Month: October 2012

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Zombies and the problem of consciousness

Seeing as it’s Halloween, I’m going to play devil’s advocate with the help of some zombies and explore the Gordian knot of consciousness. I think most scientists would hold a physicalist view when it comes to their view of how the world ‘really’ is. That is to say, objectively speaking, all there is to the universe are the various interacting fields and particles of physics. The problem with such a view is that our conscious selves prove very difficult to incorporate into this picture. We are subjective beings. Finding out how consciousness came about is known as the hard problem of consciousness.

David Chalmers, a philosopher of mind, formed a clever thought experiment to illustrate the difficulty. Okay, so imagine a world where everyone has the outside appearance of being conscious, for instance they laugh when you tell a joke,  shirk away from pain, gaze at sunsets etc., the only difference is that they have no internal subjectivity, they’re automata or zombies. I don’t see any problem with conceiving of such a place, so it looks like a possibility. But if these automata are indistinguishable from us on the outside in terms of their behaviours and actions then evolution won’t be able to distinguish between them and us, so why consciousness? It looks like an unnecessary extravagance. It also suggests that there is something more to the world than the physical, because our world isn’t like that, we, or at least I, know I’m conscious.

It seems to me that our theories as to how and why consciousness evolved have fallen short in their efforts. A lot of work is dedicated to finding the neural correlates of consciousness, but that doesn’t get us anywhere! Neurons are made up of the same material as the rest of the cells in our body, but heart cells don’t generate conscious beings so why treat neurons differently. So we’re really left with two questions. How do physical things generate subjective thought? And once we get there, why is it advantageous to be conscious? It’s called the hard problem for a reason.

Author

kanead[at]tcd.ie

Photo credit

wikimedia commons


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Dinosaur detective stories

“Being a paleontologist is like being a coroner except all the witnesses are dead and all the evidence has been left out in the rain for 65 million years” Mike Brett-Surman, 1994

I am very much for palaeontology and the enthusiasm for the science today but there was a time when even the mighty dinosaurs were out of fashion. During the 40s and 50s they were thought of as animals who had been destined for extinction, little more than children’s monsters.

Perish the thought. That changed in both academic and public circles when palaeontologist John Ostrom and his student Bob Bakker came on the scene during the 60s and 70s. The trigger of this ‘dinosaur renaissance’ was Ostrom’s description of Deinonychus which he deemed a fleet footed, endothermic, bird-like animal. This was a world apart from the view of dinosaurs as cold-blooded, tail dragging, sluggards. In Bakker’s book, the Dinosaur Heresies, he presented a persuasive body of evidence to support the idea that dinosaurs were endothermic. Bakker is a great artist too and it really helped to get his point across. You can see his influence in the similarity of the Velociraptors of Jurassic Park infamy to his artwork. This was all very exciting. Now we had animals seemingly on a physiological par with mammals and birds. What I find so impressive is that we can still make inferences about the physiology of long extinct animals so long as we marshal enough evidence.

But the case for endothermy wasn’t so clear cut. The bones of reptiles and amphibians, which are demonstrable ectotherms, show seasonal bone growth and we can see similar patterns in the fossils of dinosaurs. An impasse presented itself.

Until now anyway. The issue, it seems, is that we weren’t looking in the right place. A recent paper in Nature shows why. The authors of the study looked at the histology of modern ruminant mammals revealing that they also display seasonal bone growth and that this can be extended to all endotherms with a constant body temperature. So seasonal bone growth can no longer used as an argument for cold blooded dinosaurs. I think it’s interesting that all it took was for someone to look at modern mammals.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

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Sulawesi field report

A Lemon-bellied White-eye Zosterops chloris with nesting material in its bill, Tomia Island

July and August of this year saw members of the Behavioural and Evolutionary Ecology research group embark on another field season studying the birds of tropical south-east Sulawesi, Indonesia. Principal investigators Dr. Nicola Marples and Dr. Dave Kelly were joined this year by PhD student Seán Kelly, as well as a number of undergraduates from the university. This year’s expedition, carried out in collaboration with Operation Wallacea, consisted of two teams: the mist netting team, led by Dr. Marples and Dr. Kelly, and the behavioural team led by Seán Kelly.

The netting team trapped birds using mist nets at various locations on Buton island, mainland south-east Sulawesi and Wangi-wangi island (of the Wakatobi archipelago). While small passerines such as white-eyes, sunbirds and flowerpeckers were the target species, individuals from a total of 35 species were caught. The season proved to be a great success with over 300 birds trapped and processed. Data on plumage, morphology, age, sex and breeding condition were collected from each bird, which was colour-ringed and released unharmed. A small number of body feathers were also plucked from each bird for later genetic and stable isotope analyses.

The behavioural team spent the season on various islands of the Wakatobi archipelago collecting detailed behavioural ecology data on the white-eye, sunbird and flowerpecker species present. This included information on their diets, competitors, preferred habitats, social habits, courtship and breeding, as well as their foraging and flocking behaviours. Data collection took place in the early morning and evening, walking 1 km transects through scrub, farmland or forest edge habitats. This resulted in some fantastic insights into the behaviour and ecology of these poorly studied species.

From analysis of the plumage, morphometric and genetic data we have found a number of significant differences between bird populations on the Wakatobi archipelago and mainland Sulawesi, as well as between populations within the Wakatobi. It is hoped that the behavioural data gathered this season will help us to understand the selective pressures driving this divergence, giving us further insight into the evolution of this region’s fascinating avifauna.

Author

Seán Kelly: kellys17[at]tcd.ie

Photo credit
Seán Kelly
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The not so black and white story of why the zebra got its stripes

Why are zebra black and white? I would hazard a guess your answer is camouflage, and you would be right… well, mostly. I would then bet you got the beast from which the zebra is hiding wrong. While the black and white stripes might disrupt outline of a zebra in the eyes of an ambushing lion or sprinting cheetah, the scientific evidence points to a much smaller blood thirsty devourer of zebra.

Since the 1970s, experiments have shown that Tsetse flies are less attracted to black and white striped patterns than plain black, white or grey colours. Most recently, a series of experiments conclusively showed that another group of flies, the horseflies, are far less attracted to zebra-stripe patterns than plain, black, white, brown or grey surfaces. Furthermore, narrow bands of stripes are even more effective at keeping hidden from the horseflies, and it’s perhaps no surprise that the legs and heads of zebra contain the closest spaced stripes where blood vessels lie perilously close to the skin surface of these key anatomical locations. The legs being needed to flee from the lions and the head for thinking.

Of course, there may be other factors that simultaneously favour such a striking colour pattern. Regardless though, some interesting evolutionary points follow the “camouflage from flies” idea. Chief among them being: if stripes are so good at hiding from horseflies, then why do Eurasian horses not possess the same pattern where horseflies are also common and a nuisance?

So while the “why” of the zebras stripes seems to have some scientific evidence at last, the “how” they got their stripes is another blog topic for another day and involves leopards, cells, computers and a bit of maths.

Author

Andrew Jackson: a.jackson@tcd.ie

Photo credit

Andrew Jackson

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All the better to see you with

A recent discovery of a large eye found by a beachcomber in Florida initiated a flurry of internet speculation of its mysterious owner. The contenders for ownership included colossal squid, thresher sharks and a range of mysterious sea creatures both real and imagined.

While the owner of the tennis ball sized eye has recently been attributed to a swordfish, it is perhaps not unreasonable to attribute such a large eye to creatures of monstrous sizes, especially considering the eye rivals the size of those of the largest animals to every exist, the cetaceans.

So why don’t we always find the largest eyes in the largest creatures? Moreover, why are the largest eyes found in such an unusual and evolutionarily distant set of creatures including colossal squid, the extinct ichthyosaurs and to a lesser extent swordfish?

One study recently published in Current Biology has tried to address this mystery by looking at the football sized eyes of the Colossal squid. The eyes of Giant and Colossal squid are the largest of any extant animal with an eye diameter up to three times larger then the next largest eyes, that of swordfish and whales, hence dwarfing the eye found on the beach.

Nilsson et al used model simulation comparing the benefits arising from increasing eye size in relation to spotting point light sources, dark objects against a light background (diurnal vision) and luminescent objects against dark background. They found that in bright-lit areas the benefits arising from larger eyes diminish greatly meaning that whale eyes size represents the limit in terms of visual ability in these environments. However in cases where large luminous objects are against a dark background, extremely large eyes become beneficial again.

Such scenarios of bright objects against a dark background are found in the deepest parts of the oceans where various bioluminescent organisms live. Movement through such waters can disturb such organisms, in particular bacteria, which cause them to create a glowing silhouette of the animal. This is where the advantage arise for the squids large eyes as they can detect the disturbance of its main predator the sperm whale from over 120 meters away, allowing it to take evasive action.

This technique only seems to be advantageous for spotting large predators, which explains why colossal squid and also perhaps why ichthyosaurs had such large eyes, with large pliosaurs their potential predator.

Author

Kevin Healy: healyke@tcd.ie

Photocredit

wikimedia commons

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The tree on the web

Visualising the tree of life is a challenge for even the most artistically attuned in the scientific community. The problem is the sheer number of species that we need to represent, literally millions. But I think the latest attempt meets the challenge. The developers of OneZoom, the name of the new approach, argue that we need to escape the “paper paradigm”. We should instead make full use of the benefits that digital interactive displays grant us. Worrying that our efforts won’t translate to the printed page is an exercise in Luddism.

So, why is OneZoom so successful? The display takes its cues from Google Earth, the virtual globe, but whereas in Google Earth you move from continents to countries in OneZoom you zoom in from class to species. It’s even better than that because the whole tree has a fractal geometry, the self similar patterns you can see with real trees, which allows for an intuitive zoom function. One critique is that the fractal geometry ends up displaying the groups that diverged earlier (e.g. monotremes) as larger than the more recent groups (e.g. placentals), suggesting some significance when there is none. So far only the mammals are on show but it’s early days yet.

There are a number of other really useful features like the ability to play the evolution of the whole tree backwards and forwards in time so you can see exactly when a given species, genus or what have you, diverged. The potential for science communication as well as research is great. But enough of me talking about what is best seen and check it out for yourself. The details of OneZoom are available in PLOS Biology.

Author

Adam Kane: kanead[at]tcd.ie

Photo Credit

Rosindell J, Harmon LJ (2012) OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biol 10(10): e1001406. doi:10.1371/journal.pbio.1001406

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Hotbeds of photosynthesis evolution

Grasses rank among the world’s most ecologically and economically important plants including wheat, barley, rice and maize. Evolution of the C4 syndrome has made photosynthesis highly efficient in about half of their species, inspiring intensive efforts to engineer the pathway into C3 crops to improve drought and heat tolerance.  An international collaboration called the Grass Phylogeny Working Group (including Trevor Hodkinson, TCD) produced one of the most comprehensive phylogenetic trees of the grasses and used this to show how C4 evolution has evolved. Results published in the journal New Phytologist show that it has evolved repeatedly 22-24 times and within two groups in particular.

Author

Trevor Hodkinson: hodkinst[at]tcd.ie

Photo credit

Wikimedia commons

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What did what to what? Finding causality in chaos.

A new paper has been published in Science by George Sugihara and colleagues, which is an immediate contender for the most insightful paper I’ve ever read. In the paper they outline a new method, which they dub ‘Convergent Cross Mapping’ (CCM), for detecting causality between variables using time series data. Not only does CCM allow for the detection of causality but also its directionality. The method takes us well beyond the previous confines of Granger causality (which requires the assumption that systems are linear, or are showing linear behaviour near an equilibrium), and allows us to tease out causality in systems that show non-linearity and chaos. As examples of possible applications of their method the authors address two classic causality problems:

Predator-prey dynamics of Didinium and Paramecium. The authors show that there is bidirectional causality in this classic predator-prey system, but that top-down control is stronger than bottom up control (i.e. Didinium has a larger effect on the Paramecium population than vice-versa).

Dynamics of Pacific sardines and anchovies. There has been a long-standing debate about the cause of alternating dominance between sardines and anchovies in the Pacific. Some arguing that competition between the species is the driver, while others claim the pattern is caused by differing responses to temperature. The authors weigh in on this debate by showing that, while sardine and anchovy abundance is negatively correlated, this is a mirage as there is no causation in either direction. The authors also unambiguously show that sea surface temperature does causally affect the abundance of both species, indicating that climate is the main driver.

I think this method will be absolutely invaluable to future studies, and for me has already proved its worth from the results the authors present. The videos below are from the supplementary information of the paper and explain the method simply using beautiful illustrations.

watch?v=7ucgQE3SO0o

watch?v=NrFdIz-D2yM

watch?v=rs3gYeZeJcw

Author

Luke McNally: mcnall[at]tcd.ie

Photocredit

Wikimedia commons

 

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Darwin’s insects, Dodo skeletons and macaques with braces

macaque braces

The Natural History museum in Dublin is one of my favourite places in the city. It has a very Victorian feel to it, none of this pandering to the X-box generation, just cabinet upon cabinet of mounted skins and skeletons revealing the diversity of nature. Some of the taxidermy is pretty hilarious and you can see the bullet holes in some of the skeletons, but that adds to the charm of the place!

I did a lot of museum based work during my PhD and absolutely loved using museum collections, so now I have my own students they all have museum collection aspects to their projects (whether they like it or not!). They will be using the collections in the Dublin museum, so today we had a tour behind the scenes of the museum, and a look at the storage areas with one of the curators Nigel Monaghan.

It was awesome! In the space of a few hours we saw insects collected by Darwin during his time on the HMS Beagle, a Dodo skeleton, a macaque skull with orthodontic braces (the original owner was apparently a dentist, though no-one is sure whether the macaque had braces in life or was just used for practice after it died), an entire room full of Irish elk crania and antlers, some wild Irish grass snakes (Ireland historically has no snakes of any kind), a DNA bank for every Cetacean stranded on the Irish coast, a huge selection of bird parts collected from birds that accidentally flew into lighthouses, and probably the funniest interpretation I’ve ever seen of what a guinea pig should look like.

As we went around, many of the things Nigel told us got me thinking about what an under used resource museum collections are. Certainly many people use the big collections in London, Paris, New York and Washington DC, but few of us would think to look in our local museums. For example, Nigel told us that a geneticist did a piece to camera in the museum recently and mentioned how wonderful it was that they had managed to extract Dodo DNA from a specimen in France. They seemed completely unaware of the fact that the Dublin museum has a beautiful Dodo skeleton in its collection. So my message is go out and use your local museum collections (or at least ask the curators if they have what you’re looking for)! They’re wonderful sources of information and inspiration, whether you’re a first year undergraduate student or a tenured professor. Right, now where did I put my calipers…

Author 

Natalie Cooper: ncooper[at]tcd.ie

Photo credit

Natalie Cooper

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“To expect the unexpected shows a thoroughly modern intellect”

I spoke before of how to use mathematics to convey an idea in biology. Here, I’ll take a different tack and discuss a paper in which the author makes his argument with naked English. The author in question is Nicholas Humphrey who in his famous paper ‘The social function of the intellect’ draws a wonderful metaphor of Mother Nature as an economist,

“It is not her habit to tolerate needless extravagance in the animals on her production lines: superfluous capacity is trimmed back, new capacity added only as and when it is needed”.

His metaphor serves as an introduction to the puzzle of the seemingly unnecessarily inflated intellects of some animals, notably humans.

Humphrey questions if such a highly developed intellect is really necessary for invention. The ability to produce tools is generally not a result of deductive reasoning or creative thought but rather follows from aping other individuals or pure trial and error learning. The intellect must have some other function in his estimation and in the end, he proposes that it is as a social glue. The complex interactions that arise out of the social milieu require some serious intellectual horsepower,

“[S]ocial primates are required by the very nature of the system they create and maintain to be calculating beings; they must be able to calculate the consequences of their own behaviour, to calculate the likely behaviour of others, to calculate the balance of advantage and loss – and all this in a context where the evidence on which their calculations are based is ephemeral, ambiguous and liable to change, not least as a consequence of their own actions.”
 

Calculating the consequences of your own behaviour is one thing but understanding that others around you have motivations of their own is a huge leap in understanding. All of this is done without ever having direct access to the subjective thoughts, motives, and desires of another person. Understanding the reasons for understanding is even more impressive and Humphrey’s paper has rightly influenced the theories of scientists since its publication. Most recently a study in the school that mechanistically linked sociality and selection for intelligence.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Wikimedia commons