've never taken a good photo of an ant. I've tried plenty of times, but even when I've happened across queens, whose size should give the point'n'shooter the best chance to capture a passable shot, I've failed. I haven't given up though, and that's why I was spent about 15 minutes of this morning on my hands and knees pointing my camera at the little red, and slightly larger black, ants that patrol the paving stones in front of our house. I failed again, but if you spend 15 minutes contemplating the little creatures that run our world you are pretty much guaranteed to run into something interesting. Today I saw something I've never seen before

A baby harvestman! I've written about harvestmen before, they are spider-relatives which are mainly scavengers rather than hunters and don't have poison-delivering fangs. I don't know if this one is a native or the introduced European harvestman (Phalangium opilio), but New Zealand has a surprisingly large number of native harvestmen (several hundred, and likely more awaiting description) and a suprisingly large number of those are truly weird looking. Arachnids like harvestmen and spiders have two sets of appendeges associated with their head. The chelicerae are use to grasp food and direct it towards their mouths whereas the pedipalps are strangely dual-purpose organs, used almost like an extra set of legs and also to deliver sperm during mating. Earlier this year I ran across a native Palpatores which amazingly giant chelicerae:

Today, while I was lining up the baby harvestman another misshapen harvestmen ran across the paving stones:

This one has considerably shorter legs than than the Palpatores, and when you zoom in on that mouth-gear you can see it's the pedipals and not the chelicerae which are out-sized.

It's not clear why the pedipalps are so spikey. They might help males to fight to fight off challangers and secure mates, but they probably also contribute to these creature's excellent camouflage. The three forward spacing spikes on the carapace place this guy in the genus Aligidia. I took a few more photos before I let him go about his business:

The Nobel Disease

2011-10-08T16:56:00.001+13:00

Bruce A. Beutler, Jules A. Hoffmann, Saul Perlmutter, Brian Schmidt, Adam Riess, Ralph M. Steinman and Dan Shechtman. Seven new Nobel Laureates and seven new names to include in the most exclusive club in science.

The Nobel prize comes with a trip to Stockholm, a gold medal and a share of million dollar prize. But perhaps even more than that, it provides a cachet that extends beyond the world of science and into the every day. Nobel lauretes are recognized as the best of the best: people whose intellectual achievements have changed the way we think of the world. The gravitas we attach to people who can put 'Nobel Prize winning scientist' in front of their name means their opinions are afforded special status. Indeed, listening to people who ought to know what they're talking about is a pretty good way to learn about the world. But a Nobel Prize doesn't represent a barrier to sloppy thinking. In fact, if anything there seems to be tendency for acknowledgement of expertise in one area to provide an unfounded confidence to speak out on other subjects. Some laureates have fallen for the most appalling anit-scientific rubbish. So much so, the term "Nobel Prize Syndrome" or "Nobel Disease" has been coined to describe this phenomenom. So, without wishing to take any of the gloss of this year's Nobelists, here is a list of some of those that were brought low by the Nobel Disease.

Linus Pauling (Chemistry and Peace, Vitamin C fanatic)

Surely the saddest case. Pauling was a supreme scientist, one of the first chemists to get serious about using the tools of physical chemistry to understand the basis of biology. His most famous contribution was pioneering methods that use what we know about the nature of chemical bonds to find the structure of biological chemicals. Evolutionary biologists like me remember him as the guy the first proposed that we could use the rate of change in chemical structures to measure evolutionary time between species. He's also the only person to have won a ~~real~~ science Nobel and the Nobel Peace Prize - the latter coming for his activism for nuclear nonproliferation.

Then there was the vitamin C business. Pauling became convinced that high doses of vitamin C would cure.. well, amost everything. The initial results of Pauling's research were promising, but it soon became clear they wouldn't hold up to more rigourous tests. It seems Pauling's belief was stronger than any evidence, and he doubled down, advoacting high does of vitamin C in popular and scientific works. Today it's almost impossible to talk to an advocate of these cures without having Pauling's name thrown add you.

Kary Mullis (Chemistry, HIV denialist)

If Pauling is the saddest case of the Nobel Disease, Kary Mulllis might just be the oddest. Mullis is credited with inventing the Polymerase Chain Reaction (PCR) - a method used hundreds of thousands of times every day in molecular biology labs around the world to amplify small, specific regions of DNA. I can't even imagine how you'd do genetics without PCR, so his achievement is certainly worth the prize. But he is seriously strange. When people talk about Mullis' personality, they emphasise his use of LSD and his love of surfing and motorbikes. I guess that's quirky, but science takes all sorts and none of those would make him unique among Nobel Laureates. However, I'm not sure there has ever been an acceptance speech quite like his. Before Mullis embarked on his career in biochemistry he had a go at being a novelist, and his speech reflected this:

And now as December threatened Christmas, Jennifer, that crazy, wonderful woman chemist, had dramatically left our house, the lab, headed to New York and her mother, for reasons that seemed to have everything to do with me but which I couldn't fathom. I was beginning to learn tragedy. It differs a great deal from pathos, which you can learn from books. Tragedy is personal. It would add strength to my character and depth someday to my writing. Just right then, I would have preferred a warm friend to cook with. Hold the tragedy lessons. December is a rotten month to be studying your love life from a distance.

So, I don't think much of his writing, but he won a Nobel Prize and I'm some guy writing a blog - so it's hard for me to pick on him for that. Sadly, he's done much worse. In his autobiography he claimed the theories of Ozone depletion and climate change were the result of a conspiracy between scientists and government organisations seeking to continue their funding. Even worse, he is an HIV denialist. Mullis has never done any scientific research on HIV or AIDs, but PCR is, on rare occasions, used to diagnose HIV. You can imagine the mileage that those strange people that deny the link between HIV and AIDS get from being able to say "the inventor of the PCR test doesn't even believe it!"Mullis has gone to say anti-retrovirals don't work and agree that AIDS isn't a disease that people who lead "normal, American lifestyles" run much of a risk of developing.

Also there is something is his book about being visited by a fluorescent alien raccoon.

William Shockley (Physics, Eugenicist)

Shockley invented the transistor and thus, changed the world. Apparently, he wasn't happy with one revolution and wanted to change the word again, this time by creating a brighter future through genetics. Shockley was one of those people that think Idiocracy is a documentary, and that letting people make their own reproductive decissions will inevitably lead to a genetic meltdown for society. Almost all of the reasoning that goes into these eugenic panics is flawed, but Shockley really went a long way out on a short branch. His argument amounted to "Black Americans have a lower average IQ than whites, this is a result of genetic differences, therefore environmental interventions won't alleviate these problems". Shockely was no inhibited by an understanding of genetics at any step of the reasoning that took from his poor data to his odious proposals.

Among other things, Shockley's argued those with an IQ under 100 should be paid to be sterilised, and he provided samples to the wonderfully named "Repository for Germinal Choice" (dubbed the Nobel Prize sperm bank in the media") in the hope his sperm would make the world a better place.

Brian Josephson (Physics, Parapsychologist)

Josephson won his Nobel Prize for his PhD work on superconductivity. Having been awarded the prize while he was still a Reader at Cambridge (and academic rank equivalent to Associate Professor in many other countries) he can now pretty much do what he wants with his life. And what he mainly wants to do is explore the stange and wonderful world of "quantum mysticism" including ideas like telepathy and precognition. I don't really know what else to say about Josephson, except read his webpage and find out for yourself.

Luc Montagnier (Medicine, Homoeopathy supporter)

Montagnier is one of the people credited with discovering HIV which, Mullis and his crew notwhistanding, has been shown to the causative agent of AIDs. A huge discovery, and one that set the basis for working on treating or even curing that disease.

Then, in 2009, Montagnier set up his own journal, and published two papers that purported to show electromagnetic signals could be recorded in water that had once had DNA in it, but had subsequently been diluted such that none could remain. That would be a truly earth shattering result, as it would change pretty much everything we know about chemistry. That would be good news for homoeopaths, because, in order for their cures to work almost everything we know about chemistry would have to change. Indeed homeopaths jumped on Montagnier's work as evidence for their quackery.

Of course, the papers are rubbish. PZ Myers goes into the details, but my favourite warning sing is that one paper went from submission to re-submission to acceptance in three days. The most earth shattering result in chemistry: read, reviewed, commented on, edited, resubmitted and accepted in three days; in Montagnier's own journal; where he is the chief editor. Of course, none of that, or the fact the even the most sympathetic and credulous reading of Montagnier's papers actually supports homoeopathy as it is practised will stop him being cited by homoeopaths at every chance.

Niko Tinbergen (Medicine, supported "Refigerator Mother" theory)

The Dutch ethologist gets special mention as showing the most rapid onset of Nobel Disease. Tinbergen used his acceptence lecture to advocate for the "Refigirator mother" theory of schizophrenia and autism - an unfounded theory that led to thousands of mothers (never, it seems, fathers) being told their children's illness were a result of their poor parenting.

Sunday Spinelessness - For aussie beetles, beer bottles are an evolutionary trap

2011-10-02T17:25:00.000+13:00

It's Nobel season. Over the next month or so, we'll hear who has received a telegram summoning them to Stockholm and to fame and fortune (the cash part of the prize is worth about 1.5 million dollars). Of course, the Nobels are a big deal. Prizes are given to recognise people who have fundamentally changed the way we think about the world or the way science works. So it's nice that in the week before we start thinking about those huge sicentific acheievements we have the Ig Nobel prizes to remind us that most science is small, and sometimes it's even prettty funny. The Ig Nobels were set up to honour science that "first makes people laugh, then makes them think". This year's winner were announced on Friday and prizes went to researchers who trained a tortoise to yawn on command so they they could find out if yawning was contagious among these animals (it's not), a Japanese team who developed an alarm clock that wakes you up by spraying a fine mist of wasabi across the room and a team who finally provided an answer to that age-old question - "why do discus throwers get dizzy while hammer throwers don't?" (here's that answer). But perhaps the award that's done the most to make people laugh is the one presented to Darryl Gwynne and David Rentz in recognition of their studies into male Australian beetles that would rather mate with beer bottles than their female counterparts.

The beetles in question are Julodimorpha saundersi, a member of the jewel beetles (Buprestidae) and native to desert habitats in Australia:

J. saundersi. Thanks to Jean Hort for sharing this photo as CC2.0

Mating season has probably just finished for these beetles. Adults emerge around August and for next couple of months male J. saundersifly about the place looking for females, which are larger than the males and flightless. So, for millions of years male J. saundersihave spend their springtime looking down hoping to find large (because large females produce more eggs) shiny, amber coloured surfaces covered in dimples like those on the beetles back. And for millions of years I'm sure that worked fine. Then someone invented beer bottles, and because some people suck, beer bottles starting turning up on roadsides in the Australian desert. Apparently, some Australian stubbies* have a series of dimples across the bottom. When a J. saundersimale sees one of these bottles he presumes he's won the reproductive jackpot and found the biggest, most amber, most dimpled female to ever live and... well.. you can see what happens next for yourself:

Image © Darryl Gwynne

Gwyne and Rentz found that they could attract males just by putting beer bottles out, in 30 minutes of observation that managed to lure two of them. Sadly for J. saundersi, this battle with the bottle can have devastating effects. Gwynne observed a beetle being attacked by ants "which were biting at the soft portions of his everted genitalia" and another dead one being eaten by ants.
I have to admit, the idea of a beetle so madly fixated on a beer bottle that it will give its life in the hope of mating with it is so ridiculous as to be funny. So I'm laughing, but is there anything in this research that fulfills the Ig Nobel's other criterion and makes us think? Well, I'm not sure you and I are so different from a beetle with a pathological sexual attraction to discarded beer bottles.

J. saundersi males had a perfectly sensible approach to finding partners that only broke down when a sudden change in the environment made last generation's strategy look stupid. Any species can fall into that trap because natural selection, the process that makes organisms fit their environment, has no foresight. All that selection can do is adapt the next generation to the last habitat. Usually that's fine, but lately habitats have been changing quickly. The rapid technological change of the last few thousand years has left humans in a few evolutionary traps of our own. The most commonly cited example is about food. Until recently, foods rich in fat and sugar were pretty hard to come by. Since these foods are important for regular running of our body, we have evolved brains that reward us when we eat them. Today, our brains no longer match our environment. In most western societies fatty and sugary meals are about 10 minutes drive away and, perhaps not surprisingly, the developed world is dealing with a epidemics of obesity and type 2 diabetes.

I think there is an even more important example of this phenomenon for people that aim to live a skeptical life - our brains developed in a world quite different than the one we live in. The share volume of cognitive biases that psychologists have identified reveal how our intuitions can stray from reality. Not all of those biases arise from a mismatch between our brain and our environment. Brains aren't truth finding machines, because knowing something is true doesn't, in and of itself, provide any survival advantage. But some of these mistaken intuitions really do seem to arise from our evolutionary history. Most of the people that have ever lived have done so in bands of about 50 people. Every piece of news they ever learned about the world came through those people, and maybe a few interactions with other groups. Today, I can open a new browser tab and read one of 50 million twitter streams; or watch, read and hear news from almost anywhere on the planet. But I have still have my brain, which mainly evolved to deal with news from about 50 people, so part of me is amazed when I hear someone won the lottery three times, or someone else has given birth to three children in three different years but each at 7:43. Of course, in a world of 6.7 billion people these things have to happen, but, as much as I know that, it's hard to convince my brain these aren't amazing events.

I said this fact problem matters for skeptical types, and, indeed, our faulty intuitions can have effects at least as bad as those faced by the amorous beetles that precipitated this post. If you live in a world with 50 contacts, and one of them tells you they got sick after eating a specific sort of food, that's pretty good evidence that you should avoid that food. If you live in a world with billions of potential contacts, and one of them tells you that someone, somewhere got sick after receiving a vaccination or got better after taking a homeopathic remedy that's not evidence for anything. Just like the triple lotto winners, in a world where millions of doses of vaccine given out, someone will get sick after a vaccine whether it causes an illness or not. Thankfully, we've developed methods that help us, as much as possible, to remove our intuitions from the way we handle evidence. Together, we call those methods science and it's crucial that those methods are the heart of the way our societies develop if we are going to avoid our own evolutionary traps

So, by all means laugh at J. saundersiand his futile, fatal attempts to impregnate a glass bottle, but do try an be aware that similar traps are lurking in our own brains.

Gwynne, D. & Rentz, D. 1983 Beetles on the bottle: male buprestids mistake stubbies for females (Coleoptera). Australian Journal of Entomology, 22, p.79-80. doi: 10.1111/j.1440-6055.1983.tb01846.x

*For people outside Australiasia, a stubby is a short brown 330 mL bottle which usually contains the caramel fizz that gets called "ale" or "draught" beer down here, but is, in fact, a lager.

Thanks to Ted, the blogo-sphere's foremost beetle taxonomist for pointing out this species is not called J. saundersi, as it has been shown to be distinct from J. bakewilli the name this population bore when the paper was written

Sunday Spinelessness - How chitons are tougher than stone

2011-09-25T18:06:00.003+13:00

No time to say anything meaningful today, so here's a pretty picture of a green chiton (Chiton glaucus)

Of course, I wouldn't be a self-respecting invertebrate evangelist if I didn't try an convince you that chitons represent more than a pretty shell and a stern test for junior rock-pool hunters' ability to prize creatures from rocks. Apart from all that armour, the most interesting think about chitons is their teeth. Like most molluscs they feed with a rasp like organ called the radula, unlike most other molluscs their radulae are coated in an iron-containing mineral called magnetite. As the name suggests, magnetite is a mineral that can become magnetised (in fact, of all naturally occurring minerals its the most magnetisable) but that's not why chitons make cover their teeth in it. In order to eat, chitons need incredibly abrasive teeth that can scour away at rocks and expose algae, and that means the teeth need to be coated in a tough material.

"Normal", geologically produced magnetite is pretty tough, but, remarkably, the magnetitie that chitons produce to coat their teeth is much tougher despite being made from the same molecules. The chiton's biochemical toolkit is able to produce magnetite in which the three dimensional structure is tweaked towards a tougher end result. Professor Kate McGrath from the MacDiarmid Institute spoke about this 'biomineralisation' process as part of her contribution to the Royal Society's Marie Curie Lecture Series. Her research doesn't aim to mimic the specific ways in which organisms create chemicals, so much as learn the various tricks that evolution has discovered and see how they might be applied to either tweak or completely chain the way we make useful minerals on industrial scales.

Sunday Spinelessness - Speciation by magic

2011-09-18T21:48:00.000+12:00

For someone that writes about evolution, I don't spend much of my time talking about the 'debate' that surrounds that topic. That's probably an artifact of living in a county that doesn't allow people who are so confused about the world that they think the bible is a biology textbook to acquire any political power. But it's also because debating whether evolution happened, a fact that no serious biologists has debated since Darwin's generation and is further confirmed with each new DNA sequence, is so utterly and spectacularly boring when you compare it with some of the real debates with evolutionary biology. So here's a little something on one debate, and the land snail shells that help swing it a little towards one side.

Some of the most contentious debates within evolutionary biology are to do with how new species arise (a process we call speciation). For instance, it's not clear how much ecology* matters when it comes to speciation. Some authors argue that speciation and ecological adaptation are usually seperate processes - the second making species distinct only after speciation has separated them. Others argue that ecological adaptation can itself be an important part of the speciation process and maybe even be enough to drive species apart.

Like many ideas in evolution, this debate goes back to Darwin's time. People who really ought to know better will sometimes tell you that, despite its name, The Origin of Species doesn't have a theory of speciation. You should tell those people to read Chapter 4. Darwin did have a theory of speciation, and it explicitly placed ecological competition between newly formed species as the key to driving species apart from each other. We've learned a few things about biology since Darwin's time, and it turns out his verbal arguments don't hold up to mathematically rigorous models of the ones genes work in populations. Natural selection can't push a population apart more quickly than genetic recombination (the mixing of genes that happens in each generation) pulls it back together. So, species can't arise soley from selection. In fact, the modern conception of speciation revolves around the flow of genes between populations. If a population isn't sharing genes with others it's free to evolve independantly and take on the properties that make species distinct.

Although people have talking about gene flow with regard to speciation since Darwin's time, Ernst Mayr is probably the person most associated with establishing this idea among evolutionary biologists. Mayr took the importance of 'reproductive isolation' to its logical extremes - arguing lack of gene flow was not just a pattern that created species but actually the definition of a species (I disagree) and that speciation almost exclusively occured because of geographical barriers that keep populations apart from each other (leaving no room for selection).

But the gene-flow conception of speciation still leaves a tiny bit of room for selection as a driver of speciation. For instance, imagine a trait that could, at once, be subject to ecological competition and prevent gene flow between members that don't share the trait. Then selection would be acting to keep diverging species away form each other at the same time as adapting them to their habitat. Sergey Gavrilets, a theoretical evolutioanry biologist, called models of speciation that rely on these sort of quirks "magic trait" models, partly to represent some scepticsm that such traits could exist in the wild. But empiricists have known for a long time that these sorts of traits really are out there. For instance, many plant eating insects only mate on their host-plant. So, if two diverging species are adapting to particular hosts plants, that same adaptation process will be preventing them from mating with each other. Other examples of these magic traits include body size in fish, beak size in birds, wing colouration in butterflies and, now, shell characters in land snails.

Snails can be left- or right-handed. Or, at least, the sprial of a snail's shell can turn clockwise (making a right-handed or dextral spiral) or anti-clockwise (a left-handed or sinistral spiral) and the direction of spiraling is decided by a single gene (inherited from the mother, suggesting in may be an imprinted gene as snail's don't have sex chromosomes) . Most species are predominately right-handed and very few individuals within a species don't match the predominant spiraling direction (I only know of one exception to this rule). In fact, I've spent more time than most people looking at snails, and I've never seen a left-handed one (trust me, I check!). There's a very good reason one individuals within one species are predominately of one spiraling direction - left-handed land snails have great trouble mating with right-handed ones. Land snails are all hermaphrodites and they mate by lining up extending their gentals through a pore on the 'spiral side' of their body (if you aren't invert-phobic, there are plenty of photographs of this process here). But mirror-image snails, espacially those with relatively flat shells, struggle to line up in this way, and when they do their shells bump into each other. For this reason, 'mirror' snails (which do arise in populations all the time) struggle to reproduce and leave few descendants.

The direction in which a snail's shell coils also has ecological implications. Animals that specialise in eating snails have adapted to attacking right-handed shells. So, for instance, Pareas snakes always attack from the left and have lopsided jaws that help them work the snail out of the shell:

As you might imagine, these adaptations mean the snakes are less able to attack left-handed snails. If death by snake is a big risk in a snail population, then left-handed snails, while still having a hard time when it comes to mating, will be at a distinct ecological advantage. So the direction of snail's coil could be subject to ecological selection, and it definitely presents a potential barrier to gene flow. But to be a magic trait it needs to be doing both of these things at the same time.

The Japanese land snail genus Satsuma provides a natural experiment to test this idea. Satsuma snails come in left- and right-handed forms and some populations share their homes with the snake eating Pareas iwasakii snakes. Masaki Hoso and his colleagues (Hoso et al 2010, http://dx.doi.org/10.1038/ncomms1133) looked at the distribution of left- and right-handed Satsuma species and their relationships with each other.

From this data they concluded that sinistral Satsuma species have evolved multiple times and almost always in regions that are currently home to snail-eating snakes. So shell shape really does seem like a magic trait here - left handed shells get an ecological advantage that allows them to survive and it also prevents them from sharing genes with right handed snails.

So Satsuma snails are another example of magic traits in the wild. But I think they are an opportunity to understand a bit more about speciation. The hardest thing about studying speciation is separating the differences that cause speciation with those that arise once species stop sharing genes. In the case of Satsuma we know a change one gene caused speciation so any other traits that differentiate left- and right-handed snails living along side each other happened after the fact. The number of left-right species pairs, and the different ages of the lineages they represent gives us a unique chance to understand the how interactions between newly formed species shape their futures.

Surely that's infinitely more interesting that another round of the evolution-creation controversy?

You should also check odd Ed Yong's take on this study, which is predictably excellent.

*I'm sorry to do this, because I don't want to be one of tiresome people who complain about the way language changes, but the science of ecology is something quite different from what's fast becoming the modern definition of the word. Ecology is the study of the way organisms interact with each other and their environment and (as far as I can tell) mainly involves counting a lot of things then doing some clever statistics on the resulting numbers. It's not (directly) about conservation or sustainability and it's certainly not an idea invented by advertisers who worked out adding 'eco-' to a products name and putting it in a plain box allowed them to sell it at twice the price.

Sunday Spinelessness - Visualising fungal communities

2011-09-11T18:22:00.001+12:00

If you read the Sunday post last week you'll remember that I started a little "when my brains are completely destroyed by thesis wrangling and I need a break" project, and that I'm the sort of person that takes a break from one science project by playing around with another science project. That's just how sad I am. Anyway, last I week i set out to use existing records in GenBank to compare the diversity of fungal species living on the roots of various species of tree in New Zealand. And I failed. I only managed to find records for one species, silver beech, so all I could really say was that there seemed to be a lot of different fungal species on this tree.

Inevitably, I found myself needing a break from thinking about my snails this week, so had another crack at comparing fungal diversity by host. In particular, I've filtered through hundreds of records of fungi collected from New Zealand to isolate those collected from natural southern beech (Nothofagus) forests or plantation pine forests. The mycorrhizal fungi I talked about last week are generally considered to be highly host-specific and unable to form relationships with off-host species. If that's true we should be able to see that the community of fungi recorded for each forest type is quite distinct. But how can we see that phenomenon? Last week I used a graph of the frequency of different taxonomic families to show how diverse the community living on silver beech was, but taxonomic ranks above species don't represent anything real about biology or biodiversity. I have argued species are natural units of biodiversity (even if we can struggle mightily to identify those units), but most of the sequences I've found aren't annotated down to this level (in fact, most probably represent undescribed species). So, I gave up on a 'unit of biodiversity' and instead only included sequences for a particular gene loved by fungal geneticists called the Internal Transcribed Spacer. Using just these sequences, I can make a phylogenetic tree, which attempts to relate DNA sequences to each other based on their similarity.

So here's the tree, drawn as a big circle. Each tip represents a single DNA sequence and is shaded according to the forest it comes from - brown for pine, green for beech. As you can see, the pine and the beech forests have very different fungal communities. There are whole swathes of the tree that are unique to to beech forests (although, of course, that could be an artifact of the effort to which people have sampled) and whenever you see a brown branch within a predominantly green section of the tree, that branch is substantially distinct from its beech-living relatives. (click on the image to be taken to an interactive version, where you can add information on host species or change the shape of the tree):

So that's fun. There's still a lot more that could be done with the data set. I haven't included much data about the fungi themselves - it would be interesting, for instance, to see if the fungi living in the roots of trees showed more or less specificity than the those living elsewhere. It might also be possible to use these sequences to estimate the number of species they represent using some of the new-fangled species delmitation methods the DNA Barcorders have come up with. There are also other natural forest types in New Zealand that might be interesting to include. Both Manuka and Kanuka rely have mycorrhizal fungi and including those species might help us to understand if the differences displayed above are about natural v plantation forests or about host-specificity in the fungal species.

I didn't include any code snippets today, because I've set up a github repository as an 'open record book' instead. If you're interested in the process or the code that went into this you can check it out there (though I should warn you, there's nothing very clever going on).

Sunday Spinelessness - An online fungal foray

2011-09-04T09:15:00.007+12:00

One of my goals with these Sunday posts is to do a little to broaden the understanding of just how extraordinarily diverse the biological world is. In almost two years of writing about spineless creatures I've limited myself to animals, which, as amazing as we are, only comprise one twig in the tree of life. You can call that an institutional bias, since I'm from a Zoology Department (there are few that haven't yet been swallowed by Schools of Life Sciences) and maybe it's a necessary step to narrow the field of targets a little bit. But this is my blog, and my series, and today I want to write about fungi.

In fact, fungi are a prefect example of the gap between our everyday experience of the biological world and what's really out there. Most of us only notice fungi when mushrooms start popping up in the autumn or when the fruit we bought, and were definitely going to eat this time, starts turning furry. In fact, there might be something like one and a half million species of fungi on earth; there are deep-sea fungi, forest fungi and freshwater fungi; there are fungi that live on tree roots and others that live on human skin; there are even mind-controlling fungi that hijack the nervous system of certain ant species for their own gain:

Some fungi play important roles in ecosystems, and probably the most important of all are a taxonomically diverse group that livr in or on the roots of plants. These so called 'mycorrhizal' fungi greatly increase their host's ability to take up and process nutrients and water from the soil, while the fungi can take advantage of the plant's ability to create sugars from carbon dioxide and sunlight. Between 80 and 90 per cent of plant species can form relationships with mycorrhizal fungi (Wang and Qui 2006 doi: 10.1007/s00572-005-0033-6) and, as you might imagine, the presence or absence of mycorrhiza can have a big impact on the health of individuals plants, crops and forests.

On Wednesday, I heard David Orlovich (@davidorlovich) speak about mycorrhiza in southern beech (Nothafagus) forests in New Zealand. Beech forests form a major part of New Zealand's natural heritage, and some our most important conservation sites (Westland, Fiordland...) are covered almost exclusively by beech species. Without mycorrhizal fungi there would be no Southern Beech: seedlings raised in sterile soil simply fail to develop. David went as far as to say that we should see beech trees as giant antennae that fungi used to fix carbon from the atmosphere. I'm not sure I'd follow him quite that far, but his talk on using DNA sequences to quantify the number of fungal species associated with local silver beech forests and the the specificity of fungal species was really interesting.

It also got me thinking about a blog post by Rod Page (@rdmpage) in which he shows how we can take advantage of data that is stored in The Big DNA Database (called GenBank) but goes almost unused. Every record in GenBank has certain information attached to the DNA sequence in describes (the source of the sample, the name of the gene, a scientific paper the sequence is attached to) but the information in a given record is not limited to the required fields - researchers can add any pertinent information they want to. Researchers in biodiversity and related fields often wring their hands about the lack of any infrastructure to hold data collected on various species and taxonomic groups, but, as Rod has pointed out in the past, existing databases (and wikipedia) already contain considerably more information than we're taking advantage off.

So, when I decided I needed a break from thinking about snails this Friday night, I set out to see if there was enough information about fungal hosts in GenBank for us to start examining the fungal diversity of New Zealand forests*. You could make a start at that project using the pointy-clicky web-interface but I decided to use Biopython (a library for the Python programming language), because writing code for a project is really the best way to document what you're doing , helps make you research reproducible and allows you to pick up a project where you left it. So, the first step was finding records that corresponded to sequences from mycorrhizal fungi in New Zealand. As far as I can tell you can't search within particular submitter-defined features of a file, so here's how I did the search with Biopython's Entrez.esearch() function.

The 'ids' object collected form that search is a list of unique identifiers for sequence records that matched our search, so let's get all of those records in a sequence file and use SeqIO from Biopython to deal with them

Now the heavy lifting! We need to get the host information from each record which means looping through a bunch of attributes in the Biopython object representing that record. We want to store the data as a "one to many" relationship, since each host species might have multiple fungal species associated with it. There are couple of different ways of doing that, but I used python's very cool "defaultdict" dictionary which can create a list for each host and add new information to that list when it encounters the host.

And this is where everything went wrong. Well not quite, the search term I used found 84 records, but they were all for fungi collected from silver beech (Nothofagus menziesii) trees. So much for comparing diversity between hosts! Still, those 84 records give us a change to estimate the taxonomic diversity of fungi associated with this tree, so lets count up all the unique taxonomic names among these records:

And (dropping python for R and ggplot2) a graph (click for a larger version):

I'm not finished with this little project, I have some ideas to widen the net for fungal species next time I get really sick of snails, but even this little exercise shows some interesting things. First, silver beech have lots of fungi on their roots, and they come from lots fo different groups! It would be fascinating to know if the fungal families represented above were playing different roles in the root-tip, or if each was competing with others. Or how that make-up of the fungal biota attached to a given tree or a given forests effects its health. More importantly, GenBank is potentially a really useful way for researchers to share more than just sequence data. If people working on mycorrhizal fungi decided on a de facto standard for the way they annotated their GenBank submissions then data from hundreds of published (and unpublished) studies could be almost effortlessly combined to create a big picture of the dynamics of these important fungi. Even as it is now, there is a source of data that is almost never used by researchers or people building the various "encyclopedia of life" projects, and it doesn't take too much tinkering to see how it could be put to use.

*Yes, I'm the sort of person who takes a break from science by doing some other science. On a Friday night. What of it?

Sunday Spinelessness - Little creatures that make a world

2011-08-28T21:58:00.003+12:00

E.O. Wilson once described insects as "the little creatures that run the world". Wilson was presumably referring to the huge amounts of energy and mass that pass through insect bodies in terrestial ecosystems. There are, slightly puzzlingly, almost no insects in the sea but invertebrates still run marine ecosystems. In fact, invertebrates even create habitats in what would otherwise be unproductive waters.

We tend to think of the tropics as areas of great biological diversity - that's true for the land but less so in the ocean. The beautiful clear waters you see in tropical seas indicate a lack of nutrients and a corresponding lack of plankton. Without plankton, the normal marine food webs don't develop and, as a result, tropical seas are generally not very productive. But if you've been snorkling around a tropical island you'll know coral reefs are explosions of biolgical diversity. That's all because some coral animals can take advantage of the marginal conditions in tropical waters. These corals supplement the meager pickings that can filter from the water with energy trapped by a type of photosynthetic protozoa called zooxanthellae. In time these corals, with their protozoan helpers, can put down acres of calcium carbonate and create food and habitat for more and more animals. When those animals are anenomes, they can themselves form habitat for another animal. Like this anemone fish (or, as most people call them, NEMOS!!!) filmed earleir this year at Hideaway Island in Efate, Vanuatu:

Sunday Spinelessness - Sluglett

2011-08-21T21:36:00.003+12:00

I spend quite a lot of my time trying to convince people that very few snails or slugs are interested in eating their lettuces. But it has to be said, there are a few terrestrial gastropods that are serious pests. In New Zealand, those are all introduced species and the "grey field slug", Deroceras reticulatum, is the one we run into most often. These slugs can destroy freshly planted vege gardens, they're a major pest for commercial growers and they can force out native species in disturbed forests. So, they're unquestionably bad news. But the baby one I found in the cauliflower today was quite cute:

Sunday Spinelessness - A Sunday Spiral

2011-08-14T20:56:00.003+12:00

I had planned to write about snail shells today. Specifically, about how chance mutations that change the direction of a shell's spiral might be enough to create a new species. I guess that story will have to wait another week, today I'll just share (what I think is) a particularly beautiful spiraled shell I found recently.

I'm not sure what species of snail once lived in this shell. I found this one, and 20 or 30 more, under logs and in leaf litter in the the fuchsia-dominated remnant forest (yes, in New Zealand fuchsia comes in tree-form) in Fraser's Gully. There's a clue to the taxonomic placement of the animal that used to inhabit the shell on the flip-side.

The hollow cone shape that forms at the bottom of some snail shells is called an 'umbilicus', and it's a taxonomically informative character. In the New Zealand land snail fauna, the family Charopidae is assoicated with large open umbilcuses like this one. There are charopids that have closed shells, and there are snails from other families that have this sort of open umbilcus - so its presence isn't the final word, but it's something to go on and I'll have to do a bit of sleuthing at some stage and see if I can work out what these snails are.

Whatever their placement, I was taken by these shells because of their lovely pattern. Something I more or less failed to capture in the obligatory front-on shot of the shell (sorry, I don't even have time to photoshop the blue-tac out today!):

Sunday Spinelessness - A visit form a queen

2011-08-07T20:09:00.003+12:00

You can tell from the increasingly brief nature of these posts, that I have quite a lot on at the moment. Between trying to polish off these thesis chapters, finish edits to paper I contributed a little bit do and teaching my very first lecture last week I've been a little busy. I do have time to share a couple of photos I took to record the visit of queen bumblebee.

It's really not bumblebee season in Dunedin, so I was quite surprised to hear that familiar baritone buzz in my kitchen a couple of weeks ago. In temperate climates like Dunedin's, bumblebee nests survive the winter by putting all their investment into a few queens who mate at the tail end of summer then hibernate in some warm-looking spot (often a disused rat's nest), biding their time so they can establish a new nest in the spring. I don't know if the bee that made it to my kitchen had been fooled by a couple of warm days, or if it was a straggler from a nest that had tried to make it through the autumn (in Northern New Zealand bumbleebee colonies can find enough flowers to eek out an existence over the winter, but I can't see that working down here), by the time she got to me she wasn't doing very well (note the splayed, face down posture)

The buzzing I'd heard wasn't so much the bee flying about searching for a way out as her attempts to build enough temperature in her flight muscles to let her take off. The muscles themselves need to be around 30 °C before they can work, but bumblebees can operate when the outside temperature is as low as 6°C by uncoupling their flight muscles from their wings and vibrating them. As David Attenborough explains, bumblebees are warmblooded insects!

My visiting queen didn't appear to be winning her battle with the thermoregulation, so I scooped her and but her under a desk lamp in the hope it would help. The fact I might be able to take photos of her at the same time was, of course, just a happy side effect of trying to help her out. I really failed to take any interesting photos, but I do quite like this detail of the hairy abdomen and veined wings:

I hoped focusing on the tail-end of the bumblebee might reveal the fact that bees (and their relatives the wasps and the ants) have two pairs of wings (which is the ancestral state for insects). But, in fact, the smaller set of wings are so tightly connecting with the larger ones it's impossible to see here. You'll have to look at some disembodied wings to see that I'm not making it all up.

You'll be glad to know a couple of minutes under the lamp, and her concerted efforts, were enough get the queen back in the air - she was last seen flying upwards and hopefully towards a good spot avoid the snow that fell here recently.

Sunday Spinelessness - Butterflies!

2011-07-31T16:29:00.002+12:00

Just a couple of pretty pictures today, and what could be prettier than tropical butterfiles? There is a great butterfly house at the Otago Museum, and every time I visit I try and challenge myself to find another angle from which to photograph these beautiful creatures. Sometimes the butterflies themselves make that all too easy:

But my favourite one took a little more work, trying to approach a Heliconius while it surveyed the artificial jungle the musuem has created for the butterflies

Sunday Spinelessness is putting its feet up today

2011-07-24T08:59:00.002+12:00

Today is my birthday and a Sunday. So, I'm going to sleep in, ride my bike slowly around the peninsula (if the forecast snow doesn't evenutuate) then... well , then I'll probably have to do some work. But I'm not going to find time to write anything here. If, however, you need a fix on spinelessness to get through your Sunday then I think my post on the Scientific American guest blog should do nicely.

Sunday Spinelessness - What the... ?

2011-07-17T18:40:00.004+12:00

Issac Asimov provided one of my favourite quotes about science

The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny...

Scientific questions are almost never solved in eureka moments. Answers take time, planning, analysis and, finally, results from multiple studies made available for the scientific community to scrutinize. But there plenty of exciting moments in science, and there is nothing quite like the feeling of noticing something that doesn't quite fit with the way you think the world works. From there you can start spinning off theories that might explain the anomaly, and most excitingly, think how you might test those ideas against reality.

Something a little bit similar goes on in the life of a bug nerd. There are lots of creatures I'd love to see and never have. I've never seen a tardigrade, or a mantidfly [you really want to click that link, they're amazing] and reading Ted's blog means I'm forever looking out for one of our native tiger beetles. It's definitely a thrill seeing finally seeing some creature that you're read about and seen photos of, but it's at least as exciting to see something you didn't even know existed. For a bug nerd, "What the ..." is just as exciting a phrase as "A'huh", and that's exactly what I said when I turned some tree bark and found this spiky little guy:

Just as "That's funny ..." is a trigger to hypothesising and mentally developing a research proposal, "What the ..." is a precursor to reading searching, viewing and poking about in the hope of placing the strange creature into what we know about life. I have to admit I haven't got very far in this particular example. The thickest of those tufts mark the back end of the animal, and I'm pretty confident it's a beetle larva (you can make out two of the three legs on the near side of the body is this photo). Beyond that I'm a bit stuck, there are plenty of weevils with larvae that live under bark, but this doesn't look like any I've been able to find. Similarly, quite a few beetles in the family Dermestidae (called 'skin beetles' since some species are scavengers of animal corpses and some even specialise in eating hide) have spikey looking larvae like this one, but I can't find any helpful references for these beetles in New Zealand and don't know if there is a give away as to whether this animal fits in that family. If anyone knows what this is, or might be, I'd love to learn!

Sunday Spinelessness - The first animals (molecular biology)

2011-07-10T22:12:00.002+12:00

It's time to wrap up this series of posts on the origin of animals. If you are just tuning in here, I've already decided that early fossils are utterly fascinating but really not much help to us and had a look at some modern organisms that might give us an idea about how the major steps towards multi-cellularity might have been achieved. Today, I'm going to zoom down another level, and see if molecular biology can tell us anything about the first animals.

Life is really just a very special kind of chemistry. The organisms that emerge from the bewildering number of inter-connected chemical processes that make life tick are so complex, so varied and so far removed from the things that chemists study that we had to create a whole other science, biology, to study them. For a long time biologists and chemists more or less got on with their own problems, but in the middle of the 20th century the progress each field had made created the opportunity to actually study the molecules that make life. The so called "molecular revolution" in biology has effected almost every sub-discipline within our science, and the tools and data that revolution created can be used to try and understand the origin of animals. Over the last decade or so scientists have sequenced the genomes of an increasingly number of species, and in between the big headlines created by creatures like chimps, mice and humans; we've been able to learn about sponges, cnidarians and placozoans. Those sequences can help us understand how these animals work at a molecular level, and they can also be used to recover the relationships between different groups of animals.

Scientists call the branching trees we create to represent the relationships between species 'phylogenies', and as someone who spends quite a lot of his time working on molecular phylogenies (have you seen The Atavism's logo...) I should really be saying that this is the best way to understand the origin of animals. But that's not really true. DNA isn't quite the wonder-molecule that CSI may have lead you to believe it is, and having DNA sequences available isn't necessarily enough for us to recreate a phylogeny. At the moment, the relationships at the base of the animal family tree are very hard to untangle. We know that a group of animals called the bilatarians (you, me, insects, fish, sea urchins, nematodes, spiders and, well, really every animal you are likely to name off the top of your head) form one group distinct from the other animals, and that these animals can be further subdivided based on the way their embryology plays out. But the relationships of the non-bilatarian animals - a grab-bag of creatures including the cindarians (jellyfish, corals and their relatives), comb jellies, placozoans and sponges - are really unclear:

That uncertainty isn't a matter of us just not having enough data to throw at the problem. Molecular phylogeny works by grouping species together based on mutations that they share, having inherited them from a common ancestor. So, ideally all the branches in the true history of the species we are studying will be separated by enough time for those mutations to start racking up in the period of time that lineages shared an evolutionary history, something like this (with the mutations being the red stars occurring at random):

Sadly, the real pattern underling the base of the animal family tree doesn't appear to be like this. The initial branches fromed relatively quickly, leaving only short periods of shared ancestry for related groups to accrue mutations that would allow us to recreate their relationship. Worse yet, the branches that lead out from initial splits are really long, which means there has been millions of years for any useful mutations to have been over-written by more recent changes in DNA sequences.

There is no easy way to get around this problem. It seems like we should be able to throw more and more genetic sequences at the tree, increasing the chance the we get some informative mutations, but these trees run the risk of falling into the terrifying Felsenstein zone, in which the confidence with which we estimate the wrong tree increases as we apply more sequences to the problem. Because of the difficulties inherent in reconstructing the very early history of animals, I think we should take results based solely on molecular phylogenies with more than a few grains of salt.

A case in point is the phylogeny Casey Dunn and colleagues presented in Nature a few years ago (doi: 10.1038/nature06614). If we were trying to fill in the question marks and the base of the animal tree without considering molecular data at all, we'd probably put sponges on the first branch to split in the animal family tree. Sponges are quite different from other animals, they don't have a nervous system, their cells are not bound into tissues and, although sponges do have specialised cell-types, their cells are uniquely flexible in that mature cells can change from one type to another. It's actually quite possible that several of the early branches in the animal tree lead to different types of sponges, like this:

But, against all expectations, Dunn's phylogeny found comb jellies (creatures that look a little like jelly fish but form a phylum, Ctenophora, in their own right) to be the first group to split from the animal tree. If that were true, then we'd be less confident that the first animals were sponge-like since either (a) sponges would be radically modified animals which had lost their nervous system, given up on tissues and taken to a sedentary filter feeding life or (b) comb jellies would have evolved nervous systems and tissues independent of those of other animals.

There is no reason that such a scenario would be impossible (in fact, fungi and plants have each evolved tissues independently of animals), but when the whole idea is constructed from a method that we know is prone to biases I don't think there is much point in worrying about it (I should say, this isn't a criticism of the paper I'm talking about, which took all the sensible measures to deal with the problems inherent in there analysis and presented their tree as something to work on rather than a final result). Similarly, a phylogeny that included data from everyone's favourite animals the placozoans (Schierwater et al., 2009. doi: 10.1371/journal.pbio.1000020) was used to resurrect a hypothesis for the origin of animals that includes a flat ancestor, not unlike a modern placazoan or the 'planula' larvae of some cindarians. This scenario would again require nervous systems to evolve twice:

One of the reasons I'm skeptical of this idea comes from what we've learned about the genomes of simple animals. For my money, the discovery of Hox genes is the most remarkable result to come out of the the molecular revolution I talked about in the intro to this post. In turns out the genes that orchestrated your embryonic development have counterparts in Drosophila (or Sophophora if you'd rather) that do exactly the same job. If we move away from the bilataria, Hox genes are a bit harder to come by, but they still exist in the genomes of comb jellies, cnidarians and even palcozoans. But sponges have no Hox genes (Larroux et al, 2007. doi: 10.1016/j.cub.2007.03.008 and references therein). It's conceivable that the sponges descend from an ancestor that had Hox genes, then gave them up, but it seems much more likely that Hox genes evolved after sponges parted ways with the rest of the animal kingdom.

The contents of animal genomes tell us more than which phylogenetic patterns are likely - they can also let us know how some of the unique features of animals might have arisen. Almost every time the genome sequence of a simple animal is published you'll get a press release saying how surprising it is that genes associated with functions of more complex animals were found in this simple creature. And every time I read one of these press releases I sigh. Thesy are exactly analogous to someone that studies birds expressing surprise that therapod dinosaurs (the ancestors of birds) had forelimbs even though they couldn't fly. You can't make entirely new gene families out of nothing, new functions evolve when existing genes are retooled to attack different problems. The first animals faced two big problems when they moved from a single-celled lifestyle to a mulit-celled one: first, they needed to hold themselves together; and second, they needed ways for cells to communicate to their neighbours. Modern animals stick together with collagen (an entirely animalian invention) and a bunch of other sticky proteins including cadherins. The closest relatives of animals, the choanoflagellates which I talked about last week, have cadherins and other sticky proteins which they probably use to trap their prey (bacteria and other small cells).

Choanoflagellate genomes also give us a great insight into how the cells in the first animals started talking to each other. One of the most important pathways for cell-cell signalling in animals is called notch. Choanoflagellates don't have notch genes, but they do have the raw material from which one could be made. The proteins that notch genes make have several distinct 'domains' each of which perform particular function - and all these domains are present in choanoflagellate genomes! These different domains could have been brought together by genetic recombination, creating new genes by so called 'domain shuffling'. If we move just a little bit past the origin of animals and look at the genomes of sponges we can find the precursors of nervous system genes (see for example Liebeskinda et al., 2011. doi: 10.1073/pnas.1106363108).

So, that's three posts about 5 000 words and a whole bunch of figures on the origin of animals. What can we say we've learned? Certainly, studying modern animals seems to be the only way to approach the question of where animals came from. The models we looked at last week allow us to understand how the problems associated with a switch from single celled life, to a colonial lifestyle and finally the emergence of an individual identity for the colony. Modern genomes also tell us how those changes might have happened at the molecular level. Sometimes, as is the case of the cadherins and the evolution of the nervous system, existing genes could be re-purposed to a new tasks. Other times, new features were likely achieved with the help of new genes, cobbled together by genetic recombination. We can probably disregard theories for the origin of animals that require complex morphological changes based entirely on molecular phylogenies, since those estimates are prone to biases and the most interesting branches in them remain uncertain. If we look at morphological similarities between choanoflagellates and sponges (which goes right down to the collared and flagellated cells they use to eat) it seems likely that the first animals were filter feeders that pumped water into their cells with long flagella.

If you forced to make a bet on what the first animals were like, I reckon they'd be a bit like a sponge larva. A collection cells similar to a choanoflagellate colony, moving about in the water column with their flagella. The big question is how that individual could have emerged from the colony, and here I like Paul Rainey's ideas (described last week) about the way inter-cellular competition, which is bound to arise in a colony, could actually create the conditions that would foster cooperation. I'd be really interested to hear what any readers who made it all the way through this series think now.

Our greatest journey

2011-07-07T13:01:00.002+12:00

The Symphony of Science series of videos is probably the best justification for the continued existence of auto-tune. The latest of these videos, which put various scientists and science communicator's words to music, deals with the history of our species - the fact we all descend from African ancestors and that all populations outside Africa are the result of migrations that started around 150 000 ago:

It's a matter of continual disappointment and annoyance to me that most New Zealanders don't know that the person most responsible for finding our place in the biological world and locating the base of our family tree in Africa was a kiwi. Allan Wilson was a graduate of Otago University who went to Berkeley to use the new technologies that were developed for medical genetics to answer some of the oldest questions in biology. By sequencing DNA and looking at the cross-reactivity of immune system proteins, Wilson and his students established that humans only separated from other apes about 6 million years ago (as opposed to conformable distance of 25 million years paleontologists had favoured) and coined the term "Mitochondrial Eve" for one of the ancestors all modern humans can trace their origin to. This 'Eve' lived 150 000 years ago in Africa, so, just as Alice Roberts says in the video, we are all children of Africa.

These findings absolutely changed the way we think of ourselves as a species, and New Zealanders should know a kiwi was behind them! Thankfully the Royal Society has just announced one of Wilson's students, and a co-author on the most important papers, Rebbecca Cann is coming to New Zealand to talk about Wilson and his legacy. If you get a chance, I really encourage you to get along and hear her talk.

Sunday Spinelessness - The first animals (modern analogs)

2011-07-03T21:47:00.003+12:00

The last time I tried to work out what the first animals might have looked like I decided fossils probably weren't much help. So, today I'm going stop looking back into the depths of time, and see if any modern creatures might provide clues as how animals got their start in life.

Remember from the last post, the major challenge for ideas about the origin of animals is explaining how a group of single celled organisms, each with their own evolutionary interests, can join together to create a mutli-cellular creature in which almost all of the cells can never reproduce in their own right. Our glance at earliest animal fossils record showed us that the resolution of this record just isn't fine enough for us to isolate the first cells to go in for this sort of arrangement, but there are a wealth of modern organisms that seem to have gone some way down this road, and they provide useful models for us to study.

Let's start by looking at the closest living relatives of animals the choanoflagellates:

(photo is CC 3.0 from Choano-wiki (really!) user Mark J. Dayel)

Choanoflagellates are a widespread a diverse group of single-celled creatures that live in the ocean as well as freshwater. At first glance it might seem a stretch to propose a relationship between these ten micrometre long cells and animals, but there is good reason to believe the relationship is real. Choanoflagellates, with their characteristic 'collar' around the tip of the cell body and the the flagellum extending from it are almost identical to a class of cells called choanocytes found in sponges. In fact, the two cells work in exactly the same way - the flagellum pushes water and nutrients into the cell body through collar were than are digested or, in the case of sponges, moved from one cell to another. By comparing molecular sequences, biologists have confirmed the choanoflagelletes are close relatives to animals, and also established they aren't simply a lineage discended of a sponge¹ that gave up the multi-cellular lifestyle

The shared anatomy and feeding methods of sponge cells and choanoflagelletes gives us a clue as to how animals might have evolved. If a sponge is a bunch of cells that are held together by proteins that feeds using choanocytles, could the first animals have evolved from choanoflagellates that formed colonies? You don't have to imagine too hard here, because there are modern choanoflagellates that do just that:

In fact, colonial behaviour appears to have evolved multiple times within the choanoflagellates. This behaviour might crop up so often because even the solitary species have a wealth or sticky proteins that they use to trap bacteria and other food items in their collars. However it arises, colonial behaviour is obviously worthwhile for some choanoflagellates because they been doing it for millions of years, either forming spheres like the Sphaeroeca shown above, clusters like Protero below or as small groups sitting on a stalk like Proteospongia ²

Colonial choanoflagellates might well have been the first step on the road to true mulit-cellularity, but an agglomeration of cells each doing well out of their association with each other is still a long way from the specialisation we see in modern animals. Thankfully, there are organisms out there that give us a glimpse as to what the next step might have looked like. And some of them are stunningly beautiful:

(photo is CC 2.0 from Wellcome Images)

The sphere you see above us an alga called Volvox that makes blurs the line between a colony of single celled organisms and a multi-cellular life form. Of course, algae are only very distantly related to animals, but we are looking for models of how simple multi-cellular life might work, and Volvox is interesting because it's a very simple organism that has a clear distinction between reproductive cells and the rest of the organism. The closest realtives of these beautiful creatures are single celled algae called Chlamydomonas. Most of the time Chlamydomonas are free swimming cells, propelled about in search of sunlight for photosynthesis by two flagella:

When it comes time for them to divide they draw their flagella in and begin a series of cell-divisions, keeping between two and eight daughter cells within the 'old' cell wall before they burst out and get back to the swimming lifestyle

Volvox has ditched this two-stage life cycle, instead, the individual (or colony if you'd rather) simultaneously contains reproductive and 'swimming' cells. That dotted sphere is made up of thousands of cells very similar to swimming Chlamydomonas each connected in an extra-cellular matrix of proteins and carbohydrates. Importantly, those outer cells don't divide. Reproduction is down to a set of immobile cells within the sphere, called gonidia. Each gonidia can go through a set of programmed cell divisions that create all the cells that make up a new Volvox individual. Volvox is probably the simplest example of an organism that displays a division of labour between 'body cells' (in this case the swimming cells that move the individual around) and reproductive ones. As I said, algae are not closely related to animals, but the larvae of some sponges seem in some ways analogous to an individual Volvox. Like all sedentary animals, sponges have larvae that can move, and in sponge larvae that movement comes courtesy of a set of ciliated cells that form the lower portion of the larva:

A glass model of a sponge larvae, photo provided by Welsh Museum

So, between Volvox and sponge larvae we have an idea of what a very simple free swimming animal with specialised cell types might look like. But how might that division of labour between different cell types have evolved? Now we really are heading into some murky waters. Animal multi-cellularity happened once, at least 600 millions ago. Obviously any answer we offer as to why this happened is going to be at best a tentative explanation, but I've always like an idea developed by New Zealand evolutionary biologist Paul Rainey (and not just because he has been the head of a Centre for Research Excellence of which I'm a member!)

Rainey is an experimental evolutionary biologist, taking advantage of the speed at which miroogranisms reproduce to answer questions those of us that wander about in the field couldn't even begin to ask. One of his experiments involved growing bacteria in a stable environment, which reliably procudes mutants that are rather charmingly called "wrinkly spreaders". The wrinkly spreaders form mat-like colonies on the top of the tubes that they live in:

To be part of that mat each cell has to pay a small cost in the form proteins that stick the cells together, but that cost is more than repaid by the fact only cells in that mat can access oxygen from the barrier between the fluid in the cell and air above it. For this reason wrinkly spreaders soon take over the population in the tubes. Natural selection acts on individuals, not colonies, and very often selection acting on cells within the mat will lead to its destruction. Cells within the mat can take advantage of their neighbours by not producing the adhesive proteins that hold the mat together while still enjoying the benefit of being within it. In time, the small advantage these mutant cells gain by not paying the price in adhesive proteins will be enough to see them out compete their neighbours. But, of course, once such 'cheating' cells predominate the mat won't be able to sustain itself and it will fall apart.

Here's were is gets really interesting. Each mat seems like an evolutionary dead end, because the mats themselves can't reproduce (a prerequisite for evolution by natural selection) - when the mat falls apart the cells fall into the oxygen-free zone and die. But 'cheating' cells can reproduce and they can leave the mat and, most remarkably, because there are so many cells in a population that, in time, it's likely one of them will mutate back to the co-operative wrinkly spreader type. Now stand back and think about the big picture here. You have a larger stationary structure, the mat, that can give rise to small, mobile cells (the cheaters) that can each go on to establish a new large structure. That sounds very similar to a larval-adult life cycle, or even the distinction between body cells and reproductive cells that we are trying to explain. Since the 'cheater' cells probably arise by mutations that break existing genes, the switch between cheater and wrinkly spreader could, in time, be controlled by gene expression rather than by waiting for mutations.

Of course, I'm not trying to argue that animals evolved from wrinkly spreaders specifically, or even this sort of pattern generally. The really neat idea in Rainey's description of the dynamics of wrinkly spreaders is the way the cohesive nature of multi-cellular organisms might have evolved from competition rather than co-operation. Hundreds of co-operative systems have been identified within colonies and populations of single celled organisms and all of them are prone to sabotage by cheaters, so it's definitely something to think about, but, like all the ideas in this field, it is speculative and may turn out to be wrong.

So, modern organisms can give us a few clues as to animals might have got their start. Colonial choanoflagellates are an example of how simple colonies that feed in the same way as modern sponges could form. Volvox is an example of a very simple organism that has a distinction between reproductive and body cells and Rainey's wrinkly spreading bacteria show us one possible route to how that distinction would arise in the first place. In this peice of really presumed that the first animals fed in much they way modern sponges do, but not everyone thinks is the case. Next week I'll turn to genes, genomes and the family trees we can estimate from them to explain some of the slightly more outre ideas about the origin of animals.

¹ I really wanted to call this post "To be descended of a sponge", but I called the first "The first animals" so I guess I'm stuck with it for the series

² The world's number one protist fan, Psi Wavefunction, would like it to be known that the Proteospongia species you might read about that is meant to have specialised cell types similar to a sponge's ameboid cells probably doesn't exist (being recorded in error a in the 1880s and not seen since)

Lots of references today: Choanoflagellate biologists have their own wiki, and it's pretty cool The free online version of Molecular Biology of the Cell has a section on the evolution of multi-cellularity including Volvox as does Scitable, Nature's education website.

Paul Rainey's ideas are more thoroughly explained in:

Rainey, Paul B. 2007. “Unity from conflict.” Nature 446 (7136): 616. doi:10.1038/446616a.

Sunday Spinelessness - Snails can be speedy too

2011-06-26T23:12:00.003+12:00

Sorry for anyone looking forward to the next part of a series on the first animals - that posts needs more editing than I have time to do this evening.

Instead, I'm going to jump on an internet bandwagon and show you a surprising video that's been doing the rounds:

As I've said before, we have some seriously big invertebrates in New Zealand, but none of them are more impressive than our giant carnivorous snails. We tend to think of snails and slugs as pests that destroy our lettuce plants, but snails are the most diverse group of molluscs and they have adapted to eat a whole range of food. Most snails scrape algae and fungi off surfaces, others are plant eaters, a few are parasites with no mouth at all and a surprisingly large number of them are carnivores. The scrapers and the herbivores eat by extending a rasp-like organ called the radula out from their mouths to chip away add the food at hand and rake into their mouths:

Typical snail feeding anatomy from wikimedia user Debivort - image is CC 3.0

Great as this method is for eating immobile plants and algae, it doesn't really work for carnivorous snails whose prey has the ability to run away. Indeed, most carnivorous snails have seriously re-arranged their feeding anatomy to accommodate their lifestyle. The video above gives us a rare chance to see it in action. Once the snail has worked out where the worm is (using its two sets of tentacles - the smaller ones below are for smelling while the longer ones have eyes on their tips) its pharnyx fulls with blood and is rapidly thrust outside of its body, surrounding the worm. Once the worm is enveloped, the snail's sharp radular teeth will hold on, and start to break its body up as its dragged deeper into the digestive system. Although the actually moment of capture happens with a swiftness that belies snails' reputation as slow moving animals, the rest of the eating process takes a bit longer. The radular teeth are not particularly efficient and it will take several passes for the (still living) worm to be sloughed off into edible pieces.

All of New Zealand's carnivourous snails are from the Southern Hemisphere family Rhytididae. All told we have around 60 species in 6 genera. The video doesn't tell us what species were looking at, but it's probably from the one of the two related genera Powelliphanta and Paryphanta (if you forced me to pick, I'd says this was Po. augusta since the video comes from DoC and, as we'll see, they have a population of that species in captivity). Both these genera contain large worm-eating species with extraordinarily beautiful shells:

Image is CC 2.0from Flickr user SidPix

Most of the Powelliphanta species aren't yet formally described, and seems like there is some interesting evolutionary biology going on in this group. A number of species appear to be linked to each other in what is called a 'ring species' - a long chain of populations in which those adjacent to each other can interbreed but populations distant from each become quite distinct (and probably couldn't interbreed given the chance). I'd really love to get the chance to apply some genetic tools to understanding what's going on there, and, in fact, sorting out the number of species in this genus has important conservation implications. Unfortunately, for all their fearsome eating habits, most of our rhytidids are at risk of extinction. Like the rest of our fauna, they have no natural defence against introduced mammalian predators like possums. Habitat destruction also threatens their future, since some species appear to be adapted to very fine-scale differences in habitat, which makes the risk we took in translocating an entire species that had the temerity to live on mountain with a coal seam seem utterly crazy to me.

Sunday Spinelessness - The first animals (fossils)

2011-06-19T16:58:00.008+12:00

I see that Prime is playing a documentary by David Attenborough on the origin of the animals. One of my favourite people talking about one of my favourite topics is motivation enough to dust off one of the many posts in The Atavisms massive "drafts" folder....

You and I are connected. Trace our lineages back long enough and we are guaranteed to find a shared ancestor. In fact, we are each connected to all of life on earth. Every cell in your body can trace its existence back through an unbroken chain of cell division and DNA replication to the origin of life. The same is true of every creature on earth, so, in a very real sense you are connected to all life on this planet.

Animals are a bit weird though. Every piece of DNA in your body is the latest link in chain that goes back to the origin of life, but most of your cells can't continue that chain. Very early on in our development, there is a fundamental distinction between the cells that make our germline (and will go on to make sperms and eggs) and those that make our bodies (the so called somatic cells). It seems natural to us for some of our cells to have no chance of leaving descendants that outlive us. But how the transition from singled celled organisms, each with a chance of reproducing, to multi-celled creatures in which most cells on reproduce 'by proxy' happened is one of the most fascinating questions in biology. So, how did animals evolve?

What is an animal?

Before we can ask how animals came about, we have to know just what makes animals different from other types of life. If you studied biology at school you may remember that animals are "heterotrophs" - that is they eat food rather than make their own. Lots of singled-celled animals are heterotrophs, but almost all animals are multicellular (some very strange single-celled parasites called Myxozoa appear to have evolved from multicellular ancestors). All animals are capable of moving, at some stage in their lives. There are plenty of animals that spend their whole adult life on one spot, but they all have larval forms that can get about under their own steam. Finally, animals are the only group of organisms to go through a "blastula" stage in development, and the only creatures to use collagen to hold themselves together. Since these characters are all unique to animals, and found in all branches of the animal family tree, we'd expect the common ancestor that unites all animals to share them.

So how to we reconstruct this ur-animal? This is one of those exciting fields of science where a whole suite of different tools and methods need be used to try and arrive at a clear picture The events that we are talking about happened around 600 million years ago, there are lots of different ways to try an peer back to that time, but as we'll see, each of them has their own strengths and weaknesses. Over the next couple of weeks I'm going to look at evidence for different methods and see if we can't pull together a consensus view of what the first animals might have been like.

Fossils

If you want to know what animals looked like 600 million years ago, you'd think the obvious place to look was 600 million year old rocks. There used to be a real problem here. Until the 1950s the fossil record seemed to have a very abrupt start in rocks from the Cambrian period (around 540 million years ago). Cambrian rocks had plenty of fully developed animals, while earlier formations seemed to have no fossils at all. The problem of life seeming to arrive fully-formed in the Cambrian period has come to be known as Darwin's Dilemma. In Chapter 10 of The Origin (p308) Darwin talks about it (in a characteristic style that has been abused by creationists who seemed to think Darwin didn't believe his one theories). First he acknowledges the problem, and grants that it could be used to argue against the evolutionary origin of life

To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer... The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained.

So Darwin was happy to admit, at least at the time that he was writing, that there was no clear reason why pre-Cambrian rocks had no fossils and this lack of fossils was a mark against his theory. But, he goes on to offer a particular explanation for why pre-Cambrian rocks might be fossil free even if their were many pre-Cambrian creatures (which, as far as I can tell turned out to be wrong) and a more general reason to be skeptical about claims that rested on a lack of fossil evidence. Darwin argued that the evidence geologists had so far uncovered was only a thin slice of the full history of earth, in fact it was like:

A history of the world imperfectly kept and written in a changing dialect. Of this history we possess the last volume alone, relating only to two or three countries. Of this volume, only here and there a short chapter has been preserved, and of each page, only here and there a few lines. Each word of the slowly-changing language, more or less different in the successive chapters, may represent the forms of life, which are entombed in our consecutive formations, and which falsely appear to have been abruptly introduced. On this view the difficulties above discussed are greatly diminished or even disappear.

When we view fossils not as a complete record of life on earth, but as a few snapshots of different periods, the apparently sudden appearance of animals in the fossil record becomes less of a problem.

But Darwin was right, simply saying the fossil record was incomplete might be perfectly reasonable, but it wasn't the satisfactory answer he would have wanted. Darwin's Dilemma lacked that answer until the 1950s and the discovery of Charnia A frond-like impression in a rock discovered by a school boy in England was the first fossil to confirmed to exist in pre-Cambrian rocks.

The first pre-Cambrian fossil, holotype of the genus Charnia. CC2.5 from wiki-commons user Smith609

People had found things that looked like fossils in old rocks before, but they were dismissed or ignored either because the impression were presumed to be of an non-organic origin or because the dates of the rocks were disputed. Charina was different, the impression is clearly biological, and the rocks from which it was collected had been dated by the British Geological Survey. Once Charnia has been established as something real and something pre-Cambrian, people got a bit more serious aobut older fossils. In time an entire community of large creatures were discovered, what we now called the Ediacaran bioata

Though the Ediacarans were morphologically diverse, but there were made up from repeats of some pretty simple patterns. Charnia had is fronds growing from a rib Ediacaria left disc-like fossils and Dickinsonia was a flat oval made of tubular sections (which probably inflated like an air mattress)

Above: A Dickinsonia fossil. Below A reconstruction of an Ediacaran ocean (with way too much light!)

It's hard to say quite what the Ediacarans were. The rocks they are preserved in were formed at the bottom of deep oceans, so it's clear they were heterotrophs (because photosynthesis wouldn't work down there). The fronds like Charnia must have been filter feeders (or "absorbers" feeding by osmosis) while the surface spreaders like Dickinsonia also left trace fossils, suggesting they dragged themselves across the sea floor. It's not clear if there were any predators in these systems (leading some to call the time the "Garden of Ediacara"). So, the Ediacarans were heterotrophs, they could move and they were obviously multicellular - it seems like they must be animals. But placing them into the tree of life we've created by looking at modern animals has proved extremely difficult. When it was discovered Charnia was thought to be like a modern sea pen (a cniderian) but recent evidence evidence suggests that interpretation was wrong. Some researchers, most notably Adolf Seilacher, have argued that the Edicarans don't fit easily within modern animals because most of them aren't very closely related to them. In this view, most of the Ediacaran biota form a distinct group, which seperatley arrived at the idea of being large, multicellular heterotrophs. Others have argued that particular fossils fit into existing groups; Kimberella as a mollusc, or, more sketchily Vernanimalcula as an early Bilaterian.

It's very hard to come down on one side or another here. If the Ediacarans really are early animals, then when we look at them we are looking at the first twigs of what would go on to form the mighty branching tree of animal life. We shouldn't expect those first twigs, all those years ago, to contain the traits that would go on to define animal groups. On the other hand, the fossil record is so fragmentary, and gap between out time an theirs so great, placing any particular early fossil into a modern takes a bit of leap. It seems likely some of the creatures preserved in Ediacaran rocks are closely related to animals, and some others are experiments in multicellular life that burnt out. (For what it's worth, this guy thinks the are all lichens). Whatever the Ediacarans were, they left the scene, replaced rapidly in the fossil record by the Cambrian fauna. The amazing diversity that arose in the so called Cambrian explosion is worth more than blog post by itself, but it's not really relevant to the question at hand, reconstructing the first animals.

I should include a little discussion on some of the claims to "first animal fossil" you might have read in headlines. "Firsts" are important in paleontology, and they're a sure fire way to get your work into a good journal, but the further back we go the more circumstantial the evidence becomes. Some very old rocks have biological chemicals that are as far as we know only produced by modern animals. That is circumstational evidence for the presence of animals in those periods, but when the rocks are hundreds of millions of years older than the oldest known animals, it seems like good evidence that some animal-ancestors could make those chemicals too. Similarly, there are very old trace fossils (tracks left behind by crawling creatures), but we know modern single-celled eukaryotes are capable of producing similar tracks, so they don't provide water tight evidence for the presence of animals in the sediments that have been preserved.

So, fossils seem to leave us with as many questions as answers. The patchiness of the record means we can't be sure the Ediacarans were early animals, the earlier "animal" fossils are sketchy at best and the Cambrian fauna (wonderful as it is) is just too late to tell us about the origins of animals. Next week, I'll see if modern organisms can't help up understand how ancient animals might have got their start, but now I'm going to tune in to David Attenborough and see how much we agree with each other... (8:30, Prime TV)

Sunday Spinelessness - Razor-back

2011-06-12T22:24:00.003+12:00

The photos I share here are really not representative sample of the bugs I come across in my travels. For me to get photos of a bug I need to get pretty close to it, and that means i can't get nice pictures of creatures that are skittish or particularly fast moving. For instance, there's a longhorn beetle (Cerambycidae) species I find quite often in Dunedin but have never taken a nice photo of, because every time I line one up the subject runs out of frame or out of focus.

Even though I've never taken a good photo of this beetle, I do have one that displays it's most unusual feature. It has two ridges growing out of it's back:

I can't imagine what, if any, purpose those protuberances serve, but i quite like them. Their spikiness, and their shape makes me think of tiny little circular saw blades sticking out of a saw bench.

Sunday Spinelessness - Flat animals and biology's age of discovery

2011-06-05T23:25:00.011+12:00

Sometimes it's tempting to look back on the history of science and feel just a little envious of the people that went before us. Imagine being alive at a time when you could jump on a boat, sail to some tropical country and discover thousands of species not yet known to science. Even better, you could use your discoveries to understand some of the most important ideas in biology. Darwin is the obvious example, but imagine being Wallace and finding flying frogs and searching for birds that were said to spend their whole lives on the wing and, so, have no feet. Or being with Banks and Solander as they arrived in New Zealand and discovered an entirely new flora to describe, catalogue and learn from.

It would be pretty great to live in those times, but I wouldn't swap places for the world - biology's age of discovery is still going strong. There are probably ten times as many species on earth as we know about. In the last couple of months we've heard news of new fish species discovered in the kermadecs, a nematode that survives a mile below earth's surface, bioluminescent fungi and an antelope species discovered in a meat market. Then there's biodiversity's dark matter; whole groups of creatures for which the fac they exist is all we know about them. Recently, DNA sequences have revealed a new group of fungi discovered in a pond in Devon, and maybe, just maybe, a whole new branch of life in a set of DNA sequences that are similar to each other but like nothing else we know. In the 21st century there is no lack of species for us to discover, and, in fact, modern tools mean we don't have to get on boat to discover them. Your average shovel load of soil almost certainly has bacteria and fungi that aren't known to science.

Sunday spinelessness has, rather arbitrarily, limited itself to animals (I am from a zoology department, these things rub off) - and one of my favourite examples of how little we really know about biology comes from some very strange animals. Meet a placozoan (literally 'flat animal'):

That's really an animal. It has no tissues, no organs, no front or back (let alone a mouth) and it has only a handful of specialised cell-types. But it's an animal none the less. Placozoans have been on earth for 600 million years, but it took us until the 1880s to notice them. F.E. Schulze was a German zoologist who specialised in simple animals like sponges, and when he stumbled across these guys living in marine aquariums he recognized them as animals and created the species Trichoplax adhaerens for them. Schulze also recognized his flat animals were quite unrelated to anything else in the animal kingdom. Unfortunately, other people had different ideas. Until the 1970s, text books said Schulze's Trichoplax wasn't a species in its own right, rather, they said, it was the larval form a some cnidarian (the group containing jellyfish, corals and their kin) or other. It wasn't until the 1970s that it became clear placazoans really were animals, and the ones people were finding in aquariums were adults. So, what have we leaned since then?

What do we know about placozoans?

They're small, up to 3 mm across. They don't have organs, or tissues (sponges are often cited as the only other animals to lack these, but I think some of the recently discovered small phyla don't have them either) but they do have specialised cells. In particular they have a layer of stretched out 'contractile' cells they use to move (FC in the diagram below) , these cells sandwiched between an upper- and a lower-level of epithelial cells (UE, and LE respectively).

When you zoom back from the cells and look at the animal you get... a blob (Mike Dickison tells me he thinks "they're tiny Blobs from Mars, and are slowly striving to meet up and form a giant Blob and destroy New York.")

They live in the 'littoral zone' - the part of the sea closest to the shore. Because they're tiny, and basically see-through, they've never been studied in their natural habitat. Instead, they're collected from rocks or microscope slides suspended in the water column. As the video above shows, they can be studied in the lab.

The adherens bit of their species name refers the fact they stick to surfaces (presumably rocks and shells in their natural habitat) where they eat algae and cynanobacteria. But how do they eat? I said before, they don't have mouths. Instead, they slide their entire body over a food particle and and fold-up to form a 'digestive cavity' into which enzymes that break down the food items can be secreted.

If I was writing this post way back when I first had the idea to, I would have said that placazoans definitely reproduce asexually and that they can probably also reproduce sexually. Last month Micheal Eitel and colleagues upgraded that 'probably' to an 'almost definitely'. Using genetics and some advanced microscopy they showed evidence for active growth of sperm and eggs in adults, and also detailed the stages of embryonic development.

Amazingly, one of the few things I can say we know about the Placazoa is the complete sequence of their genome. In 2009 researchers put the 90 million DNA letters together ( that 's about 33 times smaller than our own genome, and about 150 smaller than an onion's before you get too carried away about what that number might mean). The placazoan genome is of particular interest to cancer geneticists, as it has versions of two genes that usually protect us from the mutations that kick off the uncontrolled cell growth that characterises that disease.

What don't we know about placozoans?

Placazoans are almost always described as either 'ancient', 'primitive' or, worst of all, 'a living fossil'. Ancient really doesn't make any sense, all animal phyla have been on earth for 600 or so million years, so it's hard to see how a rabbit or a chicken is anymore ancient than a particular placazoan species (even if there really is only placozoan species at the moment). Primitive is not much better. The term means "similar to the ancestral state", there is no doubt that the first animals were simple, but it doesn't follow that because placazoans are simple they are like the first animals. After all, placazoans have been evolving for 600 millions years too, and it's entirely possible that they have ancestors that were more complex than the modern examples (the idea that evolution always creates more complex organisms seems to be one of the more persistent misunderstandings of biology). I'm not even going to talk about "living fossil".

So, placazoans aren't necessarily like the first animals, but that is a hypothesis we can test. If all other modern animals are more closely related to each other than they are placozoans then it would be more likely (still not certain) that modern placazoans are similar to ancient animals. If, on the other hand, placazoans fit somewhere in the middle of the animal family tree, it's more likely that their simplicity is something they evolved (what biologists called a "derived character"). We don't know which of those scenarios is the right one. Phylogeny (the methods we use to reconstruct the relationships between organisms) is really really hard when look way back into deep time, so different studies into this question get conflicting results. The placozoan genome study included a phylogeny that suggested sponges were first group to diverge from the animal tree, with placazoans more closely related to you and me than spognes (increasing the odds that placazoans are derived forms of more complex animals) but that study didn't include many other animals, possibly reducing its power. Another study suggested placazoans form a group along with sponges and cnidarians, but that study treats a whole set of gene sequences as a single piece of data. I don't mean to be unkind, but I think that's the worst way to do phylogeny. Every gene is an independent witness to the evolution of a group, and munging a whole lot of them into a single piece of data it just a terrible idea. So, we remain uncertain as to where placazoans fit into the animal kingdom.

We also don't know how many species there are. At the moment only one is described, but there are clear morphological and genetic differences between different placazoans and it seems likely there are several more.

We really don't know where placazoans live. They've been recorded in most of the places that people have looked for them in the tropics, as well as decidedly more temperate places like the Pacific Coast of the USA and the Sea of Japan. They will almost certainly be present in Northern New Zealand, but, as far as I know, no one has looked. If anyone up there wants a more exciting animal to study for their Year 13 Biology course, the best places to look are sandy beaches with some cover and a weak current. The easiest way to collect them is to suspend a box of microscope slides in the water column and leave them for a week or two to let a nice little community of algae, and hopefully a few algae eaters, develop on their surfaces. Then you'd need a dissecting microscope to examine your slides. You might not find anything, in which case you could fall back on a sea monkey colony or whatever the usual study animal is, but wouldn't it be fun to try?

What don't we know about life?

Placazoans are just one example about how much we still have to learn about life on earth. If we limit ourselves to animals, there are two phyla (remember vertebrates and all the lions, tigers, bears, fish, eagles, frogs and lizards you can think of are only part of one phylum) that were only discovered in the late 20th century (Cycliophora and Loricifera). There is a huge amount that we still don't know about life of earth. But just as international travel gave Darwin and Wallace and Solander and Banks a new chance to understand biology; DNA technology, new imaging methods and the possibility of collaboration with experts through the Internet givens 21st century scientists a unique opportunity to fill in the gaps in our knowledge. There has never been a better time to be a biologist!

Eitel, M., and B. Schierwater. 2010. “The phylogeography of the Placozoa suggests a taxon‐rich phylum in tropical and subtropical waters.” Molecular Ecology 19: 2315-2327. doi:10.1111/j.1365-294X.2010.04617.x.

Eitel, Michael, Loretta Guidi, Heike Hadrys, Maria Balsamo, and Bernd Schierwater. 2011. “New Insights into Placozoan Sexual Reproduction and Development.” PLoS ONE 6 e19639. doi:10.1371/journal.pone.0019639.

Schierwater, Bernd, Michael Eitel, Wolfgang Jakob, Hans-Jürgen Osigus, Heike Hadrys, Stephen L Dellaporta, Sergios-Orestis Kolokotronis, and Rob Desalle. 2009. “Concatenated analysis sheds light on early metazoan evolution and fuels a modern ‘urmetazoon’ hypothesis.” PLoS Biology 7e20. doi:10.1371/journal.pbio.1000020.

Srivastava, Mansi, Emina Begovic, Jarrod Chapman, Nicholas H. Putnam, Uffe Hellsten, Takeshi Kawashima, Alan Kuo, et al. 2008. “The Trichoplax genome and the nature of placozoans.” Nature 454 (7207): 955-960. doi:10.1038/nature07191.

Sunday Spinelessness - Earth Measuring Caterpillars

2011-05-29T21:07:00.006+12:00

It's Sunday night. So, of course, it's time for me to find an excuse for not writing that post I've been going on and on about and, instead, put up some photos and get back to work (or at least, stop working in time to watch Sherock).

The excuse is same old boring one, too much work and too little time. The photos were chosen to honour Weird Bug Lady (owner of the coolest Etsy shop in the world) and her brand new blog, dedicated entirely to caterpillars.

I'm not very good at the taxonomy of butterflies and moths, but it's very easy to see what family this caterpillar belongs when you see it move (terrible photo I'm afraid...):

That's the familiar gait of the "inch-worm", "looper" or geometrid. I've talked about geometrids before, but this was a good chance to talk about the anatomy that makes their caterpillars different than those of other moths. Most caterpillars get about with a combination of six "true legs" (labeled 3 in the diagram below) combined with a set of "prolegs" (short stubby limbs not unlike the ones that propel onychophorans through the leaf litter, and labeled 4 below). Quite a few species have particularly well developed prolegs on their final segment, which are to clasp on surfaces (labeled 5)

Michał Komorniczak for making this CC 3.0

Compare that pattern to this caterpillar:

The true legs are there:

But the prolegs are gone, except for a big pair of claspers:

"Inchworms" move around by hanging on with their true legs and dragging their rear-end forward (making a loop out of their body in the process) before they clasp on the surface and extend their whole bodies forward. When you see an "looper" making its way along a leaf or a twig it really does look like it's measuring out a set distance along its length, which gave them the common name "inchworm" and the scientific name Geometridae - which means earth measurer.

I have no idea what species this caterpillar belongs to. Landcare Research has photos of adults from about fifty species from New Zealand. Browsing through those photos, you can see some lovely examples of the camouflage patterns moths have developed to hide from hungry birds while they sleep on tree branches and trunks during the day:

Sunday Spinelessness - Embracing point and shoot photography

2011-05-22T17:08:00.004+12:00

Last week I told you all that I had a great idea for a Sunday Spinelessness post, but not enough time write it. So, of course, this week I've managed my time in such a way... that there's still no way I'm going to get to write that idea up.

I'll leave that idea for another day, and, instead take inspiration from one of Alex Wild's recent posts at Myrmecos. The bug-blogo-sphere is filled with wonderful photographers, producing absolutely stunning portraits of the little creatures that run our world. When I go out fossicking for bugs, it's images like Alex's ants and Ted's beetles that I have in mind. That mindset inevitiably leads to dissapointment, since I'm restricted to a point an shoot camera. As much as I love my camera, it's never going to challenge dSLRs for image quality and its lens can't produce the sort of magnification a really good macro lens can. But, Alex points out, I shouldn't be disappointed that my camera can't do something it's not designed for, instead, I should take advantage of some of the things digicams really are good at. In partcular, the small lenses used in these cameras create a wide depth of focus, which can capture not just a bug, but a little of the the way the world looks form a bug's point of view. With this new idea in mind I went out today and... well, completely failed to get anything interesting. It was a grey sort of a morning here in Dunedin there wasn't much life out at about. Instead, here are a few older images that gel with Alex's tips:

First, a soldier beetle looking for food in masterwort flowers in the UBC Botanical Gardens in Vancouver. I tried, and failed, to get a close up of these beetle's face; but did get this one:

Flowers seem to be the over-arching theme in thse photos. A bumblebee visiting a dahlia (I probably should have thought a bit harder about the background here...):

I've taken a few decent photos of bumblebees, but I've never taken a good one of a honeybee. Or at least, I've never taken a good photo of a sinlge honey bee, I quite like this one with hundreds of bees flying in and out of their hives.

And finally, back to the dahlia for my favourite of these photos. A tiny fly, far too small for my camera to capture in any great detail, but looking pretty good in this setting:

edit: I forgot to include a link to The Geek in Question, who followed up Alex's article with some more great tips

3 tweets

2011-05-20T09:51:00.002+12:00

Let's see if Storify stories can be embedded in blogger (if not, I guess you'll have to read it here)

Sunday Spinelessness - The little guy

2011-05-15T20:43:00.006+12:00

I seem to have run out of week. I had a great idea for a Sunday post this week, but I'm not going to have time to write that one. Instead, here's a recent discovery from the backyard.

Recognise the eyes? This must be a male of the same Cycloctenid (scuttling spider) species I uncovered a couple of weeks ago. He's a good deal smaller, and a good deal slimmer than his female counterpart:

If I knew I was going to compare the male and the female I would have tried to get a better comparison shot... male on the left, female on the right

Whenever you see males and females of the same species that look conspicuously different from each other you know that each sex is subjected to different evolutionary pressures. In mammals, if there is a difference in size, males are usually the larger sex. That disparity arises because males fight with each other for access to females and big males do better than small.

In invertebrates (and fish, for what it's worth), the tables are usually turned, with females being larger than males. This pattern probably arises from the different costs that each sex has to bear in creating the next generation - eggs are expensive and sperms are cheap. That bias might be amplified in 'sit and wait' predators like these Cycloctenid spiders. Fritz Vollrath and Geoff A. Parker looked across a host of spider species and found those with relatively sedentary females tend to have smaller males, then set about trying to build a model to understand how that size difference might evolve. It turns out, if females are few and far between then the success of males has more to with the time they spend searching for females than their ability to fight off other males. So, the best bet for a male Cycloctenid that wants to leave descendants might be early maturation, even if the extra searching time that results from it comes at the cost of extra growth.

This male's search seems to be over. I found him about 5 metres from the log that the female in this first post was living under and she hasn't moved since.

Vollrath, F. & Parker, G. A. 1992 Sexual dimorphism and distorted sex ratios in spiders. Nature, 360, p.156-159. (doi:10.1038/360156a0)

Sunday Spinelessness - Playing favourites

2011-05-08T19:15:00.003+12:00

As long as I've lived in Dunedin, the Otago Museum has a run an annual wildlife photography competition. I never entered a photo, because I go through exactly the same process every year. I look back through a years worth of photos and start picking out some that I like, ending up with a list of about ten, which then needs to be whittled down to two entrants. I agonize over the whittling process for about five minutes, then reason that there's no chance of me winning anyway so forget about it. There really is no chance of me winning, but some of the better photos get included in an exhibition, and it would be a thrill to have the spineless properly represented. So, this year I'm going to 'crowd source' the whittling process. Here are some photos that I like, at the bottom of the post there is a poll - vote for your favourite and help me decide which ones to enter!

First off, a couple of photos from my run-in with a wasp nest.

The only good wasp?

Emergence

One from my trip to Vancouver and Portland

Another angle

And finally a couple form Christmas in Vanuatu (I sound like some sort of globe trotter with all these exotic locations - I was very lucky in 2010)

Hadda beetle

Crab spider

And the poll (by the way, does anyone know a nicer way of putting a poll into a blog, keeping in mind about half of the people reading this blog do so at sciblogs, the other half at blogspot):

Sunday Spinelessness - All in the eyes

2011-05-01T19:32:00.004+12:00

Can you guess what these patterns represent?

Well, having read the title of the post you may have guessed that each black dot is an eye. In fact, these pictures all represent the way a particular family of spiders arrange their eyes. For spiders, the eyes are a window into evolutionary history: the ancestor from which all spider species descent had eight eyes, and, although most modern spiders have kept all eight, they arrange them in an astounding number of patterns. Very often, the eyes are the best way of placing an unidentified spider into at family. (These pictures are from Lynette Schimming's article on BugGuide, they represent the families Ctenizidae (trapdoor spiders), Oxyopidae (lynx spiders) and Scytodidae (spitting spiders) and are Creative Commons by-nd-nc licensed).

So, when I found this spider lurking under a log, and couldn't place it into my (admittedly scant) knowledge of spider taxonomy I was very keen to get at least one photo of its eyes (as it turned out, it was also by far the best photo I took of this spider before turning its log back over):

There are a couple of families of relatively large ground dwelling spiders in New Zealand, and and first glance I thought this might be a vagrant spider but the eyes are just all wrong for that placement. I had to dig a little deeper for the answer, but between google and Flickr I found it. You are looking at a member of the family Cycloctenidae.

The drive many naturalists have to call each thing by its right name might seem oddly obsessive, but learning a creature's place in nature isn't the same as placing a stamp in the right section of an album. A taxonomic name can be a key to data collected by hundreds of people. In this case, Ray and Lyn Forster wrote about the Cycloctenidae in Spiders of New Zealand. It seems the family is restricted to New Zealand and Australia and has only a few known genera. They are commonly called "scuttlng spiders" because the arrangement of their legs allows them to run sideways as well as forwards and backwards, which means than can rapidly hide from a would-be predator. That's no-doubt a predator avoiding adaptation, but this particular spider was very happy for me to rest a camera directly in front of and get the shot that let me know what I was looking at.

Sunday Spinelessness - Incertae sedis

2011-04-24T13:44:00.004+12:00

I was going to start this post by saying taxonomy has a language of its own, but that's not really true. Taxonomy just has a whole lot of Latin. When I've given talks in schools, I've almost always been asked why scientists insist on giving creatures those strange Latinised names. The answer is, we need names that anyone anywhere can recognise and pin to particular species or group. A common name like "black bird" might make sense in conversation in New Zealand, but in other circumstances it could refer to a single species (Turdus merula), the five species that make up Turdus, or a whole bunch of species in the new world family Icteridae. When taxonomy really got started Latin was the language which scientists from different countries used to speak to each other, so modern taxonomy follows Linnaeus in using Latinised names.

But the Latin terms used by taxonomists don't stop with names, if you thought they were difficult to understand you should open a taxonomic work. The first time I did I was lost in a sea of lecto-, neo- and allo-types; homonyms junior and senior and Nomina nuda, obltum and protectum. The title of this post, Incertae sedis is another of those strange taxonomic terms and translates as "uncertain placement". Most big taxonomic reviews include a few species the author is certain are well defined, but hard to place into a higher group. Those species get placed under the heading Incertae sedis.

I used that title because today's subject is... a land snail... of some sort

I found this guy (actually, all land snails are hermaphrodites, so I need a better familiar term for them) in our garden and it's pretty tiny (this is a 50 cent coin, almost exactly the same size as a quarter for North American readers):

Allan Solem (who knew a thing or two about land snails) regarded the New Zealand land snail fauna as one of the most diverse the world. Head into a patch of native bush and pick through the leaf litter and you're bound to find small snails like this one eating the decaying matter, look around a bit more an there will be slugs like the leaf veined ones I've written about and much bigger species like giant carnivorous Powelliphanta. The massive diversity of our land snails makes their classification and identification hard work. This is probably a punctoid (a member of the super-family Punctoidea) but that's a pretty lame identification from someone who's meant to be some sort of malacologist (equivalent to a scientist specialising the cute and the cuddly saying a cat it probably some kind of mammal, since land snail families tend be much more anciently diverged groups that vertebrate families) and doesn't help us very much with getting the species name because there are probably 450 punctoids in New Zealand, only half of them formally described.

So, for now, I'm just considering it Incertae sedis and admiring its finely sculptured shell

Conserving Don Merton's achievements

2011-04-19T09:13:00.001+12:00

Don Merton holding Richard Henry, an important Kakapo. Photo is CC 3.0 from here (thanks to Errol Nye from DoC)

Don Merton probably saved more species from extinction than anyone on earth. If it wasn't for his efforts we would have lost the Chatham Island's Black Robin and the Kakakpo, and the methods he pioneered as used by conservation projects all around the world. Last week Don Merton died.

Don's most famous achievement was his heroic rescue of the black robin. The species was reduced to five adults and only one fertile female called 'Old Blue', all living on a tiny rock sticking out of the sea in the Chatham Islands. By going against the "hands off" approach to conservation that prevailed at the time and translocating the surviving birds to a larger island and 'fostering out' Old Blue's eggs to the local tomtits Don founded a population that now has 300 or so birds. Their future is a long way away from being secure, but the fact they exist at all is down to Don Merton's creative thinking, hard work and perseverance.

Don also led the team that rediscovered female kakapo after that species was considered 'functionally extinct', and the team that captured Richard Henry, the kakapo he's holding in the photo above this story. (A bird so important for the kakapo recovery program that his death was recorded by Wired magazine). On top to those achievement you can add hundreds of projects in New Zealand and overseas which Don contributed to, or made use of the methods he'd developed here

Nic Valence spoke to Don about the robin project a few years ago.

Nic also found a quote from an interview with Don that makes a fitting eulogy. Talking about New Zealand's natural heritage he said:

“They are our national monuments. They are our Tower of London, our Arc de Triomphe, our pyramids. We don’t have this ancient architecture that we can be proud of and swoon over in wonder, but what we do have is something that is far, far older than that. No one else has kiwi, no one else has kakapo. They have been around for millions of years, if not thousands of millions of years. And once they are gone, they are gone forever. And it’s up to us to make sure they never die out.

Though I struggle to understand them, there are people who are not sold on the importance of conservation by comments like that one. So here's another quote from Don, this one recorded by Douglas Adams when he visited Don and the kakapo as part of Last Chance to See

All we can do is perpetuate them during our lifetime and try to hand them on in as good a condition as possible to the next generation and hope like heck that they feel the same way about them as we do.

If we are so careless that we still lose the kakapo, or the black robin we won't just lose a unique product of our countries long history; we will lose something that Don Merton, and thousands of other people have committed their lives to. If we let that happen we are vandals, just as surely as someone who defaces a monument is.

Sunday Spinelessness - The sight of a wild slug eating

2011-04-17T21:49:00.006+12:00

Did you know that I'm in the pocket of big bussiness ? Or that I set out to bamboozle people with fancy graphs? Or that I show the typical arrogance of the modern scientist? Well, it was news to me as well, but all this, and much more, appeared in the comments underneath my article on Ken Ring's (non)ability to predict earthquakes when it was picked up by the National Business Review. One of my crtics did a little research about me and decided that... well I'm not sure what he decided:

As for people like David Winter - well he is in the pocket of people like the NBR - after all if the economy goes down the gurgler he just might not get any more freebee grants so he can go off and study snail trails. Studying snail trails wouldn't engage someone for many hours a day, no doubt why he has had time to pen the "syndicated" article above. So here we have people like David Winter and the NBR "feeding" of the Christchurch earthquake.

I've had plenty of support, both public and private, in funding my research and I'm very grateful for it, but I'm not sure propping up a right-wing newspaper would be a very good way to expand spending on basic research. As it happens, I have never studied snail trails (although there's plenty of science in that mucous), but I've looked into something I'm sure my anonymous critic would be equally dismissive of.

I want to know what my snails eat. That might seem like an easy question to answer, couldn't I just set up in the field with a notebook and write down what I see? Not really, land snails are generally only active for a small proportion of the day, and even if you can observe them feeding it's hard to tell what they're eating. The lettuce-destroying slugs and snails we are familiar with are the odd ones out in the malacolgical world - most land snails don't eat live plants, instead, they prefer decaying matter or algae and fungi growing on various surfaces (some others are carnivores). So, to try and learn something about the diet of my land snails I broke out a scalpel and started collecting the gut contents from my preserved specimens and picking through them to see what they've been eating (and if there are differences between species).

I'll talk about those results one day, but while I was doing those dissections I started finding and more of the leaf veined slugs I've written about before. Including babies:

Which made me think: what are these guys eating? As ever, I turned to google for an answer and Te Ara had it "their biology is poorly known, but they are thought to live mainly on algae and fungi on the surface of plants". Sure enough, searching through the literature on the 30 or so species of leaf veined slug in New Zealand, there is no indication of what it is that they eat. That was too depressing for me, we know so little about the biology of our native invertebrates, but this species (Athoracophorus bitentaculatus) isn't particularily rare, we should at least know what this one eats.

Don't worry, I didn't start sacrificing cute little slug-lets in the name of science. There's another way to get gut contents (note also, that even flattened slugs have the strangely twisted anatomy of the snails from which they descended):

So, I took to stepping outside an night time, finding a couple of slugs, and placing them in a bucket. In the morning I'd move them back to the shrubs from which they'd been plucked and scoop a few fecal samples out of the bucket to inspect along with my dissections. And here's what I found when I looked down the microscope:

And a little closer:

It's took me a pretty long time to work out what these three-lobed structures were, but I'm pretty sure I know now. They're pollen grains. You can tell a lot about the world from studying pollen grains, each year plants put out millions of these structures, each once identifiable to a taxonomic group. To a trained eye, a series of pollen samples from a old lake bed can reveal past climate change or the evolutionary history of our country. Pollen can even solve crimes. To my eyes... well, I think these are from the massive pine tree next door ( the smaller lobes are "bladders" designed to catch the wind and let the pollen fly, and are unique to pines and their relatives).

It's not actually clear that the slugs were going out of their way eat pollen, it might just have been on the surface they were eating from and unavoidable. It's certainly clear that a lot of grains made it through the digestive system intact. So I still hadn't really cracked the mystery of what these guys were eating. Then, a couple of weeks ago I noticed something. The railing along the pathway the leads down to our front door is covered in algae and fungi, with a very distinctive pattern:

These are slug feeding trails. As they slide across a surface, slugs and snails use an organ called the radula to rasp away and remove the food. I must have walked past this evidence a thousand times without ever thinking about it! The next night I went out with my deeply amateur night-shoot gear and, sure enough, there the slugs were:

So, now we know, leaf veined slugs do indeed live on algae and fungi (and possibly pollen too) but not only on the surface of plants!

I don't know how I managed to write this post without checking for similar posts at Snail's Tale's by Aydin Örstan, the blogosphere's preeminent malacologist (I'm sure there's a trophy for that). Remarkably, Aydin has found pine pollen in fecal samples from slugs, and has found feeding tracks left by the same species! Perhaps his Arion and my Athoracophorus fill the same niche on opposite sides of the world.

Hello boingboing readers! If you want to find some more backyard science, I've also been keeping an eye on a little colony of spiders (1 ,2,3) and I once tried to find out what makes bumblebee workers get working. If you're a fan of spineless creatures in general, you should check circus of the spineless which collects posts from all over the web (and all over the world). The last edition was hosted by Zen Faulkes at Neurodojo and you can find the older ones here.

Sunday Spinelessness - Wolf spiders make good mothers

2011-04-10T20:37:00.001+12:00

Sometimes I wish I was a better photographer. I have lots of fun sticking a lens in front of the spineless creatures I find in my travels, but every now and then I happen across something so cool I wish I could share it in some real detail:

That's a mother wolf spider (Lycosidae) clinging to the wall of our house, with hundreds of baby wolf spiders clinging to her back. Wolf spiders make good mothers. They spend their days hunting, eating whatever prey passes their course. That mobile lifestyle leaves them no chance to build a nest for their offspring, so, instead, they carry them around with them. First as an eggsac (I photographed a pair fighting over ownership of eggs last year), then. once they've hatched, as a whole mass of spiderlings. The spiderlings stay on their mothers back for a week or so, leaving just before their first moult, and they don't eat during their stay.

So, a pertty cool piece of biology, but I can't help but feel it's shame someone with a bit more skill (and some flash camera gear) had come across the sight:

What makes a great scientific talk?

2011-04-06T13:10:00.009+12:00

Genetics Otago (the group behind the Southern Genes blog at sciblogs) runs a bi-weekly meeting for postgrads to catch up, find out about each others work and perhaps even learn something about life as a budding academic. Next week I'm going to present a short talk on... how to present a short talk.

Looking about for some resources around the web, it seems most just reinforce the preferences of the author. To try and be a little more representative in my approach I'm going to present the notes I've written for my talk so anyone with an opinion can tell me what I've missed and what they think I've got wrong. This is going to be presented to postgraduate genetics students, but most of the skills that go into making a good presentation apply beyond genetics and even science, so I'd welcome feedback from anyone.

(As new tips come in, I'm adding them in italics)

Think about your audience, then tell them a story

You might know all there is to know about the protein family you study, the amazing new phylogenetic methods you used or why finding the mutation that underlies the phenotype you are studying will change the world - but does your audience? As a postgrad you've become an expert in a very narrow field, but you'll hardly ever talk to an audience in which everyone is as clued up as you are. Be generous and share some of your knowledge, think about who comes to the sort of talk you're presenting (you lab? your department? an inter-department program? the public?) and think about what they already know, what terms they'll be familiar with, and what sorts of data and results they're used to interpreting.

It seems bizarre that I should have to mention this, but you should also think about what sort of thing the members of your audience care about. You hardly ever get a chance to talk about all of your research at once, so when you prepare a talk you are always making a decision about which details to include. Think about your audience when you decide the 'angle' you want to take in your talk; are they specialist your area will be interested in how you applied a bleeding edge technology to your problem? Or are they wider audience, who are more interested in how your results will be translated into practical benefits? (That last angle is a little harder to work if you study speciation in land snails).

Once you have your angle, and you know the level at which you will pitch your work, you're well on the way to the single most important tip for any presentation: tell us a story. A week after you've given your talk, no one is going to remember the degree to which transcript NM_091299.1 was over-represented in your second experiment, but if you told them a really good story about how you found out how a certain gene plays a role in a disease it will stick with them. So how do you tell the story...

Whatever you do, don't open powerpoint now

I couldn't care less what software you use to present your story, you can make awful presentations in prezi and you can make wonderfully clear ones in powerpoint, but the worst thing you can do is start writing you presentation in powerpoint. As soon as you sit down in front of that program you're sucked into making those bullet point lists:

Capulets and Montagues
- Alike in dignity
- In Verona
- Ancient grudges
  - led to new mutiny
Romeo and Juiet
- From these loins (C&M)
- Star cross'd lovers
- death marked love
  - buried their parents' strife

There might be some sorts of information that are best presented in this way, but certainly not the whole talk. More to the point, most people use these lists to mark out the structure of their talk. That's not what slides are for. The slides are their to illustrate, back up and reinforce the things that you are saying and to present your results once you've prepared your audience for them. At the moment you should be worrying about the story you're going to tell.

Stories have structures, and almost all good scientific talks follow a similar structure. They start with a broad outline of the field you studied (tailored, of course, for the audience you are talking to) which narrows in on the one bit that you are working on. It's nice to end this introduction with a clear statement of the questions you're asking: "what genes get turned on in queen bees but not workers", "what, if anything, is a rabbit?", "Why are some sheep more resistant to parasites than others?". Then you present the results that hopefully answer the question, before finally stepping back and showing how those results have changed the big picture you presented to begin with. It goes without saying that you need to be careful and precise when you are describing your results, "telling a story" is not another way of saying that you are free to throw in wild speculations or ease over wrinkles in the data.

Take some time to design your slides

You could spend a whole session on information-design and scientific data (I contributed to one last week!), but the most important points are pretty obvious. Make all your slides clear. Don't spend hours worrying about the particular font or colour combo you use (light on dark is fine, as is the opposite) just make sure everything you present is legible and nice to look at. Don't use esoteric fonts, because they probably won't be on the computer you use to present your talk. Do proof read your slides (I'm terrible at this, and really should get other people to do it for me).

Often, cartoon style diagrams or illustrations help you explain complex ideas quickly. When it comes to graphs and data, you should really think about each element of the figure and decide whether it needs to be there to convey the point you are making: does anyone care about the precise value of the probabilities on your giant phylogenetic tree? Do you need a legend for your bar chart, or can you directly label the bars? You don't want to end up saying "I know this is hard to see but..." at any stage (that includes pie-charts of your 154 GO terms, use an ordered dot plot or bar chart instead). If you use colour, be aware about 7% of the males in your audience will be red-green colour blind, you can use one of these palettes and check your resulting graphics here.

If you are presenting the same comparison in multiple slides (wild type against mutant, or one species against another) keep the colours consistent from slide to slide. There's a lot more that could be said about this, I'll add links to some great resources on information design below.

Give you slides decent, descriptive titles ("Mutant is 100x less effective than wild-type", not "Alleles compared")

Practice your talk

Another one firmly from the "I shouldn't have to say this" category, but how many times have you been to a seminar that ran 20 minutes over time? Despite anything else, it's incredibly rude to turn up to a presentation without having rehearsed it, especially if you're at a conference in which your overflow eats into someone's time.

Rehearse your talk out loud, and preferable to a test audience.

You should consider your notes and your first set of slides as a first draft - something to be pared down into a tight presentation that you know inside-out by the time you present it. The challenge here is how to do that and still sound fresh when you present...

Be an incredibly charismatic and dynamic presenter (or just yourself, actually)

Everyone will have their own presentation style. I'm one of those people that talks a thousand miles per hour, walks about the stage and waves his hands. Some people think that's a presentation skill, but, really, I'm just a big science fan-boy and I can't stop myself. If you're not that sort of person, then there's no point pretending to be, and you can present a great talk without running around like a fool. But there are a few things you can do to to keep an audience interested in what you're saying.

Don't rote learn every line of your talk

It's much better to have a few key points or phrases you want to get to and a good idea of how you'll navigate between them that to present a dreary mantra. Knowing where each passage is headed also prevents that very kiwi trait of adding an upward inflection to each sentence, which doesn't fill anyone with confidence! You'll likely be nervous when you start your talk, knowing exactly what you'll say in the first few minutes will let you ease into the talk and feel confident once you move into the body of the talk.

Know what's on your next slide

This is a really easy and effective one, if you start talking about the next piece of data in your talk before you actually present it you are able to prepare your audience for what they're going to see, and you don't take their attention away from what you are saying. The "Presenter tools" feature in later versions of powerpoint lets you see the next slide (and a timer) on your screen.

Take a breath either side of presenting something cool/weird/important

Just like it says, use a little bit of silence to underline the things you really want people to remember. If you have a really controversial or counter intuitive point to make, think of a short sharp sentence that describes it, take a second to let it sink in then start explaining why you think it's true.

A pointer on pointers

A nervous presented makes for shaky hands, and shaky hands and laser points really don't go together. I personally like the big-pointy-stick method (as displayed by the wonderful Hans Rosling in his TED talk) if the screen your presenting on is small enough. Alternatively, you can rest your 'pointing hand' on the dais, or use the mouse to highlight sections or even draw on your slides during your talk.

Be confident

You know what your talking about, really, you've done a literature review and you've collected all this data. A lot of younger postgrads suffer from a sort of imposter syndrome: they think they've somehow snuck their way through an undergrad course and into a scholarship and PhD program without anyone noticing they don't have a clue about what they're doing. This lack of confidence is manifested in two ways: people either present their data apologetically ("I think...", "...or something", "but I don't know") or they go to the other extreme and drown their message in jargon, as if they were proving they too can wield these words, just like a real scientist. Neither of these are approachs are a good idea; if you don't believe your conclusions why will anyone else, and too much jargon will leave half the audience behind.

Leave time for questions, and be honest in answering them

Of course, you should leave time for questions and of course it's much, much better to say "I hadn't considered that, do you want to talk about it later" than to extemporise a wild and whirling answer to that guy that just has to ask the really mean question.

In powerpoint, typing the number of a slide then pressing 'enter' lets you jump to that slide. If you remember the number of "the big data slide" in your presentation (or write it on a post-it), you can skip write to it when you are asked a question about it and look like a pro.

Have fun, and ignore what I said

Don't get too worried about all these rules. If you understand why they might be helpful in some cases, then use a little judgment and decide if they work for you. It would be great to see a talk that doesn't start with a broad introduction, but instead a single slide showing the most important result to come out of your work. From there you could work back, and try and convince your audience that the slide really was worth it's place at the start of the talk. Presenting is an important skill for a scientist, and if should be one you try and develop through you career. When you go along to departmental seminars and conferences, take note of the way people present their work. Learn what works and what doesn't (especially note things that annoy you or waste your time, and try and avoid those!)

Remember, I want your ideas on how to make my advice better!

Here are some links with tips on designing charts/diagrams/illustrations (feel free to suggest more):

Mike Dickison from Canterbury runs an information design consultancy and has some useful tips on his blog. Mike also runs a short course on presenting, you can download the notes from his class [pdf] and see a whole slew of useful links here.
Elf Elridge porvided a link to some tips put together by the postgrads at the MacDiarmid Institute
Edward Tufte is kind of the grandfather of information design, lots of great stuff (but be aware his followers can be a little... fanatical)
A recent workshop entirely devoted to visualising biological data (with speaker's slides available)
Check out David Lubinkski's advice and links in the comments at sciblogs, lots of good stuff

Sunday Spinelessness - The Entomologist who invented Daylight Saving Time

2011-04-03T09:04:00.004+12:00

Today marks the end of the Daylight Savings Time in New Zealand, so local readers will have had an extra hour at their disposal to sleep through, get more work done, or explain to their children that they are meant to stay asleep for longer today. However you used that extra hour, you should take a moment to think of the extraordinary amateur entomologist that came up with the idea that gave it to you.

George Vernon Hudson was one of New Zealand's first and finest entomologists. He described hundreds of our insect species and worked out the lifecycles of still more by raring their larvae at his house in Karori, Wellington. Hudson was a not a professional entomologist - he had a day job as a shift worker at the Wellington Post Office. Working shifts gave Hudson a chance to get out and collect insects while others were working, and it also made him aware just how much daylight people were sleeping through during the summer. In 1895 Hudson read a paper to the Wellington Philosophical Society (part of what became the Royal Society of New Zealand) in which he advocated putting clocks forward in October so sunrise wouldn't happen hours before anyone woke up and the pushed-back sunset would mean "a long period of daylight leisure would be made available in the evening for cricket, gardening, cycling, or any other outdoor pursuit desired".

By all accounts Hudson's proposal wasn't well received. The paper itself wasn't printed (the quote above is from a follow-up he presented in 1898), but reactions to it were reported in the society's journal. William Maskell, the president of the society and a fellow entomologist, was particularly scathing (and inaccurate) when he said " the mere calling the hours different would not make any difference in the time. It was out of the question to think of altering a system that had been in use for thousands of years, and found by experience to be the best." Apparently, Hudson wasn't deterred by the bad reaction his paper got, and he kept pressing the idea. By 1898 he claimed the support from many people, particularly in Christchurch, but in the end, it all came to nothing. Daylight Saving Time as we know it was really the result of an English builder called William Willet, who came up with the idea independently and managed to get his plan considered by parliament. But the turning of the clocks, and GV Hudson's role in coming up with the idea, are the perfect excuse to show off one of my favourite possessions :

I have a copy of Hudson's first major scientific book, New Zealand Moths and Butterflies (1898). My copy used to belong to the Wellington Acclimatisation Society. It came to me by a circuitous route, but it seems the book spent at least some of the last hundred years sitting in a shed. It's largely a taxonomic work, full of anatomical details and the curious codes by which taxonomists speak to each other. That much is interesting to a specialist (and I really should donate the book to a research library), but the real stand-out feature is the 13 colour plates, each one full of Hudson's beautiful hand-drawn illustrations

The common copper as drawn by Hudson (Chrsophanus salustius to him) and the same insect at Sinclair Wetlands last year (it's called Lycaena salustius today).

On top of these wonderful illustrations, there are two letters tucked away inside the book, each written to the Acclimatisation Society by Hudson. They are probably not of outstanding historical interest, but they do tell us something about life as an amateur naturalist at the turn of the 20th Century, so I'm going to reproduce them here. In the first, written in 1898, Hudson writes to follow up a conversation he'd had with the members of the Acclimatisation Society about a truly hair-brained scheme to introduce English mayflies to New Zealand to feed the trout they'd already brought over

Dear Mr Morris,
Referring to our conversation of this afternoon regarding the introduction of the common English may-fly Ephemera vulgaris, into the New Zealand streams as food for the trout, I must say that I do not think its introduction is necessary. I have devoted considerable attention recently to the study of the various neropterous larvae which inhabit the streams including those of the Ephemeridae and I have been astonished at the great number of these larvae.
Apart from the fact that our native Ephimerae would appear to be amply sufficient for the requirements of the troutc etc, I should mention that the larvae of these insets are extremely difficult to keep in captivity and I thnk that it would be almost impossible to introduce themfrom England, except perhaps by the egg state ... I think therefore that any attempt to introduce th English may-fly into this country should certainly be discouraged

Four years later, Hudson had written a new book on the New Zealand Neuroptera (a taxonomic group that included mayflies and dragonflies at the time). Being an amateur, Hudson's work was funded from his salary at the Post Office and whatever money his books might make. So, he decided to try and cash-in on the advice he'd given the Acclimatisation Society:

Dear Mr Rutherford,
I enclose herewith a specimen plate and some prospectives (?) of my new book on the New Zealand Neuroptera. If you could mention the book and exhibit the plate at the meeting of the Acclimatisation Society on Thursday next I should be very much obliged. The new secutary also has a copy of the plate. During Mr Morris’s time I was asked by the Society to report as to the necessity and best means of importing the British may-flies into New Zealand and in reply I said that such an importation would in my opinion be quite unnecessary ... my recommendation probably saved the Society a considerable sum of money... I think I have some claim on the Society and its members for a liberal support of my book.

I don't know what happended to his Neuroptera plates, but, evidently someone like Hudson's work enough (or felt sufficiently grateful for his help) to buy his butterfly book.

According to Rebecca Priestly's short biography, Hudson wasn't a fan of professional science. When New Zealand's DSIR was set up, he declined the chance to join, and he even intended to donate his collection to a British museum rather than one overseen by government scientists in New Zealand. Thankfully JT Salmon convinced Hudson to give his collection to the Dominion Museum, and today its housed at Te Papa. Old insect collections are immensely valuable tools for research. When I was studying GIANT springtails we went back to old collections (including Salmon's, but not Hudson's) to find out how widespread these species were before human-impacts like logging broke up their habitat. Hudson's collections are really valuable for this sort of research because he was collecting in Wellington while there will still decent patches of native bush around that city. Comparing modern collections to Hudson's helps entomologists see how habitat changes have affected native species. Hudson's work lives on in another important way, his grandson George Gibbs took up the study of insects will have passed on his passion for the subject to many of his students at Victoria University

So, New Zealanders: enjoy your extra hour. Those readers tuning in to this post from the Northern Hemisphere: remember to honour that fact that daylight savings was first proposed by someone that wanted to spend the extra daylight ito get out and find some bugs!

Sunday Spinelessness - The rest of Vanuatu

2011-03-27T16:48:00.002+13:00

It's about time I stopped drip-feeding these Vanuatu photos and presented the "best of the rest".

I've had a very tough time trying to identify most of the bugs that I came across in Vanuatu - there aren't really any resources dedicated to invertebrates in Vanuatu or even Melanesia in general so it's a matter of trying to ID each creature as far down the taxonomic scale as possible then hope there is something recorded for that taxon in Vanuatu. Thankfully, I got a helping hand in idenfying this odd looking fly:

Ted MacRae encountered a similar looking fly in his travels through Brazil (and took a much better photo, you shold check it out) and he had the skill and the perserverance to work out his fly was from the family Neriidae (sometimes called cactus flies or stalk legged flies).

Evidently, the feature that seperates Neriids from realted families is the bristle like "arista" on the top of the antennae which is nice and clear in this photo. Neriid species from the genus Telostylinus have been recorded from New Caledonia (which is adjacent to Efate, the island on which were staying in Vanutatu) and the black and white stripes on this fly suggest its from this genus. If you look at Ted's photos, you can see the forelimbs of male Neriids are spiked, a feature you usually see in predators like crab spiders and robber flies which need to grab and hold their prey. Neriids eat rotting plant material, which is unlikely to escape their grip. It seems the spikes are used when males wrestle and strike each other in the hope of gaining access to females.

Here's the first invertebrate I saw after landing in Vanutatu:

You'd have to try very hard to miss these massive orb web spiders, in the fifteen minute drive from the airport to house at which we stayed I spotted five or six. In town, they tend to set up their webs on power lines and between houses. I gather they are Nephila plumipes, one of the golden silk orb weavers. Unfortunately, becuase they weave their webs at such great heights and I couldn't get close enough to them, these photos don't really show how massive these spiders are.

Female Nephilla are the largest of the web building spiders, their bodies alone are about 50 mm long and their webs span 2 metres. If you look closley at the photos above you'll see some much smaller spiders in the same web as the massive one. The smaller spiders could very well be 'kleoptoparasites', species that live within the webs of larger spiders and steal their host's prey. But, it's also quite possible some of the smaller spiders are males of N. plumipes, eyeing up the much larger female as a potential mate.

It seems the evolutionary process that made Nephilla females so large left the males of the genus behind. In fact, small males are probably less likely to mistaken for food by the large females, so it's even possible that males of these species got smaller at the same time as the females grew. Whatever the reason, Nephilla males are often ten times smaller than their mates. This is the bit where I would have tried to explain some of the mechanics of spider sex, but, rather wonderfully, Isabella Rosellini, has already done that:

Thanks to Alex Wild for finding that video, his post presenting includes a great photo of the difference between a male and a female Nephilla.

I think there's room for one more spider from Vanuatu as the last of terrestrial invertebrates from my trip. An unidentified orb weaver in the sun at the Mele Cascades waterfall:

Sunday Spinelessness - Dragonfly

2011-03-20T21:41:00.006+13:00

I appear to have run out of Sunday in which to write about bugs. No matter, I think I have a photo that'll more than make up for a lack of words on my part.

Face to to face with one of the orange dragonflies that spent their days zooming over (and, in this case, falling into) the swimming pool at our house in Vanuatu.

and the close up

That's all from me today (I have to get back to writing about statistics and land snail gut contents, which is actually surprisingly interesting),if you're a fan of these beautiful bugs theres a couple of posts about dragonfly's closest cousins the damselflies here.

From a blog post to TV

2011-03-17T09:04:00.001+13:00

There can't be many countries in which you could end up on national TV for staying up all night and writing a blog post criticising someone, but New Zealand is one them.

I knew when Campbell Live aired that interview with Ken Ring there was going to be a great deal of interest in his predictions, but I never imagined just how far my post on the topic would reach. It got more than a years worth of normal traffic for me and my wierd bugs and was quoted by an AFP article and Radio New Zealand's Mediawatch (one step towards my life goal of being interesting enough to be interviewed by Kim Hill). Then I got contacted by Tristam Clayton from Campbell Live, who was putting together a follow-up to that first interview and wanted to include me. I think the hour or so I spend filming that interview isthe scariest thing I've ever done, and I was very nervous from start to finish. Somehow, they managed to cut together a few minutes that make me sound as if I know what I'm talking about, and I'm very happy with the way it turned out. I don't think the TV3 site lets you embed their videos, but you can go and see it here (the site isn't geo-locked, so, foreign friends, you should be able to laugh at my accent):

Ken Ring’s quake theories – how scientific are they

Sunday Spinelessness - Why we have bumblebees

2011-03-13T22:03:00.005+13:00

We've had a stunningly beautiful day here in Dunedin. It's been feeling pretty autumnal around here lately, so there was no way I was going to spend any more time in front of a keyboard than was strictly necessary. As a result today's post is going to be short, but, I think, rather sweet. The insects in our garden seemed to be enjoying some summery weather too. Like this bumblebee I caught visiting a Tradescantia flower. In this shot you can see the ocelli - the set of "simple" eyes on the top of the head and gauge the intensity of light.

In this photo you can see the feature that brought these bees to New Zealand.

There are a few native bee species in New Zealand, but none of them have a tongue quite like Bombus hortorum, and that's why we have bumblebees. European settlers tried to introduce red clover as a pasture, but the native bees and the (already introduced) honey bee couldn't reach into the flowers well enough to pollinate them. This meant early farmers had to import fresh seed almost every season, and were desperate to work get clover to set seed. An English naturalist by the name of Charles Darwin had talked about the pollination of red clover in a little book called The Origin of Species:

From experiments which I have tried, I have found that the visits of bees, if not indispensable, are at least highly beneficial to the fertilisation of our clovers; but humble-bees alone visit the common red clover (Trifolium pratense), as other bees cannot reach the nectar *

Evidently, someone in Canterbury had read their Darwin, so the acclimatisation society asked their contacts in the UK for some queen bumblebees to establish local populations. In the end four species (B. hortorum, B. terrestris, B. subterraneus and B. ruderatis) took hold and now the lovely baritone buzz of bumblebees fliting from one flower to the next is a part of summer in New Zealand.

The acclimatisation societies which were set up in New Zealand were basically ecological vandals, introducing familiar European species with no thought to what they'd do the native inhabitants . These are the people that introduced trout to our streams (decimating native fish species) and stoats and weasels to our forests (driving native birds to extinction). So, it feels bit odd to say that, in the case of bumblebees, the acclimatisation societies actually did something very good. Bumblebees are attracted to big showy flowers of the sort our native flora is lacking in, so they don't displace any native species in forests and their introduction has come an no cost to our native ecosystems. Even better, the thriving populations of bumblebees in New Zealand have the potential to rescue the seriosuly unhealthy populations from which they were sourced . One of the introduced species, B. subterraneus, is now presumed to be extinct in Britain and all of the others are declining due to habitat loss and the overuse of pesticides. Last year, members of the British Bumblebee conservation trust came to the South Island to collect mated queens in the hope of establishing new populations of these bees back home. I gather that particular mission didn't work out, but, if the causes of the bumblebees' decline in Britain can be turned around our bees will be the prefect stock from which to re-establish these species.

*The section from which this quote is pulled is and interesting in that it's one of several proto-ecological ideas in The Origin. Here it is in full:

From experiments which I have tried, I have found that the visits of bees, if not indispensable, are at least highly beneficial to the fertilisation of our clovers; but humble-bees alone visit the common red clover (Trifolium pratense), as other bees cannot reach the nectar. Hence I have very little doubt, that if the whole genus of humble-bees became extinct or very rare in England, the heartsease and red clover would become very rare, or wholly disappear. The number of humble-bees in any district depends in a great degree on the number of field-mice, which destroy their combs and nests; and Mr H. Newman, who has long attended to the habits of humble-bees, believes that ‘more than two thirds of them are thus destroyed all over England.’ Now the number of mice is largely dependent, as every one knows, on the number of cats; and Mr Newman says, ‘Near villages and small towns I have found the nests of humble-bees more numerous than elsewhere, which I attribute to the number of cats that destroy the mice.’ Hence it is quite credible that the presence of a feline animal in large numbers in a district might determine, through the intervention first of mice and then of bees, the frequency of certain flowers in that district!

Sunday Spinelessness - Vanuatu jumping spiders

2011-03-06T12:27:00.000+13:00

So, last week my little old blog found itself in the middle of a national discussion abuot Ken Ring and his claimed ability to predict earthquakes. In this space of two days that post recieved a good deal more than a year's worth of The Atavism's normal traffic.

And now I have to tell anyone that subscribed to this blog in the wake of that article, hoping perhaps that I'd follow the news of the day and provide analysis of the key claims, that I mainly blog about bugs. I'm an invertebrate fan boy, and dedicate a post a week here to celebrating some creature from that ignored majority. Ninety five precent of animal species don't have a backbone, and the spineless multitude contains some of the most amazing creatures on earth.

Today, I'm going back to photos I took in Vanuatu over christmas and looking at my very favourite group of spiders - the jumping spiders (family Salticidae). Spiders get a bad rap generally, almost none of them pose any threat to us*, and absolutely none of them are going to go out of their way to get us. Some spiders, like the long-legged big-fanged Cambridgea in this post, seem to set of a revuslion somwhere deep within our brains, but others are just down right charasmatic. Jumping spiders are the puppies of the arachnid world: cute inquisitive and apparently unaware of how small they are. I've written about the group before, so lets skip right to the photos:

The big round forward-facing eyes are one of the charactersitc traits of the jumpers, because they are active hunters these spiders need to be able to cast a finely-focused image of their prey. Obviously, this one has used its eyes to good effect, I can't tell what it has clamped between its jaws (or chelicerae, if you want to be accurate). It has eight legs, which makes it a fellow arachnid, the body looks a little mite-like but the legs seem too long for that identification so I'm afraid I can't tell you anything more.

As much as it pains me to put up photos with zero taxonomic information, here's a another jumping spider of unknown affinity. This one was truly tiny, perhaps 3mm across the body, but quite happy to have it's host plant bent out of shape to allow a camera to intrude

That's it from me today. You should know that people much more skilled than I am have taken some terrific photos of jumping spiders. Alex Wild has a stunning ant-mimicking spider here, and Thomas Shahan is the acknowledged master in this field. Here's one example of his focus stacked images:

*In New Zealand it's only the katipo and the (introduced) redback

Ken Ring can't predict earthquakes either

2011-03-01T10:19:00.002+13:00

The New Zealand media have done a remarkably good job of covering the Christchurch earthquake. TV, newspapers and radio have all struck the difficult balance between the country’s desperate need to understand what happened on the 22nd and how people are coping with the right that each victim the quake has to privacy in such a terrible time. The media have also shown great restraint with respect to one particular story. Ken Ring, the astrological weather forecaster, claims to have predicted the earthquake. I think Ring, with all his calculations and post-hoc explanations, is the very embodiment of what Richard Feynmann called “cargo cult science” - someone who does some of the things scientists do, but fails in the most defining characteristic by not honestly testing his theories against data. I’ve had a little fun at his expense before, but, really; as much as it makes me sad that we live in a world in which Ken Ring can sell his weather forecasts and appear as an “expert” on anything in the media, the worst thing his almanac does is take money from people. In the wake the earthquake Ken Ring has done something much more serious. While thousands of people are devastated by a natural disaster, and terrified about what might happen next, Ken Ring claims to have predicted the earthquake of the 22nd and that a much worse one is due in March. So, let's do what Ring fails to and test his methods against reality.

If Ring had really made an isolated and specific prediction that a destructive earthquake would strike Christchurch on February the 22nd then he might be worth listening to. His claim revolves around this post from his website a little more than a week before the event. Here's the quotes he'd like you to pick out from that post:

The window of 15-25 February should be potent for all types of tidal action, not only kingtides but cyclone development and ground movement.
Over the next 10 days a 7+ earthquake somewhere is very likely

You might quibble that the Christchurch quake, at magnitude 6.3, was about 5 times less powerful than the M7 event he'd predicted - but I don't think anyone in Christchurch wants to argue about how strong their quake was. On the face it, it really does look like an amazing coincidence: Ring predicted a quake and it happened. But there is more to it than that, I've been through his site and Ring has also predicted earthquakes for, at least, the 24th of September, the 1st and 7th of October the first week in November, the 20th to the 27th of January, the 1st to the 5th and 19th to the 25th of March and the 17th of April. In fact, in one post, giving him the +/- one day he needs in order to claim he predicted the February 22nd quake , he paints more than half of the time between the start of January and the end of March as earthquake risk:

You can add a fair few false negatives to those false positives. In October he claimed the aftershock sequence would die down, missing the major rumble on boxing day and several times he declared that it was unlikely Christchurch would be face another major quake (tragically wrong).

Thanks to the way our brains work, we generally struggle to evaluate theories of causation and claims of prediction fairly. We are too impressed by occasional "hits" and tend to forget the many "misses" which outweigh them. If we want to be rigorous, how should we react to hearing about Ring's "hit" given the litany of "misses" I list above? As it happens there is a theorem for that. Bayes theorem is one of the most important little pieces of maths going around, because it tells us how to update our beliefs about a given question in light of new evidence, and that's exactly what we should be trying to do if we want to lead a skeptical life. It is maths, but it's not too scary. I'm the sort of person that loses contact with scientific papers as soon as 'Σ's and '∫'s start turning up, so you know if I'm writing this , you can follow it. Before we start, we need to define a couple of terms. Let's call P(KR) the probability Ken Ring can predict earthquakes and P(Prediction) the probability that Ken Ring would have successfully predicted this earthquake. From that we want to calculate how probable the claim "Ken Ring can predict earthquakes" is given his successful prediction, well call that P(KR|Prediction). Once we have those defined it's just a little 3rd form algebra:

P(KR\|Prediction) =	P(Prediction\|KR) * P(KR)
	P(Prediction)

So, how are we going to replace those terms with numbers? For now, let's not be one of those close minded skeptical types, ignore how eccentric Ring's methods and takes the evidence as it stands by saying P(KR) is 50%. P(Prediction|KR) is the probability that Ring would have predicted this quake if his methods work. You might be tempted to says this is 100%, but remember, he missed the Boxing Day aftershock and he's repeatedly said Christchurch was unlikely to be hit again, so he's not immune to false negatives either, I'll be generous and give him 90%. The really interesting bit in Bayes Theorem is the bottom term P(Prediction). If we are being agnostic about Ken Ring's abilities then we need to estimate this with regard to both the possibility his method has something going for it and the possibility that it doesn't. We've already said that Ring has an 90% chance of predicting an earthquake if his methods work, what's his chance of 'successfully' predicting a quake even if his methods don't work? This is the most important question you should ask yourself about his claims and it's where all those false alarms come in. Given the 'calendar' above, Ring would have claimed to have predicted the quake if it fell on any of half of the days between January and March. His prediction for February was a little more specific than that, but when you read the post it's still quite vague: "somewhere", "in the ring of fire", "withing 500km of the Alpine fault". I'm going to say, given the huge number of predictions he's made, there was about a 30% chance any day that had an earthquake would have been one Ring had previously predicted. To get P(Prediction) we have to balance each scenario like this:

Now, when we put the numbers in like so...

P(KR\|Prediction) =	0.9 * 0.5
	0.6

...we end up with P(KR|Prediction) being 75%. Ring's successful prediction still supports the case that his methods work, but it's hardly the decisive piece of information that allows us to say once and for all that he knows what he's doing. You almost certainly want to put different numbers than I did in that equation, and you should. The idea is not to convince you a particular value is the right one, but to show you how including those false positives in our assessment of his claim changes the way we update our ideas about it and, by extension, how much stock we should put in his future predictions. There is a Bayesian calculator here for anyone that wants to play around with other numbers, over there P(H) is what we called P(KR), P(D|H) is P(Prediction|KR) and P(D|'H) is the probability Ken Ring got it right by mistake (the one I gave 30%).

Skeptics are often accused of being closed minded for sticking to scientific orthodoxy in the light some piece of evidence or other: "If you would just let this evidence stand by itself you'd see my theory is true!". Assessing any evidence by itself, without our background of knowledge on a topic, is not being open minded - it's being willfully ignorant. When we want to compare one theory to another we should use all the evidence available to us, and that includes what we know about how the world works. Ring thinks earthquakes happen when the moon makes its closest approach to the earth (called perigee) and around full and new moons. This next sentence really pains me, but here goes. His theory is not 100% lunacy. The phases of the moon have no effect on the earth [whoops, as pointed out in comments, they kind of do, since they correlate with moons position relative to the sun and contribute to tides, this was included in the models/charts below so doesn't change their conclusions], but the position of the moon in its orbit just might. As every schoolchild knows, the moon exerts a tidal force on the planet and there really are "land tides", tiny swells and lulls in the crust of the earth analogous to the ocean's tides, that ebb and flow through the day. It's just possible that a fault that has been loading up with pressure for hundreds of years is more likely to give way when then moon is close and the tidal forces are stronger. But think about that for even a second and the problem becomes clear. Even if the moon is sometimes the straw that breaks the camels back at a particular fault, you couldn't use the moon to predict an earthquake unless you already new a fault was about to go, i.e., the moon could only predict earthquakes when you could already predict an earthquake!

Ken Ring get's a bit touchy about scientists dismissing his theories out of hand, so let's look at some data. I actually asked Ring for some help with this, but he is yet to answer my email. Luckily, since the September 4th earthquake Paul Nicholls from Canterbury University has been plotting the intensity of the aftershock sequence. He's also plotted the two lunar cycles Ring thinks are responsible for the strength of earthquakes: the lunar distance and the moon's phase. In many ways, this is the data-set in which we are most likely to find support for Ring's ideas. We know for a fact that the faults around the Canterbury plains are going to be under stress while the land sorts itself out after the upheaval in September. If the moon really was pushing already loaded faults past their breaking point we'd expect to see it in this data. Usually the most important statistical test you can perform on a data-set is having a look at it. This is Paul's plot from last night, the slimmer of the two waves on the top represents moons orbit (troughs are perigee, the point Ring thinks is most dangerous) and the larger is the moon's phase (the troughs are new moons).

If you can see any correlation between either of the lunar cycles you're doing a lot better than me. I decided to dig a littler further, and plot the intensity of each day's activity against each of the lunar cycles. First the phases of the moon. Remember, Ring thinks new and full moons are the most dangerous, so we expect a curved relationship higher at either end of the x-axis. We find no such thing (in fact, if anything, it's more dangerous between the new and the full moon):

How about the distance between the earth and the moon? This is the one that makes just a little scientific sense:

This time the relationship at least goes the right way, the quakes seem to be, on average, more powerful when the moon is close. In fact, when you put this data into a model that factors in the general tailing off in earthquake activity following the initial quake, the distance between the moon and the earth is a statistically significant variable with regard to the energy released. And there lies an incredibly important point. "Statistically significant" means unlikely to happen if the null hypothesis (in this case "the moon doesn't effect earthquakes at all") was true, it doesn't mean the result is "powerful", "meaningful", or even "capable of explaining a great deal of the variation in the data". As is often the case, we didn't really believe our null hypothesis to start with, so it's no surprise a large data-set found a significant relationship. But the actual effect of the moon is tiny, it explains about 2% of the variation in the data. The feebleness of the moon as a predictor is obvious when you look at the graph - there are plenty of days when the moon is close and there was not much energy released and, equally, there's a whole lot of days when the moon was far away and there were still magnitude 5 quakes. The moon might well be having an effect on intensity of earthquakes from day to day, but if it can barely explain any of the variance in this data-set, one that was almost designed to test Ring's theories in the best light, how could it predict an earthquake? It can't.

Let's get back to our calculation, last time we started with P(KR) at 50%. I hope you'll agree, having seen the data, that Ken Ring's methods are not the least bit plausible. I going to be outrageously generous and say there's a one in one thousand chance that he can predict earthquakes, so let's plug that into Bayes Theorem, remembering to update P(Prediction) for this new value too:

P(KR\|Prediction) =	P(Prediction\|KR) * P(KR)
	P(Prediction)
=	0.9 *0.001
	(0.90.001)+(0.30.999)

Which gives us a value of 3 in one thousand. Again, you'll want to put different numbers into the equation, but there's a really important point here. Whenever we hear evidence for some new claim, "a vaccine caused my child's autism", "light behaves as a particle and a wave", "Ken Ring can predict earthquakes (and another one's coming)", we should use that evidence to update our prior knowledge of the world. Sometimes, like the outlandish claim that light can be a particle or a wave depending on how you look at, the evidence will be enough to completely change the we think, more often it will hardly make a blip. I think we can put Ken Ring firmly in the "hardly a blip" category: once you see how implausible his methods are you realise you'd need incredible evidence to believe his predictions and once you see his run of false positives you realise that his "prediction" of last week's earthquake doesn't meet that standard.

The people of Christchurch desperately need information. In the next few weeks they want to know if they'll have to face the terror of last Tuesday again and once they city has pulled itself back up they'll want to understand the future risks for the city. In a climate of such desperation people have a duty to provide only verifiable information and to explain that information's limitations. That's exactly what scientist from GNS and Canterbury University have done when they've spoken to the media. Ken Ring, who lambasted GNS for scaring people with a "knee jerk" comment that a magnitude 6 aftershock could be expected after the September earth quake, has not lived up to that duty and I really hope no one takes him seriously.

Note: I know this is a topic people will want to comment on. I'm writing a PhD at the moment and really can't take time to moderate a comment thread. I'm happy to allow comments, but don't expect instant replies today, or(at sciblogs) for comments to clear moderation straight away.

The data I used for my graphs was scraped from Paul Nicholls site, I chucked it up on google docs for anyone that's interested. I've also uploaded the R code I used to plot/analyse the data - this is an open access debunking! (BTW, did you know both R and the ggplot library I used to make those graphs were developed by New Zealanders? We grow good geeks here.)

The very error of the Moon Man

2011-02-28T17:05:00.009+13:00

I've been very impressed with the New Zealand media's reporting of the Christchurch earthquake. They've managed to balance the need so many of us have felt to understand the terrible tragedy of the 22nd with the victims of that tragedy's right to privacy in such an awful time. Up untill today, they'd also shown great restraint in not indulging in the story Ken Ring, the astrological weather forecaster who claims to have predicted Tuedsday's quake. It seems Campbell live has given in to the temptation, and will feature Ring's 'forecast' today. I have a draft of a post dealing with Ring's claims on the way, but I won't have time to finish that today, so let's make one thing clear.

On his website, Ken Ring has predicted earthquakes for, at least, the 24th of September, the 1st and 7th of October the first week in November, the 20th to the 27th of January, the 1st to the 5th and 19th to the 25th of March and the 17th of April. In fact, in one post, giving him the +/- one day he needs in order to claim he predicted the February 22nd quake , he paints more than half of the year as a time of increased earthquake risk (those are the red circles):

He also predicted a particular pattern of aftershocks on the day following the quake, and, when that failed to happen deleted the failed prediction from his twitter stream (stay classy Ken). And he missed the boxing day aftershock. [note: it's possible Ken didn't delete his prediction for aftershocks on the 23rd, that particular tweet does show up sometimes for some people]

No matter how hard we try, our brains come pre-built to be emphasise "hits" like Ring's prediction and discount the more plentiful "misses". The real question we should ask ourselves when we hear that Ken Ring predicted the Christchurch earthquake is "how likely is that he 'predicted' this event, even if his method doesn't work". By my count, for any earthquake there's about a 50% chance Ring will claim to have predicted it no matter what. I don't think we should be amazed he got this one.

Hopefully I'll have a complete post expanding on this reasoning up by tomorrow.

update: The Campbell Live has just aired, and, boy did they do a good job! Very clearly set Ring apart from the science, but his failures to him and presented the real science of earthquakes. Nice one.

Sunday Spinelessness - My second favourite spiders

2011-02-27T09:15:00.002+13:00

I think I've already said that the jumping spiders (family Salticidae) are my absolute favourite group of spiders. As much as I like the Dictynids I've been observing in our agapanthus, if I was asked to pick the group that took the next biggest place in my heart I'd have to go for the crab spiders (family Thomisidae). I've written about these spiders before, so it you want the run down on the biology of these 'sit and wait predators read those posts, today I'm just showing off some photos of a partcularily striking crab spider I found hiding under a banana leaf in Vanuatu:

If you look closely at those enlarged "raptorial" forelegs you can see downward-facing spikes which are used to increase the spider's grip on any creature foolhardy enought to fall within their grasp:

One of the reasons I like jumping spiders so much is they really show no fear when it comes to humans. Most spiders, despite their reputation, will run away when faced with a someone snooping around their hiding place, whereas jumping spiders very clearly eye you up as possible meal. Crab spiders aren't quite so outgoing, but they aren't timid either. This one got fed up with me holding its leaf up to get a photo, and decided instead to attack the camera lens then run up my arm. Whe even that approach didn't keep the camera out if its face I got a very clear threat signal:

One day I going to run a whole set of out of focus photos of bugs attempting to attack my camera, but for now I have other work to do!

A clearinghouse for #eqnz science reports

2011-02-23T16:44:00.016+13:00

Like many New Zelanders, I'm struggling to understand what happened yesterday. We all know that a devestating earthquake struck Christchurch around lunchtime yesterday, killing at least 75 people and destroying much of that beautiful city. Of course, the tragedy of the Christchurch earthquake can be measured only in the lives it's affected, you don't need to know about rocks to understand this story, which has no doubt been repeated in a thousand different variations across the city. Obviously, the most important thing at the moment is that people in Christchurch get the help they need. Still, if you have a brain like mine, then somewhere in the struggle to understand the tragedy and the overwhelming feeling of uselessness you just need to know how this happened. I'm going to use this post to collate links to articles that do a good job of explaining some of the science behind yesterday's earthquake, but first here's what I've learned from reading them.

The quake seems to part of the sequence of aftershocks from the 7.1 Darfield earthquake of September. It might be that the massive release of pressure in that quake added to the strain at a fault that was already under stress; or it might simply by part of the pattern of aftershocks following that quake which have been progessively more shallow as they've proceeded. What's abundantly clear is that, even though this new quake was 6.3M and therefore about 5 times less intense than the Darfield one at its origin, it was much more violent than the first. The eipcentre was only 5km for the centre of the city and only 5km below the surface. The peak acceleration, one measure of the strength of the shaking from a quake was 1.88 g which is about 50% stronger than any measurement from the Darfield quake and much greater than anything recorded near to the city in that event. That powerful shaking, the lunchtime rush and already damaged buildings proved to be a terrible combination.

GNS

Science Media Centre

Blogs/News/Whatever

Video

General Aggregators

I'll keep this post updated with any new pages that add something to the story, so please pass any useful links along in comments or via email (david.winter at gmail).

Sunday Spinelessness - Misshapen by love

2011-02-20T17:11:00.004+13:00

I'm not finished with photos of spineless life from Vanuatu just yet, but I do have to interrupt that stream of posts again thanks to goings on in our backyard. Ever since I started writing this blog I've wanted to shoehorn a quote from James Thurber, and on Friday I had an encounter that gave me the chance. So here goes:

Surely nothing in the astonishing scheme of life can have nonplussed Nature so much as the fact that none of the females of any of the species she created really cared very much for the male, as such. For the past ten million years Nature has been busily inventing ways to make the male attractive to the female but the whole business of courtship, from the marine annelids up to man, still lumbers heavily along, like a complicated musical comedy. I have been reading the sad and absorbing story in in Volume 6 (Cole to Dama) of the Encyclopædia Britannica. In this volume you can learn all about cricket, cotton, costume designing, crocodiles, crown jewels and Coleridge, but none of these subjects is so interesting as the Courtship of Animals, which recounts the sorrowful lengths to which all males must to go arouse the interest of a lady.

After that memorable introduction, Thurber lists some of the absurd behaviours that males of various species resort to in their attempts to get the attention of females. The fiddler crab's odd little dance, the bowerbird's colourful treasury and the nuptiual gifts providied by some tree crickets are all covered. Thruber restricted himself to the behaviour of animals in his essay, but the pursuit of love has also wrought some very strange body modifications. The peacock flashes his fabulous tail in the hope of winning a peahen's heart, in certain deep-sea fish the male lives only to find a female to which he might attach himself, so he can be subsumed into her body and then there is the creature that ran out from under our recycling bin on Friday:

Those impossibly long and skinny legs mark him out as a harvestman (a group related to spiders) from the sub-order Palpatores. Once I'd prevented his escape, and taken a few more photos I shot an email off to Christopher Taylor who, as well as writing Catalogue of Organisms, just happens to be the brains behind the most recent taxonomic review of these harvestmen in New Zealand. Chris was kind enough to identify him, so I can tell you that you're looking at Pantopsalis albipalpis. Ordinarily an animal that appears to have crawled out of the pages of The War of the Worlds would be more than enough for a post here, but those spindly legs are as nothing when you compare them to the crane-like appendages growing from his head.

Amazingly, those are his jaws, or at least his chelicerae. Arachnids have two sets of limbs associated with their heads, the pedipalps (which spiders use almost like legs, and, in males to deliver sperm if you can imagine such a dual-purpose organ) and the chelicerae which are used to grasp prey and direct it toward the mouth (arachnids don't have chewing mouth-parts like many other arthropods).

Females from Pantopsalis and the related genus Megalopsalis have more or less normal chelicerae which point downwards, let their owners shuffle food towards their mouth and do very little else. As you can see, males are built a little differently. In fact, those massive hinged jaws are so different than the female form that males and females have frequently been mistaken for different species. Even within males, several species have two distinct forms; one with relatively low abd broad chelicerae and another with tall slender chompers.

It's not entirely clear what purpose such massive chilicerae serve, but the fact they are limited to males makes it a pretty sure bet they're just another example of the what Thurber called "the mournful burdens of the male" in the biological world. Perhaps female Pantopsalis just go mad for a giant chelicera, and in each new generation males have to sport ever more rediculous dentition if they want to turn a girls head. The mean spikes and nasty looking claws seem to suggest the giant chelicerae are more of a help to fighters than lovers. A few distantly related harvestman groups have also evovled overgrown jaws, and in those species the males fight with each other for the chance to mate. As with so much of New Zealand's invertebrate fauna, no one has ever studied our harvestmen in a behavioural or ecological sense. It would be fascinating to understand the forces that created this out-sized morphology, and how the distinct male forms are maintained (do they relate to different fighting strategies?) but until someone studies them in detail we just can't know.

However they got their giant jaws, I can't look into the eyes of this last photo without thinking this particular harvestman shares a little of Thurber's opinion on the lengths to which Nature's male have to go:

There are quite a few places you can find better pictures of New Zealand harvestmen around the web. Alan from half-pie has a Megalopsalis, Sciblogs own Brenden Moyle has photos of distantly related harvestmen that have normal sized chelicerae but massive pedipalps and TERRAIN, a forest restoration project in the Taranaki, has some great details of the claws.

The quote at the start is from Thurber's story Courtship Through the Ages which was published in the New Yorker then a collection of short stories. It's really very funny.

Christopher's paper on New Zealand's Pantopsalis is

Taylor, C., 2004. New Zealand harvestmen of the subfamily Megalopsalidinae (Opiliones: Monoscutidae)–the genus Pantopsalis. Tuhinga, 15, pp.53-76.

Sunday Spinelessness - Murdering my darlings

2011-02-13T08:49:00.006+13:00

Recently, there's been a little bit of talk among science bloggers about the need to murder your darlings. Christe, Carl and Ed are talking about excising some of your favourite passages of writing in order to let a whole post hold together, but I've been thinking about the phrase in a different context recently. I'm an invertebrate evangelist, and I utterly fail to understand how most people manage to package all the world's invertebrates into one giant and creepy category. But no matter how much you love bugs, you have admit some of them are just pests that need to be dealt with.

Lately our garden has been taken over by wasps. That's "wasp" in the every day sense in New Zealand, the murderous little yellow and black flying insects; we have thousands of native wasp species but they are all solitary and most are small and limited to native bush, so they don't really enter our consciousness. The German Wasp and its cousin the Common wasp (Vespula germanica and V. vulgaris), are something quite different. They are both social insects that build nests that support thousands of workers, each of which lives to bring up their queen's brood. Unlike honey bees and bumblebees, where the workers collect nectar and pollen to feed their young, wasp larvae need flesh. In late spring, the first generation of workers leave the nest and start collecting insects (especially caterpillars it seems) to feed to the developing larvae. The adults feed on nectar, but in the start of the season they are mainly sustained by a sugary substance the larvae produce in return for their food. In the middle of summer adults spend more time looking for their own food outside the nest, and that's why we start noticing them around fallen fruit and picnics come December or so.

There is nothing quite like these introduced wasps in the New Zealand fauna. The relative nativity of our insects, the lack of any predators and our relatively warm winters (which don't kill-off the nests every year) mean these wasps live at much greater densites in New Zealand than they do in Europe. In native beech forest, especially sourthern forests that produce honeydew thanks to native scale insects, there can be as many as ten thousand workers in one hectare, that's one wasp for every square metre of forest. In beech forests in particular, wasps are a complete disaster. They can wipe the forest floor clean of native insects and spiders and monopolise the honeydew, which is an important source of energy for native birds. Indeed, if you were to weigh all the wasps in some sections of native forests it would add up to more than the combined weight of all the native birds. In urban and rural settings wasps are a pain (literally, I was stung by one as a child and remember it well).

The only good wasp? This one was caught in a very large Eriophora pustulosa web (the most common web builder in New Zealand gardens), but the very large owner of that web didn't seem to mind this smaller spider taking her prize

So, as opposed to almost every other invertebrate that crosses my path, when I see an introduced wasp I get just a little sense of revulsion. When i tracked down the the source of our graden's yellow and black plague to two different nests on our property I hardly thought twice before I bought a bottle of carbaryl to deal to them. The first nest was no problem, it was dug into our clay bank and had a nice clear entrance site that I could sneak up to at night - letting me cover the entrance with the poisoned powder. The other nest was tougher.The entrance to that one was obscured in amongst a compost pile, right next to some weedy flowers which are visited by honey, bumble and and even native bees. Carbaryl is a broad-spectrum insecticide, and bees are having a hard enough time without being caught in the crossfire of this war, so a scorched earth policy wasn't really an option. Instead, I got a long sleeved shirt* and a spade and began to excavate the entrance to the nest. This process basically involved me clearing away a little of obscuring material before dropping the spade as a bolt of WHITE-HOT ADRENALINE passed through my body as a single wasp flew in roughly my direction for a little while. Quite a few rounds of this process ended when the last blow of my spade revealed not the entrance to the nest, but the very middle of it.

I'd cut a wall of the nest open and revealed a swarming yellow and black mass of wasps (who were more interested in attacking the spade than me) and the cells they'd constructed to house their young. Once the initial buzz had died down, I managed to extract the section of the nest that I'd dismantled and in doing so I learned something. Wasps might murderous, stinging invasive pests, but they're also quite beautiful. In all the time I'd been cursing their presence in my garden, they'd built an incredible piece of architecture out of the weeds we'd thrown away. My photos hardly do their efforts justice, but you get an idea.

A section of the wasp nest with the major stages of development (eggs, larvae and pupae) on display

One of the very few spineless creatures that I thought had no place in my heart had really amazed me. Beautiful as their creation might have been, they are still a pest and later that evening I came back to their now exposed nest and killed them, but it was a much more difficult job than the first nest.

*Really. I don't know what sort of protection I though this was going to offer...

If you want more posts dealing with ravenous hordes of social insects, Alex Wild at Mrymecos declared last week "Army Ant Week" and celebrated by producing some of the most wonderful photographs and interesting posts you're likely to find.

Sunday Spinelessness - Hadda beetle

2011-02-06T21:08:00.006+13:00

Time for another tropical beetle from Vanuatu, and what could be more charming than a ladybird*?

Or its absurdy spikey larvae?

This ladybird is probably a bit larger, a bit rounder and a bit oranger than the ones you are used to seeing in your garden. The more familiar ladybirds are more that just a pretty set of elytra, they're a force for good. Both the larvae and the adults of most of the familiar red and black ladybirds eat aphids, so having a few around in your garden saves on insecticide:

Ladybird larvae 'controlling' aphids, thanks to Gilles San Martin for making this image CC 2.0

The big orange ladybird in that first photo is not nearly so helpful. It's Henosepilachna vigintioctopunctata**, commonly known as the 28 spotted ladybird or the hadda beetle. The hadda beetle is a major agricultural best, because both the adult and larval stages are herbivorous and have a patricular liking plants of the family Solanaceae. That means potatoes, tomatoes, eggplants and (worst of all?) chilies can have their leaves skeletonised by beetles, and a beetle infestation can reduce a year's crop by up to 25% if not controlled.

You might note that this is the third post I've written about invertebrates from Vanuatu, and it's the third time I've written about an introduced pest. That's not by chance. Islands are hugely interesting for evolutionary biologists, but human introductions have seriously changed island ecosystems.

Take another look at that chewed-over leaf. Now imagine that each of those small white sections to the left of the photograph is a brand new island in a green ocean. In almost no time at all, winds would carry seeds to our little archipelago and life would start to claim the bare rocks. But we don't know which plants would make it. Dispersal and colonisation are random events, each island would collect its own subset of the seeds drifting past , and so start to develop its own flora. Once those plants have taken hold, the rain of wayward and drifting insects (and even snails) that fall everywhere on earth would have a chance to establish themselves. Again, the isolation of our islands means different species will fall on each one, and different ecological relationships will start to form. Our islands might survive for 20 million years before they're reclaimed by the sea, and in that time the unique beginnings of each island's ecosystem will mean a different evolutionary history will play out. In this way islands are evolutionary experiments, and island ecosystems have given risr to some of evolution's weirdest creations - isolation from the mainland has let iguanas become marine animals, finches become vampires and pigeons give up on flying.

But islands are no longer isolated from the rest of the world. The hadda beetle is probably native to Russia and, without humans moving plants around, would never have had a chance of making it to a Pacific islands. Now it lives in almost all the way across the tropical Pacific (here's a terrible photo of one I took in Rarotonga, 3000km away from Vanuatu):

In fact, there is an entire "tramp" assemblage including, but hardly limited to, big-headed ants, mynas, land snails, centipedes, paper wasps and mile-a-minute weed that can be found almost everywhere you find people in the tropical Pacific. These Pacific-wide introductions have pushed out native species, and together they have replaced some of evolutions most exuberant expressions with a bland mono-culture. The problem is not quite as bad as it might seem. The tramp species are mainly moved about by commerce, so many of the introduced species are associated with agriculture or at least lowland environments. In most islands, as you climb higher you find a more 'native' flora and fauna (for instance, all the partulid species left in the Society Islands are restricted to mountain tops).

By the way, the hadda beetle's bid for world domination continues: last year it was recorded in New Zealand for the first time. It's known to have set up shop in Auckland, but if you find hadda beetles somewhere else MAF might want to know about the invasion's spread.

*That's "ladybug" in American English, coccinellid or "lady beetle" among scientists and "ngoikura" in Māori

** That name might seem like a mouthful, but the species epithet at least makes sense, viginti-octo-punctatameans "twenty-eight-spotted". Most ladybird species names follow this rule

Sunday Spinelessness - Vanuatu scarab beetles

2011-01-30T22:05:00.006+13:00

As promised, it's time to add a few tropical invertebrates to the mix of more temperate bugs I usually talk about here. Let's start by redressing a bit of an imbalance in these Sunday Spinelessness posts. Up until now I've only written two posts about beetles, which something of an under-representation since about a quarter of all described species are beetles. I see plenty of beetles around our garden and in my travels around Dunedin, but few of them are large enough, or sufficiently cooperative, for me to get decent photographs. I had no such problem in Vanuatu.

For a start, there was the daily invasion of giant scarab beetles. Around 6 o'clock each morning a wave of massive bumbling beetles would arrive at one of the ~~coconut~~ betel nut palms surrounding the house at which we were staying. If you stood under the tree and looked up all you could see was the yellow-bodied beetles moving about and a rain of white stamens falling down from the flowers they were busy destroying. The beetles that came late for the feast set themselves up in the shrubs underneath the palm to scavenge what they could, and were quite happy to pose for photographs:

A few of the latecomers even got a whole flower for their patience:

I can't identify these beetles to species. Their stout bodies and legs and their particular 'clubbed' antennae mark them out as scarab beetles (family Scarabaeidae). That's the same group as most well known of our native beetles the excitingly named "brown beetle" more famous for its larvae which we call grass grubs. The only extra bit of information I have on them is from this post summarising a discussion on a mailing list that deals with emerging crop pests. It seems they're a known problem in Vanuatu, and taxonomists have at least got as far as placing them in the subfamily Cetoniinae, which are sometimes called "flower chafers". From the point of view of a snail geneticist (and not a beetle taxonomist) they actually look very similar to an Australian Cetoniine species, Eupoecila australasiae.

Had I known they were such a problem for commerical coconut growers I might have spent less time rescuing these beetles from the swimming pool. Their attraction to the bright-blue sheet of water proved lethal more than a few times, but it did make for some great photo opportunities:

Sunday Spinelessness - Return of the spineless

2011-01-23T09:03:00.003+13:00

It seems all the cool bug bloggers have escaped to the tropics just at the time I've got back to more temperate climes. I spent a couple of weeks in Vanuatu over the Christmas and New Year break and have a couple of memory cards full of Melanesian wildlife to share here over the next few weeks. I have another post based on life in Vanuatu I really want to finish editing before I talk about those bugs, and no shortage of real work to do before I can get to that. So, let's kick of a new year of spinelessness with a lame joke:

(That's a very sick Achatina fulica, one of the villains in this story and pretty common snail in and around Efate, the most populous island in Vanuatu. You can bet this very picture is going to show up as a slide is all my talks about Pacfic Island snails.)

P(KR\|Prediction) =	P(Prediction\|KR) * P(KR)
	P(Prediction)
=	0.9 *0.001
	(0.90.001)+(0.30.999)