A fortnight of links - 2013 05 13

Charlemagne’s DNA and Our Universal Royalty. Carl Zimmer on why, if you are of European descent, you are descended from Charlemagne.  This 2004 paper explains why everyone who was alive 3000 years ago who has living descendents, are the ancestors of everyone living today. Coalescence! I really like that they present results from a series of models along the realism/tractability continuum - from a simple analytic treatment to a very complicated world-wide simulation. This is pretty mind-blowing stuff. 

Fact of Fiction? The Legend of the QWERTY Keyboard. The QWERTY keyboard is often used as an example of an inefficient technology persisting through institutional inertia. The popular legend is that the QWERTY Keyboard was designed slow down typists so they would not jam mechanical typewriters. It looks like its design was really influenced to help those transcribing Morse code from telegraph machines.  Note that this still leaves the institutional inertia story intact.

The Groundbreaking Isaac Newton Invention You've Never Heard Of. Did Newton really invent the idea of averaging data to reduce variance?  That would be pretty neat, but it seems like someone would have come up with that earlier.

A Congressman's Own Peer Review. Rep. Eddie Bernice Johnson may be my new favorite lawmaker. 

What China and Russia Don't Get About Soft Power. An interesting discussion of the pitfalls of soft power.

Science Communication Round-Up:

Why do kidneys need cells? "One person's jargon is another person's technical vocabulary"

Defensive Scholarly Writing and Science Communication. Kate Clancy on why scientists often write the way they do.

Over this past fortnight, members of the UC Davis Human Behavioral Ecology Lab group have been emailing around their favorite references on good writing: Politics and the English Language, George Orwell;  Fenimore Cooper's Literary Offences, Mark Twain;  Economical Writing, Deirdre McCloskey; The Elements of Style, Strunk and White

Bonus Links (entertaining in an internet sort-of-way):

Is Your State's Highest-Paid Employee A Coach? (Probably)


How long is the average dissertation?

A Curriculum in Quantitative Evolutionary Social Science

Peter Turchin's recent post, How to become a Cliodynamicist, reminded me that a couple of years ago, for fun, I tried to put together an undergraduate curriculum for a hypothetical undergraduate majoring in quantitative evolutionary social science.  Something like the program I would have liked to have had, in retrospect, as an undergraduate. (I majored in engineering, but took a lot of biology courses.)

The idea was to put together a curriculum close to the quantitative rigor of an undergraduate engineering degree, but with an emphasis on social systems, human behavior, and evolution.

The self-imposed rules were that I (1) had to use only UC Davis undergraduate (not graduate) courses, (2) could not exceed the unit requirements of an UCD engineering degree (198 units), (3) could not ignore course prerequisites, (4) could ignore complicated university requirements on breadth/depth and whatnot.  Below is what I came up with.

I focused on applied quantitative analysis and modeling. It was really hard to leave out most of the physical sciences - especially intro physics, chemistry and thermodynamics. Also, I wish there were a introductory course in political science instead of a separate courses for each of the sub-fields.

Lower Division	Units
ANT 1. Human Evolutionary Biology	4
ANT 23. Introduction to World Prehistory	4
ANT 50. Evolution and Human Nature	4
BIS 2A  Introduction to Biology: Essentials of Life on Earth	3
BIS 2B. Introduction to Biology: Principles of Ecology and Evolution	2
BIS 2C. Introduction to Biology: Biodiversity and the Tree of Life	4
BIS 20Q. Modeling in Biology	5
ECN 1A. Principles of Microeconomics	4
ECN 1B. Principles of Macroeconomics	4
ECS 30. Introduction to Programming and Problem Solving	4
MAT 21A Calculus	4
MAT 21B Calculus	4
MAT 21C Calculus	4
MAT 22A Linear Algebra	3
MAT 22AL Linear Algebra Computer Lab	1
PHIL 30. Introduction to the Philosophy of Science	4
POL 51. Scientific Study of Politics	4
PSC 1. General Psychology	4
PSC 41. Research Methods in Psychology	4
SOC 1. Introduction to Sociology	5
SOC 46A. Introduction to Social Research	4
SOC 46B. Introduction to Social Research	4
STA 32. Basic Statistical Analysis Through Computers	3
Two freshman writing courses	8
Upper Division
ANT 105. Evolution of Societies and Cultures	4
BIS 132. Introduction to Dynamic Models in Modern Biology	4
BIS 133. Collaborative Studies in Mathematical Biology	5
EVE 100. Introduction to Evolution	4
EVE 101. Introduction to Ecology	4
EVE 101Q. Introduction to Computer Models in Ecology	1
EVE 102. Population and Quantitative Genetics	4
EVE 131. Human Genetic Variation and Evolution	3
EVE 175. Computational Genetics	3
ECN 100. Intermediate Micro Theory	4
ECN 110A. World Economic History Before the Industrial Revolution	4
ECN 110B. World Economic History Since the Industrial Revolution	4
ECN 122. Theory of Games and Strategic Behavior	4
ESP 121. Population Ecology	4
MAT 124 Mathematical Biology	4
MAT 167 Applied Linear Algebra	4
NPB 102 Animal Behavior	3
NPB 102Q Quantitative Topics in Animal Behavior	1
POL 110. The Strategy of Politics	4
PSC 100. Introduction to Cognitive Psychology	4
PSC 101. Introduction to Psychobiology	4
PSC 120. Agent-Based Modeling	4
PSC 151. Social Psychology	4
STA 131A. Introduction to Probability Theory	4
STA 131B. Introduction to Mathematical Statistics	4
STA 131C. Introduction to Mathematical Statistics	4
STA 141. Statistical Computing	4
STA 145. Bayesian Statistical Inference	4

A fortnight of links - 2013 04 29

E. O. Wilson is Wrong Again —  About Collaboration - Jon Wilkins on E.O. Wilson's WSJ op-ed I briefly mentioned a fortnight ago.

Why I Let My Students Cheat On Their Exam - This article has really been making the rounds! I have seen many positive responses. Negative responses have generally been fixated on all the free-riders. I think the main difference in attitude stems from whether one thinks the primary goal of undergraduate education is "separating the wheat from the chaff" or "maximizing student learning." 

Evolutionary psychology: You're doing it wrong (but you could do it better!) - In my experience, evolutionary psychologists tend to think of themselves as the antidote to "standard" social scientists who deny or ignore the power of evolutionary thinking. Problematic for this self-conception is that evolutionary psychology research often rubs standard evolutionary biologists the wrong way as well.

James D. Fearon: Anarchy is a Choice - A video of political scientist James Fearon discussing "anarchy" in international relations.  This is roughly the observation/idea that altruistic cooperation between countries is difficult to achieve because there is no law-giving-and-enforcing body (leviathan) that is above and constrains the actions of countries.  The actions of countries must be constrained by other things.

The (sigh) Psychopath Brain - This post gets to one of my pet peeves of science reporting - assuming that because something shows up on a brain scan it is somehow "innate" or "genetic." I plan a blog post on this soon (read: after dissertation.)

On Copycat Whales, Conformist Monkeys and Animal Cultures - A great discussion about culture in non-human animals. I would have liked something about cumulative vs simple cultural evolution - but that is really nit-picking.

Why are your friends more popular than you? - Spoiler Alert: Because people with more friends are, on average,  more likely to be friends with you

Replicated typo: Numerical vs. analytical modelling - A focus on linguistics, but a good discussion on the tractability/realism trade-off for different styles of modelling.

Cyberwar in the Underworld: Anonymous versus Los Zetas in Mexico - Cyberwarefare between non-state actors.

Are the Digits of Pi Random? - Well, what do you mean by random?

Numberphile: Why are there Infinite Primes?


Fun (most fun things are apparently space-related):

Kepler’s Tally of Planets - NYT visualization of all extrasolar planets discovered so far.

How Far Away is the Moon?

Wringing out Water on the International Space Station - for Science! 

Make XKCD-style Plots in Matlab

A Fortnight of Links

I finally have my web bookmarks sinked between computers which will make it much easier to share recent and relevant links.  I hope to make this a regular feature of this blog, especially since I need to finish a dissertation by this summer...

Mathematicians Predict the Future With Data From the Past. An article in Wired about Peter Turchin and cliodynamics - a scientific/mathematical to the dynamics of human history.  This is an interesting article. However, in the Social Evolution Forum, he points out that the title is misleading.  His models are not primarily for prediction, but for understanding historical processes. I am a big fan of Turchin's work - especially his books Historical Dynamics and War, Peace and War. [via]

We Aren't the World. A magazine article on the work of Joe Henrich and colleagues on comparing Western Educated Industrial Rich and Democratic (WEIRD) societies to others using economic and psychology experiments.  I am also a big fan of this work.

They’d Rather Be Rigorous Than Right. Andrew Gelman in Chance Magazine on the statistics of Ashraf and Galor. I wrote about their paper here. [via]

False discovery: How not to find the genetic basis of human intelligence. We have a lot of nucleotides.  This makes causal claims based on correlations of things with specific sequences of  nucleotides fraught with peril.

The bad science of Satoshi Kanazawa. The blog post that prompted The Big Think to end its relationship with evolutionary psychologist Satosh Kanazawa.

Great Scientist ≠ Good at Math. This article, by E.O. Wilson, has caused quite a stir.  Mathematical theorizing can be replaced by intuition and daydreams. "Everyone sometimes daydreams like a scientist. Ramped up and disciplined, fantasies are the fountainhead of all creative thinking. Newton dreamed, Darwin dreamed, you dream." I think it is possible to be a great scientist without being good at math (see Darwin, C.).  I think it is possible to both daydream and make some valuable contributions to mathematics (see Newton, I.)  But without some mathematics, don't expect that you will be able to test the logical consistency of your daydreams (see Fischer, R.A. saving Darwin's theory from genetics.)  If E.O. Wilson understood the mathematical theories of kin and group selection, for example, he might not be going around saying incorrect things about them.

Resurrecting a Forest. Most American Chestnut trees were wiped out by a fungus from Asia in the 20th centruty.  For my circa 1997 Eagle Scout project, I helped plant 300 trees to use as genetic stock for bringing them back.  My impression at the time was that there were two major efforts.  The first, more mainstream, effort was to breed American and fungus-resistant Asian chestnut trees to make fungus-resistant hybrids.  The second, less mainstream, effort was to accomplish similar goals through genetic engineering.  My project was part of the later effort and I have not followed up on it until seeing Carl Zimmer's article.

Bonus Links (entertaining in an internet sort-of-way):

Thumbs and Ammo. Real tough guys don't need guns,  they just need a positive, can-do attitude.

Six Degrees of Francis Bacon. Pretty much what it sounds like.

Genetic diversity and economic development

Recently two economists, Quamrul Ashraf and Oded Galor, published an article in a prominent economics journal comparing genetic diversity in various countries with economic development (ungated version here).  They found the following relationship: high and low genetic diversity is associated with low economic performance.  High economic performance is associated with moderate levels of genetic diversity.  Below is the take-home "hump-shaped" graph comparing genetic diversity to per capital income for a slew of countries (lower numbers on the x-axis represent higher genetic diversity).

Ashraf and Galor conclude that this relationship supports the hypothesis that "genetic diversity within a population confers both social costs, in the form of miscoordination and distrust arising from genetic differences across members of society, and social benefits in the form of diversity-driven knowledge accumulation."

Needless to say, this interpretation caused some controversy.  A group of anthropologists (mostly from Harvard) penned a response in Current Anthropology before the original article was even published (ungated version).  Jason Collins, at Evolving Economics, has been covering the fall-out in detail.

Much of the back-and-forth has been about the specific methods employed by Ashraf and Galor.  I am going to leave that to others and instead focus on Ashraf and Galors proposed mechanisms.  For what it is worth, I mostly agree with Andrew Gelman's take on the other issues.
 

Critique 1: If any finding is consistent with an hypothesis, finding something is not very good support for the hypothesis.

 

Ashraf and Galors's hypothesis, as quoted above, predicts that genetic diversity should have both a positive and a negative effect on economic productivity. The great thing about this sort of hypothesis is that it can explain any observed pattern in the data.

For example, in the stylized charts below, the top chart reflects the findings of Ashraf and Galor, highlighting the positive and negative effects of genetic diversity creating a "hump-shaped" curve.  The bottom chart reflects the exact opposite findings: a "trough-shaped curve."  Notice that this curve is also consistent with Ashraf and Galor's hypothesis - showing regions of "negative effects" and regions of "positive" effects.  Even a flat line would be consistent with their hypothesis (the effects cancel out!).  If any empirical pattern is consistent with an hypothesis, finding a specific empirical pattern that is consistent with the hypothesis is not too surprising.

Critique 2: Genetic Difference Only Matters on (Very) Small Scales

There is a large body of work in evolutionary biology on the scale at which genetic differences should matter in cooperation. The consistent finding is that genetic differences only matter for very close relatives, for animals like humans who have fairly limited number of offspring (unlike social insects), the scale at which genetic differences might matter is something under a dozen individuals.  Any more than that and genetic relatedness is just too diluted to make a difference. 

Countries are much bigger than a dozen individuals. Within a country, people might be more cooperative with their immediate relatives, but any genetic diversity beyond that shouldn't matter.
  
When they hypothesize that genetic differences cause "miscoordination and distrust arising from genetic differences across members of society" this sounds a lot like kin recognition.  Basically, individuals act differently towards others based on observed genetic similarities and differences. In the classic paper by François Rousset and Denis Roze, they find that even under the most ideal conditions, kin recognition only works in extremely small groups [summary here].

 

Critique 3: Genetic Diversity Cannot Explain (much) Cognitive Diversity

Political scientist Scott Page has two books summarizing research into diversity from a variety of academic disciplines. One of the books' key points is that are that the important type of diversity in group decision-making and innovation is "cognitive diversity,"  defined as "differences in how people see, categorize, understand, and go about improving the world."

For example, economists see and understand the world differently than population geneticists. This implies that a study about population genetics and economics would be better if conducted by a mixed group of economists and population geneticists, than by a group of only economists or a group of only population geneticists (see what I did there).

What are the sources of cognitive diversity? Are they likely to be genetic? The answer is no.  The basic argument is that in any given group there is much more cognitive diversity than genetic diversity. Therefore, genetic diversity cannot explain very much cognitive diversity. Most cognitive diversity seems to result from differences in training and experience.

(Update: After posting this, I saw that Jason Collins posted today on the claimed relationship between genetic diversity and innovation.)

 

Conclusion: Reasons to Be Skeptical

 
I am skeptical of the conclusions of this study for three basic reasons. (1) The hypothesis is consistent with any observed pattern in the data, (2) the hypothesized negative effects of genetic diversity are unlikely to matter on the scale of countries, (3) the hypothesized positive effects of diversity are unlikely to be a result of genetic diversity.

Political scientists and biologists have different article titling conventions

I subscribe to various biology and political science journals. When scanning tables of contents, I always have an easier time deciding what biology papers to read than what political science papers to read. At first, I assumed this was because I knew more biology than political science. However, this never really changed as I learned more political science.

Today, I noticed a big difference in the way biologists and political scientists title papers. Biologists generally use their main result as a paper's title and political scientists generally write titles that are more broad in scope.

For example, here are the most recent tables of contents from the American Political Science Review (a top political science journal) and Proceedings of the Royal Society B (a top biology journal). 

APSR	Proc B
Unemployment and the Democratic Electoral Advantage	Groups of related belugas (Delphinapterus leucas) travel together during their seasonal migrations in and around Hudson Bay
How Words and Money Cultivate a Personal Vote: The Effect of Legislator Credit Claiming on Constituent Credit Allocation	Nectar bacteria, but not yeast, weaken a plant–pollinator mutualism
Sources of Bias in Retrospective Decision Making: Experimental Evidence on Voters’ Limitations in Controlling Incumbents	The evolution of cooperation by social exclusion
Tying Your Enemy's Hands in Close Races: The Politics of Federal Transfers in Brazil	Careful cachers and prying pilferers: Eurasian jays (Garrulus glandarius) limit auditory information available to competitors
The Adverse Effects of Sunshine: A Field Experiment on Legislative Transparency in an Authoritarian Assembly	Telomere length reflects phenotypic quality and costs of reproduction in a long-lived seabird
Borrowed Power: Debt Finance and the Resort to Arms	The role of individuality in collective group movement
“Writing a Name in the Sky”: Rancière, Cavell, and the Possibility of Egalitarian Inscription	Opsin switch reveals function of the ultraviolet cone in fish foraging
Democracy's Dignity	Visual habitat geometry predicts relative morph abundance in the colour-polymorphic ornate rainbowfish
The Supreme Court's Many Median Justices	Females roam while males patrol: divergence in breeding season movements of pack-ice polar bears (Ursus maritimus)
On the Demos and Its Kin: Nationalism, Democracy, and the Boundary Problem	Direct evidence for encoding of motion streaks in human visual cortex
Does Combat Experience Foster Organizational Skill? Evidence from Ethnic Cleansing during the Partition of South Asia	Extraversion predicts longer survival in gorillas: an 18-year longitudinal study
Legislative Bargaining and the Dynamics of Public Investment	An assessment of wheat yield sensitivity and breeding gains in hot environments

I have helpfully underlined articles titles that are also the authors' key findings. These tend to be papers titled with a complete declarative sentence. In this sample, eight out of twelve (67%) of Proc B articles and zero out of twelve (0%) APSR articles follow this convention.

For someone interested in norms and institutions, this is an interesting puzzle.  My first instinct is to call this a somewhat arbitrary self-reenforcing norm.  In ecology, these titles might better meet the expectations of readers, reviewers and journal editors.  From the "journal article checklist" in Karban and Huntzinger's How to Do Ecology book:

Is there a similar expectation in political science-style titles?

Or maybe there is something about political science and biology as disciplines that make them more prone to these conventions?  Perhaps biology articles are more focused on specific questions than political science which tend to be more broad?  Certainly political science articles are longer on average. Or are political scientists more cautious about sounding like they are trying to have the final word on a subject than biologists?

There seems to be advantages to each.  I likely read more political science paper abstracts than I would if they were titled more like biology papers. So in the end, I am more broadly exposed to political science than biology. However, when pressed for time I am probably more likely to read a paper selected from a biology journal since, because I can be more discriminating, my expected returns are higher.

Do political scientists rely more heavily on authors' reputations when deciding what to read?  For example, since I know Branislav Slantchev, (who wrote one of the above APSR articles) is a game theorist working in international relations, I am pretty likely to read his paper.

Any thoughts?

PS - I originally titled this post something like "Article titling conventions in biology and political science."






  

Why Human Cooperation is Special: Part I

At the end of this article about human cooperation, West, El Mouden and Gardner (WEG), ask "Are Humans Special?"  The authors specifically consider two questions:

1) Do humans have especially high levels of altruism?

2)  Are humans special because cooperation occurs between non-relatives?

After reviewing the literature, they answer both of these questions in the negative, suggesting that human cooperation is not so special after all.  However, their argument misleads because they answer two questions separately that really should be answered together:  The special thing about cooperation in humans is that we have especially high levels of altruism that occurs between non-relatives.

Allow me to illustrate with a Venn diagram:

The left circle in the diagram represents altruistic cooperation.  This is normally defined as cooperation where an individual pays a cost and confers a benefit on another individual. In evolutionary biology, these are normally considered as reproductive costs and benefits at the level of the individual (some like to do the accounting at the level of the gene, but that is outside the scope of this post).  WEG give examples of non-altruistic cooperation:

...a number of organisms have higher levels of altruism than humans, ranging from social amoebae and bacteria to ants and cooperative breeding vertebrates... An extreme example at the altruistic end of the continuum is the long tailed tit, where helpers never reproduce and so
cooperation has been favoured purely by indirect fitness benefits.

Something to notice is that in each example (social amoeba, ants, and long-tailed tits) altruistic behavior occurs between close genetic relatives. For example, in most ant colonies workers are all the offspring of a single queen or multiple closely-related queens. And on top of that most ants are haplodiploid which makes workers even more genetically related. Because altruism promotes the fitness of similar genes in close relatives, this allows for large-scale altruistic cooperation in ants.  This is what WEG means by "purely indirect fitness benefits."

In contrast, the right circle represents cooperation in non-kin. WEG write:

...cooperation between nonrelatives occurs in a range of organisms. Many forms of cooperation occur between nonrelatives in birds and mammals (Clutton-Brock, 2002). In cooperative breeding vertebrates, there are several examples where non-relatives cooperate, the indirect fitness benefits of cooperation appear to be negligible and it is thought that cooperation is driven by direct fitness benefits...

They do not give specific examples but this review by zoologist Tim Clutton-Brock describes cooperation between meerkats, pied babblers, and African wild dogs.  Something to notice about these examples is that cooperation is not altruistic. Instead, it is what is called mutualistic cooperation, which occurs where an individual's behavior provides reproductive benefits to both itself and another individual. This is what WEG mean by "direct fitness benefits."

For example, if an African wild dog goes hunting by itself, it can capture food which will help it reproduce. If more dogs join in the hunt, the expected return to the hunt increases with the number of dogs. If the returns to the hunt are only shared by participants, there is no reproductive cost to cooperation and, thus, cooperation is not altruistic (more about this in my encyclopedia article.)


But don't take my word for it.  Here is WEG earlier in their paper:

Cooperation is defined as a behaviour which provides a benefit to another individual (recipient) and which is selected for because of its beneficial effect on the recipient (West et al., 2007b). This definition of cooperation therefore includes all altruistic (–/+) and some mutually
beneficial (+/+) behaviours.

If you were paying close attention to the Venn diagram you will notice that there is only one animal that is enclosed in both circles - humans - and this is the only animal described by WEG as being a member of both. This seemingly unique position is what makes human cooperation special - our willingness (or even eagerness) to cooperate altruistically with very distant genetic relatives. You see this type of cooperation all around us and we mostly take it for granted. There are extreme examples, like the willingness to sacrifice oneself for unrelated comrades in war, but also everyday examples like throwing trash in a can instead of on the street. Economic experiments have long established that individuals will often behave altruistically even when their behavior is completely anonymous and one-shot.

So why do humans cooperate altruistically with non-relatives? I am of the school that thinks this is a result of the unique properties of human social learning (i.e., human culture) - a topic I will discuss in a Part II of this post.