Tag Archives: evolution

The Evolution of House Cats

Photo shows Fritz the Cat – see photos Fritz took.

Scientific American has a long and interesting article on: The Evolution of House Cats

It is by turns aloof and affectionate, serene and savage, endearing and exasperating. Despite its mercurial nature, however, the house cat is the most popular pet in the world. A third of American households have feline members, and more than 600 million cats live among humans worldwide.
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Together the transport of cats to the island and the burial of the human with a cat indicate that people had a special, intentional relationship with cats nearly 10,000 years ago in the Middle East. This locale is consistent with the geographic origin we arrived at through our genetic analyses. It appears, then, that cats were being tamed just as humankind was establishing the first settlements in the part of the Middle East known as the Fertile Crescent.
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Over time, wildcats more tolerant of living in human-dominated environments began to proliferate in villages throughout the Fertile Crescent. Selection in this new niche would have been principally for tameness, but competition among cats would also have continued to influence their evolution and limit how pliant they became. Because these proto–domestic cats were undoubtedly mostly left to fend for themselves, their hunting and scavenging skills remained sharp. Even today most domesticated cats are free agents that can easily survive independently of humans, as evinced by the plethora of feral cats in cities, towns and countrysides the world over.
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So are today’s cats truly domesticated? Well, yes—but perhaps only just. Although they satisfy the criterion of tolerating people, most domestic cats are feral and do not rely on people to feed them or to find them mates. And whereas other domesticates, like dogs, look quite distinct from their wild ancestors, the average domestic cat largely retains the wild body plan. It does exhibit a few morphological differences, however—namely, slightly shorter legs, a smaller brain and, as Charles Darwin noted, a longer intestine, which may have been an adaptation to scavenging kitchen scraps.

Cats are Cool 🙂

Intel Science and Engineering Fair 2009 Webcasts

Tara Adiseshan, 14, of Charlottesville, Virginia; Li Boynton, 17, of Houston; and Olivia Schwob, 16, of Boston were selected from 1,563 young scientists from 56 countries, regions and territories for their commitment to innovation and science. Each received a $50,000 scholarship from the Intel Foundation.

(video removed, so the embed code has been removed)

In the webcast, Tara Adiseshan, talks about her project studying the evolutionary ties between nematodes (parasites) and sweat bees. She identified and classified the evolutionary relationships between sweat bees and the nematodes (microscopic worms) that live inside them. Tara was able to prove that because the two have such ecologically intimate relationships, they also have an evolutionary relationship. That is to say, if one species evolves, the other will follow.

Li Boynton developed a biosensor from bioluminescent bacteria (a living organism that gives off light) to detect the presence of contaminants in public water. Li’s biosensor is cheaper and easier to use than current biosensors, and she hopes it can be used in developing countries to reduce water toxicity. Li Boynton on What’s Great About Science:

Olivia Schwob isolated a gene that can be used to improve the intelligence of a worm. The results could help us better understand how humans learn and even prevent, treat and cure mental disabilities in the future.

In addition to the three $50,000 top winners, more than 500 Intel International Science and Engineering Fair participants received scholarships and prizes for their groundbreaking work. Intel awards included 19 “Best of Category” winners who each received a $5,000 Intel scholarship and a new laptop. In total, nearly $4 million is scholarships and awards were provided.

Evolutionary Robotics

Evolutionary Robotics, chapter of Handbook of Robotics, is interesting and includes a good explanation of the difference between evolution and learning:

Evolution and learning (or phylogenetic and ontogenetic
adaptation) are two forms of biological adaptation that differ in space and time. Evolution is a process of selective reproduction and substitution based on the existence of a population of individuals displaying variability at the genetic level. Learning, instead, is a set of modifications taking place within each single individual during its own life time.

Evolution and learning operate on different time scales. Evolution is a form of adaptation capable of capturing relatively slow environmental changes that

might encompass several generations (e.g., the perceptual characteristics of food sources for a given species). Learning, instead, allows an individual to adapt to environmental modifications that are unpredictable at the generational level. Learning might include a variety of mechanisms that produce adaptive changes in an individual during its lifetime, such as physical development, neural maturation, variation of the connectivity between neurons, and synaptic plasticity. Finally, whereas evolution operates on the genotype, learning affects only the phenotype and phenotypic modifications cannot directly modify the genotype.
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Recent research showed that teams of evolved robots can: (a) develop robust and effective behavior, (b) display an ability to differentiate their behavior so
to better cooperate; (c) develop communication capabilities and a shared communication system.

Resurrection of the Human IRGM Gene

Interesting open access paper on Death and Resurrection of the Human IRGM Gene. Author summary:

The IRG gene family plays an important role in defense against intracellular bacteria, and genome-wide association studies have implicated structural variants of the single-copy human IRGM locus as a risk factor for Crohn’s disease. We reconstruct the evolutionary history of this region among primates and show that the ancestral tandem gene family contracted to a single pseudogene within the ancestral lineage of apes and monkeys.

Phylogenetic analyses support a model where the gene has been “dead” for at least 25 million years of human primate evolution but whose ORF became restored in all human and great ape lineages. We suggest that the rebirth or restoration of the gene coincided with the insertion of an endogenous retrovirus, which now serves as the functional promoter driving human gene expression. We suggest that either the gene is not functional in humans or this represents one of the first documented examples of gene death and rebirth.

Darwin’s Jellyfishes

Palau’s marine-lake jellyfish actually diverged very quickly from their common ancestor, the spotted jellyfish. Like other jellyfish, the spotted jellies are cnidarians, a scientific grouping that includes reef-building corals. The spotted jellyfish drift in Palau’s lagoon, zapping the occasional zooplankton with their stinging nettles and absorbing the sugary by-products of photosynthesizing algae living in their tissues.

Like many jelly species, the spotted jellyfish has a multi-stage life cycle. Adult males and females with the familiar bell-shaped bodies are called medusae, but you would not recognize very young jellyfish as jellyfish at all. After medusae release eggs and sperm into the water, fertilized eggs hatch as larvae that drift for a few days before attaching to solid objects, such as rocks. The larvae morph into polyps resembling tiny anemones. Polyps can bud off into more polyps or, when conditions are right, into new young medusae.
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the jellyfish do not “eat” algae. Like their lagoon ancestors, the jellyfish simply absorb their algae’s photosynthetic leftovers. The jellies get about three-fourths of their energy from algal excretions and the remainder from prey. In essence, the jellyfish are landlords that hunt a bit on the side.

The jellyfish-algae partnership did not originate in the lakes, either. Ancestral spotted jellyfish brought the arrangement with them. “Spotted jellyfish in the lagoon have basic behaviors that help ‘sun’ their algae,” Martin explains. “They move eastward in the morning. The lake jellies have adapted this migration to each individual lake. The most spectacular migration is in Jellyfish Lake.”

The jellies’ migration delicately balances time in the sun (to benefit their algae) and predator avoidance. The gelatinous masses of peanut-shaped Jellyfish Lake begin their day in the western basin. As the sun rises they pulsate eastward toward the rising sun—but not too far east, because the lakeshore is covered with jellyfish-eating anemones. The jellies stop swimming east when they hit the shade cast by mangrove trees lining the shore.
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At nightfall the jellies switch to a vertical migration. Jellyfish Lake reaches depths of 100 feet, but only the top 45 feet contain oxygen. The bottom is a toxic vat of hydrogen sulfide. Bacteria do a brisk business at the interface, metabolizing both the oxygen above and hydrogen sulfide below. Every night the jellies bob up and down from the surface to the bacterial layer. Besides helping the jellyfish stay in place, dipping down treats the jellies’ algae to a midnight snack of nutrients excreted by the microbial masses.

Very Cool.

Macropinna Microstoma: Fish with a Transparent Head

That is a pretty awesome fish. The eyes were believed to be fixed in place and seemed to provide only a “tunnel-vision” view of whatever was directly above the fish’s head. A new paper by Bruce Robison and Kim Reisenbichler shows that these unusual eyes can rotate within a transparent shield that covers the fish’s head. This allows the barreleye to peer up at potential prey or focus forward to see what it is eating.

Deep-sea fish have adapted to their pitch-black environment in a variety of amazing ways. Several species of deep-water fishes in the family Opisthoproctidae are called “barreleyes” because their eyes are tubular in shape. Barreleyes typically live near the depth where sunlight from the surface fades to complete blackness. They use their ultra-sensitive tubular eyes to search for the faint silhouettes of prey overhead.

Full press release

Gene Duplication and Evolution

Roughly 10 million years ago, a major genetic change occurred in a common ancestor of gorillas, chimpanzees, and humans. Segments of DNA in its genome began to form duplicate copies at a greater rate than in the past, creating an instability that persists in the genome of modern humans and contributes to diseases like autism and schizophrenia. But that gene duplication also may be responsible for a genetic flexibility that has resulted in some uniquely human characteristics.

“Because of the architecture of the human genome, genetic material is constantly being added and deleted in certain regions,” says Howard Hughes Medical Institute investigator and University of Washington geneticist Evan Eichler, who led the project that uncovered the new findings. “These are really like volcanoes in the genome, blowing out pieces of DNA.”

Eichler and his colleagues focused on the genomes of four different species: macaques, orangutans, chimpanzees, and humans. All are descended from a single ancestral species that lived about 25 million years ago. The line leading to macaques broke off first, so that macaques are the most distantly related to humans in evolutionary terms. Orangutans, chimpanzees, and humans share a common ancestor that lived 12-16 million years ago. Chimps and humans are descended from a common ancestral species that lived about 6 million years ago.

By comparing the DNA sequences of the four species, Eichler and his colleagues identified gene duplications in the lineages leading to these species since they shared a common ancestor. They also were able to estimate when a duplication occurred from the number of species sharing that duplication. For example, a duplication observed in orangutan, chimpanzees, and humans but not in macaques must have occurred sometime after 25 million years ago but before the orangutan lineage branched off.

Eichler’s research team found an especially high rate of duplications in the ancestral species leading to chimps and humans, even though other mutational processes, such as changes in single DNA letters, were slowing down during this period.

Darwin’s Beetles Still Producing Surprises

As part of National Science Foundation-funded research on the evolution of male dimorphism in insects, biology professors J. Mark Rowland, UNM, and Douglas J. Emlen, UM, were surprised to find that many species of beetles are capable of producing not only two, but three different types of males.

The sex lives of animals is known to be complicated business. Where competition in mating is particularly intense, many kinds of animals produce enlarged weapons that function in male combat and utilize alternative tactics in deploying them. Such exaggerated structures include horns in dinosaurs and deer, and tusks in elephants and walrus.

Elaborate male weapons are also known to occur in many types of insects. Now it appears, as the research of Rowland and Emlen illustrates, that male weaponry and alternative mating tactics can be much more complex in the lives of beetles than previously imagined.

“We discovered a novel mating system in which the individual males of various species of beetles have the capacity to express one of three alternative morphologies,” said Rowland. “In many dung beetles , smaller males are unlikely to prevail in direct contests with alpha males. These beta males develop disproportionally smaller horns and employ alternative, less aggressive, reproductive tactics.

“The trimorphic species reported here have alpha, beta and gamma (completely hornless) male – three qualitatively distinct forms. A mating strategy with three such tactics implies considerable complexity, but may actually involve operational rules reminiscent of the old rock, paper, scissors game.”
Continue reading →

Evolution, Methane, Jobs, Food and More

Photo from May 2005 by NASA’s Mars Exploration Rover Spirit as the Sun sank below the rim of Gusev crater on Mars.

Science Friday is a great National Public Radio show. The week was a great show covering Antimicrobial Copper, Top Jobs for Math and Science, Human-Driven Evolution, Methane On Mars, Fish with Mercury and more. This show, in particular did a great job of showing the scientific inquiry process in action.

“Fishing regulations often prescribe the taking of larger fish, and the same often applies to hunting regulations,” said Chris Darimont, one of the authors of the study. “Hunters are instructed not to take smaller animals or those with smaller horns. This is counter to patterns of natural predation, and now we’re seeing the consequences of this management.” Darimont and colleagues found that human predation accelerated the rate of observable trait changes in a species by 300 percent above the pace observed within purely natural systems, and 50 percent above that of systems subject to other human influences, such as pollution

Very interesting stuff, listen for more details. A part of what happens is those individuals that chose to focus on reproducing early (instead of investing in growing larger, to reproduce later) are those that are favored (they gain advantage) by the conditions of human activity. I am amazed how quickly the scientists says the changes in populations are taking place.

And Methane On Mars is another potentially amazing discovery. While it is far from providing proof of live on Mars it is possibly evidence of life on Mars. Which would then be looked back on as one of the most important scientific discoveries ever. And in any even the podcast is a great overview of scientists in action.

This week astronomers reported finding an unexpected gas — methane — in the Martian atmosphere. On Earth, a major source of methane is biological activity. However, planetary scientists aren’t ready to say that life on Mars is to blame for the presence of the gas there, as geochemical processes could also account for the finding. The find is intriguing especially because the researchers say they have detected seasonal variations of methane emissions over specific locations on the planet.

Martian Methane Reveals the Red Planet is not a Dead Planet
The Mars Methane Mystery: Aliens At Last?

So What are Genetic Algorithms?

Genetic Algorithms: Cool Name and Damn Simple is a very nice explanation with python code of genetic algorithms.

What Can Genetic Algorithms Do?
In a word, genetic algorithms optimize. They can find better answers to a question, but not solve new questions. Given the definition of a car, they might create a better car, but they’ll never give you an airplane.
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For each generation we’ll take a portion of the best performing individuals as judged by our fitness function. These high-performers will be the parents of the next generation.

We’ll also randomly select some lesser performing individuals to be parents, because we want to promote genetic diversity. Abandoning the metaphor, one of the dangers of optimization algorithms is getting stuck at a local maximum and consequently being unable to find the real maximum. By including some individuals who are not performing as well, we decrease our likelihood of getting stuck.