research – Page 2 – Replicated Typo

Bonobos Extract Meaning from Call Sequences

A new study appeared yesterday on PlosOne by Clay and Zuberbühler of St Andrews University on the communicative ability of bonobos.

Studies have been done in the past on language-trained bonobos such as Kanzi which have revealed some remarkable abilities that the species has with regards to representational and communication tasks.

These studies have focussed on trained apes which are reared in unnatural environments and extensively trained on artificial languages. This has produced some interesting results though research into bonobos’ natural communication has been thin on the ground until now.

Clay and Zuberbühler address this gap in the research with a playback study on the natural vocal communication of bonobos.

Bonobos are known to produce five distinct vocal signals when finding food, these have been demonstrated to be combined together to make longer call sequences. The study found that individual call types were poor indicators of food quality but that calls which displayed a concatenation of signals were much better indicators.

The study looked into whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences.

They started by training four captive bonobos to find two types of foods in two different locations, those which are more preferred such as kiwis and those which are less preferred such as apples. The apes were recorded when finding these different food types and these recordings were used in the playback experiments. When the bonobos discovered their preferred food they emitted higher pitched long barks and short “peeps” and when they discovered the less-preferred food they made lower pitch “peep-yelps” and yelps. Sequences of the four calls which used different compositions were played back to bonobos who were familiar with those apes who had originally made the calls. All sequences contained the same number of calls. In response to these playbacks the study found that the apes devoted significantly more effort and time searching the space which was known to contain the food type indicated by the call sequence (shown in the graph below).

The bonobos were shown to attend not just to individual calls but to the entire sequences before they made inferences about the food encountered by a caller.

These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to natural vocal sequences made by other bonobos. This study really highlights the importance of call combinations in their natural communication system.

References
Clay Z, Zuberbühler K, 2011 Bonobos Extract Meaning from Call Sequences. PLoS ONE 6(4): e18786. doi:10.1371/journal.pone.0018786

Replicated Hauser Results

Some of you may remember last summer Marc Hauser was found guilty of research misconduct. This investigation raised questions about several publications including a paper from 2007 in Science. This paper looked into the ability of non-human primates to understand the intentions of a human experimenter by interpreting his gestures.

Today Science has published a partial replication of the study in question which confirms the original findings that chimpanzees, cotton-top tamarins, and rhesus macaques can distinguish intentional gestures, such as pointing to indicate a container with food inside, from “accidental” actions such as a hand flopping against a container.

The Science wesite states the following:

Following the Harvard misconduct investigation, first author Justin Wood, now an assistant professor at the University of Southern California in Los Angeles, wrote to Science in June 2010 to notify the journal that the investigation had revealed that the original field notes for the rhesus experiments could not be found:

“An internal examination at Harvard University determined that there are no field notes, records of aborted trials, or subject identifying information associated with the rhesus monkey experiments; however, the research notes and videotapes for the tamarin and chimpanzee experiments were accounted for. Professor Hauser states that “most of the rhesus monkey observations were hand written by [co-author David D.] Glynn on a piece of paper, and then the daily results tallied and reported to Wood over email or by phone” and then the raw data were discarded. The research assistant who performed the experiments (Glynn) confirmed that these field notes were discarded.”

Hauser and Wood returned to Cayo Santiago island in Puerto Rico to redo the experiments from the 2007 paper with the same population of free-ranging rhesus monkeys. Their findings, including field notes and video trials, are available online and they essentially match those reported in the original paper.

It is still not known what went wrong with the original experiment, a statement issued by Science today only says the following:

We stress that this new publication aims only to determine whether the original rhesus monkey experiments from the 2007 paper can be replicated. It has no bearing on questions raised about Dr. Hauser’s larger body of work.

This article from Science Inside quotes Dario Maestriperi as saying:

“The results of this replication are straightforward and entirely consistent with those of the original study. If the authors’ interpretation of their results is correct, these findings are very important and represent one of the clearest demonstrations that nonhuman primates can interpret the behavior of other individuals as intentional or non-intentional….Since the experimenter who tested the rhesus monkeys in the replication study appeared from the video to be the first author on the paper, Justin Wood, he was clearly knowledgeable of the hypotheses being tested and had some strong expectations and desires about the monkeys’ performance on the test.”

So is this replication a clarification of groundbreaking findings or could the monkey’s behaviour be down to the Clever Hans effect?

Meanwhile investigations into Hauser’s research are still ongoing and he is still banned from teaching for the next academic year.

Emergence of linguistic diversity in the lab

There is a huge amount of linguistic diversity in the world. Isolation and drift due to cultural evolution can explain much of this, but there are many cases where linguistic diversity emerges and persists within groups of interacting individuals. Previous research has identified the use of linguistic cues of identity as an important factor in the development of linguistic diversity (e.g. Nettle, 1999). Gareth Roberts looks at this issue with an experimental paradigm.

This experiment was a game where individuals had to trade commodities in a series of rounds. At each round, individuals were paired up either with a team-mate or a competitor, though the speaker’s true identity was hidden. Players were given random resources, but scored points based on how ‘balanced’ their resources were after trading (that is, you were punished for having much more meat than corn, for example). A commodity given to another individual was worth twice as much to the receiver as to the donor.

Players could only interact through an ‘alien’ language via an instant-messaging system. Prior to the game, individuals learned an artificial language which they were to use in these interactions. All participants were initially given the same starting language. There were several conditions that manipulated the frequency with which you interacted with your team-mate and whether the task was competitive or co-operative. In the co-operative condition, four players were considered as part of the same team and the task was to get a high a score as possible. In the competitive condition the four players were split into two groups and the task was to score more than the other team. In this condition, then, the main task was to identify whether your partner was a co-operator or a competitor.

The results showed that, if players interacted frequently enough with their team-mates and were in competition with another group, then linguistic diversity emerged. Over the course of the game each team developed its own ‘variety’, and this was used as a marker of group identity. For example, in one game two forms of the word for ‘you’ arose. Players in one team tended to use ‘lale’ while players in the other team tended to use ‘lele’, meaning that players could tell group membership from this variation. Thus, linguistic variation arose due to the linguistic system evolving to encode the identity of the speakers.

The diversity seemed to arise both from drift and intentional change, both of which have been documented in the sociolinguistic literature. Roberts suggests that linguistic markers make good social markers because they are costly to obtain (so difficult for free-riders to fake), salient and flexible enough to cope with changing group dynamics. In the next post, I’ll be thinking about a similar experiment looking at how linguistic variation might arise in a co-operative scenario.

Roberts, G. (2010). An experimental study of social selection and frequency of interaction in linguistic diversity Interaction Studies, 11 (1), 138-159 DOI: 10.1075/is.11.1.06rob

Variation in Experiment Participant Applications

What do people expect when they sign up to a linguistics experiment?

I’m currently running an experiment and so I posted an ad for participants. It simply states “You will take part in a linguistics experiment. You will be paid £6.”, and gives my email. I got 30 replies in a few hours, but was struck by the variation in the responses. Here are some pointless graphs:

First, a look at the distribution of email subjects. This reveals that most people know they are going to participate in an experiment, but fewer realise that they will contribute to research. One person thought that they would be doing a “Research Study”. What’s one of them?

However, here’s the killer. Analysing the first lines of the emails, I noticed a distinct power law relationship between frequency and casualness.

People just don’t respect linguists any more.

And that’s why I make people do hours of mind-bending iterated learning experiments with spinning cats.

Prairie Dog Communication

istockphoto.com A recent NPR radio show covered the research of the biosemiotician Con Slobodchikoff of the Univeristy of Arizone on prairie dog calls. The piece is very public-orientated, but still might be worth listening to.

We’ve all (I hope) heard of the vervet monkeys, which have different alarm calls for different predators, such as for leopard (Panthera pardus), martial eagle (Polemaetus bellicosus), and python (Python sebae). (Seyfarth et al. 1980) For each of these predators, an inherent and unlearned call is uttered by the first spectator, after which the vervet monkeys respond in a suitable manner – climb a tree, seek shelter, etc. It appears, however, that prairie dogs have a similar system, and that it is a bit more complicated.

Slobodchikoff conducted a study where three girls (probably underpaid, underprivaleged, and underappreciated (under)graduate students) walked through a prairie dog colony wearing shirts of the colors green, yellow, and blue. The call of the first prairie dog to notice them was recorded, after which the prairie dogs all fled into their burrows. The intern then walked through the entire colony, took a break for ten minutes, changed shirts, and did it again.

What is interesting is that the prairie dogs have significantly different calls (important, as they are pretty much exactly the same to human ears) for blue and yellow, but not for yellow and green. This is due to the dichromatic nature of praire dog eyesight (for a full study of the eyesight of retinal photoreceptors of subterranean rodents, consult Schleich et al. 2010). The distinction between blue and yellow is important, however, as there isn’t necessarily any reason that blue people are any more dangerous to praire dogs than yellow ones. “This in turn suggests that the prairie dogs are labeling the predators according to some cognitive category, rather than merely providing instructions on how to escape from a particular predator or responding to the urgency of a predator attack.” (Slobodchikoff 2009, pp. 438)

Another study was then done where two towers were built and a line was strung between them. When cut out shapes were slung down the line, the prairie dogs were able to distinguish a triangle from a circle, but not a circle from a square. So, the prairie dogs are not entirely perfect at encoding information. The conclusion still stands however that more information is encoded in the calls than is entirely relevant to a suitable reaction (unless one were to argue that evolutionary pressure existed on prairie dogs to distinguish blue predators from yellow ones.)

NPR labels this ‘prairiedogese’, which makes me shiver and reminds me of Punxatawney Pennsylvania, where Bill Murray was stuck on a vicious cycle in the movie Groundhog Day, forced every day to watch the mayor recite the translated proclamation of the Groundhog, which of course spoke in ‘groundhogese’. Luckily, however, there won’t be courses in this ‘language’.

References:

Schleich, C., Vielma, A., Glösmann, M., Palacios, A., & Peichl, L. (2010). Retinal photoreceptors of two subterranean tuco-tuco species (Rodentia, Ctenomys): Morphology, topography, and spectral sensitivity The Journal of Comparative Neurology, 518 (19), 4001-4015 DOI: 10.1002/cne.22440

Seyfarth, R., Cheney, D., & Marler, P. (1980). Monkey responses to three different alarm calls: evidence of predator classification and semantic communication Science, 210 (4471), 801-803 DOI: 10.1126/science.7433999

Slobodchikoff CN, Paseka A, & Verdolin JL (2009). Prairie dog alarm calls encode labels about predator colors. Animal cognition, 12 (3), 435-9 PMID: 19116730

Python: Your one stop shop for social science research.

Python is easy to use and pretty solid across platforms. Drew Conway has written an essential list of python tools for social science researchers. From running experiments to analysis and modelling, Python can do practically anything you’d ever want, mostly in two or three lines. Hooray!

http://www.drewconway.com/zia/?p=204

Bored birds, busy brains: Habituation to song initiates significant molecular changes in auditory forebrain of zebra finch

When we think of habituation, we tend to think of a process in which there is a decrease in psychological and behavioural response(s) over time following an organism’s exposure to a stimulus. Conceptualising habituation in this manner seems to imply the loss of something once an initial learning event has taken place. Although this may accurately describe what occurs at the psychological and behavioural levels, a study by a group of scientists from the University of Illinois (Dong et al. 2010), which examines habituation at the neurobiological level, shows that contrary to this conceptualisation, both initial exposure and habituation to song playbacks initiates a vast array of genetic activity in the zebra finch brain.

The systematic regulation of FoxP2 expression in singing zebra finches has been the subject of previous posts, but there is also a growing literature, of which Dong et al’s study is a part, documenting increases in ZENK gene (which encodes a transcription factor protein that in turn regulates the expression of other target genes) expression in zebra finch auditory forebrain areas in response to playbacks of song or the song of a conspecific. Studies showed that ZENK expression seems to mirror the typical decline in response associated with habituation in that after a certain amount of repetition, presentation of the song that originally elicited upregulation of ZENK no longer did so, and that ZENK returned to baseline levels – although upregulation of ZENK would occur if a different song or an aspect of novelty was introduced (i.e. the original song was presented in a different visual or spatial context).

What Dong et al. have demonstrated by conducting a large scale analysis of gene expression at initial exposure, habituation, and post-habituation stages however, is that unexpectedly profound genetic changes occur as a result of habituation in the absence of any additional novel stimuli following the surge of activity observed during initial exposure to novel song. Thus, the resounding merits of the Dong et al. (2010) study lie in the broadness of their approach, providing a true sense of magnitude with respect to genomic involvement in vocal communication and illuminating important influences that have gone unnoticed by studies with a narrower focus. I summarise the experimental design and findings of the paper below.

Continue reading “Bored birds, busy brains: Habituation to song initiates significant molecular changes in auditory forebrain of zebra finch”

Fungus, -i. 2nd Decl. N. Masculine – or is it?: On Gender

In an attempt to write out my thoughts for others instead of continually building them up in saved stickies, folders full of .pdfs, and hastily scribbled lecture notes, as if waiting for the spontaneous incarnation of what looks increasingly like a dissertation, I’m going to give a glimpse today of what I’ve been looking into recently. (Full disclosure: I am not a biologist, and was told specifically by my High School teacher that it would be best if I didn’t do another science class. Also, I liked Latin too much, which explains the title.)

It all started, really, with trying to get my flatmate Jamie into research blogging. His intended career path is mycology, where there are apparently fewer posts available for graduate study than in Old English syntax. As he was setting up the since-neglected Fungi Imperfecti, he pointed this article out to me: A Fungus Walks Into A Singles Bar. The post explains briefly how fungi have a very complicated sexual reproduction system.

Fungi are eukaryotes, the same as all other complex organisms with complicated cell structures. However, they are in their own kingdom, for a variety of reasons. Fungi are not the same as mushrooms, which are only the fruiting bodies of certain fungi. Their reproductive mechanisms is rather unexpectedly complex, in that the normal conventions of sex do not apply. Not all fungi reproduce sexually, and many are isogamous, meaning that their gametes look the same and differ only in certain alleles in certain areas called mating-type regions. Some fungi only have two mating types, which would give the illusion of being like animal genders. However, others, like Schizophyllum commune, have over ten thousand (although these interact in an odd way, such that they’re only productive if the mating regions are highly compatible (Uyenoyama 2005)).

Some fungi are homothallic, meaning that self-mating and reproduction is possible. This means that a spore has within it two dissimilar nuclei, ready to mate – the button mushroom apparently does this (yes, the kind you buy in a supermarket.) Heterothallic fungi, on the other hand, merely needs to find another fungi that isn’t the same mating type – which is pretty easy, if there are hundreds of options. Other types of fungi can’t reproduce together, but can vegetatively blend together to share resources, interestingly enough. Think of mind-melding, like Spock. Alternatively, think of mycelia fusing together to share resources.

In short, the system is ridiculously confusing, and not at all like the simple bipolar genders of, say, humans (if we take the canonical view of human gender, meaning only two.) I’m still trying to find adequate research on the origins of this sort of system. Understandably, it’s difficult. Mycologists agree:

“The molecular genetical studies of the past ten years have revealed a genetic fluidity in fungi that could never have been imagined. Transposons and other mobile elements can switch the mating types of fungi and cause chromosonal rearrangements.Deletions of mitochondrial genes can accumulate as either symptomless plasmids or as disruptive elements leading to cellular senescence…[in summary,] many aspects of the genetic fluidity of fungi remain to be resolved, and probably many more remain to be discovered.” (Deacon, 1997: pg. 157)

At this point you’re probably asking why I’ve posted this here. Well, perhaps understandably, I started drawing comparisons between mycologic mating types and linguistic agreement immediately. First, mating-type isn’t limited to bipolarity – neither is grammatical gender. Nearly 10% of the 257 languages noted for number of genders on WALS have more than five genders. Ngan’gityemerri seems to be winning, with 15 different genders (Reid, 1997). Gender distinctions generally have to do with a semantic core – one which need not be based on sex, either, but can cover categories like animacy. Gender can normally be diagnosed by agreement marking, which, taking out genetic analysis of the parent, could be analogic to fungi offspring. Gender can be a fluid system, susceptible to decay, mostly through attrition, but also to reformation and realignment – the same is true of mating types. (For more, see Corbett, 1991)

As with all biologic to linguistic analogues, the connections are a bit tenuous. I’ve been researching fungal replication partly for the sake of dispelling the old “that’s too complex to have evolved” argument, which is probably the most fun point to argue against creationists with. However, I’ve mostly been doing this because fungi and linguistic gender distinctions are just so damn interesting.

If anyone likes, I’ll keep you updated on mycologic evolution and the linguistic analogues I can tentatively draw. For now, though, I’ve really got to get back to studying for my examination in two days. Which means I’ve got to stop thinking about a future post involving detailing why “Prokaryotic evolution and the tree of life are two different things” (Baptiste et al., 2009)…

References:

Corbett, G. Gender. Cambridge University Press, Cambridge: 1991.
Deacon, JW. Modern Mycology. Blackwell Science, Oxford: 1997.
Reid, Nicholas. and Harvey, Mark David, Nominal classification in aboriginal Australia / edited by Mark Harvey, Nicholas Reid John Benjamins Pub., Philadelphia, PA : 1997.

Uyenoyama, M. (2004). Evolution under tight linkage to mating type New Phytologist, 165 (1), 63-70 DOI: 10.1111/j.1469-8137.2004.01246.x
Bapteste E, O’Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, & Martin W (2009). Prokaryotic evolution and the tree of life are two different things. Biology direct, 4 PMID: 19788731

On Phylogenic Analogues

A recent post by Miko on Kirschner and Gerhart’s work on developmental constraints and the implications for evolutionary biology caught my eye due to the possible analogues which could be drawn with language in mind. It starts by saying that developmental constraints are the most intuitive out of all of the known constraints on phenotypic variation. Essentially, whatever evolves must evolve from the starting point, and it cannot ignore the features of the original. Thus, a winged horse would not occur, as six limbs would violate the basic bauplan of tetrapods. In the same way, a daughter language cannot evolve without taking into account the language it derives from and language universals. But instead of viewing this as a constraint which limits the massive variation we see biologically or linguistically between different phenotypes, developmental constraints can be seen as a catalyst for regular variation.

A pretty and random tree showing variation among IE languages.

Looking back over my courses, I’m surprised by how little I’ve noticed (different from how much was actually said) about reasons for linguistic variation. The modes of change are often noted: <th> is fronted in Fife, for instance, leading to the ‘Firsty Ferret’ instead of the ‘Thirsty Ferret’ as a brew, for instance. However, why the <th> is fronted at all isn’t explained beyond cursory hypothesis. But that’s a bit besides the point: what is the point is that phenotypic variation is not necessarily random, as there are constraints – due to the “buffering and canalizing of development” – which limit variation to a defined range of possibilities. There clearly aren’t any homologues between biological embryonic processes and linguistic constraints, but there are developmental analogues: the input bottleneck (paucity of data) given to children, learnability constraints, the necessity for communication, certain biological constraints to do with production and perception, etc. These all act on language to make variation occur only within certain channels, many of which would be predictable.

Another interesting point raised by the article is the robustness of living systems to mutation. The buffering effect of embryonic development results in the accumulation of ‘silent’ variation. This has been termed evolutionary capacitance. Silent variation can lay quiet, accumulating, not changing the phenotype noticeably until environmental or genetic conditions unmask them. I’ve seen little research (not that I don’t expect there to be plenty) on the theoretical implications of the influence of evolutionary capacitance on language change – in other words, how likely a language is to make small variations which don’t affect language understanding before a new language emerges (not that the term language isn’t arbitrary based on the speaking community, anyway). Are some languages more robust than others? Is robustness a quality which makes a language more likely to be used in multilingual settings – for instance, in New Guinea, if seven languages are mutually indistinguishable, is it likely the that local lingua franca is forced by its environment to be more robust in order to maximise comprehension?

The article goes on about the cost of robustness: stasis. This can be seen clearly in Late Latin, which was more robust than the daughter languages as it was needed to communicate in different environments where the language had branched off into the Romance languages, and an older form was necessary in order for communication to ensue. Thus, Latin retained usage well after the rest of it had evolved into other languages. Another example would be Homeric Greek, which retained many features lost in Attic, Doric, Koine, and other dialects, as it was used in only a certain environment and was therefore resistant to change. This has all been studied before better than I can sum it up here. But the point I am making is that analogues can be clearly drawn here, and some interesting theories regarding language become apparent only when seen in this light.

A good example, also covered, would be exploratory processes, as Kirschner and Gerhart call them. These are processes which allow for variation to occur in environments where other variables are forced to change. The example given is the growth of bone length, which requires corresponding muscular, circulatory, and other dependant systems to also change. The exploratory processes allow for future change to occur in the other systems. That is, they expedite plasticity. So, for instance, an ad hoc linguistic example would be the loss of a fixed word order, which would require that morphology step in to fill the gap. In such a case, particles or affixes or the like would have to have already paved the way for case markers to evolve, and would have had to have been present to some extent in the original word order system. (This may not be the best example, but I hope my point comes across.)

Naturally, much of this will have seemed intuitive. But, as Miko stated, these are useful concepts for thinking about evolution; and, in my own case especially, the basics ought to be brought back into scrutiny fairly frequently. Which is justification enough for this post. As always, comments appreciated and accepted. And a possible future post: clade selection as a nonsensical way to approach phylogenic variation.

References:

Caldwell, M. (2002). From fins to limbs to fins: Limb evolution in fossil marine reptiles American Journal of Medical Genetics, 112 (3), 236-249 DOI: 10.1002/ajmg.10773

Gerhart, J., & Kirschner, M. (2007). Colloquium Papers: The theory of facilitated variation Proceedings of the National Academy of Sciences, 104 (suppl_1), 8582-8589 DOI: 10.1073/pnas.0701035104

Mapping Linguistic Phylogeny to Politics

In a recent article covered in NatureNews in Societes Evolve in Steps, Tom Currie of UCL, and others, like Russell Gray of Auckland, use quantitative analysis of the Polynesian language group to plot socioanthropological movement and power hierarchies in Polynesia. This is based off of previous work, available here, which I saw presented at the Language as an Evolutionary Systemconference last July. The article claims that the means of change for political complexity can be determined using linguistic evidence in Polynesia, along with various migration theories and archaeological evidence.

I have my doubts.

Note: Most of the content in this post is refuted wonderfully in the comment section by one of the original authors of the paper. I highly recommend reading the comments, if you’re going to read this at all – that’s where the real meat lies. I’m keeping this post up, finally, because it’s good to make mistakes and learn from them. -Richard

§§

I had posted this already on the Edinburgh Language Society blog. I’ve edited it a bit for this blog. I should also state that this is my inaugural post on Replicated Typo; thanks to Wintz’ invitation, I’ll be posting here every now and again. It’s good to be here. Thanks for reading – and thanks for pointing out errors, problems, corrections, and commenting, if you do. Research blogging is relatively new to me, and I relish this unexpected chance to hone my skills and learn from my mistakes. (Who am I, anyway?) But without further ado:

I have my doubts. The talk that was given by Russell Gray suggested that there were still various theories about the migratory patterns of the Polynesians – in particular, where they started from. What his work did was to use massive supercomputers to narrow down all of the possibilities, by using lexicons and charting their similarities. The most probable were then recorded, and their statistical probability indicated what was probably the course of action. This, however, is where the ability for guessing ends. Remember, this is massive quantificational statistics. If one has a 70% probability chance of one language being the root of another, that isn’t to say that that language is the root, much less that the organisation of one determines the organisation of another. But statistics are normally unassailable – I only bring up this disclaimer because there isn’t always clear mapping between language usage and migration.

Continue reading “Mapping Linguistic Phylogeny to Politics”