Biology: May 2008 Archives


May 31, 2008

Predicting Human Brain Activity Associated with the Meanings of Nouns
Tom M. Mitchell, Svetlana V. Shinkareva, Andrew Carlson, Kai-Min Chang, Vicente L. Malave, Robert A. Mason, Marcel Adam Just

The question of how the human brain represents conceptual knowledge has been debated in many scientific fields. Brain imaging studies have shown that different spatial patterns of neural activation are associated with thinking about different semantic categories of pictures and words (for example, tools, buildings, and animals). We present a computational model that predicts the functional magnetic resonance imaging (fMRI) neural activation associated with words for which fMRI data are not yet available. This model is trained with a combination of data from a trillion-word text corpus and observed fMRI data associated with viewing several dozen concrete nouns. Once trained, the model predicts fMRI activation for thousands of other concrete nouns in the text corpus, with highly significant accuracies over the 60 nouns for which we currently have fMRI data.

This paper is pretty interesting. Basically, they have measured fMRI activation data for 60 words. So, voxel v has activation level A_v_w for word w. For each word, they have measurements of a bunch of linguistic parameters P_1, P_2, P_3..., etc. They then fit a predictive model for the effect of each parameter on the activation level of each voxel, so for instance you could say that if a word is associated with "sight" (i.e., it appears near "sight" in text corpii) that increases the activation of voxel v by .1 units. This is fairly straightforward regression modelling stuff.

Once you have the model fitted, you can then predict the activation of each voxel for a novel word by taking its linguistic parameter values and plugging them into the model. Their results are actually pretty good. They have a corpus of 60 word/fMRI pairs and they use 58 as a training set and 2 as a test set. They then try to differentiate the two test words by asking which predicted activation pattern is closer. The results are significantly better than chance: mean=.77 for what appears to be arbitrary words and mean=.62 when the words are from the same semantic category (e.g., "celery" and "corn"). Moreover, a significant amount of the error appears to come from head motion by the subjects.

I'm not sure how to interpret this from a scientific perspective. It's a long way from knowing which brain cells are used in processing certain words to knowing how the brain actually processes those words. On the other hand, it's not clear you ned that deep an understanding to build a brain-scanning fMRI gizmo that does something useful. Though we're a long way from that too. Even ignoring the fact that we don't understand the brain well enough, hanging out with your head in a noisy magnet probably isn't a lot of fun.


May 24, 2008

For some reason I checked out Conservapedia today. Sort of an amazing artifact, if basically insane. It's like—well, it actually is—they want to create a whole alternate reality where the normal rules of intellectual discourse don't apply. Here's the (somewhat famous) article on the kangaroo:
According to the origins theory model used by young earth creation scientists, modern kangaroos are the descendants of the two founding members of the modern kangaroo baramin that were taken aboard Noah's Ark prior to the Great Flood. It has not yet been determined by baraminologists whether kangaroos form a holobaramin with the wallaby, tree-kangaroo, wallaroo, pademelon and quokka, or if all these species are in fact apobaraminic or polybaraminic.

After the Flood, these kangaroos bred from the Ark passengers migrated to Australia. There is debate whether this migration happened over land[6] with lower sea levels during the post-flood ice age, or before the supercontinent of Pangea broke apart[7] The idea that God simply generated kangaroos into existence there is considered by most creation researchers to be contra-Biblical.

Other views on kangaroo origins include the belief of some Australian Aborigines that kangaroos were sung into existence by their ancestors during the "Dreamtime" [8] and the evolutionary view that kangaroos and the other marsupials evolved from a common marsupial ancestor which lived hundreds of millions of years ago.[9] In accordance with their worldviews, a majority of biologists regard evolution as the most likely explanation for the origin of species including the kangaroo.

Uh, yeah. Incidentally, that passage contains links to Baraminology, the study of Biblical kinds. I almost expect there to be a page on the Turtles all the way down theory of cosmology. I was going to try to make a serious argument about this, but it's just laughable.

Incidentally, Mrs. G noted the weird juxtaposition of Pangea and flood theory. Unsurprisingly, there's a footnote pointing to this uh, explanation about how Pangea is compatible with flood theory. In case you're curious, it's that the rate of geologic activity was higher during the flood.


May 16, 2008

Interesting fact: there's a significant amount of evidence that sleeping on the left hand side as opposed to the right hand side significantly reduce GERD. For instance: Khoury et al. (1999(:
METHODS: Ten patients, three female and seven male (mean age 47.6 yr, range 30-67 yr) with abnormal recumbent esophageal pH <4 on 24-h pH-metry participated. A standardized high fat dinner (6 PM) and a bedtime snack (10 PM) were administered to all patients. GER during spontaneous sleep positions was assessed with a single channel pH probe placed 5 cm above the lower esophageal sphincter (LES) and with a position sensor taped to the sternum. Data were recorded with a portable digital data logger (Microdigitrapper-S, Synectics Medical) and analyzed for recumbent percent time pH <4 and esophageal acid clearance time in each of four sleeping positions. Time elapsed between change in sleeping position and GER episodes was also calculated.

See also Katz et al. (1994), van Herwaarden et al. (2000). The mechanism doesn't appear to be entirely clear, however.