The differential biology reader

"Whenever you get two people interpreting the same data in different ways, that’s metaphysics."

Mon, 28 May 2012 10:45:21 +0100

“Whenever you get two people interpreting the same data in different ways, that’s metaphysics.”

- Thomas Kuhn. Interview by John Horgan. Via @PsychScientists.

Turtles all the way down. cshalizi: The Game of Life,...

Fri, 25 May 2012 09:25:38 +0100

Turtles all the way down.

cshalizi:

The Game of Life, implemented in the Game of Life. (Best watched with the sound off, unless you like high-pitched whines.) Via Tozier.

This model shows the genetic structure of psychological...

Thu, 24 May 2012 09:49:43 +0100

This model shows the genetic structure of psychological well-being. A general genetic factor underlies six components of well-being while four additional mechanisms influence more specific facets. Interestingly the environmental covariances showed no such structure, leading m’colleagues Despina, Gary, and Tim to conclude “that environmental experiences are not, in general, the source of the psychological structure for well-being”

Archontaki, D., Lewis, G. J., & Bates, T. C. (2012). Genetic influences on psychological well-being: A nationally representative twin study. Journal of Personality. doi:10.1111/j.1467-6494.2012.00787.x

GREML

Wed, 23 May 2012 21:29:12 +0100

It’s always nice when a new technique gets a catchy name so you can refer to it in conversation more easily. The technique to estimate heritability from SNP data now seems to be called GREML: genomic-relatedness-matrix restricted maximum likelihood.

Benjamin, D. J., Cesarini, D., van der Loos, M. J. H. M., Dawes, C. T., Koellinger, P. D., Magnusson, P. K. E., Chabris, C. F., et al. (2012). The genetic architecture of economic and political preferences. Proceedings of the National Academy of Sciences of the United States of America.

"ELEMENTARY discussions of the development of personality usually involve the familiar debate over..."

Tue, 22 May 2012 20:59:00 +0100

“ELEMENTARY discussions of the development of personality usually involve the familiar debate over the relative importance of heredity and environment. Such discussions sometimes proceed on the obviously fallacious assumption that the personality is merely the sum total of these two constituents-inherited tendencies and environmental influences. The truth is, of course, that the self develops through a complex chain of interactions with the environment, so that the resultis not a mixture of heredity and environmental factors but a compound, the character of which is determined both by the constituent interacting elements and by the (usually very complicated) “laws of composition” by which these elements are united. Thus the analysis of personality development must include not only (1) heredity, and (2) environ- ment, but also a third factor, namely, (3) the laws of composition or principles of organization of the self in its various stages. These “laws of composition” describe the new structural and functional patterns which emerge from the interacting elements.”

- Phenix, Philip H. (1953). A Note on Heredity, Environment, and Personality. The Journal of Philosophy. via Eric Turkheimer.

"…it is an immense benefit to have institutions I can trust to tell me ‘these claims about..."

Tue, 22 May 2012 14:52:14 +0100

“…it is an immense benefit to have institutions I can trust to tell me ‘these claims about cortical columns, or locally compact Hausdorff spaces, are at least not crazy’.”

- Cosma Shalizi, If Peer Review Did Not Exist, We Would Have to Invent Something Very Like It to Serve Highly Similar Ends

Ramón y Cajal, Chick cerebellum. From Sotelo Nature Reviews...

Mon, 07 May 2012 20:42:34 +0100

Ramón y Cajal, Chick cerebellum. From Sotelo Nature Reviews Neuroscience 2003 via neurolove

Figure 1. Optimality model for peer-review filters and the...

Sun, 06 May 2012 10:30:36 +0100

Figure 1. Optimality model for peer-review filters and the progress of science.
Aarssen, L. (2012). Are peer-review filters optimal for the progress of science in ecology and evolution? Ideas in Ecology and Evolution, 5(0). doi:10.4033/iee.v5i0.4322

Can we model the peer review process and adjust it to maximize the difference between benefits and costs?

"The one respect in which I was overly pessimistic is that I have not, in fact, had to spend much..."

Fri, 04 May 2012 16:01:00 +0100

“The one respect in which I was overly pessimistic is that I have not, in fact, had to spend much time ‘de-programming students [who] read A New Kind of Science before knowing any better’”

- Cosma Shalizi, Ten Years of Monster Raving Egomania and Utter Batshit Insanity

A pair of Long Tailed Tits making a new nest by...

Fri, 04 May 2012 09:40:47 +0100

A pair of Long Tailed Tits making a new nest by gautonphotography

Maintenance of genetic variation in personality

Fri, 04 May 2012 06:55:50 +0100

A new paper by Verweij et al tests competing theories about the maintenance of genetic variation in personality (neutrality, mutation–selection balance, and balancing selection) against SNP-derived heritability estimates. Each hypothesis makes different predictions about the number of causal variants, the proportion of nonadditive genetic variance, and the proportion of additive genetic variance explained by common variants:

They tested these predictions in four samples using the Yang et al method of calculating heritability from SNP genotypes. The result was that around 7% of the variance in personality (using Clonginer’s dimensions) could be explained by common variants. Thus personality is more likely to be explained by rare variants or nonadditive genetic effects. This is consistent with balancing selection as well as the high proportion of nonadditive genetic effects found in studies of humans, orang-utans, and tits.

Verweij et al. (in press) Maintenance of genetic variation in human personality: testing evolutionary models by estimating heritability due to common causal variants and investigating the effect of distant inbreeding. Evolution.

Caroline BriggsStuart and Tony from BBC News via...

Fri, 06 Apr 2012 12:29:00 +0100

Caroline Briggs
Stuart and Tony

from BBC News via @christopheradam.

"it’s easy to forget that anyone who publishes enough will end up with some skeletons in their..."

Tue, 13 Mar 2012 15:46:57 +0000

“it’s easy to forget that anyone who publishes enough will end up with some skeletons in their closet”

- Russ Poldrack, Skeletons in the closet. via @hardsci.

Fisher's influence

Thu, 08 Mar 2012 09:10:34 +0000

Fisher's influence:

Simply Statistics catalogs some of Fisher’s contributions to statistics:

P-values: 3 million citations
Analysis of variance (ANOVA): 1.57 million citations
Maximum likelihood estimation: 1.54 million citations
Fisher’s linear discriminant: 62,400 citations
Randomization/permutation tests: 37,940 citations
Genetic linkage analysis: 298,000 citations
Fisher information: 57,000 citations
Fisher’s exact test: 237,000 citations

And this doesn’t even touch on his contributions to population genetics and evolutionary biology. The University of Adelaide has a collection of his manuscripts related to evolution and genetics.

Lytro Light Field Camera

Sun, 04 Mar 2012 10:21:29 +0000

Lytro Light Field Camera:

The Lytro embodies a new concept in how cameras work: instead of capturing a single image, it course a “light field” containing information on the angle of each ray of light. This allows you to refocus the shot after you’ve taken the image. This is one case where you can’t believe it until you see it.

While the Lytro is getting panned in reviews (poor image quality, small screen) and for consumers the the ability to focus a shot post hoc feels a bit like a gimmick, this sounds perfect for scientific applications such as fieldwork photography. Pointing the camera at your subject without having to worry about focussing greatly simplifies the process, which is important when you are out in the field having to attend to a lot of things at once.

The other thing I picked up from the video review by Richard Butler for dpreview is just how small the Lytro is. You could almost hang it from the strap of your binoculars. With a DSLR, it would be the other way around.

Molecular Psychiatry - Meta-analysis of genome-wide association studies for personality

Fri, 24 Feb 2012 08:00:05 +0000

Molecular Psychiatry - Meta-analysis of genome-wide association studies for personality:

Even samples sizes in the tens of thousands only uncover a handful of genome wide associations for personality. The effect sizes of genes influencing personality are either small or not tagged by the current crop of SNPs. High nonadditive genetic variance may mean that models incorporating epistasis are required to find the underlying genetic variance.

via @StuartJRitchie

Somtimes simple methods outperform complicated ones. Simply...

Thu, 23 Feb 2012 16:39:34 +0000

Somtimes simple methods outperform complicated ones. Simply Statistics find that just using the top 10 predictors (a method they dub the ‘Leekasso’) can be better than the Lasso under certain conditions.

January 9, 1973 — see The Complete Peanuts 1971-1974

Wed, 22 Feb 2012 20:48:43 +0000

January 9, 1973 — see The Complete Peanuts 1971-1974

ERVs are sexed-up bivariate heritabilities

Sun, 29 Jan 2012 11:54:00 +0000

Complex diseases such as major depression show considerable heritability but linkage and genome-wide association studies have so far not identified a sufficient number of genetic variants to account for the observed genetic variance. One problem might be that the observed phenotype of interest, such as incidence of major depression, is too far removed from the underlying genetic variants to produce a strong enough signal to detect given the power of current techniques. To aid both genetic studies and to understand the underlying biology and physiology of a disease, the search is now on for endophenotypes: heritable, biological markers that are associated with the disease but that do not depend on disease state (Gottesman & Gould 2003). I got on to this topic after a presentation by @anamariafernand to our journal club.

To speed the identification of endophenotypes for mental illness, Glahn et al (2012) present the concept of an endophenotype ranking value (ERV)

$$\mathrm{ERV}_{ie} = \left | \sqrt{h^2_i} \sqrt{h^2_e} \rho_g \right |$$

between an illness $ i $ and endophenotype $ e $ where $ h^2_i $ and $ h^2_e $ are the heritabilities and $ \rho_g $ is the genetic correlation between $ e $ and $ i $. The ERV is useful as it goes in that it allows Glahn et al to detect several potential neurocognition, brain structure, and gene expression endophenotypes.

However, in quantitative genetic terms, the ERV is not anything new. Michelle pointed out that if you carry through the equation and drop the absolute value signs, the ERV formula reduces to

$$h_i h_e \rho_g$$

which is the same as the bivariate heritability (Falconer & Mackay 1996)

$$h_x h_y r_G$$

between two traits $ x $ and $ y $. So the main innovation is in using this standard quantity as part of a ranking scheme for identifying which phenotypes merit further exploration.

Gottesman, I., & Gould, T. (2003). The Endophenotype Concept in Psychiatry: Etymology and Strategic Intentions. Am J Psychiat, 160(4), 636. doi:10.1176/appi.ajp.160.4.636
Glahn, D. C., Curran, J. E., Winkler, A. M., Carless, M. A., Kent, J. W., Charlesworth, J. C., Johnson, M. P., et al. (2012).High Dimensional Endophenotype Ranking in the Search for Major Depression Risk Genes. BPS, 71(1), 6–14. Elsevier Inc. doi:10.1016/j.biopsych.2011.08.022

"…it’s very tempting to believe things when they imply many self-serving benefits. This is why..."

Sat, 28 Jan 2012 08:00:05 +0000

“…it’s very tempting to believe things when they imply many self-serving benefits. This is why integrity is a virtue, because it’s hard, uncommon, and helpful.”

- Eric Falkenstein, Do Academics Overfit?