The Atavism

Sunday, March 28, 2010

Sunday Spinlessness - The Other Damsel

This week's Sunday Spinelessness is dedicated to those people who wash up at this post after googling for "Austrolestes colensonis" only to be disappointed. At the time I wrote that post on our damselflies I didn't have a photo of the the New Zealand Blue Damselfly, let me correct that now. A full body shot:


And a close up:


These photos were taken at Fensham Reserve in the Wairarapa. We walked through the bush there on a bright summer's afternoon and every time we passed a break in the canopy we found a little flight of Austrolestes basking in the sun. The reflective wings were beautiful, but, as you're about to see, not easily photographed:


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Posted by David Winter 11:40 AM | comments(2)| Permalink |

Friday, March 26, 2010

Does a forty thousand year old finger point to another human species?
DNA extracted from a 40 000 year old finger bone found in a cave in Siberia might be evidence for a previously unrecognized human species. Or it might not be. The bone, which comes from what New Zealanders call a "little finger", Americans call a"pinky" and paleo-anthropologists call the "distal manual phalanx of the fifth digit", was found in the Denisova cave, in a region of Siberia from which remains of members of both our own species (Homo sapiens) and Neanderthals (H. neanderthalensis) have previously been found. The mitochondrial DNA (mtDNA) sequences generated from the finger bone are distinct from both modern human sequences and from previously published neanderthal sequences, but inferring species boundaries is a tricky business and the mtDNA sequences are not, in and of themselves, proof that the finger belonged to a member of a third human species.

Here's the big figure from the paper, which was presented by Johannes Krause and colleagues in Nature yesterday. It's a phylogenetic tree which relates the little finger's mtDNA to H. sapiens and H. neanderthalensis sequences (click to see a high-resolution version):

The Denisnova sequence is red, Neanderthal sequences are in blue and modern humans are grey. So, the Denisova mtDNA forms a distinct lineage that isn't represented in modern humans or in previously published Neanderthal sequences. By using the tree as the basis for molecular dating the researchers were able to estimate that Denisova lineage separated from other human mitochondrial lineages between 0.78 and 1.3 million years ago. The temporal context the molecular dating adds to the phylogenetic tree helps to us understand where this new mitochondrial lineage might fit into humanity's family tree.

I've said before that most of our species' history was played out in Africa, and, in fact, the same is true when we step up a taxonomic level and look at our genus. All the human species that have been found outside of Africa descend from migrants that moved out of that continent at some stage. Here's a schematic representing some of the species in the wider human family tree and the timing of the migrations that moved them out of Africa.

How does the new evidence presented by Krausse et al. fit into that scheme? Perhaps the simplest interpretation is the the Denisova lineage represents a new species. The estimated age of the Denisova lineage makes it too young to have been carried out of Africa by the first wave of H. erectus migrants to leave Africa and apparently too old to have been inherited from the migrants that went on to form the Neanderthal lineage. If the Denisova sequence is something new then we'll have to update our family tree, adding a new branch and a fourth migration out of Africa.

John Hawks thinks we should hold off on updating the family tree too qucikly. The Desinova specimen might be a Neanderthal. At first glance the tree presented by Krausse et al. seems to dispel that possibility since previously identified Neanderthal sequences are more closely related to modern human sequences than the new linaeage, but that tree is based entirely on mtDNA. The mitochondrial genome is inherited as if it was a single gene. We can often use trees estimated from a single gene ("gene trees") as a proxy for species-level relationships ("species trees") but, in fact, every gene in a population has its own history and there there are scenarios that can push a given gene tree away from underlying species tree. Perhaps the easiest way to visualise how you'd end up with mitochondrial lineages that diverged millions of years ago within a single species is to think about genetic lineages moving through a population while speciation happens. New species form when populations stop sharing genes with each other, in the diagram below the big black triangle represents a barrier to gene flow. What happens if multiple different gene lineages are present in the ancestral population at the time that this gene flow stops? Usually, given enough time, each species will "sort" into specific gene lineages that descend from just one of the lineages in the ancestral population, but it's also possible for one (or both) species to maintain multiple lineages for some time. Such "incomplete lineage sorting" makes gene trees bad proxies for species trees and it's just possible that something like this has happened in Neanderthals:

Perhaps by moving to the very Easterm edge of the Neanderthals range we've sampled for the first time a lineage that existed in that species for the whole time it was in Europe. Maybe, and Hawks surely knows a lot more about paleobiology than I do, but I don't really buy it. It's certainly possible for a species to harbour deeply divergent mitochondrial lineages, but the time it takes for gene-lineages to sort within a species is relative to the effect population size of that species. Neanderthals probably had a relatively small effective population size (and mtDNA definitely does, since only females pass it on and then in only one copy) making the retention of multiple lineages over hundreds of thousands of years seem like a long shot. As Hawkes argues, strong geographic structure in Neanderthal populations might have aided the retention of divergent genetic lineages against those odds, maybe the Denisova mitochondrial lineage was extinct in Western Europe but common in Central Asia? It's possible, but I wouldn't bet on it.

Finally, the Denisova sample might be our first look at H. erectus DNA. H. erectus remains have been recovered from China so it seems possible they were in Siberia too. As I've said, the molecular dating of the Denisova lineage probably makes it too young to be a descendant of the first wave of migration form Afirca (though, of course, there is some uncertainty associated with that dating), but it might be evidence of genetic exchange between African and the H. erectus diaspora. As we've come to understand the origin of our species we've realised that the simple "Out of Africa" model is just that, a model, and the true pattern is more complex. H. sapiens really did have its start in Africa and it really did push out into the rest of the world in the last 50 000 years or so, but during that expansion populations have continued to exchange genes. There's no reason to believe that that H. erectus could not have done the same, perhaps the main thrust of the H. erectus expansion was 1.6-2 million years ago but genes continued to flow in and out of Africa for sometime after that.

So, there are three possibilities for the Denisova sample:

  1. It could be a new species,
  2. It could be an ancient mitochondrial lineage retained in eastern Neanderthal populations but lost elsewhere
  3. It could be the first H. erectus sequence.
We'll need more genes (Krausse et al. report they are working on sequencing genes from the nuclear genome) or more complete specimens to know for sure but I'll throw caution to the wind and say I think the first scenario to be the most likely and the second the least probable (remembering of course, that I'm not an anthropologist and these are pretty subjective estimates!). Perhaps I'm displaying some biases because I also think numbers one and three would be the cooler results. If either of those scenarios are true then we can add a third human species (alongside the Neanderthals and the 'Hobbit' H. floresiensis) that modern humans might have interacted with - it's just so fascinating to imagine our ancestors living alongside other human species and how differently the world might have turned out if those other species had survived the few thousand years that separate us.

You should read Carl Zimmer's post on the paper, he's compiling expert opinions as they come to him. There's also some more qualified comments via The Independent who made up for their poor news article on the story by having Chris Stringer from the Natural History Museum write a piece on it.

Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature DOI: 10.1038/nature08976

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Posted by David Winter 5:20 PM | comments(24)| Permalink |

Sunday, March 21, 2010

Sunday Spinlessness - Waste Not

Just a quick one today. A few weeks a go I used a picture of a male Cambridgea spider to spring off into a half-baked conversation on arachnophobia. That male had probably wandered into the warmth of our house after paying a visit to a female who has a web attached to the downpipe by our kitchen window:

cambridgea web

During the day the web's owner hides in a retreat (in this case right behind the joint in the downpipe) but at night you can see a very impressive spider sitting under her web, waiting for some tasty morsel to get trapped. Cambridgea are really forests spiders, if you hunt around a decent piece of native forest and you are bound to find a similarly constructed, but much larger, web. In the forest expectant Cambridgea mothers obscure their egg cases with twigs and dried leaves. Apparently our kitchen wall did offer much camouflage when our Cambridgea mother


You really should click on that image and see the high-res version, it's pretty cool. In order to grow, spiders have to cast off their rigid exoskeleton. You can see here our Cambridgea mother has used her discarded exoskeleton to help obscure her egg case!

The exoskeleton also gives you a clue as to how the spider has achieved its moult - the cephalothorax (the part of an arachnid body that includes the head and the thorax) is popped off and the spider pulls itself, legs and all, out through that gap. The last step of the process is photographed here.

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Posted by David Winter 10:56 AM | comments(0)| Permalink |

Thursday, March 18, 2010

Illustrating Carl Zimmer's Readers

Carl Zimmer has been wondering what to do next. Obviously, he's going to keep writing his wonderful science stories and continue to maintain the Science Tattoo Emporium but where to do that , and how to make money from it, is less clear. Carl's a scientific kind of guy, so he wanted get some data to inform his decision. The results of his reader's survey are out and they're interesting. But, for all Carl's skill with words data wants to be pretty, so here are a couple of the the key conclusions of his reader's survey illustrated with the help of ggplot.

Where do readers of The Loom get their science news?

How much would they pay for an e-book from a scince writer they liked?

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Posted by David Winter 12:45 PM | comments(0)| Permalink |

Wednesday, March 17, 2010

Lawrence Krauss on a bad day

Dunedin got to see Lawrence Krauss on a good day and a bad day this week, but that’s not to say one of his presentations was better than the other. Yesterday the award winning physicist and scientific communicator revealed to his audience that his outlook on life changes from day to day. On good days he can revel in the wonder of a universe that could come to know itself due to a series of accidents that started 10-31 seconds after the big bang and allowed the creation of first matter then atoms, stars and planets and finally astronomers. On bad days he despairs at the lack of scientific thinking in journalism and politics and thinks these problems, and the anti-scientific forces that fuel them, will probably prevent us from doing anything meaningful about climate change.

Krauss' awe inspiring story of an atom's journey from the birth of the universe to its death will gain nothing from my retelling it. If you weren't able to see it then you'l be glad to know his talk was a précis of his excellent book ATOM: An Odyssey from the Big Bang to Life on Earth...and Beyondand covers similar ground to this recored lecture. Perhaps I'm a masochist and a pessimist, but I'm going to skip the awe inspiring story to focus on what Lawrence Krauss thinks about on a bad day. His talk on "Science, Non-Science and Nonsense" described the sources of scientific confusion in society and the tactics used by those groups that seek to take advantage of it.

Krauss argued that the goal of science education and science communication should be to make sure everyone develops a functioning bullshit filter. He didn't express his thesis quite as bluntly as that, but his core idea is that spreading a scientific mindset would allow us to short circuit needless debates (is global warming real?) and let us get on to the important ones (what are we going to do about it?). He used a neat example to illustrate how this sort of scientific common sense could stop nutty ideas before they get started. UFO enthusiasts often cite the ability of the lights they observe to perform right angle turns at speed as evidence of their otherworldliness. In fact, Krauss pointed out, common sense should tell us that these apparently amazing maneuvers are evidence that the lights in question are not being emitted by a massive object moving through the sky. The only way to turn at a right angle is to stop then change direction, for a UFO to do all its slowing down and stopping so quickly a human observer couldn't perceive it would generate G-forces with a strength about 2000 times greater than earth's gravity. And quite a mess.

If the evidence used by UFO junkies is so silly then why do continue prosper? Why aren't people already filtering this sort of nonsense? The standard of scientific reporting in the media certainly has a lot to answer for. Krauss cited the normal concerns, a fractionated media market means viewers can choose a source of news that confirms their biases and the innate need of journalists to present balance is misplaced in science stories when, in almost every case, one side is wrong and we usually know which side that is. He also mentioned something I hadn't thought about before. According to Krauss, part of the problem with science coverage in mainstream reporting is that journalists don't feel qualified to make scientific pronouncements. Writers and broadcasters are happy to make bold statements on politics, financial markets and sports but will shy away from even a scientifically uncontroversial statement like "evolution is a fact."

Scientific understanding might not be helped by meek journalists and the false equality of balance but most journalists aren't setting out to deliberately mislead the public on science. Unfortunately, there are forces at work that are doing just that. Krauss had a tonne of examples from the culture wars in his native USA to draw on but he also took the time reminded us of our home grown cranks, citing the New Zealand Climate "Science" Coalition and Ray Comfort (The Apologists Nightmare [youtube video]) as evidence we aren't immune to anti-science in New Zealand. As you'd expect Krauss exposed just how vacuous the claims of intelligent design creationism and the objections of climate change denialists are, but he also attempted to deconstruct the PR strategies each group use. Both campaigns seek to take advantage of the public's sense of fairness and journalists' willingness to provide balance to any point of view. The Discovery Institute would have you believe their goal is simply to get their science a fair hearing in the classroom. But they don't have a science. For normal science, theories only make it into the school curriculum after they've been proposed, tested, retested and confirmed. The ID crowd don't want fair treatment, they want special treatment, to avoid that boring scientific process and start in the classroom!

Krauss could hardly have known this, but our own climate cranks play the same game. I hate to make an example of this article because the author usually covers science well, nevertheless it highlights the point. In an effort to provide balance to a story on how the IPCC might be made better the author contacted Vincent Gray for comment, here's the paragraph

Wellington scientist and climate change sceptic Vincent Gray said the researchers were continually coming up with "new models" but they were still "fiddling the figures" and were unlikely to restore public confidence in their work until their projections were proven

That sounds pretty fair doesn't it? Climate scientists can run their model forward in time and if their projections match observations we'll take action. Actually, it's absurd. As Krauss emphasised in his talk, the evidence for climate change doesn't only come from models, we have tonnes of data that tell us the earth is warming and the seas are rising. Combine those data with the fact recent temperature records are within the uncertainties of the IPCC's projections and sea levels are near to the upper bound of those projections and Gray's sound bite seem less fair.

Krauss had more problems than solutions in his hour long presentation. In fact, it's a testament to the passion he has for his science and skill he has as a scientific communicator that he managed make a talk made almost entirely of depressing facts seem invigorating. The only ray of hope Krauss offered us was that when people's backs are to the wall they abandon their their preconceptions and to turn to science. In 2003 George W. Bush said that he believed "both sides" of the "evolution debate" should be taught in schools. In 2005 Bush was faced with the prospect of Avian flu becoming able infect humans. Confronted with threat of a flu pandemic the Bush administration dispensed with its evolutionary agnosticism and planned for the possibility of genetic mutations allowing viruses to pass from human to human. That sort of infectivity requires conformational changes in surface proteins which create a new function, exactly the sort of phenomenon the ID crowd think is so improbable as to be effectively impossible.

Krauss will be presenting something very similar to his Dunedin talk in Auckland next week. I'd encourage anyone who has the chance to get out and seem him, he's a very chrasmatic and interesting speaker. You might even ask the question I really wish I did now- how are we going to fix all these problems?

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Posted by David Winter 5:17 PM | comments(0)| Permalink |

Sunday, March 14, 2010

Sunday Spinelessness - Extreme Close-up

Almost all the photos I've used to illustrate these Sunday Spinelessness posts have been taken with my fixed lens digital camera. I think it does a pretty nice job in macro mode but sometimes you just want to get a little closer to your subject. I photographed each of the landsnails I collected for my PhD research so that I could have a record of their pigmentation, which degrades once you preserve a specimen in ethanol. Obviously, the more detail I could get the better so I borrowed some very exciting toys from the department's photography office:


The camera is a DSLR with a 100mm f2.8 macro lens, an extension tube and a twin flash. The mammal crashing this invertebrate-celebrating series is me.

Of course, I couldn't have a toy like this to play with and limit myself entirely to photographing snails. In amongst those important snail photos I have jumping spiders, hornets, geckos and really anything else that chanced across the porch I was taking photos on. One of the more striking subjects is this red-eyed fly:


And the head-on shot...


It turns out the pretty red-eyed fly is Oxysarcodexia taitensis, one of the Sarcophagidae. That family name gives you a clue to how this fly makes its living, it translates as "flesh eating" (it stems from the same root words as sarcophagus, the Greeks believed limestone ate away at corpses sealed in it). Most of the flesh-flies feed on dead animals but a few have earned a place in vertebrate nightmares, horror movies and even medical practice by depositing their maggots in on open wounds.

Relying on dead animals for food is a chancy business. Corpses are usually patchily distributed and there a plenty of other scavangers out there to compete with. This problem is especially bad for the larval stages of insects, without wings to get them to the next corpse their entire future depends on the continued existence of the flesh they are born on. The sarcophogids have developed a neat trick for making the most of corpse when they find one - they give birth to live maggots. Technically, the flesh flies are ovo-larviparous, meaning the larva develops inside an egg which is retained in the female until the larva hatches. Flesh-fly maggots can start eating as soon as they are born, maximizing their chances of getting through their lifecycle before another scavenger eats the corpse they live in.

It's easy to get freaked out about a creature that spends it's life eating decaying flesh but we should remember that flesh-flies play an important role in ecosystems. Sarcophigids and other scavengers turn dead flesh into living flesh. WD Hamilton, one of evolutionary biology's most insightful and original thinkers, recognised the important role of carrion feeding insects in his burial instructions:

"I will leave a sum in my last will for my body to be carried to Brazil and to these forests. It will be laid out in a manner secure against the possums and the vultures just as we make our chickens secure; and this great Coprophanaeus beetle will bury me. They will enter, will bury, will live on my flesh; and in the shape of their children and mine, I will escape death. No worm for me nor sordid fly, I will buzz in the dusk like a huge bumble bee. I will be many, buzz even as a swarm of motorbikes, be borne, body by flying body out into the Brazilian wilderness beneath the stars, lofted under those beautiful and un-fused elytra which we will all hold over our backs. So finally I too will shine like a violet ground beetle under a stone.".

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Posted by David Winter 7:52 AM | comments(3)| Permalink |

Wednesday, March 10, 2010

Talking about talking about science

I've been swamped by the requirements of my real work for the last couple of weeks which has meant I've more or less neglected The Atavism just when a set of new scientific posts might have impressed voters in the Research Blogging Awards with this blog's vitality. I do have a couple of substantive posts on the boil but for now I'm going to resort to flinging out a few links and half digested ideas on science communication


Let's start at sciblogs where Ken Perrot has a review of Cornelia Dean's guide for scientists Am I making myself clear? It's particularly interesting to read that Dean urges scientists to write for newspapers in the same week that Grant Guilford publihsed some clear thinking in response to nonsense about climate science. The nonsense was in The Herald and no doubt read by thousands, the sensible reply is on some obscure piece of the University of Auckland's website...


Dean suggests scientists shouldn't write books unless they really can't help themselves. Still, if you sufficiently helpless and want to go down that route there's been plenty of advice published recently. Nature has a a special 'web focus' on writing science books featuring, among others, the inimitable Carl Zimmer. In a similar vein, Brian Switek, the writer behind Laelaps, is about to have his first book Written in Stone appear on the shelves. He has already documented parts of that journey on Laelaps and now he's going to start a series of posts dedicated to the process


I don't think I'll be writing a pop-sci book anytime soon but, obviousy, I do think science blogs have a place in getting science out to the public so I don't quite know what to make of this very odd paper on scientific blogging. The authors take a set of posts from 11 widely read science blogs and draw the following conclusions

Science blogs are a virtual water cooler for graduate students, postdoctoral associates, faculty, and researchers from a variety of disciplines and areas of inquiry. The conversations in science blogs are also of “water cooler” quality ...
To become a tool for non-scientist participation, science blogs need to stabilize as a genre or as a set of subgenres where smaller conversations may facilitate more meaningful participation from members of the public. Science bloggers need to become more aware of their audience, welcome non-scientists, and focus on explanatory, interpretative, and critical modes of communication rather than on reporting and opinionating.

Which is what happens when you presume 11 blogs is a representative sample of the thousands of people who are writing about science on the net. Of course there are blogs that are pitched at other experts and other blogs that deal mainly in links but presumably that's because that's what the authors want to do with their blogs!

If the authors of the paper wanted to see how blogging fits in to describing scientific ideas and news to non-scientists then they might have started, not with 11 blogs plucked from google, but by selecting blogs that are aimed at a lay audience . If you want interpretation and explanation of the day's science news there are superb writers like Carl Zimmer and Ed Yong to help you out. If you want a scientist to bring their expertise to bear on some topic then there's a whole mess of blogs (1, 2 3, 4, 5... and another thousand or so here) that do just that (and I like to think The Atavism fills one small niche in that sprawling ecosystem). A thoughtful review of those blogs would have served a real purpose, it's hard to see that the published paper does. One good thing came from that paper though, I now know there is a Journal of Science Communication, I trust some of the other papers will be more useful. (If you are interested The Panda's Thumb and Blog around the Clock have more detailed reviews of the paper)


Finally, congratulations to Elizabeth Connor who has won the inaugural Prime Minster's Science Media Communication Prize (really, that's the flowing title given to a prize for communicating difficult ideas...) which gives her $150 000 to undertake a program that focuses on "the mystery intrigue and uncertainty of science."

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Posted by David Winter 12:32 PM | comments(7)| Permalink |

Sunday, March 7, 2010

Sunday Spinelessness - Survivor

Until today these Sunday Spinelessness posts have been severely unrepresentative. I've talked about molluscs and myriopods and shown you photos of anthozoans and arachinids but nowhere in these posts have I included a post about a beetle. Which is a shame because, to a first approximation, every species on earth is a beetle. Really. Most animals are arthropods, most arthropods are insects and most insects are beetles. In all, 350 000 species have been described so far, about a third of the total number of species from all groups. The star of today's piece is one of New Zealand's 4 500 described species.


I found our star stuck in one of those deadly rhododendron shoots . I guess if I was a cold-hearted documentarian, interested only in recording the happenings of the natural world, I would have left him there to struggle. But, really, I'm just a sucker for handsomely striped elytron so I helped disentangle him from the sticky shoot.


Those impressive antennae place our specimen in the order Cerambycidae, the long horn beetles, which includes the famous huhu beetle. I can't identify it down to species but it's likely in the genus Coptomma (for what it's worth, the taxonomic shorthand for 'some species in Coptomma' is 'Comptomma. sp'). Our Coptomma didn't seem to have any long lasting effects from his run in with the rhododendron's sticky trap, he wandered off my life-raft leaf and set about cleaning himself up:


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Posted by David Winter 4:20 PM | comments(0)| Permalink |