Tag: genome

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.

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Some Links #17: The Return of Whorf

The famous Klingon linguist, Whorf, has returned with his theories on linguistic relativity (I know, terrible joke).

The Largest Whorfian Study Ever. The Lousy Linguist looks at the paper Ways to go: Methodological considerations in Whorfian studies on motion events. As you can probably guess, the paper deals with the methodological issues surrounding linguistic relativity. It’s all interesting stuff, bringing to light important questions about how the brain handles language. I’m fairly lay when it comes to this topic, so for more background on the current events, see similar posts over at Language Log: Never Mind the Conclusions, What’s the Evidence? and SLA Blog: Linguistic Relativity, Whorf, Linguistic Relativity.

But Science Doesn’t Work That Way: Miller & Chomsky (1963). Many of you who read this blog will be familiar with the position taken by Melody’s post over at Child’s Play: against a strong nativist position in language acquisition. It’s the first part in a series of posts so I’ll reserve judgement on her conclusions until she’s finished. But much of her post is drawn from a brilliant paper by Scholz and Pullum (2005): Irrational Nativist Exuberance. Key paragraph:

Do we really want to say that phonemes are ‘innate’?

I haven’t yet addressed how we know — with all but certainty — that the model Miller and Chomsky used had to be a poor approximation of human learning capabilities.  It has to do with phonemes.

Experiments have shown that people are remarkably sensitive to the transitional probabilities between phonemes in their native languages, both when speaking and when listening to speech.  If Miller and Chomsky’s assessment of probabilistic learning is correct, then the problem of “parameter estimation” should apply not only to learning the probabilities between words, but also to learning the probabilities between phonemes.  Given that people do learn to predict phonemes, Miller and Chomsky’s logic would force us to conclude that not only must ‘grammar’ be innate, but the particular distribution of phonemes in English (and every other language) must be innate as well.

We only get to this absurdist conclusion because Miller & Chomsky’s argument mistakes philosophical logic for science (which is, of course, exactly what intelligent design does).  So what’s the difference between philosophical logic and science? Here’s the answer, in Einstein’s words, “No amount of experimentation can ever prove me right; a single experiment can prove me wrong.”

PLoS Blogs. Yet another blogging network. This time it’s with the Public Library of Science. The most notable move, for me at least, is Neuroanthropology. That move hasn’t seemed to impact upon their ability to produce good articles, the latest of which being in regards to Uner Tan Syndrome (I’m sure there was a documentary about this on BBC…).

Hap Map 3: more people ~ more genetic variation. Razib has a cool read on the new HapMap dataset. The current paper (Integrating common and rare genetic variation in diverse human populations) looked for variants across the genome in 11 populations, consisting of 1184 samples. It’s been especially useful with less common variants. As with previous versions, you can also explore the data. Here’s the conclusion from the paper:

With improvements in sequencing technology, low-frequency variation is becoming increasingly accessible. This greater resolution will no doubt expand our ability to identify genes and variants associated with disease and other human traits. This study integrates CNPs and lower-frequency SNPs with common SNPs in a more diverse set of human populations than was previously available. The results underscore the need to characterize population-genetic parameters in each population, and for each stratum of allele frequency, as it is not possible to extrapolate from past experience with common alleles. As expected, lower-frequency variation is less shared across populations, even closely related ones, highlighting the importance of sampling widely to achieve a comprehensive understanding of human variation.

Mathematics: From the Birth of Numbers. Someone gave this in to the charity store I work at: it’s a brilliant book by Jan Gullberg on (surprise, surprise) the history of mathematics. The first chapter was on mathematics and language, so I had to pick it up, and not just for that chapter alone, as there are plenty of gaps in my mathematical knowledge I’m sure this will clear up.

Answering Wallace's challenge: Relaxed Selection and Language Evolution

ResearchBlogging.orgHow does natural selection account for language? Darwin wrestled with it, Chomsky sidestepped it, and Pinker claimed to solve it. Discerning the evolution of language is therefore a much sought endeavour, with a vast number of explanations emerging that offer a plethora of choice, but little in the way of consensus. This is hardly new, and at times has seemed completely frivolous and trivial. So much so that in the 19th Century, the Royal Linguistic Society in London actually went as far as to ban any discussion and debate on the origins of language. Put simply: we don’t really know that much. Often quoted in these debates is Alfred Russell Wallace, who, in a letter to Darwin, argued that: “natural selection could only have endowed the savage with a brain a little superior to that of an ape whereas he possesses one very little inferior to that of an average member of our learned society”.

This is obviously relevant for those of us studying language evolution. If, as Wallace challenged, natural selection (and more broadly, evolution) is unable to account for our mental capacities and behavioural capabilities, then what is the source behind our propensity for language? Well, I think we’ve come far enough to rule out the spiritual explanations of Wallace (although it still persists on some corners of the web), and whilst I agree that biological natural selection alone is not sufficient to explain language, we can certainly place it in an evolutionary framework.

Such is the position of Prof Terrence Deacon, who, in his current paper for PNAS, eloquently argues for a role for relaxed selection in the evolution of the language capacity. He’s been making these noises for a while now, as I previously mentioned here, with him also recognising evolutionary-similar processes in development. However, with the publication of this paper I think it’s about time I disseminated his current ideas in more detail, which, in my humble opinion, offers a more nuanced position than the strict modular adaptationism previously championed by Pinker et al (I say previously, because Pinker also has a paper in this issue, and I’m going to read it before making any claims about his current position on the matter).

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Culture and the human genome: a synthesis of genetics and the human sciences

ResearchBlogging.orgHumans are immersed in culture from birth. It is so fundamental to our experience, and what it means to be human itself, yet we often overlook the consideration that “cultural practices might have transformed the selection pressures acting on humans” (Laland, Odling-Smee & Myles, 2010, pg. 137).

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Guns, Germs and Predictable Reviews

If, like me, you generally like the Guardian’s science features, then please avoid reading Tim Radford‘s book club discussion of Jared Diamond‘s Guns, Germs and Steel. Ever since I noticed this book was on the Guardian’s reading list, it’s been an ongoing curiosity of mine as to how they will tackle the subject. Mainly because Diamond’s book, along with Richard Dawkins’ The Selfish Gene, urged me to move into studying evolution. Sadly, and perhaps not very surprisingly, you get little from the discussion bar an unequivocal acceptance of Diamond’s central thesis: that of environmental determinism.

Nowhere is there a mention of ideas that stand somewhat in opposition to Diamond’s, such as those in the 10,000 Year Explosion. Namely, the consequences of agriculture on recent human evolution, and the growing mountain of evidence supporting the contention that different human populations have adapted to their local environments.

And just to be clear: I think Diamond’s book is a well-written, scholarly account of human history, and it’s influence is not to be understated. But I also think he overlooked a large portion of the argument.

How Culture Shaped The Human Genome

The study of culture, cultural evolution, gene-culture coevolution and niche construction have all received much more attention over the last decade. So it’s nice to see Nature taking on-board a fascinating review by Kevin Laland, John Odling-Smee and Sean Myles about how culture shaped the human genome: bringing genetics and the human sciences together. It’s really worth reading for anyone interested in the interactions between biology and culture. In particular, I was pleased to see them put forward the notion of culture having accelerated recent evolution, contra Stephen J. Gould’s claim that “there’s been no biological change in humans for 40,000 or 50,000 years”. Here’s the abstract:

Researchers from diverse backgrounds are converging on the view that human evolution has been shaped by gene–culture interactions. Theoretical biologists have used population genetic models to demonstrate that cultural processes can have a profound effect on human evolution, and anthropologists are investigating cultural practices that modify current selection. These findings are supported by recent analyses of human genetic variation, which reveal that hundreds of genes have been subject to recent positive selection, often in response to human activities. Here, we collate these data, highlighting the considerable potential for cross-disciplinary exchange to provide novel insights into how culture has shaped the human genome.

What conclusions can we draw from Neanderthal DNA pt.2

ResearchBlogging.org4. Nuclear DNA: Forays into 3 billion base pairs

4.1 Before Vi-80

The Vindija-80 (Vi-80) specimen is an important find for geneticists: it yielded a minimally contaminated sample and provided those first steps into Neanderthal genomics.

Previously, attempts at retrieving ancient nuclear DNA sequences proved to be a notoriously difficult process, plagued with problems of degradation, contamination and chemical damage (Hofreiter et al., 2001). Researchers also need to contend with quantities of nuclear genome available: for every nuclear genome there are approximately several hundred mtDNAs (Green et al., 2008). The severity of these problems, especially contamination, is magnified through Neanderthal genetic similarity with humans (Green et al., 2006). This is troubling because nuclear DNA presents far less variability than mtDNA (Russell, 2002). As a result, huge stretches of nuclear sequences are required to find a significant number of polymorphisms (ibid). Such implications meant that discovering endogenous DNA sequences requires sifting through a large corpus of “[…] more than 70 Neanderthal bone and tooth samples from different sites in Europe and western Asia” (Green et al., 2006, pg. 331).

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What conclusions can we draw from Neanderthal DNA pt.1

ResearchBlogging.orgIn recent times, genetic technology has progressed sufficiently to elucidate upon some of the questions normally preserved for archaeologists. One such question concerns the fate of a group of hominins that roamed Europe and East Asia for at least 250,000 years. During this time, this species adapted and endured some of the harshest environments on offer, all while showing signs of a unique culture. Only for them to suddenly disappear from the fossil record approximately 30,000 years before present (BP) (cf. Barton et al. 2007). So, what happened to our closest evolutionary relatives, the Neanderthals?

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Reading Round Up

Here’s some stuff I’ve been reading over the last month or so:

Okay, so that brings you up to date with my reading from May through to July. Next round up will cover August. How fascinating :-/


Neanderthal Genome Published

…Well, 60% of the genome at least. Not much has been said yet in regards to the nitty gritty aspects of Svante and colleagues’ findings. No doubt John Hawks and many others will offer their own perspectives over the next couple of days. If you’re interested in the immediate gist then here’s a link to the press release. Also, here is a quote from the BBC offering a succinct summary:
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