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Archive for the ‘Evolution’ Category

First Support for a Physics Theory of Life

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Natalie Wolchover writes in Quanta:

The biophysicist Jeremy England made waves in 2013 with a new theory that cast the origin of life as an inevitable outcome of thermodynamics. His equations suggested that under certain conditions, groups of atoms will naturally restructure themselves so as to burn more and more energy, facilitating the incessant dispersal of energy and the rise of “entropy” or disorder in the universe. England said this restructuring effect, which he calls dissipation-driven adaptation, fosters the growth of complex structures, including living things. The existence of life is no mystery or lucky break, he told Quanta in 2014, but rather follows from general physical principles and “should be as unsurprising as rocks rolling downhill.”

Since then, England, a 35-year-old associate professor at the Massachusetts Institute of Technology, has been testing aspects of his idea in computer simulations. The two most significant of these studies were published this month — the more striking result in the Proceedings of the National Academy of Sciences (PNAS) and the other in Physical Review Letters (PRL). The outcomes of both computer experiments appear to back England’s general thesis about dissipation-driven adaptation, though the implications for real life remain speculative.

“This is obviously a pioneering study,” Michael Lässig, a statistical physicist and quantitative biologist at the University of Cologne in Germany, said of the PNAS paper written by England and an MIT postdoctoral fellow, Jordan Horowitz. It’s “a case study about a given set of rules on a relatively small system, so it’s maybe a bit early to say whether it generalizes,” Lässig said. “But the obvious interest is to ask what this means for life.”

The paper strips away the nitty-gritty details of cells and biology and describes a simpler, simulated system of chemicals in which it is nonetheless possible for exceptional structure to spontaneously arise — the phenomenon that England sees as the driving force behind the origin of life. “That doesn’t mean you’re guaranteed to acquire that structure,” England explained. The dynamics of the system are too complicated and nonlinear to predict what will happen.

The simulation involved a soup of 25 chemicals that react with one another in myriad ways. Energy sources in the soup’s environment facilitate or “force” some of these chemical reactions, just as sunlight triggers the production of ozone in the atmosphere and the chemical fuel ATP drives processes in the cell. Starting with random initial chemical concentrations, reaction rates and “forcing landscapes” — rules that dictate which reactions get a boost from outside forces and by how much — the simulated chemical reaction network evolves until it reaches its final, steady state, or “fixed point.”

Often, the system settles into an equilibrium state, where it has a balanced concentration of chemicals and reactions that just as often go one way as the reverse. This tendency to equilibrate, like a cup of coffee cooling to room temperature, is the most familiar outcome of the second law of thermodynamics, which says that energy constantly spreads and the entropy of the universe always increases. (The second law is true because there are more ways for energy to be spread out among particles than to be concentrated, so as particles move around and interact, the odds favor their energy becoming increasingly shared.)

But for some initial settings, the chemical reaction network in the simulation goes in a wildly different direction: In these cases, it evolves to fixed points far from equilibrium, where it vigorously cycles through reactions by harvesting the maximum energy possible from the environment. These cases “might be recognized as examples of apparent fine-tuning” between the system and its environment, Horowitz and England write, in which the system finds “rare states of extremal thermodynamic forcing.”

Living creatures also maintain steady states of extreme forcing: We are super-consumers who burn through enormous amounts of chemical energy, degrading it and increasing the entropy of the universe, as we power the reactions in our cells. The simulation emulates this steady-state behavior in a simpler, more abstract chemical system and shows that it can arise “basically right away, without enormous wait times,” Lässig said — indicating that such fixed points can be easily reached in practice.

Many biophysicists think something like what England is suggesting may well be at least part of life’s story. But whether England has identified the most crucial step in the origin of life depends to some extent on the question: What’s the essence of life? Opinions differ.

Form and Function

England, a prodigy by many accounts who spent time at Harvard, Oxford, Stanford and Princeton universities before landing on the faculty at MIT at 29, sees the essence of living things as the exceptional arrangement of their component atoms. “If I imagine randomly rearranging the atoms of the bacterium — so I just take them, I label them all, I permute them in space — I’m presumably going to get something that is garbage,” he said earlier this month. “Most arrangements [of atomic building blocks] are not going to be the metabolic powerhouses that a bacterium is.”

It’s not easy for a group of atoms to unlock and burn chemical energy. To perform this function, the atoms must be arranged in a highly unusual form. According to England, the very existence of a form-function relationship “implies that there’s a challenge presented by the environment that we see the structure of the system as meeting.”

But how and why do atoms acquire the particular form and function of a bacterium, with its optimal configuration for consuming chemical energy? England hypothesizes that it’s a natural outcome of thermodynamics in far-from-equilibrium systems.

The Nobel-Prize-winning physical chemist Ilya Prigogine pursued similar ideas in the 1960s, but his methods were limited. Traditional thermodynamic equations work well only for studying near-equilibrium systems like a gas that is slowly being heated or cooled. Systems driven by powerful external energy sources have much more complicated dynamics and are far harder to study.

The situation changed in the late 1990s, when the physicists Gavin Crooks and Chris Jarzynski derived “fluctuation theorems” that can be used to quantify how much more often certain physical processes happen than reverse processes. These theorems allow researchers to study how systems evolve — even far from equilibrium. England’s “novel angle,” said Sara Walker, a theoretical physicist and origins-of-life specialist at Arizona State University, has been to apply the fluctuation theorems “to problems relevant to the origins of life. I think he’s probably the only person doing that in any kind of rigorous way.”

Continue reading.

Life as a natural result of matter, energy, and the second law of thermodynamics, which seems to be a primal force. Everything then follows by one or another sort of selection (shades of Darwinian evolution) until life emerges and then evolution speeds up a lot, and then memes emerge and evolution speeds up more.

What is missing in the discussion is line-drawing and emergent phenomena: as life is an emergent phenomenon from thermodynamically driven chemical reactions. Interesting book: The Emergence of Everything. Also interesting: The Evolution of Everything. Different authors, though.

Written by LeisureGuy

26 July 2017 at 12:10 pm

Posted in Books, Evolution, Science

How Nature Solves Problems Through Computation

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A very interesting interview of Jessica Flack by Joshua Sokol in Quanta:

here are many patterns of collective behavior in biology that are easy to see because they occur along the familiar dimensions of space and time. Think of the murmuration of starlings. Or army ants that span gaps on the forest floor by linking their own bodies into bridges. Loose groups of shoaling fish that snap into tight schools when a predator shows up.

Then there are less obvious patterns, like those that the evolutionary biologist Jessica Flack tries to understand. In 2006, her graduate work at Emory University showed how just a few formidable-looking fighters could stabilize an entire group of macaques by intervening in scuffles between weaker monkeys, who would submit with teeth-baring grins rather than risk a fight they thought they would lose. But when Flack removed some of the police, the whole group became fractured and chaotic.

Like flocking or schooling, the policing behavior arises from individual interactions to produce a macroscopic effect on the entire ensemble. But it is subtler, perhaps harder to visualize and measure. Or, as Flack says of macaque society and many of the other systems she studies, “their metric space is a social coordinate space. It’s not Euclidean.”

Flack is now a professor at the Santa Fe Institute, where she has spent all of her postgraduate career, except for a stint at the University of Wisconsin, Madison. Her “collective computation” group, C4, which she co-runs with her collaborator, David Krakauer, probes not just macaques but neurons, slime molds and the internet for the rules that underlie each model, as well as the general rules underlying them all.

Flack describes her work as an investigation into three interlocking questions. She wants to understand how phenomenological rules in biology, which seem to work in aggregate, emerge from microscopic ground truths. She wants to understand how groups solve problems and come to decisions. And she wants to know how complex systems stay robust in the face of shocks, like the macaques with their own police force that acts as social glue.

At its root, though, Flack’s focus is on information: specifically, on how groups of different, error-prone actors variously succeed and fail at processing information together. “When I look at biological systems, what I see is that they are collective,” she said. “They are all made up of interacting components with only partly overlapping interests, who are noisy information processors dealing with noisy signals.”

Over the phone, by Skype and via email, Quanta Magazine caught up with Flack to ask about C4’s current projects, her own career path, and the overarching philosophy behind her work. An edited and condensed version of our conversations follows.

How did you get into research on problem solving in nature, and how did you wind up at the Santa Fe Institute?

I’ve always been interested in how nature solves problems and where patterns come from, and why everything seems so organized despite so many potential conflicts of interest. Those sorts of questions have been with me since I was really little.

At Cornell, I was taking evolutionary biology classes, but none of the material really addressed these questions. I would spend a lot of time in Mann Library, which was where all the good biology books were. So I would sit on the floor in the dusty, dimly lit stacks with this pile of books around me. And in that way I discovered that there was a community of people working on these questions in evolutionary biology that I found more interesting.

They weren’t in the mainstream. One of the main places that turned out to be home to a lot of these people was the Santa Fe Institute. This was in the early to mid-’90s. I emailed the Santa Fe Institute and I requested something like 40 working papers. I was being a really annoying undergraduate. And someone mailed them to me! They actually snail-mailed me 40 of these papers, and I was thrilled, and I read them all.

Now that you’ve ended up there, can you break down what your C4 research group means by “collective computation”?

Collective computation is about how adaptive systems solve problems. All systems are about extracting energy and doing work, and physical systems in particular are about that. When you move to adaptive systems, you’ve got the additional influence of information processing, which we think allows a system to extract energy more efficiently even though it has to expend a little extra energy to do the information processing. Components of adaptive systems look out at the world, and they try to discover the regularities. It’s a noisy process.

Unlike in computer science where you have a program you have written, which has to produce a desired output, in adaptive systems this is a process that is being refined over evolutionary or learning time. The system produces an output, and it might be a good output for the environment or it might not. And then over time it hopefully gets better and better.

What we are doing at C4 is taking messy, conceptually challenging problems and turning them into something rigorous. We’re very philosophically oriented, but we’re also very quantitative, particularly in thinking about how nature can overcome subjectivity in information processing through collective computation. We really think the answer to these questions requires combining insights from statistical physics, theoretical computer science, information theory, evolutionary biology and cognitive science.

Can you walk us through an example? In a recent paper, your group looked at communication between neurons in the brains of macaques.

The human brain contains roughly 86 billion neurons, making our brains the ultimate collectives. Every decision we make can be thought of as the outcome of a neural collective computation. In the case of our study, which was lead by my colleague Bryan Daniels, the data we analyzed were collected during an experiment by Bill Newsome’s group at Stanford from macaques who had to decide whether a group of dots moving across a screen was traveling left or right. Data on neural firing patterns were recorded while the monkey was performing this task. We found that as the monkey initially processes the data, a few single neurons have strong opinions about what the decision should be. But this is not enough: If we want to anticipate what the monkey will decide, we have to poll many neurons to get a good prediction of the monkey’s decision. Then, as the decision point approaches, this pattern shifts. The neurons start to agree, and eventually each one on its own is maximally predictive.

We have this principle of collective computation that seems to involve these two phases. The neurons go out and semi-independently collect information about the noisy input, and that’s like neural crowdsourcing. Then they come together and come to some consensus about what the decision should be. And this principle of information accumulation and consensus applies to some monkey societies also. The monkeys figure out sort of semi-independently who is capable of winning fights, and then they consolidate this information by exchanging special signals. The network of these signals then encodes how much consensus there is in the group about any one individual’s capacity to use force in fights.

I noticed that another recent paper uses the same macaque data set you produced during your graduate work at the Yerkes National Primate Research Center in Lawrenceville, Georgia. What did you find when you returned to thinking about this system?

We wanted to understand how social systems or other biological systems go from state A to state B. How a group of fish goes from shoaling to schooling, or how a social system goes from having a few super-powerful animals to a setup where there is less inequalityOne mechanism known to facilitate switching between different states like this is for the system to sit near what’s called a . . .

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Written by LeisureGuy

7 July 2017 at 8:15 pm

Posted in Evolution, Science

Can Microbes Encourage Altruism?

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Interesting idea. Lifeforms are much more intricate and interrelated than we think: the “web of life” really does reflect how you (and I) are attached to other lifeforms, including the microbiome that has such an influence on our health and without which we could not live. Elizabeth Svoboda writes in Quanta:

arasites are among nature’s most skillful manipulators — and one of their specialties is making hosts perform reckless acts of irrational self-harm. There’s Toxoplasma gondii, which drives mice to seek out cats eager to eat them, and the liver fluke Dicrocoelium dendriticum, which motivates ants to climb blades of grass, exposing them to cows and sheep hungry for a snack. There’s Spinochordodes tellinii, the hairworm that compels crickets to drown themselves so the worm can access the water it needs to breed. The hosts’ self-sacrifice gains them nothing but serves the parasites’ hidden agenda, enabling them to complete their own life cycle.

Now researchers are beginning to explore whether parasitic manipulations may spur host behaviors that are selfless rather than suicidal. They are wondering whether microbes might be fundamentally responsible for many of the altruistic behaviors that animals show toward their own kind. Altruism may seem easy to justify ethically or strategically, but explaining how it could have persisted in a survival-of-the-fittest world is surprisingly difficult and has puzzled evolutionary theorists going all the way back to Darwin. If microbes in the gut or other tissues can nudge their hosts toward generosity for selfish reasons of their own, altruism may become less enigmatic.

A recently developed mathematical model and related computer simulations by a trio of researchers at Tel Aviv University appear to validate this theory. The researchers showed that transmissible microbes that promoted altruism in their hosts won the survival battle over microbes that did not — and when this happened, altruism became a stable trait in the host population. The research was published in Nature Communications earlier this year.

“The story is fascinating, because we don’t think of altruism in terms of the host-microbiome relationship,” said John Bienenstock, a biologist at McMaster University in Hamilton, Ontario, and director of the Brain-Body Institute at St. Joseph’s Healthcare Hamilton, who was not involved with the simulation work. “You can’t ignore the possible effect of what your bug population is doing.”

Even when Darwin was developing his theory that the strongest and fittest individuals in each generation were most likely to control resources and leave progeny, he recognized altruism as a befuddling challenge. “It is extremely doubtful whether the offspring of the more sympathetic and benevolent parents … would be reared in greater numbers than the children of selfish and treacherous parents,” he wrote in The Descent of Man.

Darwin hypothesized that altruism might survive if individuals’ cooperative behaviors gave the group to which they belonged a collective advantage. The entire group’s fitness might then trend upward, enabling it to out-compete other groups with more selfish members. That “group selection” model of evolution was developed further by later scientists, and it found powerful advocates such as the leading naturalist Konrad Lorenz.

But in the 1960s, work by influential evolutionary theorists such as John Maynard Smith and George C. Williams dealt a blow to group selection by demonstrating that altruistic traits were hard to maintain in an evolutionary context. Selfish individuals would still appear spontaneously and would tend to have more offspring, edging out more generous members of a species and ensuring the persistence of selfishness.

The biologist William D. Hamilton made an end run around this problem in 1964 by invoking a strategy that Maynard Smith had called kin selection. Hamilton proposed that altruism could persist if helpful individuals’ actions allowed family members to pass on enough of their shared genes to compensate for any reduction in the altruistic individuals’ own progeny. This principle is laid out in a formula called Hamilton’s rule (C < rB), which states that if the cost to a giver (C) is less than the benefit to a recipient (B) multiplied by their genetic relatedness (r), altruism will come to dominate within a population.

Hamilton’s rule explains why altruistic behavior evolved among ants and bees, which are famously social insects. Because of quirks of their haplodiploid genetics, female workers share more genes with their sisters than with their own offspring, so it makes competitive sense for them to sacrifice their own fecundity to help their colony queen mother produce more sisters. The relevance to other animals, however, is murkier. (The geneticist J.B.S. Haldane, who explored early concepts of kin selection in the 1930s, is sometimes alleged to have joked that, as a human being, he would lay down his life for two brothers or eight cousins.)

Kin selection is one example of “inclusive fitness” theories that have been advanced to explain altruism since the 1970s. “Multilevel selection” theories that would include forms of group selection have also had a resurgence, championed by biologists such as David Sloan Wilson of Binghamton University, but they remain contentious.

Still, when it comes to altruism, “there are many explanations, but it still sounds like a mystery,” said Ohad Lewin-Epstein, an evolutionary biologist and programmer at Tel Aviv University. As a student in the biology laboratory of Lilach Hadany, he took part in research on how cooperation among members of a population can affect the evolution of new traits. The team came to feel that the classical explanations for the evolution of cooperation weren’t the whole story. In particular, Hadany and Lewin-Epstein, with Ranit Aharonov, a computer scientist visiting the university from IBM Research, wondered if microbes could manipulate their hosts to encourage them to help others.

The researchers in Tel Aviv wanted to lend context and focus to an idea that had been debated for some time: Can transmissible “piggybacking” factors encourage altruism? In 2013, Sorcha Mc Ginty, a biologist then at the University of Zurich, and her colleagues created a computer model showing that plasmids — genes that move from one bacterium to another — help spur the evolution of cooperation within bacterial communities. In 2015, a group at Paris Descartes University experimentally demonstrated that when bacteria exchange certain plasmids, the plasmids reprogram the recipient bacteria with genetic information that compels them to contribute to the common good. The bacteria secrete proteins that destroy antibiotics in the vicinity — a strategy that protects the entire bacterial community. To Lewin-Epstein and Hadany, results like these raised the question of whether microbes or parasites that move between complex hosts might drive cooperation as well.

To explore this question in depth, the Tel Aviv group created both a mathematical model and a computer simulation that analyzed interactions among members of a population over hundreds (and in some cases, thousands) of generations. The model assumed that altruistic members incurred some fitness cost when they interacted with others, while the recipients of altruistic acts benefited. The definition of altruism the study uses is broad, Lewin-Epstein says, with costs to the giver that can range from minor to a high degree of self-sacrifice.

The researchers then pitted two types of virtual microbes against each other in the simulation. One microbe promoted altruism in its hosts, while the second did not. In each generation, individuals interacted in ways that allowed both types of microbes to pass from one host to the next, and each individual’s microbes were then transmitted to its offspring. Over the generations, microbes that encouraged altruism in their hosts out-competed their rivals when both passed from one host to another and were subsequently passed from parent to child. This was true even when the population of “pro-altruism” microbes was very small at the outset. Pro-altruism microbe recipients were fitter in that they had benefited from another host’s generosity, meaning they were more likely to produce offspring carrying the same microbe.

By the end of the simulation, the host population consisted mostly of individuals carrying the altruism-promoting microbe — in some scenarios, 100 percent of hosts ended up with the microbe. That outcome led to the sustained expression of altruistic behavior within the population. A stable level of altruism persisted even when there were selfish hosts in the mix that refused to reciprocate. The mathematical models and simulations also demonstrated that microbe-transmitted altruism ultimately became more stable within a host population than selflessness that had genetic origins.

“Previous works considered altruism only from the perspective of the host,” Hadany said. “Where classical models would explain the evolution of altruism under some circumstances, this [could explain the] evolution of altruism under wider conditions.” Andrew Moeller, an evolutionary biologist at the University of California, Berkeley, who studies gut microbiomes, said the findings warrant further study. “Microbes can influence the behaviors of animal hosts, so it is not outside the realm of possibility that microbes could promote altruistic behaviors.” . . .

Continue reading.

Written by LeisureGuy

29 June 2017 at 3:34 pm

Moonlighting Genes Evolve for a Venomous Job

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Christie Wilcox writes in Quanta:

Venoms are among nature’s fiercest adaptations. The geographer’s cone snail, for example, only injects about a tenth of a milligram of venom when it stings, and yet, this is more than enough to kill a person in under an hour. These chemical cocktails contain some of the most potent compounds known, and their fearsome power has awed people since the dawn of history. It wasn’t until modern advances in genetics, though, that scientists were able to study how the genes encoding for such potent toxins arise, providing glimpses into the workings of evolution at the molecular level. From such studies came the current canonical model of how venom genes evolve through the chance replication and mutation of genes for enzymes, peptides and other proteins.

But new findings published today in Current Biology challenge this model, finding that the majority of toxin genes for parasitoid wasp species are instead “moonlighting” from other physiological roles. A further exciting implication is that if this discovery is relevant to compounds other than venoms, it might be a pathway that nature uses to develop other evolutionary solutions rapidly.

“I’ve been working on parasitoid wasps for a very long time,” remarked Jack Werren, a professor of biology at the University of Rochester. His fascination with these animals centers on their specialized venoms, which allow the wasps to be masterful physiological puppeteers. Parasitoid wasps are an enormous group of between 100,00 and 600,000 species that are parasitic when they are larvae, living on or frequently inside a host they eat alive. As free-living adults, they must find and subdue an appropriate creature to play host to their young, which they do with the aid of behavior-altering venoms. The emerald cockroach wasp, for example, transforms its formidable targets — cockroaches many times its size — into complacent meals for the wasps’ hungry offspring by manipulating the animals’ brain chemistry. The Glyptapanteles wasp goes even further, turning its caterpillar offerings into zombie bodyguards that protect the young wasps that have just eaten their way out of the caterpillars’ tissues. Another wasp, Reclinervellus nielseni, forces its arachnid victims to transform their webs into sturdy nests that will continue to protect the wasp larvae after the spiders expire.

“The venoms of parasitoids are quite different from those of most of the venomous animals that have been studied because they’ve evolved to manipulate metabolism” rather than to kill outright, Werren explained. He and Ellen O. Martinson, a postdoctoral fellow in his lab, were interested in understanding the diversity of toxins in parasitoid venoms and how those toxins evolve. They and their colleagues started by assembling genomes for several closely related wasp species, and they found something striking: Even close relatives among the wasps shared only about 30 to 40 percent of their venom genes. That surprisingly low number suggested the evolution of new species was accompanied by rapid turnover of the venom genes, with old genes being abandoned and new ones with novel venom functions suddenly arising. “Our next question was, okay, well what happened?” Werren said. “These genes that are being picked up, where are they coming from? And that got us into this broad question of: How do new genes’ functions evolve?”

Based largely on studies of snakes, spiders and other species dangerous to our own, it is thought that most venom genes arise through the mechanism of gene duplication followed by mutation and repurposing (which scientists refer to as neofunctionalization). The process begins when a gene for a molecule with a potentially toxic function, like a protein-chopping enzyme, is accidentally duplicated, typically during the formation of egg cells and sperm. The extra copy, free of the burden of performing the original gene’s biological duties, can accumulate changes through random mutations. Those changes may render the duplicate gene or its protein worthless, and it may disappear. Sometimes, however, those changes alter the protein in such a way that it becomes a useful toxin — and voilà, a venom toxin is born.

But when Martinson, Werren and their colleagues compared the venom proteins and genes from four closely related species of parasitoid wasps, that’s not what they saw. In stark contrast to studies of other venomous animals, they found that nearly half of the 53 most recently recruited venom genes uncovered through their genetic analyses were single-copy, meaning they were not duplicates of other genes with which evolution had tinkered. In fact, less than 10 percent of the toxin genes clearly arose through duplication and mutation. . .

Continue reading.

Written by LeisureGuy

22 June 2017 at 7:36 pm

Posted in Evolution, Science

What Duck Sex Reveals about Human Nature

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In an interview with Der Spiegel, Richard Prum, an ornithologist and curator at the Peabody Museum of Natural History at Yale University, discusses the violent mechanics of duck sex, the beauty of bird-mating rituals and why human civilization was made possible by love.

SPIEGEL: Professor Prum, among all the wonders of nature you were most inspired by the sex of ducks. Why?

Prum: For a long time, I have been fascinated by the sex life of birds. But there is probably no other species where the deep sexual conflict between male and female sex is as blatant as in ducks.

SPIEGEL: And so you started studying their genitalia?

Prum: No, it was actually even more simple than that. I had a prospective post-doctoral student who was looking for something to do, and she was interested in studying genitalia. I said to myself: Well, I have never worked on that end of the bird before. As a result, we studied duck sex intensively for six, seven years.

SPIEGEL: What surprised you most?

Prum: Oh, there were many surprises. Not the least that we had all these descriptions of duck genitalia, and when we looked ourselves, we said: There is almost nothing to see. How could this be? That is how we discovered that the genitalia of ducks regress and regrow each year, so that a 10- or 15-centimeter penis in the summer will reduce to less than 1 centimeter in the winter and then grow back the next year.

SPIEGEL: This is part of the sexual conflict you mentioned before?

Prum: Yes, indeed. Mate choice occurs first. In winter the males do these elaborate displays, and the females choose the one they like most. Because, parallel to the evolution of the males’ display behavior, the females have evolved preferences for these displays. We call this “coevolution.”

SPIEGEL: So far, this sounds quite harmonious.

Prum: Yes, it is. The pairs stay together until the clutch is laid and the females incubate. The conflict part comes next. Because now some of the males pursue an alternative mating strategy, which is to violently enforce copulation. For this they make use of their penis, which is regrown by now. This penis is a very bizarre structure. It is counterclockwise coiled, and erection takes place in less than half a second. Erection, penetration and ejaculation in ducks is one and the same event, and it happens very, very rapidly.

SPIEGEL: How do the females react?

Prum: It’s very interesting. Of course, in the short run, females struggle to escape from forced copulations. But in the long run, female ducks coevolve vaginal morphologies for the purpose of preventing forced intromission (or insertion of the penis) — sort of dead end cul-de-sacs and a series of clockwise spirals that have a chiral (or non-superimposable) mismatch with the shape of the penis. These are literally anti-screw devices.

SPIEGEL: Why all this effort? Wouldn’t it be easier to just give in to the aggressor’s assault?

Prum: To understand this, you have to consider the evolutionary mechanisms involved: If the female gets the mate she likes, then her offspring will inherit the green head and the quack-quack-quack, all those displays that she likes so much. And since all other females have coevolved to prefer those same traits, her sons will be very successful and she will have lots of grandchildren from him. But if she’s fertilized by force, then some random male will father her kids, which means that her offspring are less likely to inherit the attractive traits that she and other females like. That means fewer grandkids. Therefore, evolution will favor any mutation that allows her to get her own choice — for example by protecting her vagina against forced sex.

SPIEGEL: Are you saying that nature works to protect female rights?

Prum: You can put it like that. Sexual autonomy matters to animals. It’s not just a political idea invented by feminists, but an evolved feature of social species.

SPIEGEL: In other words, nature created a sex that is focused on autonomy and another that is focused on violence — a good and an evil sex?

Prum: You are right: In our world, we do associate violations of autonomy with abuses of power. But this doesn’t mean, of course, that there are ethical standards among ducks as there are among humans. Females are not the inherently more ethical sex, but it is just that there is something about female reproduction that limits the potential for the sexual abuse of power.

SPIEGEL: Somehow birds seem to be particularly successful in achieving their sexual autonomy. Among them, female mate choice is more common than among other animals. Why?

Prum: For a very simple reason: Unlike ducks, 97 percent of birds cannot be forcibly fertilized, because the males don’t have a penis. Copulation in most birds is achieved by a cloacal kiss, just an apposition (or touching) of orifices. So, to be fertilized, the female has to actively take up the sperm, which means that she retains full control of her sexual choice. By the way, I think this is the essential reason why birds are so beautiful. Since they have the freedom of choice, females exhibit aesthetic preferences. And, as a result of these preferences, males developed amazingly elaborate ornaments.

SPIEGEL: Does that mean beauty arises wherever there is female mate choice?

Prum: Wherever you have mate choice, period — not necessarily because the females are choosing. There are examples of male mate choice, or mutual mate choice as well. Take puffins for example. They court each other with elaborate displays, and therefore both sexes look the same. They both have the same colorful beaks and the same preferences for these beaks.

SPIEGEL: How about humans? Does our conception of beauty also stem from mate choice?

Prum: I’m convinced it does. Socrates was interested in Eros as the source of art and beauty, but it is important to be aware that our sense of aesthetics was reinvented over the course of human evolution. Because looking at the lives of chimpanzees and gorillas, our nearest relatives, we don’t see much evidence for sexual choice. In chimpanzees, males will pursue every sexual opportunity they get and females will acquiesce to every sexual request made to them.

SPIEGEL: And because chimps are sexually indiscriminate they don’t have any sense of beauty?

Prum: Yes, I think their lives are basically devoid of the aesthetic.

SPIEGEL: How did this transformation happen — when did beauty enter our world as humans?

Prum: This question is very difficult to answer. But just posing it already represents substantial progress. If you look in any current textbook of human evolutionary biology you will find that mate choice as a topic is almost entirely absent.

SPIEGEL: Do you think it was more likely to have been the males or the females that introduced mate choice into human evolution?

Prum: Initially, it was the females, for sure. Males didn’t need to become choosy until they were actively engaging in the upbringing of their offspring. And that happened much, much later.

SPIEGEL: What do you think were the criteria for female choice then?

Prum: Well, we don’t know for sure, of course. But I propose that the main male ornament females were selecting for was social personality itself. . .

Continue reading.

And see also “Duck Sex and the Patriarchy,” by Richard Prum in the New Yorker:

Four years ago, as the country was wrestling with a federal-budget crisis, conservative news outlets turned their attention, once again, to the topic of wasteful government spending. That March, a reporter with CNS News, a Web site devoted to countering “liberal bias” in the media, came across what seemed to be the quintessential example of such waste—a National Science Foundation grant to Yale University for a study of duck penises. Within days, the story had made its way to Fox News. “It’s part of President Obama’s stimulus plan, and it’s just one example of the kind of spending decisions that have added up to massive debt and deficits,” Shannon Bream told viewers. The following week, Sean Hannity piled on. “Don’t we really need to know about duck genitalia, Tucker Carlson?” he asked. To which Carlson responded, with a smirk, “I know more than I want to know already!” The controversy, dubbed Duckpenisgate by Mother Jones, roared back to life some months later, when Senator Tom Coburn, of Oklahoma, included the N.S.F. grant in his “Wastebook 2013.” At $384,949, it accounted for only a thousandth of one per cent of all the spending that Coburn had tallied up, but it made headlines again. Clearly, the combination of money, sex, and power—your money, ducks’ sex, and Ivy League power—was irresistible to the graying male demographic for conservative news.

I followed Duckpenisgate with particular trepidation, since I was one of the co-investigators on the maligned study. For the past decade, in collaboration with Patricia Brennan, of Mount Holyoke College, and other colleagues, I have explored the sexual behavior and genital evolution of waterfowl. Contrary to what Carlson thinks, it is a fascinating business. It can also be shockingly brutal. In the wintry months before breeding begins, male ducks flaunt their plumage, putting on dramatic courtship displays in an effort to entrance a mate. The females can be choosy, often picking a male only after extensive deliberation. (Their preferences tend to coalesce, like a genetic fashion trend, around a shared ideal of male beauty, with each species evolving off in its own distinct aesthetic direction.) When spring arrives, the pairs migrate together to the breeding grounds. But, as the nest-building and egg-laying season approaches, unpaired males start causing trouble. Many attempt to force copulation with paired females, sometimes even ganging up on them in groups. The female ducks resist strenuously; often they are injured, or even killed, in the process.

The males’ sexual attacks are made possible by the fact that, unlike most birds, ducks still have a penis. It is not, however, an organ that most humans would recognize, being shaped like a counterclockwise corkscrew and possessing a ribbed or spiky surface. Ducks’ erections are driven by lymphatic, not vascular, pressure, which means that their penises never become stiff. Rather, they erect flexibly, but explosively, into the female’s body in less than half a second. Ejaculation takes place immediately. And duck penises can be long—really long. A breeding male mallard in your typical city park has a five-inch penis. In the case of the diminutive Argentine lake duck, the penis is longer than the duck itself—more than sixteen inches.

What, exactly, is the function of these bizarre organs? To find out, Brennan dissected the genitalia of fourteen species of waterfowl. By comparing the results, we discovered that, as males have evolved longer penises with more heavily armed surfaces, females have coevolved increasingly complex vaginal structures—dead ends, cul-de-sac side pockets, clockwise spirals. We hypothesized that these twists and turns create a mechanical barrier to the penis, frustrating forced intercourse and lowering the likelihood of a female duck being fertilized against her will. Our subsequent experiments—high-speed videos of duck penises erecting into glass tubes of various shapes—suggested we were right. (Our observations also revealed that when a female duck solicits sex with a chosen mate, her cloacal muscles dilate to allow uninhibited entry.) The result is that, even for species in which nearly forty per cent of all copulations are violently coerced, only between two and five per cent of ducklings come from extra-pair matings. As a method of contraception, ducks’ vaginal barriers can be ninety-eight-per-cent effective—a level of reliability that the U.S. Food and Drug Administration would readily approve.

A female duck’s vaginal barriers cannot shield her from physical harm. On an evolutionary level, though, they protect her in another way—by allowing her to choose the father of her offspring. If she has ducklings with her chosen mate, then they will inherit the fancy plumage that she and other females prefer. But, if she is fertilized by force, then her offspring will inherit either random display traits or traits that she has specifically rejected as less attractive. These extra-pair offspring will, on average, be less attractive to their peers, which could mean fewer grand-ducklings for the mother duck—and fewer of her genes passed on to posterity. By using her vaginal barriers, she is able to maintain her sexual autonomy in the face of sexual violence. Freedom of choice, in other words, matters to animals; even if they lack the capacity to conceptualize it, there is an evolutionary difference between having what they want and not having it. Unfortunately for female ducks, though, evolving complex vaginal structures doesn’t solve the scourge of sexual violence; it exacerbates it. Each advance results in males with longer, spikier penises, and the coevolutionary arms race continues.

Although many duck species are trapped in costly and unproductive sexual battles, other birds have pursued different evolutionary paths toward male disarmament. In bowerbirds, for instance, females have used mate choice to transform male behavior in ways that have advanced their own sexual autonomy. Male bowerbirds build elaborate seduction theatres, called bowers, out of sticks, which they decorate with gathered artifacts such as feathers, fruits, and flowers. When the time comes to breed, females visit a number of prospective mates, choosing one based on the attractiveness of the male, his bower, and his ornaments. As a result, the architecture of the bowers is shaped by females’ aesthetic preferences. Males work from a blueprint that actually prevents them from successfully coercing copulations. A so-called avenue bower, for example, features two parallel walls of sticks. The female sits cozily between them while the male does his dance at a safe remove. To copulate with her, he must go around the walls and mount her from behind, which gives her a chance to pop out the front, if she prefers, with her freedom of choice intact.

Scientists admonish one another, often with good reason, to avoid anthropomorphizing animals. But they themselves regularly redraw the line between good science and anthropomorphism as a way of policing scientific discourse and favoring particular ideas. Most of us, for example, learned a strictly adaptationist version of Charles Darwin’s theory of evolution; we were told that almost every feature of the biotic world, no matter how tiny, could be explained by how it contributed to an organism’s ability to survive and reproduce. In fact, though, Darwin also proposed a theory of sexual selection, in which animals may choose their mates according to aesthetic standards—their own subjective desires. This view has frequently been rejected as too anthropomorphic precisely because it implies that sexual selection can act independently of natural selection—an unsettling thought for the typical adaptationist.

When it comes to the sexual politics of birds and people, there are, of course, enormous differences. Birds don’t have elaborate social cultures, money, or any notion of their own histories. Humans do. But, in seeking to understand the complexities of human evolution and sexuality, we can learn a lot by examining the diversity of life on Earth and acknowledging the parallels where they exist.

Consider, for a moment, that the sexual arms race between male and female ducks is not really a fair fight. . .

Continue reading.

Written by LeisureGuy

14 June 2017 at 9:21 am

Posted in Evolution, Science

“The Evolution of Culture,” from Matt Ridley’s The Evolution of Everything

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Here are a few pages from the beginning of Chapter 5 of The Evolution of Everything, by Matt Ridley:

Chapter 5: The Evolution of Culture

And therefore to assume there was one person gave a name
To everything, and that all learned their first words from the same,
Is stuff and nonsense. Why should one human being from among
The rest be able to designate and name things with his tongue
And others not possess the power to do likewise? . . .

Lucretius, De Rerum Natura, Book 5, lines 1041–5

The development of an embryo into a body is perhaps the most beautiful of all demonstrations of spontaneous order. Our understanding of how it happens grows ever less instructional. As Richard Dawkins writes in his book The Greatest Show on Earth, ‘The key point is that there is no choreographer and no leader. Order, organisation, structure – these all emerge as by-products of rules which are obeyed locally and many times over.’ There is no overall plan, just cells reacting to local effects. It is as if an entire city emerged from chaos just because people responded to local incentives in the way they set up their homes and businesses. (Oh, hang on – that is how cities emerged too.)

Look at a bird’s nest: beautifully engineered to provide protection and camouflage to a family of chicks, made to a consistent (but unique) design for each species, yet constructed by the simplest of instincts with no overall plan in mind, just a string of innate urges. I had a fine demonstration of this one year when a mistle thrush tried to build a nest on the metal fire escape outside my office. The result was a disaster, because each step of the fire escape looked identical, so the poor bird kept getting confused about which step it was building its nest on. Five different steps had partly built nests on them, the middle two being closest to completion, but neither fully built. The bird then laid two eggs in one half-nest and one in another. Clearly it was confused by the local cues provided by the fire-escape steps. Its nest-building program depended on simple rules, like ‘Put more material in corner of metal step.’ The tidy nest of a thrush emerges from the most basic of instincts.

Or look at a tree. Its trunk manages to grow in width and strength just as fast as is necessary to bear the weight of its branches, which are themselves a brilliant compromise between strength and flexibility; its leaves are a magnificent solution to the problem of capturing sunlight while absorbing carbon dioxide and losing as little water as possible: they are wafer-thin, feather-light, shaped for maximum exposure to the light, with their pores on the shady underside. The whole structure can stand for hundreds or even thousands of years without collapsing, yet can also grow continuously throughout that time – a dream that lies far beyond the capabilities of human engineers. All this is achieved without a plan, let alone a planner. The tree does not even have a brain. Its design and implementation emerge from the decisions of its trillions of single cells. Compared with animals, plants dare not rely on brain-directed behaviour, because they cannot run away from grazers, and if a grazer ate the brain, it would mean death. So plants can withstand almost any loss, and regenerate easily. They are utterly decentralised. It is as if an entire country’s economy emerged from just the local incentives and responses of its people. (Oh, hang on . . .)

Or take a termite mound in the Australian outback. Tall, buttressed, ventilated and oriented with respect to the sun, it is a perfect system for housing a colony of tiny insects in comfort and gentle warmth – as carefully engineered as any cathedral. Yet there is no engineer. The units in this case are whole termites, rather than cells, but the system is no more centralised than in a tree or an embryo. Each grain of sand or mud that is used to construct the mound is carried to its place by a termite acting under no instruction, and with no plan in (no) mind. The insect is reacting to local signals. It is as if a human language, with all its syntax and grammar, were to emerge spontaneously from the actions of its individual speakers, with nobody laying down the rules. (Oh, hang on . . .)

That is indeed exactly how languages emerged, in just the same fashion that the language of DNA developed – by evolution. Evolution is not confined to systems that run on DNA. One of the great intellectual breakthroughs of recent decades, led by two evolutionary theorists named Rob Boyd and Pete Richerson, is the realisation that Darwin’s mechanism of selective survival resulting in cumulative complexity applies to human culture in all its aspects too. Our habits and our institutions, from language to cities, are constantly changing, and the mechanism of change turns out to be surprisingly Darwinian: it is gradual, undirected, mutational, inexorable, combinatorial, selective and in some vague sense progressive.

Scientists used to object that evolution could not occur in culture because culture did not come in discrete particles, nor did it replicate faithfully or mutate randomly, like DNA. This turns out not to be true. Darwinian change is inevitable in any system of information transmission so long as there is some lumpiness in the things transmitted, some fidelity of transmission and a degree of randomness, or trial and error, in innovation. To say that culture ‘evolves’ is not metaphorical.

The evolution of language

There is an almost perfect parallel between the evolution of DNA sequences and the evolution of written and spoken language. Both consist of linear digital codes. Both evolve by selective survival of sequences generated by at least partly random variation. Both are combinatorial systems capable of generating effectively infinite diversity from a small number of discrete elements. Languages mutate, diversify, evolve by descent with modification and merge in a ballet of unplanned beauty. Yet the end result is structure, and rules of grammar and syntax as rigid and formal as you could want. ‘The formation of different languages, and of distinct species, and the proofs that both have been developed through a gradual process, are curiously parallel,’ wrote Charles Darwin in The Descent of Man.

This makes it possible to think of language as a designed and rule-based thing. And for generations, this was the way foreign languages were taught. At school I learned Latin and Greek as if they were cricket or chess: you can do this, but not that, to verbs, nouns and plurals. A bishop can move diagonally, a batsman can run a leg bye, and a verb can take the accusative. Eight years of this rule-based stuff, taught by some of the finest teachers in the land for longer hours each week than any other topic, and I was far from fluent – indeed, I quickly forgot what little I had learned once I was allowed to abandon Latin and Greek. Top–down language teaching just does not work well – it’s like learning to ride a bicycle in theory, without ever getting on one. Yet a child of two learns English, which has just as many rules and regulations as Latin, indeed rather more, without ever being taught. An adolescent picks up a foreign language, conventions and all, by immersion. Having a training in grammar does not (I reckon) help prepare you for learning a new language much, if at all. It’s been staring us in the face for years: the only way to learn a language is bottom–up.

Language stands as the ultimate example of a spontaneously organised phenomenon. Not only does it evolve by itself, words changing their meaning even as we watch, despite the railings of the mavens, but it is learned, not taught. The prescriptive habit has us all tut-tutting at the decline of language standards, the loss of punctuation and the debasement of vocabulary, but it’s all nonsense. Language is just as rule-based in its newest slang forms, and just as sophisticated as it ever was in ancient Rome. But the rules, now as then, are written from below, not from above.

There are regularities about language evolution that make perfect sense but have never been agreed by committees or recommended by experts. For instance, frequently used words tend to be short, and words get shorter if they are more frequently used: we abbreviate terms if we have to speak them often. This is good – it means less waste of breath, time and paper. And it is an entirely natural, spontaneous phenomenon that we remain largely unaware of. Similarly, common words change only very slowly, whereas rare words can change their meaning and their spelling quite fast. Again, this makes sense – re-engineering the word ‘the’ so it means something different would be a terrific problem for the world’s English-speakers, whereas changing the word ‘prevaricate’ (it used to mean ‘lie’, it now seems mostly to mean ‘procrastinate’) is no big deal, and has happened quite quickly. Nobody thought up this rule; it is the product of evolution.

Languages show other features of evolutionary systems. For instance, as Mark Pagel has pointed out, biological species of animals and plants are more diverse in the tropics, less so near the poles. Indeed, many circumpolar species tend to have huge ranges, covering the whole of an ecosystem in the Arctic or Antarctic, whereas tropical rainforest species might be found in just one small area – a valley or a mountain range or on an island. The rainforest of New Guinea is a menagerie of millions of different species with small ranges, while the tundra of Alaska is home to a handful of species with vast ranges. This is true of plants, insects, birds, mammals, fungi. It’s a sort of iron rule of ecology: that there will be more species, but with smaller ranges, near the equator, and fewer species, but with larger ranges, near the poles.

And here is the fascinating parallel. It is also true of languages. The native tongues spoken in Alaska can be counted on one hand. In New Guinea there are literally thousands of languages, some of which are spoken in just a few valleys and are as different from the languages of the next valley as English is from French. Even this language density is exceeded on the volcanic island of Gaua, part of Vanuatu, which has five different native languages in a population of just over 2,000, despite being a mere thirteen miles in diameter. In forested, mountainous tropical regions, human language diversity is extreme.

One of Pagel’s graphs shows that the decreasing diversity of languages with latitude is almost identical to the decreasing diversity of species with latitude. At present neither trend is easily explained. The great diversity of species in tropical forests has something to do with the greater energy flowing through a tropical ecosystem with plenty of warmth and light and water. It may also have something to do with the abundance of parasites. Tropical creatures are subjected to a constant barrage of parasitic invasions, and being an abundant creature makes you more of a target, so there is an advantage to rarity. And it may reflect a lower extinction rate in a more climatically equable zone. As for languages, the need to migrate with the seasons must homogenise the linguistic diversity of extremely seasonal landscapes, in contrast to tropical ones, where populations can fragment into smaller groups and each can survive without moving. But whatever the explanation, the phenomenon illustrates the way human languages evolve automatically. They are clearly human products, but they are not consciously designed.

Moreover, by studying the history of languages, Pagel finds that when a new language diverges from an ancestral language, it appears to change very rapidly at first. The same seems to be true of species. When a geographical subset of a species becomes isolated it evolves very rapidly at first, so that evolution by natural selection seems to happen in bursts, a phenomenon known as punctuated equilibrium. There are intensely close parallels between the evolution of languages and of species.

Written by LeisureGuy

4 June 2017 at 10:24 pm

Posted in Books, Evolution, Memes, Science

Darwinian Evolution Explains Lamarckism

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Extremely interesting article by Pradeep Mutalik in Quanta:

Our May Insights puzzle was inspired by recent discoveries of some rare, intriguing patterns of inheritance that hark back to Jean-Baptiste Lamarck’s theory of evolution and its emphasis on the “inheritance of acquired characteristics.” Elementary textbooks often present Lamarck’s theory as a failed 19th-century rival to Charles Darwin’s theory of evolution by natural selection. But reality, as usual, is far more complicated. There is indeed a great deal of evidence that most acquired characteristics are not inherited, but as the new findings have shown, this proscription is not absolute. The famous Överkalix study, for example, showed that men who were exposed to a poor food supply between the ages of 9 and 12 were found, two generations later, to have conferred a measurably lower risk of diabetes and cardiovascular death to their grandchildren. Adaptive Lamarckian inheritance does seem to be possible, and epigenetic mechanisms for it have been found. These mechanisms modify DNA in ways that differ from those of heredity.

But at a deeper level this kind of inheritance can be naturally selected for in the traditional Darwinian way, provided certain environmental conditions are satisfied. So Darwinian natural selection remains the fundamental basis of evolution and can produce Lamarckian inheritance: The theories are not rivals after all! Using simple models, our puzzles show how natural selection can sustain Lamarckian inheritance. The requirement is that environmental conditions, such as famines, follow patterns that persist across several generations and are repeated over long stretches of evolutionary time.

Question 1:

Imagine there exists an animal that has a new generation every year. Every normal individual has . . .

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Written by LeisureGuy

2 June 2017 at 7:21 pm

Posted in Evolution, Science

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