Mathematics posts
- June 25, 2010
- 04:12 AM
- 819 views
The A Team Sets fMRI to Rights
by Neuroskeptic in Neuroskeptic
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
- June 21, 2010
- 08:00 AM
- 1,041 views
The rational crayfish, Procambarus economicus?
by Zen Faulkes in NeuroDojo
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
Schmidt, F. (2010) Detecting and Correcting the Lies That Data Tell. Perspectives on Psychological Science, 5(3), 233-242. DOI: 10.1177/1745691610369339
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
- June 20, 2010
- 11:47 AM
- 968 views
Looking at your statistical models...
by egonw in Chem-bla-ics
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
- June 18, 2010
- 12:40 AM
- 529 views
Sciencey goodness Pt I
by aimee in misc.ience
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
- June 17, 2010
- 07:28 PM
- 865 views
Do Not Log-Transform Count Data, Bitches!
by jebyrnes in I'm a chordata, urochordata!
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.
Onwards.
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 »
O’Hara, R., & Kotze, D. (2010) Do not log-transform count data. Methods in Ecology and Evolution, 1(2), 118-122. DOI: 10.1111/j.2041-210X.2010.00021.x
- June 12, 2010
- 12:26 AM
- 775 views
Structural Causes of Increasing Life Expectancy
by Reason in Fight Aging!
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
- June 9, 2010
- 05:59 PM
- 1,252 views
Gulf Oil Spill Disaster: Spawn of the Living Dead for Atlantic Bluefin Tuna?
by GrrlScientist in Living the Scientific Life (Scientist, Interrupted)
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
- June 6, 2010
- 06:00 PM
- 764 views
Species area curves & neutral theory
by Thomas Kluyver in Thomas' Plant-Related Blog
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
- June 3, 2010
- 12:28 PM
- 907 views
Mathematician Vladimir Arnold dies in France
by Olexandr Isayev in olexandrisayev.com
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 »
Tabachnikov, S. (2007) Arnold’s Problem. The Mathematical Intelligencer, 29(1), 49-52. DOI: 10.1007/BF02984760
- May 31, 2010
- 10:53 PM
- 975 views
Discrete observations and classical confidence intervals
by Ponder Stibbons in The truth makes me fret.
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 »
Cousins, R. (1995) Why isn’t every physicist a Bayesian?. American Journal of Physics, 63(5), 398. DOI: 10.1119/1.17901
- May 31, 2010
- 06:00 AM
- 751 views
Simpson’s Paradoxical Card Trick
by Rense Nieuwenhuis in Curving Normality
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:/
- May 18, 2010
- 12:00 PM
- 1,435 views
Punishing Cheaters Promotes the Evolution of Cooperation
by Eric Michael Johnson in The Primate Diaries
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
- May 7, 2010
- 06:50 PM
- 843 views
So it turns out that software and living beings are different...
by David Basanta in Cancerevo: Cancer evolution
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
- May 4, 2010
- 09:12 AM
- 652 views
Simple Counting: an innate ability of humans to know what the chances are
by Vahid Motlagh in Ideas for a deeper sense of life
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
- May 3, 2010
- 09:45 AM
- 962 views
Fanciful mathematics and ecological fantasy
by CJA Bradshaw in ConservationBytes
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
- April 30, 2010
- 11:28 AM
- 936 views
New, Voodoo-Free fMRI Technique
by Neuroskeptic in Neuroskeptic
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
- April 13, 2010
- 11:57 AM
- 814 views
Why (and How) People of a Feather Flock Together
by David Berreby in Mind Matters
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
Nagy, M., Ákos, Z., Biro, D., & Vicsek, T. (2010) Hierarchical group dynamics in pigeon flocks. Nature, 464(7290), 890-893. DOI: 10.1038/nature08891
- March 24, 2010
- 07:22 PM
- 676 views
Voodoo and Type II: Debate between Piotr Winkielman and Matt Lieberman
by The Neurocritic in The Neurocritic
"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
- March 10, 2010
- 05:10 PM
- 874 views
Can We Rely on fMRI?
by Neuroskeptic in Neuroskeptic
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 [citation needed] 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:/
- February 15, 2010
- 04:41 PM
- 851 views
Viva la Neo-Fisherian Liberation Front!
by jebyrnes in I'm a chordata, urochordata!
p≤0.05
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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