A. Kabakçıoğlu, D. Yuret, M. Gür, B. Erman. 2010 Phys. Biol. 7 046005 doi: 10.1088/1478-3975/7/4/046005 (PDF, PDF, HTML, Online, Hermite code)
Abstract: We develop a general framework for the analysis of residue fluctuations that simultaneously incorporates anharmonicity and mode-coupling in a unified formalism. We show that both deviations from the Gaussian model are important for modeling the multidimensional energy landscape of the protein Crambin (1EJG) in the vicinity of its native state. The effect of anharmonicity and mode-coupling on the fluctuational entropy is in the order of a few percent.
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October 27, 2010
October 19, 2010
Istanbul Marathon 2010
Some pictures from the Istanbul Marathon...Here is our route from runkeeper.com:
Some useful links:
evolutionrunning.com: How to run without injury.
Galloway's Marathon book: Everybody can do it!
Born to run: To get inspired.
And some pictures:
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September 19, 2010
Adam's Tongue by Derek Bickerton
Bickerton presents his theory on the origin of language. Some notes:
- Human language is qualitatively distinct from animal communication systems (ACSs): most words are incomplete by themselves and need to be combined to express meaning whereas animal calls are self sufficient.
- A better model for origins of language may be pidgins (languages created by people that live together but do not share a common language).
- A protolanguage would have words as we know them that combine but no well defined rules of syntax or morphology.
- ACSs are all about the here and now, most words refer to things outside the current happenings.
- ACSs are mainly manipulative whereas language mainly informative.
- Communicative units come in three flavors: icons resemble the thing talked about, indices point to them, and symbols do neither. (function words which do not refer at all form a separate group). Displacement (referring to things that are not in the here/now) is only possible with symbols and icons. Iconic signs may have been the first displaced ones paving the way for symbols.
- "Since we usually regard language as no more than the means by which we express our thoughts, it seems natural to think that language should issue from intelligence, rather than vice versa. It seemed equally obvious, to naive observers, that the earth was the center of the universe, and the sun, moon, and planets all went around it." pp.58
- Categories are different from concepts. pp.87. Concepts you can think about or think with, whereas all you can do with categories is to tell whether something belongs in them. pp.205
- The ACSs of ants and bees may be closer to humans because they exhibit displacement (about food sources distant in time and space). ch.7
- Crucial as speciation is, it's still far from completely understood. pp.149
- The real breakthrough in language had to be displacement rather than arbitrariness (of signs). pp.160
- Bickerton's sequence:
1. Animals have concepts that won't merge.
2. Protohumans start talking.
3. Talking produces typically human concepts.
4. Merge appears and starts merging concepts.
5. The brain maybe gets rewired.
6. Capacities for complex thought planning etc. develop.
Chomsky's version has concepts appear first and talking last. pp.189.
- Thoughts like "roses are red" are offline as opposed to online thinking about here and now. (still makes the hearer do stuff: think of roses, think of red, merge...) pp.193
- Categories have to be only detailed enough to distinguish between appropriate reactions (affordances?). pp.206.
- I don't quite know what he's saying about memory pp.207 or recursion pp.244.
- Posted using BlogPress from my iPhone
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- Human language is qualitatively distinct from animal communication systems (ACSs): most words are incomplete by themselves and need to be combined to express meaning whereas animal calls are self sufficient.
- A better model for origins of language may be pidgins (languages created by people that live together but do not share a common language).
- A protolanguage would have words as we know them that combine but no well defined rules of syntax or morphology.
- ACSs are all about the here and now, most words refer to things outside the current happenings.
- ACSs are mainly manipulative whereas language mainly informative.
- Communicative units come in three flavors: icons resemble the thing talked about, indices point to them, and symbols do neither. (function words which do not refer at all form a separate group). Displacement (referring to things that are not in the here/now) is only possible with symbols and icons. Iconic signs may have been the first displaced ones paving the way for symbols.
- "Since we usually regard language as no more than the means by which we express our thoughts, it seems natural to think that language should issue from intelligence, rather than vice versa. It seemed equally obvious, to naive observers, that the earth was the center of the universe, and the sun, moon, and planets all went around it." pp.58
- Categories are different from concepts. pp.87. Concepts you can think about or think with, whereas all you can do with categories is to tell whether something belongs in them. pp.205
- The ACSs of ants and bees may be closer to humans because they exhibit displacement (about food sources distant in time and space). ch.7
- Crucial as speciation is, it's still far from completely understood. pp.149
- The real breakthrough in language had to be displacement rather than arbitrariness (of signs). pp.160
- Bickerton's sequence:
1. Animals have concepts that won't merge.
2. Protohumans start talking.
3. Talking produces typically human concepts.
4. Merge appears and starts merging concepts.
5. The brain maybe gets rewired.
6. Capacities for complex thought planning etc. develop.
Chomsky's version has concepts appear first and talking last. pp.189.
- Thoughts like "roses are red" are offline as opposed to online thinking about here and now. (still makes the hearer do stuff: think of roses, think of red, merge...) pp.193
- Categories have to be only detailed enough to distinguish between appropriate reactions (affordances?). pp.206.
- I don't quite know what he's saying about memory pp.207 or recursion pp.244.
- Posted using BlogPress from my iPhone
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September 04, 2010
Author Alerts
I have looked for a way to get alerted about new releases from my favorite authors for a long time. I think Amazon used to support this in the past but they no longer do. Barnes and Noble has writer alerts for only a small list of authors. This is such an obvious feature for a bibliophile that I do not understand why nobody supports it. I was about to write my own code but luckily ran into www.authoralerts.com first. Highly recommended.
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August 26, 2010
Unsupervised Part of Speech Tagging Using Unambiguous Substitutes from a Statistical Language Model
Mehmet Ali Yatbaz and Deniz Yuret. Coling 2010. pp. 1391--1398. Beijing, China. (PDF, Poster)
Abstract: We show that unsupervised part of speech tagging performance can be significantly improved using likely substitutes for target words given by a statistical language model. We choose unambiguous substitutes for each occurrence of an ambiguous target word based on its context. The part of speech tags for the unambiguous substitutes are then used to filter the entry for the target word in the word--tag dictionary. A standard HMM model trained using the filtered dictionary achieves 92.25% accuracy on a standard 24,000 word corpus.
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Abstract: We show that unsupervised part of speech tagging performance can be significantly improved using likely substitutes for target words given by a statistical language model. We choose unambiguous substitutes for each occurrence of an ambiguous target word based on its context. The part of speech tags for the unambiguous substitutes are then used to filter the entry for the target word in the word--tag dictionary. A standard HMM model trained using the filtered dictionary achieves 92.25% accuracy on a standard 24,000 word corpus.
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