Post List

  • September 22, 2010
  • 12:00 PM

To gape or not to gape? Some mussels’ choices influence their place in a habitat

by Matt Soniak in

The segregation of habitat between native and invasive species often comes down to a competition between their physiological and behavioral abilities. This is especially true in habitats prone to frequent change; as both indigenous and invasive species respond to environmental variations in a habitat, it’s the difference in their responses that can determine their success [...]... Read more »

  • September 22, 2010
  • 11:31 AM

Horned Dinosaurs: When It Rains, It Pours

by Andrew Farke in The Open Source Paleontologist

2010 will surely go down as the annus mirabilis of horned dinosaur research. Between the publications of the horned dinosaur symposium volume (with its myriad new taxa and other exciting pieces of research), a "bagaceratopsid" in Europe, a true ceratopsid in Asia, the hypothesis that Torosaurus and Triceratops are growth stages of the same taxon, and more, it's really tough for a "ceratophile" (to borrow Peter Dodson's term) to keep up!Today continues the embarrassment of ceratopsian riches. With my co-authors Scott Sampson, Mark Loewen, Cathy Forster, Eric Roberts, Alan Titus, and Josh Smith, I'm pleased to introduce you to Utahceratops gettyi and Kosmoceratops richardsoni (at top and bottom, respectively, in the image at right), freshly published in PLoS ONE. Although it's been a long time coming, our hope is that these new critters will really knock your socks off!So what's so special about these two animals? Well, for one they're new dinosaurs. And new horned dinosaurs at that. On a broader note, our new critters (along with careful radiometric dating of the Kaiparowits Formation, the rock unit in southern Utah from which they originated) provide important evidence for dinosaur provincialism during the Late Cretaceous. In other words, these big, elephant-sized dinosaurs weren't traveling far. They're the same age as dinosaurs known from much further to the north, yet represent a very different part of the horned dinosaur family tree. This is strange, especially when you consider that today there is only one (or maybe two, depending on whom you ask) elephant species in all of Africa! 75 million years ago, there were three or four closely related species of horned dinosaur living simultaneously on that little strip of beachfront property that comprised western North America. And that's not counting a few more less closely-related horned dinosaurs (centrosaurines) that lived at the same time! Truly weird.There's been a lot said more eloquently elsewhere about these animals, so I'm just going to close with an answer to the question that should be at the top of many people's minds. Given the possibility that Torosaurus and Triceratops might be growth stages of a single species, how do we know that Utahceratops and Kosmoceratops aren't just growth stages of one species? After all, they lived at the same time in the same place, and end up somewhat close together on the phylogenetic analysis. Well, we certainly haven't done much in the way of histology yet, which would lay the issue completely to rest. However, as readers of the paper will note, we have obvious juveniles (based on sutural fusion and cranial element size) of both species. Although these remain to be published, in my opinion they pretty firmly demonstrate that both species of dinosaur were very different very early on in their development.So, go read the paper!Full disclosure: I am a section editor at PLoS ONE, the journal at which this new paper was published. However, I had absolutely no involvement in the handling of the manuscript (assigning the academic editor, selecting reviewers, making a publication decision, etc.).Image credit: Lukas PanzarinCitationSampson, S., Loewen, M., Farke, A., Roberts, E., Forster, C., Smith, J., & Titus, A. (2010). New horned dinosaurs from Utah provide evidence for intracontinental dinosaur endemism PLoS ONE, 5 (9) DOI: 10.1371/journal.pone.0012292... Read more »

  • September 22, 2010
  • 11:24 AM

Renewed Muck, Stuck

by Journal Watch Online in Journal Watch Online

Nobody said it was going to be easy – and they were right. A landmark effort to restore a huge swath of Florida’s wetlands isn’t bringing native plants back to some areas, a new study finds. And to add insult to injury, an invasive exotic shrub appears to be gaining ground due to the restoration. […] Read More »... Read more »

  • September 22, 2010
  • 11:00 AM

Y Chromosome VI: Palindromes!

by Kele in Kele's Science Blog

Synopsis: Why does the ampliconic sequence of the Y chromosome show such high sequence similarity to other regions of the Y? Palindromes. Find out more below! First, a brief review of what the ampliconic class is. From my Y Chromosome II post: The final sequence class, the ampliconic, is more complex than the previous two [...]... Read more »

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T.... (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature, 423(6942), 825-37. PMID: 12815422  

  • September 22, 2010
  • 10:50 AM

Flightlessness in azhdarchids, marsupial brains and pelagic desmostylians: SVPCA 2010 (part II)

by Darren Naish in Tetrapod Zoology

In the previous article on the 58th Symposium on Vertebrate Palaeontology and Comparative Anatomy (SVPCA), held in Cambridge, UK, I discussed some of the work that was presented on stem-tetrapods and sauropods. This time round, we look at more Mesozoic stuff - pterosaurs in particular - before getting on to Cenozoic mammals.

Read the rest of this post... | Read the comments on this post...... Read more »

  • September 22, 2010
  • 10:16 AM

How Doth the Hypercarnivorous Crocodile…

by Laelaps in Laelaps

Not long after her trip down the rabbit hole, the reluctant heroine of Charles Lutwidge Dodgson’s Alice’s Adventures in Wonderland is left shaken by the nonsensical strangeness of her surroundings. She tries reciting her school lessons to settle her nerves, but practicing does not provide her with any comfort. Her arithmetic doesn’t add up, geography [...]... Read more »

  • September 22, 2010
  • 10:00 AM

How Do We Design Effective Video Games for Learning? (VG Series Part 4/10)

by Richard Landers in NeoAcademic

Part 4 of my series examining research evidence for the value of video games. This time: a framework for educational games research.... Read more »

  • September 22, 2010
  • 09:58 AM

The citation game

by Hadas Shema in Information Culture

Although "Publish or perish" is more catchy, I believe it should be "Get cited or perish". Why? Because many people (without naming names, we're talking about your promotion committee)also rely on citation data when deciding a scientist's future.While citations often correlate with other measurements of scientific influence (awards, research grants, etc.) citations are hardly objective, and depend on more factors than someone finding your work useful.Time-dependent factors: Recent publications are more likely to get cited than older ones.The Matthew effect: "The rich get richer and the poor get poorer." The name was given by Merton (1968) who based it upon the Gospel of Matthew: "For to all those who have, more will be given, and they will have an abundance; but from those who have nothing, even what they have will be taken away."—Matthew 25:29, New Revised Standard Version.What it means is that the more cited a paper is, the more it will continue to get cited. Works for famous scientists as well. Field-dependent factors: Your chances for citing go up when you work in a bigger field with more publications and vice-versa.Journal-dependent factors: Getting published in a high-factor journal doesn't necessarily mean your paper is the best thing since sliced bread, but it means more people are likely to think so. Also, the first paper in a journal usually gets cited more often (I wonder if that's still relevant, given how wide-spread electronic access is these days).Paper-dependent factors: The frequency of citations for the paper correlates positively with the number of co-authors and the length of the reference list. Cite more, get cited more. Longer papers get cited more often than shorter ones, simply because they have more content.Author/reader dependent factors: Developing a good social network with colleagues can get you cited more often. Availability of publication: Do people have access to your paper? Open Access papers get cited more often (given that many universities' policy regarding paid subscriptions is "NOT", that's hardly surprising). Technical problems: Errors in the citing of your paper may prevent the citing from counting when a paper's references list is analysed. Another important rule is to pick one form of your name and stick to it (if you're John Smith, don't start being John K. Smith all of a sudden). Above all, write a good paper (it can't hurt). An important note: most of the material in this post is from Bornmann and Daniel's excellent review (2008). Bornmann, L., & Daniel, H. (2008). What do citation counts measure? A review of studies on citing behavior Journal of Documentation, 64 (1), 45-80 DOI: 10.1108/00220410810844150Eysenbach, G. (2006). Citation Advantage of Open Access Articles PLoS Biology, 4 (5) DOI: 10.1371/journal.pbio.0040157... Read more »

  • September 22, 2010
  • 09:06 AM

Simulation of Supply Chain Disruptions

by Daniel Dumke in SCRM Blog - Supply Chain Risk Management

Still too many cooperations do not analyze their supply networks using consistent and scientifically proven methods. Some already do. One case of a company (ABC) is described below.

Goals and Methods
ABC company wanted to know more about their exposure to supply chain disruptions originating from their own plants but also the connected transportation links, suppliers and customers. Specifically, the goals were:Assess the current level of supply chain disruption risk in the systemTest different mitigation strategiesProvide a tool that can be used in the case of a disruption to validate recovery steps before putting them into actionIdentify redundancy in the system that can be removed without affecting the risk level
The authors therefore designed a supply chain model for two major products (one high, one low volume product) using discrete event simulation in Arena, one of the most often used simulation environments. To obtain distributions for the resulting performance measures the authors take advantage of Monte Carlo simulation using an excel tool called @Risk. Simulation
The demand and risk patterns were evaluated using available data and expert interviews. In the second step mathematical distribution functions were adjusted to fit the empirical observations / forecast to input those into the model.
The company was very concerned with the effects of the disruptions on their customer service, so the Fill Rate was chosen as the relevant performance measure.

The model was analyzed in two ways: First in an steady state analysis the current risk levels in the model were analyzed. In a second step the model was adjusted, by implementing one of the following strategies: implementation of inventory control and improvement of sourcing.
Even though only one simple measure was used, the ABC company was able to gain valuable insights into their supply chain.
Status Quo: All runs of the risk model experienced at least one week where 0% of the incoming orders were satisfied for the available inventory levels (two to six weeks)Mitigation Strategies: The output clearly showed that reducing response times or increasing capacity of back-up methods were able to reduce the impact of a disruption and speed recovery.ABC realized that they lack a database with historic distribution information for disruptionsThere were no formal strategic-level mitigation proceduresRisk exposure is very dependent on the current state of the models parameters (eg. if a disruption occurs in a low inventory state, recovery lasts much longer)The most important result is that the process of implementing such a simulation model can help the company think about supply chain disruptions more intensively and such a project can be used as a starting point for systematically documenting the risks and contingency plans in case of a disruption.

Schmitt, Amanda J., & Singh Mahender (2009). Quantifying Supply Chain Disruption Risk Using Monte Carlo and Discrete-Event Simulation Proceedings of the 2009 Winter Simulation Conference, 1237-1248
... Read more »

Schmitt, Amanda J., & Singh Mahender. (2009) Quantifying Supply Chain Disruption Risk Using Monte Carlo and Discrete-Event Simulation. Proceedings of the 2009 Winter Simulation Conference, 1237-1248. info:/

  • September 22, 2010
  • 09:05 AM

Tip of the Week: PathCase for pathway data

by Mary in OpenHelix

We spend a lot of time exploring genomic data, variations, and annotations. But of course a linear perspective on the genes and sequences is not the only way to examine the data. Understanding the pathways in which genes and molecular entities interact is crucial to understanding systems biology.
There are a number of tools which can help you to visualize and explore this kind of data. KEGG is one of the most venerable tools in bioinformatics, BioCyc is well known and used, Reactome is one of our favorites. Recently NCBI BioSystems has come along, and the BioModels tool at EBI provides more data of this type as well. Pathway Interaction Database is another place to try. What you’ll find is that each one has different emphasis, species focus or data sets available, and different tools to use to graphically display the databases. The ways to customize or interact with the data will vary as well. So you may need to try several to find the one you want for your purposes.
But for today’s tip of the week I will highlight PathCase, a Pathways Database System from Case Western Reserve University. This is a  tool I’ve  had my eye on for a number of years, and they continue to add new features and data sets to their visualization and search interface which are very nicely done.
PathCase offers you several ways to browse and search for pathways, processes, organisms, and also molecular entities (such as ATP, ions, etc) as well as genes and proteins. It’s all integrated into the system, so when you find an item of interest you can move to the other related pieces.  For example, from the Pathways you can find genes and learn more about the genes. From genes you can load the pathways in which they participate.
When you have the pathway graphics loaded, you can interact with that pathway by clicking, dragging, re-organizing and more. Right-clicking offers more details about the items and ways to visualize the data. One option I didn’t have time to show in the movie is that you can use the H20/CO2 box to load up pathways that are linked to the one you are looking at and load those up, going even further along any route that you might be interested in. Here’s just a quick sample of that: from the NARS2 gene page I loaded the alanine pathway, and then added the fatty acid metabolism pathway. Now I can explore both of them with all the standard PathCase tools and understand many of their relationships. Once you start exploring these pathways you be amazed at how complex visualizations are possible.

So if you are interested in biological pathways, exploring them and representing them, check out PathCase.
PathCase site:
Elliott, B., Kirac, M., Cakmak, A., Yavas, G., Mayes, S., Cheng, E., Wang, Y., Gupta, C., Ozsoyoglu, G., & Meral Ozsoyoglu, Z. (2008). PathCase: pathways database system Bioinformatics, 24 (21), 2526-2533 DOI: 10.1093/bioinformatics/btn459

... Read more »

Elliott, B., Kirac, M., Cakmak, A., Yavas, G., Mayes, S., Cheng, E., Wang, Y., Gupta, C., Ozsoyoglu, G., & Meral Ozsoyoglu, Z. (2008) PathCase: pathways database system. Bioinformatics, 24(21), 2526-2533. DOI: 10.1093/bioinformatics/btn459  

  • September 22, 2010
  • 09:00 AM

The Wolverine Leaf

by Brit Trogen in Science in Seconds


What once was a man, is now the Wolverine. And what once was a leaf, is now... a magnetic leaf?


Chemists at the Max Planck Institute of Colloids and Interfaces have taken the next step in merging nature with technology by devising a method to convert the skeleton of a rubber tree leaf into iron carbide. And just like Wolverine, the newly converted leaves are magnetic, able to withstand extremely high amounts of stress, and looking for blood. 


Okay... Everything but that last one. The leaf skeletons are also able to stand up to high temperatures and conduct electricity. But the exciting thing isn't necessarily the properties of the leaves. It's the process that was taken to convert them, and the broader mind-set behind using nature's structures as catalysts for the production of synthetic materials; in this case, wafer-thin metal carbides.


Through a process that starts by soaking in iron acetate, and ends with heating to 700 degrees Celsius, the researchers have opened the door for a new wave of synthetic polymers; using fine natural structures as the starting point for chemical reactions. What works for a leaf could work just as well for a porous sponge, after all. Or creeping vines, perhaps. And with some tweaking, fibers or networks derived from these processes could potentially go on to replace much more expensive metals like platinum in fuel cell electrodes, according to Dr. Zoë Schnepp, the leading researcher of the team.


I can't imagine a more perfect combination of science with nature. I mean, everybody wins in this one, right? We get a more sustainable and cost-effective method of producing synthetic materials, the rubber tree loses a couple leaves but is left mostly unharmed, and we keep a secret government agency watching over the mutant leaves so they never learn of their origins and come back to hunt us down in the future. 


What could go wrong?


Schnepp Z, Yang W, Antonietti M, & Giordano C (2010). Biotemplating of metal carbide microstructures: the magnetic leaf. Angewandte Chemie (International ed. in English), 49 (37), 6564-6 PMID: 20715026
... Read more »

Schnepp Z, Yang W, Antonietti M, & Giordano C. (2010) Biotemplating of metal carbide microstructures: the magnetic leaf. Angewandte Chemie (International ed. in English), 49(37), 6564-6. PMID: 20715026  

  • September 22, 2010
  • 08:32 AM

Intelligent Nihilism

by gameswithwords in Games with Words

The latest issue of Cognitive Science, which is rapidly becoming one of my favorite journals, carries an interesting and informative debate on the nature of language, thought, cognition and learning, between John Hummel at University of Illinois-Urbana-Champaign, and Michael Ramscar, at Stanford University. This exchange of papers highlights what I think is the current empirical standstill between two very different world-views.

Hummel takes up the cause of "traditional" models on which thought and language is deeply symbolic and involves algebraic rules. Ramscar defends more "recent" alternative models that are built on associate learning -- essentially, an update on the story that was traditional before the symbolic models.

Limitations of Relational Systems

The key to Hummel's argument, I think, is his focus on explicitly relational systems:
John can love Mary, or be taller than Mary, or be the father of Mary, or all of the above. The vocabulary of relations in a symbol system is open-ended ... and relations can take other relations as arguments (e.g., Mary knows John loves her). More importantly, not only can John love Mary, but Sally can love Mary, too, and in both cases it is the very same "love" relation ... The Mary that John loves can be the very same Mary that is loved by Sally. This capacity for dynamic recombination is at the heart of a symbolic representation and is not enjoyed by nonsymbolic representations.That is, language has many predicates (e.g., verbs) that seem to allow arbitrary arguments. So talking about the meaning of love is really talking about the meaning of X loves Y: X has a particular type of emotional attachment to Y. You're allowed to fill in "X" and "Y" more or less how you want, which is what makes them symbols.

Hummel argues that language is even more symbolic than that: not only do we need symbols to refer to arguments (John, Mary, Sally), but we also need symbols to refer to predicates as well. We can talk about love, which is itself a relation between two arguments. Similarly, we can talk about friendship, which is an abstract relation. This is a little slippery if you're new to the study of logic, but doing this requires a second-order logic, which has a number of formal properties.

Where Hummel wants to go with this is that associationist theories, like Ramscar's, can't represent second-order logical systems (and probably aren't even up to the task of the types of first-order systems we might want). Intuitively, this is because associationist theories represent similarities between objects (or at least how often both occur together), and it's not clear how they would represent dissimilarities, much less represent the concept of dissimilarity:
John can be taller than Mary, a beer bottle taller than a beer can, and an apartment building is taller than a house. But in what sense, other than being taller than something, is John like a beer bottle or an apartment building? Making matters worse, Mary is taller than the beer bottle and the house is taller than John. Precisely because of their promiscuity, relational concepts defy learning in terms of simple associative co-occurrences.It's not clear in these quotes, but there's a lot of math to back this stuff up: second-order logic systems are extremely powerful and can do lots of useful stuff. Less powerful computational systems simply can't do as much.

The Response

Ramscar's response is not so much to deny the mathematical truths Hummel is proposing. Yes, associationist models can't capture all that symbolic systems can do, but language is not a symbolic system:
We think that mapping natural language expressions onto the promiscuous relations Hummel describes is harder than her does. Far harder: We think you cannot do it.Ramscar identifies a couple old problems: one is polysemy, the fact that words have multiple meanings  (John can both love Mary and love a good argument, but probably not in the same way). Fair enough -- nobody has a fully working explanation of polysemy.

The other problem is the way in which the symbols themselves are defined. You might define DOG in terms of ANIMAL, PET, FOUR-LEGGED, etc. Then those symbols also have to be defined in terms of other symbols (e.g., FOUR-LEGGED has to be defined in terms of FOUR and LEG). Ramscar calls this the turtles-all-the-way-down argument.

This is fair in the sense that nobody has fully worked out a symbolic system that explains all of language and thought. It's unfair in that he doesn't have all the details of this theory worked out, either, and his model is every bit as turtles-all-the-way-down. Specifically, concepts are defined in terms of cooccurrences of features (a dog is a unique pattern of co-occurring tails, canine teeth, etc.). Either those features are themselves symbols, or they are always patterns of co-occuring features (tail = co-occurrence of fur, flexibility, cylindrical shape, etc.), which are themselves patterns of other other feature co-occurrences, etc. (It's also unfair in that he's criticizing a very old symbolic theory; there are newer, possibly better ones around, too.)

Implicit in his argument is the following: anything that symbolic systems can do that associationist systems can't do are things that humans can't do either. He doesn't address this directly, but presumably this means that we don't represent abstract concepts such as taller than or friendship, or, if we do, it's via a method very different from formal logic (what that would be is left unspecified).

It's A Matter of Style

Here's what I think is going on: symbolic computational systems are extremely powerful and can do lots of fancy things (like second-order logics). If human brains instantiate symbolic systems, that would explain very nicely lots of the fancy things we can do. However, we don't really have any sense of how neurons could instantiate symbols, or even if it's possible. So if you believe in symbolic computation, you're basically betting that neurons can do more than it seems.

Associationist systems face the opposite problem: we know a lot about associative learning in neurons, so this seems like an architecture that could be instantiated in the brain. The problem is that associative learning is an extremely underpowered learning system. So if you like associationist systems, you're betting that humans can't actually do many of the things (some of) us think humans can do.

Over at Child's Play, Dye claimed that the argument in favor of Universal Grammar was a form of Intelligent Design: we don't know how that could be learned/evolve, so it must be innate/created. I'll return the favor by labeling Ramscar's argument Intelligent Nihilism: we don't how the brain could give rise to a particular type of behavior, so humans must not be capable of it.

The point I want to make is we don't have the data to choose between these options. You do have to work within a framework if you want to do research, though, and so you pick the framework that strikes you as most plausible. Personally, I like symbolic systems.

John E. Hummel (2010). Symbolic versus associative learning Cognitive Science, 34, 958-865 : 10.1111/j.1551-6709.2010.01096.x

... Read more »

John E. Hummel. (2010) Symbolic versus associative learning. Cognitive Science, 958-865. info:/10.1111/j.1551-6709.2010.01096.x

Michael Ramscar. (2010) Computing machinery and understanding. Cognitive Science, 966-971. info:/

  • September 22, 2010
  • 08:00 AM

Shock Therapy – A Thing of the Past or the Only Way Out?

by Shaheen Lakhan in Brain Blogger

When most people think of electroconvulsive therapy (ECT), the first thing that comes to mind may be a scene in the 1975 film “One flew over the Cuckoo’s nest,” where Jack Nicholson undergoes the treatment, in a way more akin to torture than medical care. There are people holding him down, he is not under [...]... Read more »

Coentre R, Barrocas D, Chendo I, Abreu M, Levy P, Maltez J, & Figueira ML. (2009) [Electroconvulsive therapy: myths and evidences]. Acta medica portuguesa, 22(3), 275-80. PMID: 19686628  

  • September 22, 2010
  • 07:33 AM

Through the Language Glass (Part 2)

by Chris in The Lousy Linguist

This is part 2 of my review of Guy Deutscher's new book Through the Language Glass: Why the World Looks Different in Other Languages. This covers The Language Lens (129-249). Part 1 is here. This review will cover the scientific evidence that Deutscher reviews suggesting that language affects thought, and will end with a shocking proposal.To sum up my review of part one: meh. Okay, we've established that culture can influence language. This is a lot less controversial than Deutscher makes it seem and he spent a large amount of text defending that position. Okay, whatever, time to move on. In part 2 he again begins with historical review explaining why he thinks Whorf was a con man, but also why he thinks the core insights of early linguist relativity deserve closer, honest investigation. He complains that based his Hopi claims on just one lonely informant (p142). We'll see later that Deutscher himself falls for the same trap. He replaces Whorf with the Boas-Jakobson principle that languages differ in what they must convey, not what they may convey” (151). I respect Deutscher for making this a central theme in his book because I think he's right. To parrot his own recitation of Humbolt: any thought can be expressed in any language. It is what our native language forces us to foreground that makes linguistic relativity an interesting topic.Deutscher spends most of the second part of the book reviewing three areas of language that have provided evidence that language affects thought: spatial coordinates, grammatical gender, and color terms (familiar from part 1). The general point I want to make about his evidence is that it is far weaker than he maintains. But is is interesting. A brief set of reactions:Spatial Coordinates -- everything is embodiedMost of his argumentation about the affect of spacial coordinate terms on thought stems from Levinson's evidence from speakers of the Australian language Guugu Yimithirr which is famous for giving us the word “kangaroo.” Speakers of GY do not generally use ego-centric terms like "right" and "left" but rather use cardinal direction terms like "east" and "west." As a result, Deutscher claims, they remember information about situations differently than speakers of English. They have, so the argument goes, a perfect pitch for direction and they are always attuned to where north is. Deutscher's claim is that only the linguistic repetition of such terms can possibly account for this. Hence, their language affects what they pay attention to and what they remember, hence language affects thought.I've never found this line of research all that convincing regarding linguistic relativity and Deutscher does not really add much to the debate. Like Deutscher's complaint above regarding Whorf's one lonely Hopi speaker, it turns out there are not many native speakers of Guugu Yimithirr left and haven't been for a while. These experiments on directional language involve very few speakers, and most of them have both cardinal direction and ego-centric direction in their dialect. If we're going to complain about Whorf's restricted subject pool, we must complain about Levinson's too.But more to the point, I believe all direction terms are ultimately ego-centric insofar as they are embodied. The terms "north" and "south" are not magically universal. They are based on a human being's body and orientation (i.e., ego-centric). Don't believe me, ask yourself, what does "north" mean in space? What does "north" mean to an amoeba? Mostly what Deutscher does in his discussions of direction terms is reiterate the point he belabored in Part 1: culture affects language. Yeah, we got that already.The rise of similarity judgmentsThat is until he discusses the table experiments. These experiments show subjects tables with objects on them and ask them to arrange them in accordance with a target. Basically, they ask for similarity judgement. How can you make this table arrangement similar to the previous table. This methodological paradigm has become prominent in psycholinguistics and cognitive linguistics, especially studies testing linguistic relativity. In fact, all of the studies Deutscher discusses are similarity judgment studies of one sort or another. The point is that I show you one target thing, then two test things and ask, which test is MORE SIMILAR to the target than the other? Ultimately Deutscher himself problematizes spatial coordinate terms so much, they fall flat and remain unconvincing as a base of evidence for linguistic relativity.Grammatical GenderMost languages have terms for classifying things. Some languages have more elaborate classifier systems than others. In German, the term for the fork is die Gabel, marked by feminine die. Ultimately, most languages with elaborate classifiers have systems that can be described as incoherent in so far as most things given one classification have no inherent properties that signify that classification (there is nothing inherently feminine about a fork). However, Deutscher provides evidence that speakers of languages with grammatical gender will evoke properties of things in keeping with their gender classifier, suggesting that the classifier is causing them to imagine a fork would speak with a female voice, for example. But these experiments mainly test vague associations of imagination, not linguistic causality, as Deutscher admits.Color TermsIt is not until chapter 9 Russian Blues that Deutscher really delivers the goods. It is this chapter which provides the most interesting evidence for the effect of language on thought. Pity it is only about 15 pages of the book. The whole book should have been more like this. The facts he discusses involve the basic point that the brain sees what it wants to see. It turns out our perception of color has little to do with any objective feature of the thing we're looking at (he explains this fact brilliantly in the Appendix which I highly recommend, and frankly, should have been the first chapter, not relegated to the attic of an appendix). The point is that our brains change the input. As our eyes take in objective photons, our brain photoshops the input (a great analogy from Deutscher which really brings the point home).The experimental results Deutscher discusses involve more similarity judgements, albeit with a twist. Instead of relying solely on the similarity judgments, researchers studied the more objective reaction time. They showed people different color patches and asked them to judge the sameness. Despite the various and clever variations on this theme, they all relied on subjective judgements of similarity. And this is where they fail to extricate themselves from the problem of strategizing.Unfortunately they all share the critical flaw that making a similarity judgment is a logical reason act and may be mitigated by strategizing. Deutscher discusses this fact, but doesn't realize that none of the fixes work. A similarity judgment is always a logical process susceptible to the effects of strategizing. This will be a major issue in my Shocking Proposal at the end. You see, regardless of how clever the test, as long as you are basically asking a subject to make a similarity judgment, you are asking them to reason about the task. So your results will be tinged by the strategizing of human subjects as they logically try to game the system. This is well known in psycholinguistics and difficult to avoid. So how do you objectively test what colors a person considers blue?A Shocking ProposalThe paradigm already exists. How can you objectively prove that English speakers really do consider aspirated /kh/ and unaspirated /k/ both the same phoneme? You condition them to fear aspirated /kh/ by shocking them every time they hear it (measuring their galvanic skin response). Once they are conditioned, you then play them unaspirated /k/ (with no shock) and check to see if you get the same GSR spike (in anticipation).Okay, now apply this to color terms. Condition subjects to fear center of the category blue, then show them gradations. What causes the GSR spike? That's what they consider blue. now do that with speakers of 40 different languages.If the hippies on the human subjects review board let you do it, there's your dissertation.... Read more »

Guy deutscher. (2010) Through the Language Glass: Why the World Looks Different in Other Languages. Metropolitan Books. info:/

  • September 22, 2010
  • 07:11 AM

Sociopathic Dementia

by Neuroskeptic in Neuroskeptic

Frontotemporal dementia (FTD) is a tragic, but scientifically fascinating, disease.FTD only accounts for a small fraction of dementias in total (estimates range from 2% to 10%), but it typically strikes people aged in their 50s or 60s, i.e. much earlier than the average for Alzheimer's disease, the most common cause of dementia. As a result, FTD accounts for a large proportion of early-onset cases.The symptoms are different to those of Alzheimer's, at least in the early stages. Memory problems and confusion are not prominent. Nor are hallucinations and delusions, which are seen in 20% of Alzheimer's, but only 2% of FTD.Instead, patients often present with language problems - either forgetting what words mean, starting with uncommon words and progressing to easy ones ("semantic dementia"), or losing the ability to articulate speech ("nonfluent aphasia").But the most disturbing effects are behavioural and personality changes. These are not seen in all cases, but in some people (the "behavioural variant"), they are the main symptom. Patients may begin to act entirely out of character, including criminal acts.Aggressive behaviour is also sometimes seen in Alzheimer's, but it's usually associated with confusion or hallucinations: people "don't know what they're doing". In FTD, patients can commit serious crimes even though their cognitive function is pretty much intact: they do know what they're doing.Mario F. Mendez discusses this in a new paper, The Unique Predisposition to Criminal Violations in Frontotemporal Dementia, and asks whether people who commit crimes while suffering from FTD should be considered legally responsible for their apparantly "sociopathic" actions. He presents 4 case histories.Patient 1: A left-handed male in his sixties began stalking and attempting to molest children for the first time in his life. He followed children home from school and tried to touch them... On another occasion, he stood at the foot of a pool and stared at the children for a prolonged time.When he exposed himself to his neighbor’s children, he was arrested. The patient did not deny his actions, could describe them in detail, and endorsed them as wrong and harmful. Despite this, he stated that he did not feel that he was causing harm at the time of his acts.The patient’s personality had deteriorated over the prior four years, with decreased concern for others, disinhibition, and compulsive hoarding. He had caused disturbances at work, such as intruding into others’ conversations and walking into others’ offices... constantly pilfering... hiding money.... In addition, he ate indiscriminately, even going through waste containers and eating garbage. He stopped showering and wore the same clothes every day.Neuropsychological testing and brain scans suggested early FTD, and his mother had reportedly suffered unspecified dementia; FTD is often genetic. He was not prosecuted. This case has a lot in common with the man who became a pedophile after surgery for a brain tumour: not just the pedophilia, but other symptoms like compulsive hoarding, over-eating, etc.Patient 4: A right-handed man in his early fifties had a hit-and-run accident and left the scene without concern. He had struck a van with passengers but kept driving. The police stopped him a short distance away from the scene, and he did not deny his action.Leaving the scene of an accident was not characteristic of his premorbid personality, yet he had had several recent traffic violations... He could recall and describe the accident, knew that it was wrong to leave the scene, but did not feel the need to stop at the time.Over the prior two years, the patient’s pervasive behavior had significantly changed. He had become disengaged and emotionally detached; for example, he did not react to the death of his mother...He was no longer embarrassed over passing gas or belching in public or appearing partially clothed in front of others. The patient had a tendency toward hyperorality, especially for peanuts, and had a decline in personal hygiene. Other aspects of the history included dysarthria and a recent tendency to choke on liquids.This patient showed clear signs of motor neuron disease, which occurs in up to 15% of FTD cases. He died, as a result of the progression of the motor neuron disease, one year later, after developing other symptoms of FTD. His death meant he could not be tried for the hit-and-run.Mendez notes that legally, these patients would probably not qualify for the "insanity defence". Under the British M'Naghten Rules, also adopted by the USA, the defendant is only eligible if they werelabouring under such a defect of reason, from disease of the mind, as not to know the nature and quality of the act he was doing; or, if he did know it, that he did not know he was doing what was wrong.These patients do not fit that bill.Finally, why does FTD cause sociopathic behaviour? Mendez says that it is because it involves degeneration of the vmPFC, linking FTD patients to the classic case of Phineas Gage whose vmPFC was destroyed by a flying iron rod. But Gage, while he did show personality changes, actually managed to function fairly well in society.So temporal lobe degeneration probably also contributes to the FTD behavioural syndrome, especially since many of the symptoms (like compulsive eating) are seen in monkeys with temporal lobe lesions.Mendez MF (2010). The unique predisposition to criminal violations in frontotemporal dementia. The journal of the American Academy of Psychiatry and the Law, 38 (3), 318-23 PMID: 20852216... Read more »

Mendez MF. (2010) The unique predisposition to criminal violations in frontotemporal dementia. The journal of the American Academy of Psychiatry and the Law, 38(3), 318-23. PMID: 20852216  

  • September 22, 2010
  • 05:33 AM

Courting artists to revitalize American cities

by SAGE Insight in SAGE Insight

Artist garret as growth machine? Local policy and artist housing in U.S. cities From Journal of Planning Education and Research In the last ten years the arts, and artists, have come to be seen as catalysts for the revitalization of American cities. This article demonstrates that in most cities, artist housing programs are considered part [...]... Read more »

  • September 22, 2010
  • 01:01 AM

On local greens and homegardens and local greens

by Jeremy in Agricultural Biodiversity Weblog

Great too see two papers by our friends at Bioversity come out in rapid sequence recently relating to two project with which I was marginally connected in their early stages back in the 90s. One is on African leafy vegetables (ALV), a common subject here. And the other on homegardens. The ALV paper tries to [...]... Read more »

  • September 22, 2010
  • 12:21 AM

Neuroscience Journal Club: Misconceptions about Androgens

by Allison in Dormivigilia

It appears that DHT regulates AVP expression through ESTADIOL, redefining preconceived notions about male and female physiology. ... Read more »

Toni R. Pak, Wilson C. J. Chung, Laura R. Hinds and Robert J. Handa. (2007) Estrogen Receptor-ß Mediates Dihydrotestosterone-Induced Stimulation of the Arginine Vasopressin Promoter in Neuronal Cells. Endocrinology. info:/

  • September 21, 2010
  • 08:23 PM

Hump-day cock-ups – Médecins sans responsabilité

by thomastu in Disease Prone

Most medical residents are irresponsible jerks to their patients, a recent paper in the Journal of the American Medical Association has found. In a self-reported study of 537 respondents, 60% of second and third year medical residents admitted to turning up to work while sick; 31% more than once. In one hospital, 100% of the [...]... Read more »

Jena AB, Baldwin DC Jr, Daugherty SR, Meltzer DO, & Arora VM. (2010) Presenteeism among resident physicians. JAMA : the journal of the American Medical Association, 304(11), 1166-8. PMID: 20841527  

  • September 21, 2010
  • 08:13 PM

Hot Off The Press

by Journal Watch Online in Journal Watch Online

They are dry and brittle now, the showy orchids that Victorian-era flower-lovers plucked from English meadows and carefully pressed onto vellum sheets. But the faded blooms confirm that spring flowers are blooming earlier in the United Kingdom (UK) due to a warming climate, according to a new study.
Field records have long suggested climate change […] Read More »... Read more »

Karen M. Robbirt, Anthony J. Davy, Michael J. Hutchings and David L. Roberts. (2010) Validation of biological collections as a source of phenological data for use in climate change studies: a case study with the orchid Ophrys sphegodes. Journal of Ecology. info:/10.1111/j.1365-2745.2010.01727.x

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