Cornell Engineers Solve a Biological Mystery and Boost Artificial Intelligence

By simulating 25,000 generations of evolution within computers, Cornell University engineering and robotics researchers have discovered why biological networks tend to be organized as modules – a finding that will lead to a deeper understanding of the evolution of complexity.

The new insight also will help evolve artificial intelligence, so robot brains can acquire the grace and cunning of animals.

From brains to gene regulatory networks, many biological entities are organized into modules – dense clusters of interconnected parts within a complex network. For decades biologists have wanted to know why humans, bacteria and other organisms evolved in a modular fashion. Like engineers, nature builds things modularly by building and combining distinct parts, but that does not explain how such modularity evolved in the first place. Renowned biologists Richard Dawkins, Günter P. Wagner, and the late Stephen Jay Gould identified the question of modularity as central to the debate over “the evolution of complexity.”

For years, the prevailing assumption was simply that modules evolved because entities that were modular could respond to change more quickly, and therefore had an adaptive advantage over their non-modular competitors. But that may not be enough to explain the origin of the phenomena.

The team discovered that evolution produces modules not because they produce more adaptable designs, but because modular designs have fewer and shorter network connections, which are costly to build and maintain. As it turned out, it was enough to include a “cost of wiring” to make evolution favor modular architectures.

This theory is detailed in “The Evolutionary Origins of Modularity,” published today in the Proceedings of the Royal Society by Hod Lipson, Cornell associate professor of mechanical and aerospace engineering; Jean-Baptiste Mouret, a robotics and computer science professor at Université Pierre et Marie Curie in Paris; and by Jeff Clune, a former visiting scientist at Cornell and currently an assistant professor of computer science at the University of Wyoming.

Chimpanzees successfully play the Ultimatum Game

Researchers at the Yerkes National Primate Research Center, Emory University, are the first to show chimpanzees possess a sense of fairness that has previously been attributed as uniquely human. Working with colleagues from Georgia State University, the researchers played the Ultimatum Game with the chimpanzees to determine how sensitive the animals are to the reward distribution between two individuals if both need to agree on the outcome.

The researchers say the findings, available in an early online edition of the Proceedings of the National Academy of Sciences (PNAS) available this week, suggest a long evolutionary history of the human aversion to inequity as well as a shared preference for fair outcomes by the common ancestor of humans and apes.

According to first author Darby Proctor, PhD, “We used the Ultimatum Game because it is the gold standard to determine the human sense of fairness. In the game, one individual needs to propose a reward division to another individual and then have that individual accept the proposition before both can obtain the rewards. Humans typically offer generous portions, such as 50 percent of the reward, to their partners, and that’s exactly what we recorded in our study with chimpanzees.”

Co-author Frans de Waal, PhD, adds, “Until our study, the behavioral economics community assumed the Ultimatum Game could not be played with animals or that animals would choose only the most selfish option while playing. We’ve concluded that chimpanzees not only get very close to the human sense of fairness, but the animals may actually have exactly the same preferences as our own species.” For purposes of direct comparison, the study was also conducted separately with human children.

In the study, researchers tested six adult chimpanzees (Pan troglodytes) and 20 human children (ages 2 – 7 years) on a modified Ultimatum Game. One individual chose between two differently colored tokens that, with his or her partner’s cooperation, could be exchanged for rewards (small food rewards for chimpanzees and stickers for children). One token offered equal rewards to both players, whereas the other token favored the individual making the choice at the expense of his or her partner. The chooser then needed to hand the token to the partner, who needed to exchange it with the experimenter for food. This way, both individuals needed to be in agreement.

Both the chimpanzees and the children responded like adult humans typically do. If the partner’s cooperation was required, the chimpanzees and children split the rewards equally. However, with a passive partner, who had no chance to reject the offer, chimpanzees and children chose the selfish option.

Chimpanzees, who are highly cooperative in the wild, likely need to be sensitive to reward distributions in order to reap the benefits of cooperation. Thus, this study opens the door for further explorations into the mechanisms behind this human-like behavior.

Humanity becomes technology

Humanity’s merge with its technology, which began shortly after the taming of fire, is still happening today. Many predict that the fine-tuning of our DNA-based biology through stem cell and genetic research will spark a powerful nanotech revolution that promises to redesign and rebuild our bodies and the environment, pushing the limits of today’s understanding of life and the world we live in.

Nanotech will change our physical world much the same way that computers have transformed our information world. Physical things such as cars and houses could follow the same path of computers, when Moore’s Law correctly predicted value-to-cost would increase by 50% every 18 months.

Existing products that are now expensive, such as photovoltaic solar cells, will become so cheap in the decades ahead, that it may one day be possible to surface roads with solar-collecting materials that would also gather energy to power cars, ending much of the world’s dependency on fossil fuels.

In addition, imagine machines that create clothing, medicine, food and most essentials, with only your voice needed to command the action. Today, such devices are not available, but by early 2030s, experts predict, a home nanofactory will provide most of your family’s needs at little or no cost.

Now bring on the most amazing impending revolution – human-level robots – with intelligence derived from us, but with redesigned bodies that exceed human capabilities. These powerful android creatures expected by 2030, will enable us to tap into their super-computer minds to increase our own intelligence. Constructed with molecular nanotech processes, they will be affordable for every family.

Finally, by mid-century, many people will complete the technology merge by replacing more of their biology with nanomaterials, creating a powerful body that can automatically repair itself when damaged. No more concerns over sickness, accidents, or unwanted death.

Evolution created humanity; humanity created technology, humanity will soon become technology. This is simply our next evolutionary step. Where this trip will take us may be beyond present day knowledge, but whatever the future holds, many people alive today can expect to experience all of its wonders.

Of course, not everyone may hold such a glowing vision of how life may unfold, but for one who has seen so many amazing changes over the past eighty two years, I think it difficult to imagine a negative outcome as we trek through what promises to be an incredible future.

Bonobos will share with strangers before acquaintances

You’re standing in line somewhere and you decide to open a pack of gum. Do you share a piece with the coworker standing to one side of you, or with the stranger on the other?

Most humans would choose the person they know first, if they shared at all.

But bonobos, those notoriously frisky, ardently social great apes of the Congo, prefer to share with a stranger before sharing with an animal they know. In fact, a bonobo will invite a stranger to share a snack while leaving an acquaintance watching helplessly from behind a barrier.

"It seems kind of crazy to us, but bonobos prefer to share with strangers," said Brian Hare, a professor of evolutionary anthropology at Duke University. "They’re trying to extend their social network." And they apparently value that more than maintaining the friendships they already have.

To measure this willingness to share, Hare and graduate student Jingzhi Tan ran a series of experiments with bonobos living in the Lola ya Bonobo sanctuary in Kinshasa, Democratic Republic of Congo. The experiments involved piles of food and enclosures that the test subjects were able to unlock and open. Tan and Hare describe their work in a paper in the January 2, 2013 edition of PLOS ONE.

In the first series of experiments, a pile of food was placed in a central enclosure flanked by two enclosures, each of them holding another animal. The test subject had the knowledge and ability to open a door to either of the other chambers, or both. On one side was a bonobo they knew from their group (not necessarily a friend or family member) and in the other was a bonobo they had never really met, but had only seen at a distance.

Upon entering the chamber with the food, the test subjects could easily just sit down and consume it all themselves, or they could let in one or both of the other animals to share.

Nine of the 14 animals who went through this test released the stranger first. Two preferred their groupmates. Three showed no particular preference in repeated trials. The third animal was often let in on the treat as well, but more often it was the stranger, not the test subject, who opened the door for them.

Tan said that by letting the third animal into the enclosure, the stranger voluntarily outnumbered himself or herself with two bonobos who knew each other, which a chimpanzee would never do. In 51 trials of the experiment, there was never any aggression shown, although there was quite a bit of typical bonobo genital rubbing between the strangers.

To isolate how much motivation the animals receive from social interaction, the researchers ran a second set of experiments in which the subject animal wouldn’t receive any social contact with another animal. In the first of these experiments, the subjects couldn’t get any food for themselves regardless of whether they chose to open the door to allow the other animal to get some food. Nine out of ten animals shared with the stranger at least once.

In the final experiment without social contact, the subject animal was given access to the food in such a way that opening the door to share with the other animal would cost them some food. But they still wouldn’t have any social contact as a reward. In this instance, the animals chose not to share. “If they’re not going to see a social benefit, they won’t share,” Hare said.

This second test is similar to something called the dictator game in which humans are given the chance to share cash with a stranger, Hare said. Most people will share anonymously, but they share even more when they aren’t anonymous. Bonobos won’t share at all in the anonymous condition if it costs them food.

"They care about others," Hare said, but only in a sort of selfish way. "They’ll share when it’s a low-cost/low-benefit kind of situation. But when it’s a no-benefit situation, they won’t share. That’s different from a human playing the dictator game. You really have to care about others to give anonymously."

The findings, which Hare calls “one of the crazier things we’ve found” in more than a decade of bonobo research, form yet another distinction between bonobos and chimpanzees, our two closest relatives. “Chimps can’t do these tests, they’d be all over each other.”

Are Babies Born Good?

Arber Tasimi is a 23-year-old researcher at Yale University’s Infant Cognition Center, where he studies the moral inclinations of babies—how the littlest children understand right and wrong, before language and culture exert their deep influence.“What are we at our core, before anything, before everything?” he asks. His experiments draw on the work of Jean Piaget, Noam Chomsky, his own undergraduate thesis at the University of Pennsylvania and what happened to him in New Haven, Connecticut, one Friday night last February.

It was about 9:45 p.m., and Tasimi and a friend were strolling home from dinner at Buffalo Wild Wings. Just a few hundred feet from his apartment building, he passed a group of young men in jeans and hoodies. Tasimi barely noticed them, until one landed a punch to the back of his head.

There was no time to run. The teenagers, ignoring his friend, wordlessly surrounded Tasimi, who had crumpled to the brick sidewalk. “It was seven guys versus one aspiring PhD,” he remembers. “I started counting punches, one, two, three, four, five, six, seven. Somewhere along the way, a knife came out.” The blade slashed through his winter coat, just missing his skin.

At last the attackers ran, leaving Tasimi prone and weeping on the sidewalk, his left arm broken. Police later said he was likely the random victim of a gang initiation.

After surgeons inserted a metal rod in his arm, Tasimi moved back home with his parents in Waterbury, Conn­­ecticut, about 35 minutes from New Haven, and became a creature much like the babies whose social lives he studies. He couldn’t shower on his own. His mom washed him and tied his shoes. His sister cut his meat.

Spring came. One beautiful afternoon, the temperature soared into the 70s and Tasimi, whose purple and yellow bruises were still healing, worked up the courage to stroll outside by himself for the first time. He went for a walk on a nearby jogging trail. He tried not to notice the two teenagers who seemed to be following him. “Stop ca­tastrophizing,” he told himself again and again, up until the moment the boys demanded his headphones.

The mugging wasn’t violent but it broke his spirit. Now the whole world seemed menacing. When he at last resumed his morality studies at the Infant Cognition Center, he parked his car on the street, feeding the meter every few hours rather than risking a shadowy parking garage.

“I’ve never been this low in life,” he told me when we first met at the baby lab a few weeks after the second crime. “You can’t help wonder: Are we a failed species?”

At times, he said, “only my research gives me hope.”

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Human Intelligence Secrets Revealed by Chimp Brains

Despite sharing 98 percent of our DNA with chimpanzees, humans have much bigger brains and are, as a species, much more intelligent. Now a new study sheds light on why: Unlike chimps, humans undergo a massive explosion in white matter growth, or the connections between brain cells, in the first two years of life.

The new results, published in the Proceedings of the Royal Society B, partly explain why humans are so much brainier than our nearest living relatives. But they also reveal why the first two years of life play such a key role in human development.

"What’s really unique about us is that our brains experience rapid establishment of connectivity in the first two years of life," said Chet Sherwood, an evolutionary neuroscientist at George Washington University, who was not involved in the study. "That probably helps to explain why those first few years of human life are so critical to set us on the course to language acquisition, cultural knowledge and all those things that make us human."

Chimpanzees

While past studies have shown that human brains go through a rapid expansion in connectivity, it wasn’t clear that was unique amongst great apes (a group that includes chimps, gorillas, orangutans and humans). To prove it was the signature of humanity’s superior intelligence, researchers would need to prove it was different from that in our closest living relatives.

However, a U.S. moratorium on acquiring new chimpanzees for medical research meant that people like Sherwood, who is trying to understand chimpanzee brain development, had to study decades-old baby chimpanzee brains that were lying around in veterinary pathologists’ labs, Sherwood told LiveScience.

But in Japan, those limitations didn’t go into place till later, allowing the researchers to do live magnetic resonance imaging (MRI) brain scans of three baby chimps as they grew to 6 years of age. They then compared the data with existing brain-imaging scans for six macaques and 28 Japanese children.

The researchers found that chimpanzees and humans both had much more brain development in early life than macaques.

"The increase in total cerebral volume during early infancy and the juvenile stage in chimpanzees and humans was approximately three times greater than that in macaques," the researchers wrote in the journal article.

But human brains expanded much more dramatically than chimpanzee brains during the first few years of life; most of that human-brain expansion was driven by explosive growth in the connections between brain cells, which manifests itself in an expansion in white matter. Chimpanzee brain volumes ballooned about half that of humans’ expansion during that time period.

The findings, while not unexpected, are unique because the researchers followed the same individual chimpanzees over time; past studies have instead pieced together brain development from scans on several apes of different ages, Sherwood said.

The explosion in white matter may also explain why experiences during the first few years of life can greatly affect children’s IQ, social life and long-term response to stress.

"That opens an opportunity for environment and social experience to influence the molding of connectivity," Sherwood said.

Evolution: It’s all in how you splice it

MIT biologists find that alternative splicing of RNA rewires signaling in different tissues and may often contribute to species differences.

When genes were first discovered, the canonical view was that each gene encodes a unique protein. However, biologists later found that segments of genes can be combined in different ways, giving rise to many different proteins.

This phenomenon, known as alternative RNA splicing, often alters the outputs of signaling networks in different tissues and may contribute disproportionately to differences between species, according to a new study from MIT biologists.

After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns — which determine the segments of those genes included or excluded — vary from species to species.

“The core things that make a heart a heart are mostly determined by a heart-specific gene expression signature. But the core things that make a mouse a mouse may disproportionately derive from splicing patterns that differ from those of rats or other mammals” says Chris Burge, an MIT professor of biology and biological engineering, and senior author of a paper on the findings in the Dec. 20 online edition of Science.

Lead author of the paper is MIT biology graduate student Jason Merkin. Other authors are Caitlin Russell, a former technician in Burge’s lab, and Ping Chen, a visiting grad student at MIT.

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Researchers uncover major source of evolutionary differences among species

University of Toronto Faculty of Medicine researchers have uncovered a genetic basis for fundamental differences between humans and other vertebrates that could also help explain why humans are susceptible to diseases not found in other species.

Scientists have wondered why vertebrate species, which look and behave very differently from one another, nevertheless share very similar repertoires of genes. For example, despite obvious physical differences, humans and chimpanzees share a nearly identical set of genes.

The team sequenced and compared the composition of hundreds of thousands of genetic messages in equivalent organs, such as brain, heart and liver, from 10 different vertebrate species, ranging from human to frog. They found that alternative splicing — a process by which a single gene can give rise to multiple proteins — has dramatically changed the structure and complexity of genetic messages during vertebrate evolution.

The results suggest that differences in the ways genetic messages are spliced have played a major role in the evolution of fundamental characteristics of species. However, the same process that makes species look different from one another could also account for differences in their disease susceptibility.

"The same genetic mechanisms responsible for a species’ identity could help scientists understand why humans are prone to certain diseases such as Alzheimer’s and particular types of cancer that are not found in other species," says Nuno Barbosa-Morais, the study’s lead author and a computational biologist in U of T Faculty of Medicine’s Donnelly Centre for Cellular and Biomolecular Research. "Our research may lead to the design of improved approaches to study and treat human diseases."

One of the team’s major findings is that the alternative splicing process is more complex in humans and other primates compared to species such as mouse, chicken and frog.

"Our observations provide new insight into the genetic basis of complexity of organs such as the human brain," says Benjamin Blencowe, Professor in U of T’s Banting and Best Department of Research and the Department of Molecular Genetics, and the study’s senior author.

"The fact that alternative splicing is very different even between closely related vertebrate species could ultimately help explain how we are unique."

Human hands have ‘evolved for fighting’