In the Hamadryas baboon, males are substantially larger than females. A troop of baboons is subdivided into a number of ‘one-male groups’, consisting of one adult male and one or more females with their young. The male prevents any of ‘his’ females from moving too far from him. Kummer (1971) performed the following experiment. Two males, A and B, previously unknown to each other, were placed in a large enclosure. Male A was free to move about the enclosure, but male B was shut in a small cage, from which he could observe A but not interfere. A female, unknown to both males, was then placed in the enclosure. Within 20 minutes male A had persuaded the female to accept his ownership. Male B was then released into the open enclosure. Instead of challenging male A , B avoided any contact, accepting A’s ownership.

Evolution and the Theory of Games

The Righteous Mind: Why Good People Are Divided by Politics and Religion Jonathan Haidt Pantheon Books, 2012One has likely heard that, for the sake of decorum, religion and politics should never be topics of conversation with strangers. Even amongst friends or even when it is known that others hold opposing political or religious views, why is it that discussion of religion and politics leads to visceral-level acrimony and that one's views are right and the other's views are wrong? Professor Jonathan Haidt of the University of Virginia examines the psychological basis of our "righteous minds" without resorting to any of the pejorative labeling that is usually found in a book on politics and religion and eschews a purely comparative approach. Haidt proposes the intriguing hypothesis that our visceral reaction to competing ideologies is a subconscious, rather than leaned, reaction that evolved over human evolution to innate senses of suffering, fairness, cheating and disease, and that moral foundations facilitated intra-group cooperation which in turn conferred survival advantages over other groups. These psychological mechanisms are genetic in origin and not necessarily amenable to rational and voluntary control - this is in part the reason debating one's ideological opposite more often leads to frustration rather than understanding. Haidt also suggests that morality is based on six "psychological systems" or foundations (Moral Foundations Theory), similar to the hypothesized adaptive mental modules which evolved to solve specific problems of survival in the human ancestral environment.While decorum pleads for more civility, it would be better, as Haidt suggests, dragging the issue of partisan politics out into the open in order to understand it and work around our righteous minds. Haidt suggests a few methods by which the level of rhetoric in American politics can be reduced, such that the political parties can at least be cordial as they have been in the past and work together to solve truly pressing social problems.There are a number of fascinating points raised in the current book, but most intriguing is the one that morality, ideology and religion are products of group selection, as adaptations that increased individual cooperation and suppressed selfishness, thereby increasing individual loyalty to the group. That morality, political ideology and religion buttress group survival is probably highly intuitive. However, given the contemporary focus on the individual as the source of adaptations, to the exclusion of all else, to suggest that adaptations such as religion and political ideology arose to enhance survival of groups is heresy or, as Haidt recounts, "foolishness". While previous rejection of group selection itself was due in part to conceptual issues, one could also point out the prevailing individualist social sentiment, "selfish gene" mentality and unrelenting hostility against those who supported the view that group selection did indeed apply to humans and not just to insects. Haidt gives a lengthy and convincing defense of group selection, his main point being that humans can pursue self- interest at the same time they promote self-interest within a group setting - humans are "90 percent chimp, 10 percent bees". One can readily observe in the news and entertainment mediate that religion is a frequent target of derision, even within the scientific community - Haidt points to the strident contempt that the "New Atheists" hold for religion. They claim that religion is purely a by-product of an adaptive psychological trait and as a mere by-product religion serves no useful purpose. However, the religious "sense" has somehow managed to persist in the human psyche. One explanation by the New Atheists of how religion propagated itself is that it is a "parasite" or "virus" which latches onto a susceptible host and induces the host to "infect" others. As a "virus" or "parasite" that is merely interested in its own survival, religion causes people to perform behaviors that do not increase their own reproductive fitness and may even be detrimental to survival, but religion spreads nonetheless. …

The Righteous Mind: Why Good People Are Divided by Politics and Religion

The genomes of large multicellular eukaryotes are mostly comprised of non-protein coding DNA. Although there has been much agreement that a small fraction of these genomes has important biological functions, there has been much debate as to whether the rest contributes to development and/or homeostasis. Much of the speculation has centered on the genomic regions that are transcribed into RNA at some low level. Unfortunately these RNAs have been arbitrarily assigned various names, such as “intergenic RNA”, “long non-coding RNAs” etc., which have led to some confusion in the field. Many researchers believe that these transcripts represent a vast, unchartered world of functional non-coding RNAs (ncRNAs), simply because they exist. However, there are reasons to question this Panglossian view because it ignores our current understanding of how evolution shapes eukaryotic genomes and how the gene expression machinery works in eukaryotic cells. Although there are undoubtedly many more functional ncRNAs yet to be discovered and characterized, it is also likely that many of these transcripts are simply junk. Here we discuss how to determine whether any given ncRNA has a function. Importantly, we advocate that in the absence of any such data, the appropriate null hypothesis is that the RNA in question is junk.

/pdf/non-coding-rna-what-is-functional-and-what-is-junk-89gw6fwzr3.pdf

Non-coding RNA: what is functional and what is junk?

On the nature of

A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as “affirming the consequent,” by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

http://nsmn1.uh.edu/dgraur/pdf/genome biol evol-2013-graur-gbe_evt028.pdf

On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE.

Recent work has revealed a new class of “zero-determinant” (ZD) strategies for iterated, two-player games. ZD strategies allow a player to unilaterally enforce a linear relationship between her score and her opponent’s score, and thus to achieve an unusual degree of control over both players’ long-term payoffs. Although originally conceived in the context of classical two-player game theory, ZD strategies also have consequences in evolving populations of players. Here, we explore the evolutionary prospects for ZD strategies in the Iterated Prisoner’s Dilemma (IPD). Several recent studies have focused on the evolution of “extortion strategies,” a subset of ZD strategies, and have found them to be unsuccessful in populations. Nevertheless, we identify a different subset of ZD strategies, called “generous ZD strategies,” that forgive defecting opponents but nonetheless dominate in evolving populations. For all but the smallest population sizes, generous ZD strategies are not only robust to being replaced by other strategies but can selectively replace any noncooperative ZD strategy. Generous strategies can be generalized beyond the space of ZD strategies, and they remain robust to invasion. When evolution occurs on the full set of all IPD strategies, selection disproportionately favors these generous strategies. In some regimes, generous strategies outperform even the most successful of the well-known IPD strategies, including win-stay-lose-shift.

https://www.pnas.org/content/pnas/110/38/15348.full.pdf

From extortion to generosity, evolution in the Iterated Prisoner’s Dilemma

Self-serving, rational agents sometimes cooperate to their mutual benefit. However, when and why cooperation emerges is surprisingly hard to pin down. To address this question, scientists from diverse disciplines have used the Prisoner’s Dilemma, a simple two-player game, as a model problem. In PNAS, Press and Dyson (1) dramatically expand our understanding of this classic game by uncovering strategies that provide a unilateral advantage to sentient players pitted against unwitting opponents. By exposing these results, Press and Dyson have fundamentally changed the viewpoint on the Prisoner’s Dilemma, opening a range of new possibilities for the study of cooperation.

/pdf/extortion-and-cooperation-in-the-prisoner-s-dilemma-vkfozagpqp.pdf

Extortion and cooperation in the Prisoner’s Dilemma

Gene expression is controlled primarily by transcription factors, whose DNA binding sites are typically 10 nt long. We develop a population-genetic model to understand how the length and information content of such binding sites evolve. Our analysis is based on an inherent trade-off between specificity, which is greater in long binding sites, and robustness to mutation, which is greater in short binding sites. The evolutionary stable distribution of binding site lengths predicted by the model agrees with the empirical distribution (5–31 nt, with mean 9.9 nt for eukaryotes), and it is remarkably robust to variation in the underlying parameters of population size, mutation rate, number of transcription factor targets, and strength of selection for proper binding and selection against improper binding. In a systematic data set of eukaryotic and prokaryotic transcription factors we also uncover strong relationships between the length of a binding site and its information content per nucleotide, as well as between the number of targets a transcription factor regulates and the information content in its binding sites. Our analysis explains these features as well as the remarkable conservation of binding site characteristics across diverse taxa.

https://www.genetics.org/content/genetics/192/3/973.full.pdf

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner’s Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players’ payoffs as well as their strategies to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the coevolution of strategies and payoffs in arbitrary iterated games. We show that, when there is a tradeoff between the benefits and costs of cooperation, coevolution often leads to a dramatic loss of cooperation in the Iterated Prisoner’s Dilemma. The collapse of cooperation is so extreme that the average payoff in a population can decline even as the potential reward for mutual cooperation increases. Depending upon the form of tradeoffs, evolution may even move away from the Iterated Prisoner’s Dilemma game altogether. Our work offers a new perspective on the Prisoner’s Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the coevolution of strategies and payoffs in iterated interactions.

https://www.pnas.org/content/pnas/111/49/17558.full.pdf

Collapse of cooperation in evolving games

People must integrate disparate sources of information when making decisions, especially in social contexts. But information does not always flow freely. It can be constrained by social networks1–3 and distorted by zealots and automated bots4. Here we develop a voter game as a model system to study information flow in collective decisions. Players are assigned to competing groups (parties) and placed on an ‘influence network’ that determines whose voting intentions each player can observe. Players are incentivized to vote according to partisan interest, but also to coordinate their vote with the entire group. Our mathematical analysis uncovers a phenomenon that we call information gerrymandering: the structure of the influence network can sway the vote outcome towards one party, even when both parties have equal sizes and each player has the same influence. A small number of zealots, when strategically placed on the influence network, can also induce information gerrymandering and thereby bias vote outcomes. We confirm the predicted effects of information gerrymandering in social network experiments with n = 2,520 human subjects. Furthermore, we identify extensive information gerrymandering in real-world influence networks, including online political discussions leading up to the US federal elections, and in historical patterns of bill co-sponsorship in the US Congress and European legislatures. Our analysis provides an account of the vulnerabilities of collective decision-making to systematic distortion by restricted information flow. Our analysis also highlights a group-level social dilemma: information gerrymandering can enable one party to sway decisions in its favour, but when multiple parties engage in gerrymandering the group loses its ability to reach consensus and remains trapped in deadlock. In a voter game, information gerrymandering can sway the outcome of the vote towards one party, even when both parties have equal sizes and each player has the same influence; and this effect can be exaggerated by strategically placed zealots or automated bots.

Alexander J. Stewart

Papers

From extortion to generosity, evolution in the Iterated Prisoner’s Dilemma

Extortion and cooperation in the Prisoner’s Dilemma

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

Collapse of cooperation in evolving games

Information gerrymandering and undemocratic decisions