Monthly Archives: June 2017

June 7, 2017 (A) Switchgrass root hair growth promotion in the presence of the dark septate endophyte (DSE) fungus, cidomelania panicicola. Warm season C4 grasses such as switchgrass rely on their symbiome to persist in stressful environments such as the Pine Barrens of New Jersey, USA.(B) Symbiosis between the water fern Azolla and the cyanobacteriumAnabaena that involves vertical inheritance of the cyanobacterium via the mega-spore apparatus of the water fern. This is a transverse section of the megaspore apparatus that shows themegaspore (m), the floats (f), and the cyanobacteria (c; red region at the top of the megaspore apparatus).(C) Examples of the obligate lichen symbiosis. Top two rows show examples of lichen species present in the southern Appalachian Mountains. The lower row shows light micrographs of different types of algal associations (indicated witharrows, from L to R: Trebouxia, Trentepohlia, Nostoc) in lichen thalli. Credit: (A) Images prepared by E. Walsh, Rutgers University.(B) Image prepared by H. Schneider.(C) Images by E.A. Tripp and J.C. Lendemer.

In 1859, Charles Darwin included a novel tree of life in his trailblazing book on the theory of evolution, On the Origin of Species. Now, scientists from Rutgers University-New Brunswick and their international collaborators want to reshape Darwin's tree.

A new era in science has emerged without a clear path to portraying the impacts of microbes across the tree of life. What's needed is an interdisciplinary approach to classifying life that incorporates the countless species that depend on each other for health and survival, such as the diverse bacteria that coexist with humans, corals, algae and plants, according to the researchers, whose paper is published online today in the journal Trends in Ecology and Evolution.

"In our opinion, one should not classify the bacteria or fungi associated with a plant species in separate phylogenetic systems (trees of life) because they're one working unit of evolution," said paper senior author Debashish Bhattacharya, distinguished professor, Department of Ecology, Evolution and Natural Resources, in the Rutgers School of Environmental and Biological Studies. "The goal is to transform a two-dimensional tree into one that is multi-dimensional and includes biological interactions among species."

A tree of life has branches showing how diverse forms of life, such as bacteria, plants and animals, evolved and are related to each other. Much of the Earth's biodiversity consists of microbes, such as bacteria, viruses and fungi, and they often interact with plants, animals and other hosts in beneficial or harmful ways. Forms of life that are linked physically and evolve together (i.e. are co-dependent) are called symbiomes, the paper says.

The authors propose a new tree of life framework that incorporates symbiomes. It's called SYMPHY, short for symbiome phylogenetics. The idea is to use sophisticated computational methods to paint a much broader, more inclusive picture of the evolution of organisms and ecosystems. Today's tree of life fails to recognize and include symbiomes. Instead, it largely focuses on individual species and lineages, as if they are independent of other branches of the tree of life, the paper says.

The authors believe that an enhanced tree of life will have broad and likely transformative impacts on many areas of science, technology and society. These include new approaches to dealing with environmental issues, such as invasive species, alternative fuels and sustainable agriculture; new ways of designing and engineering machinery and instruments; enlightened understanding of human health problems; and new approaches to drug discovery.

"By connecting organisms to their microbial partners, we can start detecting patterns of which species associate under specific ecological conditions," Bhattacharya said. "For example, if the same microbe is associated with the roots of very different plants that all share the same kind of habitat (nutrient-poor and high in salt, for example), then we have potentially identified a novel lineage that confers salt and stress tolerance and could be used to inoculate crop plants to provide this valuable trait."

In general, any question that would benefit from the knowledge of species associations in symbiomes could be addressed using SYMPHY, he said.

"We'd actually have trees interacting with trees, and that sort of network allows you to show connections across multiple different organisms and then portray the strength of the interactions between species," he said.

The scientists are calling for the U.S. National Science Foundation, National Natural Science Foundation of China and other funding agencies to support a working group of diverse researchers who would propose plans to create the new SYMPHY system.

"What we wish to clearly stress is that we are not engaged in Darwin-bashing. We consider Darwin a hero of science," Bhattacharya said. "New technologies have brought radical new insights into the complex world of microbial interactions that require a fresh look at how we classify life forms, beyond classical two-dimensional trees."

"We should also aim to unify systematics (methods of classifying life) research under the SYMPHY umbrella so that departments with different specialties, such as zoology, botany, microbiology and entomology, work together to portray how biotic interactions impact species evolution, ecology and organismal biology in general," he added.

Explore further: Microscopic soil creatures could orchestrate massive tree migrations

More information: Trends in Ecology and Evolution (2017). DOI: 10.1016/j.tree.2017.05.002

Warming temperatures are prompting some tree species in the Rocky Mountains to "migrate" to higher elevations in order to survive.

The first ever global database of trees on Wednesday revealed that 9,600 tree species are threatened with extinction and identified a total of 60,065 in existence.

How can we depict diversity? Biologists of the 19th century faced this question as they became aware not only of the huge variety of plant and animal species, but also of the connections between these species. Ultimately ...

A new paper published Jan. 13 in Science reveals that the relationship between soil fungi and tree seedlings is more complicated than previously known. The paper was co-written by Ylva Lekberg, an assistant professor of soil ...

Forests, especially tropical forests, are home to thousands of species of treessometimes tens to hundreds of tree species in the same foresta level of biodiversity ecologists have struggled to explain. In a new study ...

Evolutionary distances that conservationists use to identify and target distinct species may be unreliable, Oxford University research suggests.

Economists agree that natural ecosystems store large quantities of wealth, but the challenge of measuring that wealth has prevented it from being included in typical accounting systems.

According to recent studies, declines in wild and managed bee populations threaten the pollination of flowers in more than 85 percent of flowering plants and 75 percent of agricultural crops worldwide. Widespread and effective ...

In 1859, Charles Darwin included a novel tree of life in his trailblazing book on the theory of evolution, On the Origin of Species. Now, scientists from Rutgers University-New Brunswick and their international collaborators ...

You've been there: Trying to carry on a conversation in a room so noisy that the background chatter threatens to drown out the words you hear. Yet somehow your auditory system is able to home in on the message being conveyed ...

A team led by University of Idaho researchers is calling into question a widely publicized 2016 study that concluded eastern and red wolves are not distinct species, but rather recent hybrids of gray wolves and coyotes. In ...

Worms, it appears, are good at keeping secrets.

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why not a 3d tree, one dimension being genetic relations and another being spacial relations and the third being time

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Scientists propose a new paradigm that paints a more inclusive picture of the evolution of organisms and ecosystems - Phys.Org

Recently, new school rappers primarily Lil Uzi Vert, Jaden Smith, and Young Thug have been criticized for how they dress. Uzi dresses like hes the missing member of The Clash, while Thugger and Jaden have broken gender barriers time and time again sporting dresses and other accessories, but for some reason people are shocked. Why though?

Since the 70s, hip hop has been changing and expanding its identity as more rappers and artists enter the game with their own unique personalities and swag. From MC Hammerss vibrant parachute pants, to Kris Kross rocking their clothes backwards, to Kanye West sporting a leather skirt, rap has always had fearless artist who arent afraid to push the boundaries of fashion. So, for those concerned about what Uzi and Jaden are rocking (were looking at your rap old heads), hip hop has already been doing for decades. They are just continuing the trend.

Lets take a look at the evolution of rule breaking style moments in hip hop fashion.

Before Kanye and Pharrell, Notorious B.I.G. was one of the fashion trendsetters in hip hop. Remember his influential style moments in the video below.

See the rest here:

The Evolution of Hip Hop Style That Broke All the Rules - VH1.com (blog)

June 6, 2017

Around 250 million years ago, terrestrial-bound turtles began to explore the aquatic environments, and with it, a profound, new ability first developed.

Breathable skin, made possible by the loss of their hard shells. Losing the hard shell is a feature that evolved independently in three turtle lineages during the Late Cretaceous, providing greater swimming speed and maneuverability.

And the loss of hard shells at different evolutionary branch points resulted in adaptive changes because of changes in respiration. They could maintain aerobic respiration for longer periods of time, and sustain deeper dives.

Now, scientists Tibisay Escalona, and Agostinho Antunes from the CIIMAR research institute in Porto, Portugal, and Cameron Weadick from Sussex University in Brighton, United Kingdom have traced the origin of these adaptations to different genes that are part of the mitochondrial respiratory complex in soft shelled turtles.

"It's reasonable to hypothesize that turtle mitochondrial DNA-encoded proteins may have undergone adaptive evolutionary changes associated with the loss of shell scutes and the invasion of highly aquatic eco-physiological niches," said the authors.

Mitochondria, which are passed along solely from mothers to offspring, are known as the powerhouses of the cell, responsible for aerobic respiration and 95 percent of the cell's energy currency in the form of ATP.

The research team investigated patterns of evolution in the mitochondrial DNA (mtDNA) protein coding genes across 53 Cryptodiran turtle species (representing a total of 10 families), testing for adaptive or divergent patterns of mtDNA evolution associated with the evolution of soft-shells.

The researchers identified positively selected sites that occurred in the mitochondrial-encoded proteins of the oxidative phosphorylation system byusing various models and mapped these mutations onto the three-dimensional structures of the proteins, and predicted the severity of these structural changes on respiratory function.

They've shown that subtle amino acid changes can have large functional effects and saw the largest changes effecting complex one, the first and the largest domain of the OXPHOS pathway. Complex I, is responsible for an estimated 40 percent of the proton current that drives ATP synthase.

"Our data supports the notion that the adoption of highly aquatic lifestyles in soft-shelled turtles was associated with altered patterns of selection on mitochondrial function. Our analyses thus revealed that positive selection strongly affected mtDNA evolution along two (Trionychidae and Carettochelyidae) of the three lineages associated with the evolution of soft-shells, and that positive selection targeted multiple mtDNA genes in both cases," said the authors.

However, they did not see this adaptation in leatherback sea turtles. Why not? "This suggests that the evolution of a soft-shell in leatherbacks may have been linked to thermoregulation, not respiration, enabling the species to regulate heat gain and loss," said the authors.

Their findings highlight the valuable role of mitochondrial in the larger context of mitochondrial protein biochemistry, human diseases and turtle ecology.

Explore further: How to protect cells from selfish mitochondrial DNA

More information: Molecular Biology And Evolution (2017). DOI: 10.1093/molbev/msx167

Using yeast cells as a model, scientists from the A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University investigated the mechanisms that allow cells to protect themselves from invasion of ...

One of the wonders of evolutionary innovation in animals is the turtle shell, which differs from any other reptilian defense adaptation, giving up teeth or venom in exchange for an impenetrable shield.

In a new study, researchers at the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science examined how the interaction of two genomes in animal cellsthe mitochondrial and nuclear genomesinteract ...

Mitochondria are the power stations of human cells. They provide the energy needed for the cellular metabolism. But how did these power stations evolve, and how are they constructed? Researchers from the University of Freiburg ...

One of the unique and most iconic features of many modern turtles is that they can withdraw their neck and head to hide and protect them within their shells. The group name of species which do this, Cryptodira, even means ...

Through careful study of an ancient ancestor of modern turtles, researchers now have a clearer picture of how the turtles' most unusual shell came to be. The findings, reported on May 30 in Current Biology, help to fill a ...

Economists agree that natural ecosystems store large quantities of wealth, but the challenge of measuring that wealth has prevented it from being included in typical accounting systems.

According to recent studies, declines in wild and managed bee populations threaten the pollination of flowers in more than 85 percent of flowering plants and 75 percent of agricultural crops worldwide. Widespread and effective ...

In 1859, Charles Darwin included a novel tree of life in his trailblazing book on the theory of evolution, On the Origin of Species. Now, scientists from Rutgers University-New Brunswick and their international collaborators ...

You've been there: Trying to carry on a conversation in a room so noisy that the background chatter threatens to drown out the words you hear. Yet somehow your auditory system is able to home in on the message being conveyed ...

A team led by University of Idaho researchers is calling into question a widely publicized 2016 study that concluded eastern and red wolves are not distinct species, but rather recent hybrids of gray wolves and coyotes. In ...

Worms, it appears, are good at keeping secrets.

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New study identifies energy metabolism adaptations linked to soft ... - Phys.Org

My 2000 Mathematical Intelligencer article, A Mathematicians View of Evolution,presented two arguments against Darwinian evolution. The first was the more traditional argument from irreducible complexity showing that, contrary to what Darwin believed, major advances in the evolution of life, like major advances in the evolution of software (I focused on my own partial differential equation solving software), cannot be built up through many very small improvements. I have since written several Evolution News posts on this topic, most recently Why Similarities Do Not Prove the Absence of Design.

The second point was that the development of an advanced civilization on a previously barren planet seems to violate in a most spectacular way the more general statements of the second law of thermodynamics, at least the basic principle underlying this law, even if the Earth is an open system. I have written on this topic for Evolution News numerous times in the last few years, most recently Why Should Evolutionary Biology Be So Different?I have continued to develop this argument further in scientific papers, which have passed peer-review four times (most recently inPhysics Essays), and editor-review twice, as documented in the video below.

Although many other mathematicians and physicists find these arguments persuasive, the understandable reaction of most biologists seems to be, How can you possibly say anything important about evolution without even discussing the details of evolutionary theory? But it is important to remember that this is not a new argument I invented. It is the age-old, intuitive observation that there is something very unnatural about advanced civilizations arising spontaneously on barren planets. My contribution is only to show how absurd is the compensation argument always advanced to silence anyone who draws the obvious conclusions.

Since I am not a biologist, my contributions to the debate about intelligent design versus Darwinism have been limited. Nearly everything I have written since the 2000 MI article has just expanded on one of the two points made there. My latest and clearest such contribution is a video (above) that I produced with the help of my brother Kirk. It presents these same two points, in reverse order: the second law argument is presented in the first 13 minutes.

But I believe anyone who takes the time to watch this video will realize that you can indeed draw some important conclusions about evolution without becoming an expert on evolutionary theory. In fact I think he or she will realize that sometimes it helps to step back from the details and look at the bigger picture, which is what I have always tried to do.

Photo credit: Math professor, by Ed Brambley via Flickr.

Excerpt from:

What Can a Mathematician Contribute to the Evolution Debate? - Discovery Institute