The differential biology reader

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?

"I claim that some of the reasons why so many people who have greatness within their grasp..."

Thu, 26 Jan 2012 09:43:26 +0000

“I claim that some of the reasons why so many people who have greatness within their grasp don’t succeed are: they don’t work on important problems, they don’t become emotionally involved, they don’t try and change what is difficult to some other situation which is easily done but is still important, and they keep giving themselves alibis why they don’t. They keep saying that it is a matter of luck. I’ve told you how easy it is; furthermore I’ve told you how to reform. Therefore, go forth and become great scientists!”

- Richard Hamming, You and Your Research via @dantekgeek via @PsychScientists

Photography by Martin Schoellerfrom Peter Miller, “A thing...

Fri, 06 Jan 2012 11:26:00 +0000

Photography by Martin Schoeller
from Peter Miller, “A thing or two about twins”, National Geographic

Timothy BatesTheory-driven behavior genetics: An example from...

Wed, 04 Jan 2012 14:15:39 +0000

Timothy Bates
Theory-driven behavior genetics: An example from psychological wellbeing
ISSID 2011

Behavior genetics has shown that almost all behaviors are heritable. And ‘if everything is heritable, then behavior genetic designs are essential to test almost all social science theories.”

Whatever you do, somebody in psychometrics already did it long before

Fri, 30 Dec 2011 08:00:05 +0000

Whatever you do, somebody in psychometrics already did it long before:

Andrew Gelman notes a long-standing principle in statistics.

Heart of Darwin

Wed, 28 Dec 2011 21:58:00 +0000

It is hard summarizing the heart of a great idea or the intellectual history of a paradigm being integrated in a few words or even a paragraph. I think I have a hard time doing it, so I am interested in instances that don’t quite seem to capture it.¹

Going over various thinking on the evolution of psychological diversity, I came across Tooby & Cosmides² contending that

At the heart of Darwin’s theory of the origin of adaptations is the following precept. The more important the adaptive problem, the more intensely selection should have specialized and improved the performance of the mechanism for solving it. (p 27)

This is not the heart of Darwin’s theory (which is instead modification by differential reproduction, i.e., natural selection) and seems to be the opposite of his thinking. Darwin notes that that highly specialized adaptations (such as the eye) present “difficulties” for this theory (Origin p 186). Morever, he did not see nature as crafting ‘perfection’ but only sufficiency. You don’t have to be great, just better than your competiion.³

Tooby & Cosmides then define the Modern Synthesis:

Neo-Darwinism is an account of how functional integration in biological systems can arise through selective retention of a superior functional variant—superior in the sense that the variation modifies the functioning of the system in ways that promote the variant’s own propagration. (p 28-29)

The Modern Synthesis was the formal integration of Darwinian natural selection with Mendelian and Weismannian conceptions of transmission and inheritance. I don’t see what ‘functional integration’ has to do with it.

It is bothersome to get caught up on small details like this in an essay, where you can skip over these glosses and get to the new arguments made by the authors. But it sharpens in one’s own mind the exact expression of these ideas by previous thinkers and how we got to where we are now. Perhaps it is the quality of the rest of Tooby & Cosmides explanations (even if I do not agree with many of their conclusions) that make these two minor scuffs stand out.

As Montaigne notes, we profit more by listening to a poor argument than a good one: “A good equerry does not make me sit up straight in the saddle as much as the sight of a lawyer or a Venetian out riding” (III:8. On the art of conversation. Trans. M. A. Screech) ↩
“On the universality of human nature and the uniqueness of the individual”. Journal of Personality 58. ↩
“Natural selection tends only to make each organic being as perfect as, or slightly more perfect than, the other inhabitants of the same country with which it has to struggle for existence” (Origin p 201). ↩

Phylogenetic inertia in primate sociality

Wed, 28 Dec 2011 12:52:00 +0000

Social structure seems to evolve more slowly than morphological adaptations. Shultz and co. tested alternative models of the evolution of social structure in primates and challenge the notion that social structure adapts fluidly to ecological conditions (the ‘socioecological hypothesis’). This fits with the observation that social and behavioral evolution in macaques is also highly constrained by phylogeny.

I wouldn’t go so far as Nick Wade’s summary that this finding suggests genes play a major role as one could imagine a parallel cultural transmission system that would be perfectly confounded with the phylogenetic signal.

So social behavior in primates is uncoupled quite a bit from ecological functioning.

Shultz Opie Atkinson. 2011. Stepwise evolution of stable sociality in primates. Nature 479: 219–222.

Aegithalos caudatus (Linnaeus, 1758)Vitaliy Khustochka

Sat, 17 Dec 2011 12:37:00 +0000

Aegithalos caudatus (Linnaeus, 1758)
Vitaliy Khustochka

Total Impact

Mon, 05 Dec 2011 13:38:00 +0000

Total Impact:

Interesting new search-citation engine that tracks down how many people are reading, citing, bookmarking, and blogging about articles, data, presentations, genes, and code. This generalized the citation of traditional articles and makes them only on instance of a research object.

I searched for a few of my papers and Total Impact turned up Mendeley listings and a blog post by Elizabeth Preston on our orang-utan happiness/death study that I hadn’t seen before.

via @kaythaney

"A wonderful fact to reflect upon, that every human creature is constituted to be that profound..."

Tue, 22 Nov 2011 09:15:40 +0000

“A wonderful fact to reflect upon, that every human creature is constituted to be that profound secret and mystery to every other.”

- Charles Dickens, A Tale of Two Cities
(via psychotherapy)

"Even people who only run randomized experiments could benefit from a little more depth than the..."

Tue, 20 Sep 2011 07:07:35 +0100

“Even people who only run randomized experiments could benefit from a little more depth than the sophomore-year slogan that seems to be all some researchers (AHEM, Reviewer B) have been taught about causation.”

- Sanjay Srivastava, Do not use what I am about to teach you.

An elephant having an ‘aha’ moment. Foerder P....

Fri, 19 Aug 2011 09:47:33 +0100

An elephant having an ‘aha’ moment.

Foerder P. 2011. Insightful Problem Solving in an Asian Elephant. PLoS ONE.

"This foundation [for sociobiologists concerned with cooperation] includes Hamilton’s..."

Wed, 10 Aug 2011 19:59:19 +0100

“This foundation [for sociobiologists concerned with cooperation] includes Hamilton’s reformulation of natural selection as a force that maximizes “inclusive fitness” rather than individual fitness, George Williams’ expository evisceration of old-school group selection, Robert Trivers’ explanation of cooperation between unrelated individuals with the theory of reciprocity, and John Maynard Smith’s application of game theory to the study of animal behavior. Sadly, too few of us include George Price in this august company.”

- Panchanathan K. George Price, the Price equation, and cultural group selection. Evol Hum Behav

Nonhuman primate ageing resembles its human counterpart…We...

Tue, 05 Jul 2011 14:11:25 +0100

Nonhuman primate ageing resembles its human counterpart…We examined whether, as in humans, orang-utan subjective well-being was related to longer life. The sample included 184 zoo-housed orang-utans followed up for approximately 7 years. …in a model that included, and therefore, statistically adjusted for, sex, age, species and transfers, orang-utans rated as being “happier” lived longer. The risk differential between orang-utans that were one standard deviation above and one standard deviation below baseline in subjective well-being was comparable with approximately 11 years in age. This finding suggests that impressions of the subjective well-being of captive great apes are valid indicators of their welfare and longevity.

Our analysis was prospective rather than causal, but it is good evidence for a general covitality factor in our and allied species. The figure shows the year-over-year risk of death depending on subjective well-being (SWB, i.e., happiness).

The BBC have some comments from Alex and Dick Byrne.

Weiss, Adams, King. Happy orang-utans live longer lives. Biology Letters.
figure CC-by the authors.

"Happiness is more like knowledge than like belief. There are lots of things we believe but don’t..."

Mon, 04 Jul 2011 08:32:55 +0100

“Happiness is more like knowledge than like belief. There are lots of things we believe but don’t know. Knowledge is not just up to you, it requires the cooperation of the world beyond you — you might be mistaken. Still, even if you’re mistaken, you believe what you believe. Pleasure is like belief that way. But happiness isn’t just up to you. It also requires the cooperation of the world beyond you. Happiness, like knowledge, and unlike belief and pleasure, is not a state of mind.”

- David Sosa, “The Spoils of Happiness,” via brainpicker (via dianakimball)

"It’s probably just a coincidence that when people get exercised about the reasoning behind inferring..."

Mon, 27 Jun 2011 13:46:16 +0100

“It’s probably just a coincidence that when people get exercised about the reasoning behind inferring function from form, it just happens to be in the context of one tiny part of the natural world, the computational mechanisms that underlie human social behavior.”

- Robert Kurzban, To Which Organisms, If Any, Does The Logic Of Adaptationism Apply?

"A test is said to be face valid if it appears to measure what it purports to measure, especially to..."

Mon, 20 Jun 2011 11:27:02 +0100

“A test is said to be face valid if it appears to measure what it purports to measure, especially to subjects. Face validity bears no relation to true validity and is important only in so far as adults will generally not co-operate on tests that lack face validity, regarding them as silly and insulting. Children, used to school, are not quite so fussy.”

- Paul Kline, A handbook of test construction: introduction to psychometric design, 1986 via Mind Hacks

thingsorganizedneatly: SUBMISSION: Elements of Happiness How...

Thu, 09 Jun 2011 19:26:34 +0100

thingsorganizedneatly:

SUBMISSION: Elements of Happiness

How can a life be visualized? Can a happy life be captured in numbers and diagrams?

The Harvard Study of Adult Development is the longest prospective study of mental and physical well-being ever conducted. For 72 years, researchers at Harvard have been following 824 individuals through war, career, marriage and divorce, parenthood and grandparenthood, and old age.

In this book, I’ve taken 10 representative case studies and visualized their salient character traits, personal timeline, social supports, and physical health to draw conclusions about “the happy life.”

Gorilla traditions for eating nettles. Byrne, Hobaiter,...

Wed, 11 May 2011 09:05:24 +0100

Gorilla traditions for eating nettles.

Byrne, Hobaiter, Klailova. 2011. Local traditions in gorilla manual skill: evidence for observational learning of behavioral organization. Animal Cognition.