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BEST OF SCIENCE

Best of Last Week – New explanation for dark matter, a simulation of the universe and the randomness of cancer

21 hours ago by Bob Yirka report
Dawn spacecraft begins approach to dwarf planet Ceres
This artist’s concept shows NASA’s Dawn spacecraft heading toward the dwarf planet Ceres. Credit: NASA/JPL-Caltech
(Phys.org)—Despite the celebrations leading up to the New Year last week, progress in science marched on—a paper by molecular geneticist Edward Kipreos, with the University of Georgia, for example, describing a study that found a possible alternative explanation for dark energy made news. He suggested that changing the way people think about time dilation might offer an alternative explanation of the mysterious force that drives the expansion of the universe. Also, a team of physicists at City College of New York published a paper describing their work which involved unveiling new half-light, half-matter quantum particles in very thin semiconductors—which could help pave the way to computing technology based on quantum properties of light. And in an interview with Phys.org, Professor David Pines of the University of California and the Santa Fe Institute described a paper he had published with Dr. Yi-feng Yang of the Chinese Academy of Sciences, regarding how a novel experiment-based expression can explain the behavior of unconventional superconductors.

COMSOL Handbook Series

In other news, NASA announced that the Dawn spacecraft began its approach to the dwarf planet Ceres—which is situated between the orbits of Mars and Jupiter in the asteroid belt and holds many secrets which will very soon be revealed. An international team of researchers published a paper in Monthly Notices of the Royal Astronomical Society, describing a simulation of the universe with realistic galaxies they have created—it is called the EAGLE project and they have also released an iPhone app based on one of the simulations.

In an interesting development, a team of researchers at the University of Cape Town Medical School in South Africa, announced that they believe they have found the cause of death of the enigmatic Mrs. Oscar Wilde—complications from surgery meant to cure her of multiple sclerosis. Also interesting were the findings by a pair of researchers who found that those who take part in violent conflict have more wives and children—at least those in an East African herding tribe who engage in violent raids on neighboring groups.

And finally, if you are one of the millions of people who wonder why they or a loved one have been afflicted, a new study suggests that the “bad luck” of random mutations plays a predominant role in cancer. A team at Johns Hopkins Kimmel Cancer Center found that roughly two thirds of cancers come about due to mutations that occur in genes that drive cancer that are not due to inherited genes or the environment—it is just the luck of the draw.

Special Note: You may also be interested in checking out ten of the biggest science and technology stories of 2014 on Phys.org or ten of the top medical research discoveries of 2014 on Medical Xpress.

ADAPTIVE ASSEMBLY?

Very, very interesting. Adaptive assembly without prior instructional encoding. Is it then possible that many amino acids may have a molecularly adaptive equivalency function similar to undifferentiated stem cells (at a higher level) which allows disparate proteins to guide assembly in emergency situations in an almost ad hoc fashion – yet still produce biologically viable proteins?

If so that would mean far more than mere instructional assembly in biological construction and replication, it would mean adaptive biological construction at near the very base level of Life (animate matter).

That could not possibly be accidental for it would mean that base construction rates did not lose adaptive function as they advanced and differentiated but retained such functions (at least as a potential that can be later restimulated) throughout all stages of development.

It would also mean a near plethora of medicinal applications.

This definitely goes into my research files.

Defying Textbook Science, Study Finds New Role for Proteins

Published: January 1, 2015.
Released by University of Utah Health Sciences

Open any introductory biology textbook and one of the first things you’ll learn is that our DNA spells out the instructions for making proteins, tiny machines that do much of the work in our body’s cells. Results from a study published on Jan. 2 in Science defy textbook science, showing for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added.

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“This surprising discovery reflects how incomplete our understanding of biology is,” says first author Peter Shen, Ph.D., a postdoctoral fellow in biochemistry at the University of Utah. “Nature is capable of more than we realize.”

To put the new finding into perspective, it might help to think of the cell as a well-run factory. Ribosomes are machines on a protein assembly line, linking together amino acids in an order specified by the genetic code. When something goes wrong, the ribosome can stall, and a quality control crew is summoned to the site. To clean up the mess, the ribosome is disassembled, the blueprint is discarded, and the partly made protein is recycled.

Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. Before the incomplete protein is recycled, Rqc2 prompts the ribosomes to add just two amino acids (of a total of 20) – alanine and threonine – over and over, and in any order. Think of an auto assembly line that keeps going despite having lost its instructions. It picks up what it can and slaps it on: horn-wheel-wheel-horn-wheel-wheel-wheel-wheel-horn.

“In this case, we have a protein playing a role normally filled by mRNA,” says Adam Frost, M.D., Ph.D., assistant professor at University of California, San Francisco (UCSF) and adjunct professor of biochemistry at the University of Utah. He shares senior authorship with Jonathan Weissman, Ph.D., a Howard Hughes Medical Institute investigator at UCSF, and Onn Brandman, Ph.D., at Stanford University. “I love this story because it blurs the lines of what we thought proteins could do.”

Like a half-made car with extra horns and wheels tacked to one end, a truncated protein with an apparently random sequence of alanines and threonines looks strange, and probably doesn’t work normally. But the nonsensical sequence likely serves specific purposes. The code could signal that the partial protein must be destroyed, or it could be part of a test to see whether the ribosome is working properly. Evidence suggests that either or both of these processes could be faulty in neurodegenerative diseases such as Alzheimer’s, Amyotrophic lateral sclerosis (ALS), or Huntington’s.

“There are many interesting implications of this work and none of them would have been possible if we didn’t follow our curiosity,” says Brandman. “The primary driver of discovery has been exploring what you see, and that’s what we did. There will never be a substitute for that.”

The scientists first considered the unusual phenomenon when they saw evidence of it with their own eyes. They fine-tuned a technique called cryo-electron microscopy to flash freeze, and then visualize, the quality control machinery in action. “We caught Rqc2 in the act,” says Frost. “But the idea was so far-fetched. The onus was on us to prove it.”

It took extensive biochemical analysis to validate their hypothesis. New RNA sequencing techniques showed that the Rqc2/ribosome complex had the potential to add amino acids to stalled proteins because it also bound tRNAs, structures that bring amino acids to the protein assembly line. The specific tRNAs they saw only carry the amino acids alanine and threonine. The clincher came when they determined that the stalled proteins had extensive chains of alanines and threonines added to them.

“Our job now is to determine when and where this process happens, and what happens when it fails,” says Frost.

THE LOBISON

It’s awful weird, but it’s kinda cool too. I have heard much of the 7th son of the 7th son, but never this hairy tale/tail.

President of Argentina adopts Jewish godson to ‘stop him turning into a werewolf’

The tradition to stop stigma about the ‘lobison’ has continued for a century

The President of Argentina has adopted a young Jewish man as her godson to stop him turning into a werewolf.

President Christina Fernández de Kirchner met Yair Tawil and his family at her office last week to mark the unusual ceremony, which dates back more than 100 years.

According to Argentinian folklore, the seventh son born to a family turns into the feared “el lobison”.

The werewolf-like creature shows its true nature on the first Friday after boy’s 13th birthday, the legend says, turning the boy into a demon at midnight during every full moon, doomed to hunt and kill before returning to human form.

As well as feeding on excrement, unbaptized babies, and the flesh of the recently dead, the lobison was said to be unnaturally strong and able to spread its curse with a bite.

Fear of the lobison was so rife in 19th Century Argentina that some families abandoned or even murdered baby boys – an atrocity that sparked the unusual Presidential practice of adoption, aimed at stopping the deadly stigma.

Starting in 1907, the tradition was formally established by a decree in 1973 by Juan Domingo Peron, which also extended the practice to baby girls.
Seventh sons or daughters – now much rarer than 100 years ago – gain the President as their official godparent as well as a gold medal and full educational scholarship.

Even now, reports of dog-like creatures attacking livestock continue, as does the tradition.

Ms Fernandez said Yair is the first Jewish boy to be adopted, as the tradition only applied to Catholic children until 2009.She described her meeting with him and his family on 23 December as a “magical moment”.

Calling the Tawils a “marvellous family” she described Yair as “a total sweety” and dubbed his mother “Queen Esther.”

Shlomo and Nehama Tawil, parents of seven boys, had written the President a letter in 1993 and got their wish this year, the Jewish Telegraphic Agency reported, attending the ceremony with their son and three of his brothers.

Pictures showed them lighting Hanukkah candles together on a menorah from Israel presented to the president by the Tawil family.