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Sherlock

Discovery of jumping gene cluster tangles tree of life


These are Vanderbilt evolutionary biologists Antonis Rokas, right, and Jason Slot.
Since the days of Darwin, the "tree of life" has been the preeminent metaphor for the process of evolution, reflecting the gradual branching and changing of individual species.

The discovery that a large cluster of genes appears to have jumped directly from one species of fungus to another, however, significantly strengthens the argument that a different metaphor, such as a mosaic, may be more appropriate.

"The fungi are telling us something important about evolution ... something we didn't know," said Antonis Rokas, assistant professor of biological sciences at Vanderbilt. He and research associate Jason Slot reported their discovery in the Jan. 25 issue of the journal Current Biology.

Rokas and Slot discovered that millions of years ago, a cluster of 23 genes jumped from one strain of mold commonly found on starchy foods like bread and potatoes, Aspergillus, to another strain of mold that lives in herbivore dung and specializes in breaking down plant fibers, Podospora.

The findings came as a major surprise, as there are only a handful of cases in recent evolutionary history where this type of gene transfer between organisms, known as horizontal gene transfer, has been reported in complex cells like those found in plants, animals and fungi.

"Because most people didn't believe that such large gene clusters could be transferred horizontally, they haven't looked for them and they haven't been found," Rokas said.

Comment: Whereas this article barely touches the gaps and holes in the evolutionary theory, it does raise the issue that species - including human beings - may acquire genetic material from other species other than their own. For more information on this topic, don't miss our next issue of the Dot Connector Magazine where Laura Knight-Jadczyk shares her latest research in the special feature "The Golden Age, Psychopathy and the Sixth Extinction."

Einstein

Time Travel Without Regrets

Time Travel
© iStockphoto/head-off
Groundhog Day for particles. A quantum particle can travel around a loop in time and keep returning to the same moment of interaction with another particle without creating any paradoxes, but it must meet strict consistency criteria.
Time travel is not ruled out by general relativity, but it might well create problems for the laws of common sense. In the 28 January Physical Review Letters, a team proposes a new way of deciding the possibility or impossibility of quantum states that travel forward and backward in time. The new criterion automatically disallows quantum versions of the "grandfather paradox," in which a person travels back in time and kills her ancestor, thereby ensuring her own demise. The team also performed an experiment that illustrates the paradox-nullifying mechanism.

General relativity, Einstein's theory of space and time, allows the existence of closed timelike curves (CTCs)--paths that go forward in time, then back again to reconnect and form closed loops. Although it's unclear whether CTCs can be created, physicists have nevertheless explored their possible consequences, including their influence on quantum mechanics.

An ordinary quantum event might involve two particles moving forward in time, changing each other by interacting at some time, then going their separate ways into the future. However, if one outgoing particle enters a CTC, it can double back and become one of the ingoing particles--thus influencing its own transformation. In 1991, Oxford University physicist David Deutsch proposed a consistency condition to avoid time-travel paradoxes: a particle that loops back in time in this way should be in the same quantum state when in reappears in the immediate past of the interaction as it was when it departed the interaction for the immediate future.[1]
Telescope

NASA Kepler Discovers Six Habitable Planets

NASA's Kepler mission has discovered its first Earth-size planet candidates and its first candidates in the habitable zone, a region where liquid water could exist on a planet's surface. Five of the potential planets are near Earth-size and orbit in the habitable zone of smaller, cooler stars than our Sun.

Candidates require follow-up observations to verify they are actual planets. Kepler also found six confirmed planets orbiting a Sun-like star, Kepler-11. This is the largest group of transiting planets orbiting a single star yet discovered outside our solar system.

"In one generation we have gone from extraterrestrial planets being a mainstay of science fiction, to the present, where Kepler has helped turn science fiction into today's reality," said NASA Administrator Charles Bolden. "These discoveries underscore the importance of NASA's science missions, which consistently increase understanding of our place in the cosmos."
Info

Scientific Evidence Suggests Race is an Artificial Construct

Race
© Charlote Observer
John Mackay, CEO of Discovery Place.

Very few subjects can polarize and fracture a community like race and racism. We like to talk about diversity and being socially aware, and accepting seems to be en vogue in today's world. But without a doubt, a racial divide persists. Recently, here in our own community, issues have grabbed headlines because they've taken on racial tones and exploded into volatile controversies. Economic urgencies add pressure, causing situations to become racially tinged and in turn threatening our community's vitality, something we cannot afford and which will only deepen our disunity.

But what if our fundamental understanding of race were really only skin deep?

On Saturday, Discovery Place will open a new exhibition called RACE: Are We So Different? A project of the American Anthropological Association, the exhibition investigates race through the framework of science, exploring the crossroads of science, history, society and culture as they are all affected by the ideologies of race and racism. RACE contemplates humankind at its core, examining the countless ways we perceive ourselves as individuals, cultures and other social groups.
Sherlock

World's largest prehistoric bear found in Argentina

© Robert Bruce Horsfall 1913
Life restoration of Arctotherium bonariense from W.B. Scott's A History of Land Mammals in the Western Hemisphere. New York: The Macmillan Company
An article in the January issue of the Journal of Paleontology records the discovery of the world's largest bear by paleontologist from Argentina and the United States. The report was made public on Feruary 2, 2011.

The bear stood eleven feet tall and is estimated to have weighed between 3500 and 3855 pounds.

The size of the specimen is related to the lack of competitive species at the time. The bear is dated to the Pleistocene era and could be 500,000 to 2 million years old.

The bear is a South American giant short-faced bear (Arctotherium angustidens).

© Ryan Somma
Arctodus skull
The fossils showed signs of serious injury that may be the result of mating competition or prey activity as a hunter or as prey for the only other carnivore that lived in the region, the saber toothed cat.
Sherlock

DNA caught rock 'n rollin'

DNA, that marvelous, twisty molecule of life, has an alter ego, research at the University of Michigan and the University of California, Irvine reveals.

On rare occasions, its building blocks "rock and roll," deforming the familiar double helix into a different shape.


"We show that the simple DNA double helix exists in an alternative form - for one percent of the time - and that this alternative form is functional," said Hashim M. Al-Hashimi, who is the Robert L. Kuczkowski Professor of Chemistry and Professor of Biophysics at U-M. "Together, these data suggest that there are multiple layers of information stored in the genetic code." The findings were published online Jan. 26 in the journal Nature.

It's been known for some time that the DNA molecule can bend and flex, something like a rope ladder, but throughout these gyrations its building blocks - called bases - remain paired up just the way they were originally described by James Watson and Francis Crick, who proposed the spiral-staircase structure in 1953. By adapting nuclear magnetic resonance (NMR) technology, Al-Hashimi's group was able to observe transient, alternative forms in which some steps on the stairway come apart and reassemble into stable structures other than the typical Watson-Crick base pairs.

The question was, what were these alternative stable structures?
Info

Genetic Study Uncovers New Path to Polynesia

Oceania Map
© Kahuroa / Wikimedia Commons
Micronesia, Melanesia, and Polynesia.

Surprising new evidence which overturns current theories of how humans colonised the Pacific has been discovered by scientists at the University of Leeds.

The islands of Polynesia were first inhabited around 3,000 years ago, but where these people came from has long been a hot topic of debate amongst scientists. The most commonly accepted view, based on archaeological and linguistic evidence as well as genetic studies, is that Pacific islanders were the latter part of a migration south and eastwards from Taiwan which began around 4,000 years ago.

But the Leeds research - published today in The American Journal of Human Genetics - has found that the link to Taiwan does not stand up to scrutiny. In fact, the DNA of current Polynesians can be traced back to migrants from the Asian mainland who had already settled in islands close to New Guinea some 6-8,000 years ago.

The type of DNA extracted and analysed in this kind of study is that stored in the cell's mitochondria. Mitochondrial DNA (mtDNA) is passed down the maternal line, providing a record of inheritance which goes back thousands of years. The scientists look for genetic signatures which enable them to classify the DNA into different lineages and then use a 'molecular clock' to date when these lineages moved into different parts of the world.

Lead researcher, Professor Martin Richards, explains: "Most previous studies looked at a small piece of mtDNA, but for this research we studied 157 complete mitochondrial genomes in addition to smaller samples from over 4,750 people from across Southeast Asia and Polynesia. We also reworked our dating techniques to significantly reduce the margin of error. This means we can be confident that the Polynesian population - at least on the female side - came from people who arrived in the Bismarck Archipelago of Papua New Guinea thousands of years before the supposed migration from Taiwan took place."
Beaker

Progenitor Cell in Zebrafish May Treat Renal Disease

© Summit medical group
Transferring the cell from one zebrafish to another produces nephrons, which are necessary to prevent kidney failure

Researchers at Massachusetts General Hospital, Brigham and Women's Hospital and the University of Pittsburgh have found a cell in zebrafish that could potentially improve kidney function in humans.

Dr. Alan Davidson, from the Center for Regenerative Medicine at the Massachusetts General Hospital, along with Dr. Robert Handin, of the Hematology Division in the Department of Medicine at the Brigham and Women's Hospital, and Dr. Neil Hukriede, of the University of Pittsburgh, have found a cell in zebrafish that could improve human kidney function and help those with a form of renal disease.

Approximately 10 percent of U.S. citizens have a form of renal disease, or kidney failure, where 450,000 patients are experiencing end stage renal disease (ESRD). Thirty-three percent of these patients on dialysis have a five-year survival rate, and the "epidemic" of this disease is expected to increase due to poor nutrition, lack of exercise and obesity leading to diabetes and hypertension. Currently, it costs $32 billion per year to treat ESRD.
Meteor

Extinction, Metamorphosis, Evolutionary Apoptosis, and Genetically Programmed Species Mass Death

© Unknown
Abstract

Genes, cells, and entire species undergo evolutionary apoptosis and are continually pruned from the tree of life. Programmed death is essential to life and evolution, and genetically programmed evolutionary apoptosis is one of the many causes of species death and extinction. Evolution and extinction can be likened to embryogenesis and metamorphosis as all involve the selectively turning on and off of specific genes and nucleotide sequences, the shedding of cells and tissues which are replaced, and dramatic alterations in the organs and skeletal muscular system. "Evolution" is under genetic regulatory control, in coordination with the biological activity of single celled prokaryotes (archae, bacteria, Cyanobactera), their donated and horizontally transferred genes (including those which gave rise to mitochondria), and the genetically engineered environment. The interaction between the environment and genetic activity, the secretion of chemicals, enzymes and gasses such as oxygen and calcium, regulates the emergence of new species, and the elimination of yet others--a form of evolutionary-apoptosis. Genes act on the environment, and the changing environment acts on gene selection, activating specific genes, silencing others, and giving rise to new species which emerge from the old, with entire populations of genes, cells, tissues, and species proliferating and others dying out. Like programmed cell death, extinction is often intrinsic to and necessary for the development, evolution, and metamorphosis of increasingly complex species.
Telescope

NASA's Kepler Spacecraft Discovers Extraordinary New Planetary System

Earth Like System
© NASA/Tim Pyle
Kepler-11 is a sun-like star around which six planets orbit. At times, two or more planets pass in front of the star at once, as shown in this artist's conception of a simultaneous transit of three planets observed by NASA's Kepler spacecraft on Aug. 26, 2010.

Scientists using NASA's Kepler, a space telescope, recently discovered six planets made of a mix of rock and gases orbiting a single sun-like star, known as Kepler-11, which is located approximately 2,000 light years from Earth.

"The Kepler-11 planetary system is amazing," said Jack Lissauer, a planetary scientist and a Kepler science team member at NASA's Ames Research Center, Moffett Field, Calif. "It's amazingly compact, it's amazingly flat, there's an amazingly large number of big planets orbiting close to their star - we didn't know such systems could even exist."

In other words, Kepler-11 has the fullest, most compact planetary system yet discovered beyond our own.

"Few stars are known to have more than one transiting planet, and is the first known star to have more than three," said Lissauer. "So we know that systems like this are not common. There's certainly far fewer than one percent of stars that have systems like Kepler-11. But whether it's one in a thousand, one in ten thousand or one in a million, that we don't know, because we only have observed one of them."

All of the planets orbiting Kepler-11, a yellow dwarf star, are larger than Earth, with the largest ones being comparable in size to Uranus and Neptune. The innermost planet, Kepler-11b, is ten times closer to its star than Earth is to the sun. Moving outwards, the other planets are Kepler-11c, Kepler-11d, Kepler-11e, Kepler-11f, and the outermost planet, Kepler-11g, which is twice as close to its star than Earth is to the sun.

"The five inner planets are all closer to their star than any planet is to our sun and the sixth planet is still fairly close," said Lissauer.
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