Remember the voodoo correlations and double-dipping controversies that rocked the world of fMRI last year? Well, the guys responsible have teamed up and written a new paper together. They are...The paper is Everything you never wanted to know about circular analysis, but were afraid to ask. Our all-star team of voodoo-hunters - Ed "Hannibal" Vul (now styled Professor Vul), Nikolaus "Howling Mad" Kriegeskorte, Russell "B. A. Baracus" Poldrack - provide a good overview of the various issues and ........ Read more »
Kriegeskorte, N., Lindquist, M., Nichols, T., Poldrack, R., & Vul, E. (2010) Everything you never wanted to know about circular analysis, but were afraid to ask. Journal of Cerebral Blood Flow . DOI: 10.1038/jcbfm.2010.86
You might expect a paper whose title starts with “Neural control” to include neurons.
This new paper by Liden and collegues doesn’t. It’s straight behaviour paper in the style of classic neuroethology. It starts by explicitly trying to tie itself to a hot new field: neuroeconomics. Neuroeconomics is about value assessment and decision making in humans. In many cases, this means doing brains scans of people while they play with experimenter’s money.
Liden and company argue that humans........ Read more »
Liden, William H., Phillips, Mary L., & Herberholz, Jens. (2010) Neural control of behavioural choice in juvenile crayfish. Proceedings of the Royal Society B. info:/10.1098/rspb.2010.1000
Yeh, S., Fricke, R., & Edwards, D. (1996) The Effect of Social Experience on Serotonergic Modulation of the Escape Circuit of Crayfish. Science, 271(5247), 366-369. DOI: 10.1126/science.271.5247.366
I do not think I have ever blogged the paper that played an important role in my thesis (doi:10.1021/ci990038z); research of one of the papers in my thesis, started with the hypothesis proposed therein. The paper had a really good idea; but, unfortunately, it did not contain the data to support the hypothesis. That gets me to one important lesson I learned: a QSAR data set of less than 100 molecules is not enough to make untargeted statistical models.
The paper reads quite nicely, and the resul........ Read more »
Bursi, R., Dao, T., van Wijk, T., de Gooyer, M., Kellenbach, E., & Verwer, P. (1999) Comparative Spectra Analysis (CoSA): Spectra as Three-Dimensional Molecular Descriptors for the Prediction of Biological Activities. Journal of Chemical Information and Modeling, 39(5), 861-867. DOI: 10.1021/ci990038z
Willighagen, E., Denissen, H., Wehrens, R., & Buydens, L. (2006) On the Use of H and C 1D NMR Spectra as QSPR Descriptors . Journal of Chemical Information and Modeling, 46(2), 487-494. DOI: 10.1021/ci050282s
Sometimes I am able to write posts on Friday. Sometimes not.
At least part of the reason for this is that I spend my Thursday afternoons and Fridays (or at least parts thereof) research for and writing the SMC weekly newsletter. Which is awesome.
And you should sign up! Why? Because it’s well interesting, of course. Peter [...]
[Click on the hyperlinked headline for more of the goodness]... Read more »
Greer, E., Maures, T., Hauswirth, A., Green, E., Leeman, D., Maro, G., Han, S., Banko, M., Gozani, O., & Brunet, A. (2010) Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans. Nature. DOI: 10.1038/nature09195
Verma, M., & McOwan, P. (2010) A semi-automated approach to balancing of bottom-up salience for predicting change detection performance. Journal of Vision, 10(6), 3-3. DOI: 10.1167/10.6.3
OK, so, the title of this article is actually Do not log-transform count data, but, as @ascidacea mentioned, you just can’t resist adding the “bitches” to the end.
If you’re like me, when you learned experimental stats, you were taught to worship at the throne of the Normal Distribution. Always check your data and [...]... Read more »
As I'm sure you're all aware by now, human life expectancy for both young and old in the most developed regions of the world is slowly increasing, and this has been the case for some time. As medical technology advances and our wealth grows, we benefit in ways that lead to less biochemical damage to the complex machinery of our body accumulated over the course of a lifetime - and thus a greater likelihood of living longer. That the medical and research establishments have achieved this ongoing b........ Read more »
Rousson, V., & Paccaud, F. (2010) A set of indicators for decomposing the secular increase of life expectancy. Population Health Metrics, 8(1), 18. DOI: 10.1186/1478-7954-8-18
A recently published study suggests that the Deepwater Horizon oil leak may devastate the endangered Atlantic bluefin population, causing it to completely collapse or possibly go extinct.... Read more »
Steven L. H. Teo, & Barbara A. Block. (2010) Comparative Influence of Ocean Conditions on Yellowfin and Atlantic Bluefin Tuna Catch from Longlines in the Gulf of Mexico. PLoS ONE, 5(5). info:/10.1371/journal.pone.0010756
How many species are there here? It’s a beguilingly simple question, and a fundamental area of interest. A moments thought shows that the bigger here is, the more species there will be. So, if we start from a little patch of my lawn, and take successively larger heres until we’ve included the whole world, we [...]... Read more »
O'Dwyer, J., & Green, J. (2010) Field theory for biogeography: a spatially explicit model for predicting patterns of biodiversity. Ecology Letters, 13(1), 87-95. DOI: 10.1111/j.1461-0248.2009.01404.x
Rosindell, J., & Cornell, S. (2009) Species–area curves, neutral models, and long-distance dispersal. Ecology, 90(7), 1743-1750. DOI: 10.1890/08-0661.1
Mathematician Vladimir Arnold, perhaps one of the best known and highly cited Russian scientist, has died yesterday today at the age of 72. He was receiving treatment in France, but his disease was stronger, reports lenta.ru, citing a source close to the family. Arnold was one of the greatest mathematicians of the XX century [...]... Read more »
In particle physics, experimentalists often aim to set limits on certain physical quantities, in part to verify theories. Say a theory predicts that a particle called Gobbledygook has a 10-8 chance of decaying into two Gooks and a chance of decaying into three Gobbles. Often, the ratio between these two decay modes are closely related [...]... Read more »
Imagine this card trick. A statistician divides a regular deck of cards into two sets: one of 20 and one of 32 cards. Then, he lets students prove that in both sets, the proportion of court cards is larger among the black ones than among the red cards. How is this possible and what are the consequences for statistical analyses?... Read more »
Simpson, E.H. (1951) The Interpretation of Interaction in Contingency Tables. Journal of the Royal Statistical Society. Series B (Methodological), 13(2), 238-241. info:/
Could punishing bad behavior be the origin of human cooperation?Humans are one of the most cooperative species on the planet. Our ability to coordinate behavior and work collaboratively with others has allowed us to create the natural world's largest and most densely populated societies, outside of deep sea microbial mats and a few Hymenoptera mega-colonies.
A key problem........ Read more »
Boyd, R., Gintis, H., & Bowles, S. (2010) Coordinated Punishment of Defectors Sustains Cooperation and Can Proliferate When Rare. Science, 328(5978), 617-620. DOI: 10.1126/science.1183665
Mathematical and computational biologists use algorithms to model and understand biological phenomena but as useful as computer systems are to modellers they also represent an example of what biological systems are not: designed. A recent study by researchers in...... Read more »
Yan KK, Fang G, Bhardwaj N, Alexander RP, & Gerstein M. (2010) Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20439753
A couple of days ago Steven Strogatz, the chaos and complexity theorist, wrote a lucid article in the New York Times about the daunting task of teaching probability theory. In particular he dealt with the cerebrally demanding topic of formalizing and analyzing “conditional probability”. What he suggests is quite reasonable, "comporting with human intuition instead of confounding it."Strogatz recommends skipping the mathematical formalism and avoid using Bayes’s theorem, much as his student........ Read more »
Teglas, E., Girotto, V., Gonzalez, M., & Bonatti, L. (2007) Intuitions of probabilities shape expectations about the future at 12 months and beyond. Proceedings of the National Academy of Sciences, 104(48), 19156-19159. DOI: 10.1073/pnas.0700271104
Bear with me here, dear reader – this one’s a bit of a stretch for conservation relevance at first glance, but it is important. Also, it’s one of my own papers so I have the prerogative :-) As some of you probably know, I dabble quite a bit in population dynamics theory, which basically means [...]... Read more »
Clark, F., Brook, B.W., Delean, S., Reşit Akçakaya, H., & Bradshaw, C.J.A. (2010) The theta-logistic is unreliable for modelling most census data. Methods in Ecology and Evolution. DOI: 10.1111/j.2041-210X.2010.00029.x
MIT brain scanners Fedorenko et al present A new method for fMRI investigations of language: Defining ROIs functionally in individual subjects. Also on the list of authors is Nancy Kanwisher, one of the feared fMRI voodoo correlations posse.The paper describes a technique for mapping out the "language areas" of the brain in individual people, not for their own sake, but as a way of improving other fMRI studies of language. That's important because while everyone's brain is organized roughly th........ Read more »
Fedorenko, E., Hsieh, P., Nieto Castanon, A., Whitfield-Gabrieli, S., & Kanwisher, N. (2010) A new method for fMRI investigations of language: Defining ROIs functionally in individual subjects. Journal of Neurophysiology. DOI: 10.1152/jn.00032.2010
Seeking the hidden causes of behavior, some scientists work on the scale of brain regions and neurons, searching inside people's heads. Others work on the scale of crowds, neighborhoods and nations, seeking hidden patterns in the way multitudes behave. What's unusual about this paper in PLoS One is that it combines both those perspectives: Mehdi Moussaïd and his co-authors have worked out the physical effects of a psychological motivation. That gave them a new way to predict how people wa........ Read more »
Moussaïd, M., Perozo, N., Garnier, S., Helbing, D., & Theraulaz, G. (2010) The Walking Behaviour of Pedestrian Social Groups and Its Impact on Crowd Dynamics. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010047
"Voodoo correlations in social neuroscience" was the original title of a paper that first caused a stir in late December 2008, when a manuscript accepted by Perspectives on Psychological Science was made available on the authors' websites. Vul, Harris, Winkielman, and Pashler produced a "bombshell of a paper" that questioned the implausibly high correlations observed in some fMRI studies in the field of Social Neuroscience. Ed Vul et al. surveyed the authors of 54 papers to determine the an........ Read more »
Lieberman, M., Berkman, E., & Wager, T. (2009) Correlations in Social Neuroscience Aren't Voodoo: Commentary on Vul et al. (2009). Perspectives on Psychological Science, 4(3), 299-307. DOI: 10.1111/j.1745-6924.2009.01128.x
Craig Bennett (of Prefrontal.org) and Michael Miller, of dead fish brain scan fame, have a new paper out: How reliable are the results from functional magnetic resonance imaging?Tal over at the  blog has an excellent in-depth discussion of the paper, and Mind Hacks has a good summary, but here's my take on what it all means in practical terms.Suppose you scan someone's brain while they're looking at a picture of a cat. You find that certain parts of their brain are activated to ........ Read more »
Bennett CM, Miller MB. (2010) How reliable are the results from functional magnetic resonance imaging?. Annals of the New York Academy of Sciences. info:/
Significant p-values. For so many scientists using statistics, this is your lord. Your master. Heck, it has its own facebook group filed under religious affiliations (ok, so, maybe I created that.) And it is a concept to whose slavish devotion we may have sacrificed a good bit of forward progress [...]... Read more »
Hurlbert, S. H., & Lombardi, C. M. (2009) Final collapse of the Neyman-Pearson decision theoretic framework and rise of the neoFisherian. Annales Zoologici Fennici, 311-349. info:/
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