The First Images of Molecules Breaking and Reforming Chemical Bonds

Microscopy is advancing in leaps and bounds these days. It was just last week that scientists produced the first image of a hydrogen atom’s orbital structure. Not to be outdone, Berkeley chemists have now captured a series of images showing molecules as they break and reform their chemical bonds. It looks almost... textbook.

Holy crap, is it incredible when scientists present actual, tangible visual evidence to reaffirm theoretical models. As any chemistry student knows, molecular bonds, or covalent bond structures, are typically represented in science class with a stick-like nomenclature. But as the work of Felix Fischer, Dimas de Oteyza and their Berkeley Lab colleagues beautifully demonstrates, these models are startlingly accurate.

And like so many good scientific discoveries, it all happened somewhat by accident.

The Berkeley scientists were actually working on a way to precisely assemble nanostructures made from graphene using a new cutting-edge approach to chemical reactions. They were trying to build a single-layer material in which carbon atoms are arranged in repeating, hexagonal patterns — but they needed to take a closer look to see what was happening at the single-atom level. So, they pulled out a powerful atomic force microscope — and what they saw was “amazing,” to quote Fischer.

In this image you can see the positions of individual atoms and bonds in a molecule having 26 carbon atoms and 14 hydrogen atoms structured as three connected benzene rings.

Specifically, they managed to capture the specific outcomes of the reactions themselves — a totally unexpected and happy consequence of the research.

“Nobody has ever taken direct, single-bond-resolved images of individual molecules, right before and immediately after a complex organic reaction,” Fischer noted through a release.

To create the image, the researchers used the fine tip of the non-contact atomic force microscope to “feel” or read the electrical forces produced by the molecules. Each time the tip moved near a molecule’s surface, it was deflected by the different charges. The resulting movements of the stylus were detected by a laser beam, which in turn provided the data required to produce an image of how the atoms and bonds were aligned. What’s more, they were also able to visualize the bonds between them.

Taking a look at the top image, you can see the original molecule at left before the reaction takes place. At right, the two most common final products of the reaction are shown. The clumps are about a billionth of a meter across (3 angstroms).

You can read the entire study at the journal Science: “Direct Imaging of Covalent Bond Structure in Single-Molecule Chemical Reactions.”

via io9

World's Oldest Primate Fossil Discovered

A tiny, beady-eyed, long-tailed primate with hand-like feet is now the world’s oldest known fossil primate skeleton. In a study to be released in the journal Nature this week, an international team of researchers describe their discovery of the Archicebus achilles and how it’s adding to what we understand about our own evolution.

The Archicebus achilles--named for its long tail and strange feet--was found in an ancient lakebed in China. The lack of oxygen at the bottom of the lake means that this specimen is remarkably complete and well-preserved. Recovered from sedimentary rock strata deposited in an ancient lake roughly 55 million years ago, this fossil is the oldest primate fossil, beating the previous record-holders--including Darwinius from Messel in Germany and Notharctus from the Bridger Basin in Wyoming --by 7 million years.

“It’s not just that it’s the oldest primate, but it turns out that this fossil tells us that primates had already been evolving for quite some time. This primate was already fairly advanced in terms of the evolutionary tree,” says Christopher Beard, a coauthor of the study and paleontologist from the Carnegie Museum of Natural History.

The Archicebus sits at a branch of the evolutionary tree, which goes in two directions: one toward living tarsiers—large-eyed night-dwelling small primates—and anthropoids, the monkeys, apes and humans, which have smaller eyes and are most active during the day.

This is the first time that we have had such a complete picture of the divergence between these two branches.

“Any time you find a specimen like this, it’s a bit special. It’s adding a lot of depth of history,” says John Flynn, another coauthor and curator for the American Museum of Natural History.

Given Archicebus’s size—weighing about an ounce and measuring 7 to 9 inches long including the tail—and its basal evolutionary position, this discover supports the idea that the common ancestor of both tarsiers and anthropoids were quite small. These two branches, anthropoids and tarsiers, have been thought to be evolutionarily linked for some time, and now scientists are starting to understand the age of that split.

Beyond its addition to our understanding of evolution, the ancient primate is also unique in its physique. One of the most curious characteristics of the Archicebus is its feet. Tarsiers tend to have elongated heel bones, which help give them leverage for their giant leaps. Anthropoids have feet specially designed for grasping—though humans are a bit of a special case, given our unique disposition of walking bipedally.

“I was convinced pretty early on by the foot of this creature, which looked like nothing else but a little marmoset, which is a type of monkey from South America. I was convinced this thing was going to be a very primitive anthropoid,” Beard says. “Here’s an animal that combines features that we’ve just never seen before in one fossil primate.”

But after the exhaustive analysis, it became clear that Archicebus was also closely linked to tarsiers.

To fully analyze the fragile fossil, researchers collaborated with the European Synchrotron Radiation Facility in Grenoble, France. Using a high-intensity X-ray beam, the Synchrotron scanned the fossil, producing high-resolution data. This data was then rendered into 3-D versions to be analyzed and compared with other primates, both living and fossilized.

The analysis and data-gathering was one of the longest and most extensive phases of the study. Researchers created a matrix that included data from more than 150 species and more than 2,000 different characteristics. All told, the process took 10 years and required collaboration from many institutions internationally. But the patience and practice is now finally paying off.

“[The Archicebus is like] what we find so often in paleontology, but we can never predict it, and that’s an animal that’s unlike everything else we’ve ever seen,” Beard says. “It’s a kind of hybrid or mosaic of different features that are found in different animals today, but never together in one. It’s truly a unique creature.”

via PopSci

Life-Producing Phosphorus Carried to Earth by Meteorites

We are wondering whether there is life living in outer space and researches are continuing to provide information about the question. Now new research from a team of scientists led by a University of South Florida astrobiologist now shows that one key element that produced life on Earth was carried here on meteorites.

In an article published in the new edition of the Proceedings of the National Academy of Sciences, USF Assistant Professor of Geology Matthew Pasek and researchers from the University of Washington and the Edinburg Centre for Carbon Innovation, revealed new findings that explain how the reactive phosphorus that was an essential component for creating the earliest life forms came to Earth.

The scientists found that during the Hadean and Archean eons -- the first of the four principal eons of Earth's earliest history -- the heavy bombardment of meteorites provided reactive phosphorus that when released in water could be incorporated into prebiotic molecules. The scientists documented the phosphorus in early Archean limestone, showing it was abundant some 3.5 billion years ago.

The scientists concluded that the meteorites delivered phosphorus in minerals that are not seen on the surface of Earth, and these minerals corroded in water to release phosphorus in a form seen only on the early Earth.

Via ScienceDaily

Artificial Magnetic Monopoles Discovered

A team of researchers from Cologne, Munich and Dresden have managed to create artificial magnetic monopoles. To do this, the scientists merged tiny magnetic whirls, so-called skyrmions. At the point of merging, the physicists were able to create a monopole, which has similar characteristics to a fundamental particle postulated by Paul Dirac in 1931. In addition to fundamental research, the monopoles may also have application potential. The question of whether magnetic whirls can be used in the production of computer components one day is currently being researched by a number of groups worldwide.

via ScienceDaily

Scientists Capture First Images of Molecules Before and After Reaction

Every chemist's dream -- to snap an atomic-scale picture of a chemical before and after it reacts -- has now come true, thanks to a new technique developed by chemists and physicists at the University of California, Berkeley.

Using a state-of-the-art atomic force microscope, the scientists have taken the first atom-by-atom pictures, including images of the chemical bonds between atoms, clearly depicting how a molecule's structure changed during a reaction. Until now, scientists have only been able to infer this type of information from spectroscopic analysis.

The ability to image molecular reactions in this way will help not only chemistry students as they study chemical structures and reactions, but will also show chemists for the first time the products of their reactions and help them fine-tune the reactions to get the products they want. Fischer, along with collaborator Michael Crommie, a UC Berkeley professor of physics, captured these images with the goal of building new graphene nanostructures, a hot area of research today for materials scientists because of their potential application in next-generation computers.

via ScienceDaily

Brain overload explains lack of memories during childhood

It is hard to understand why we don’t remember anything that happened before age 3. Even some momentous event in a toddler’s life has not left behind a wisp of memories.

Scientist call this phenomenon “infantile amnesia”. Now a new study, which was presented Friday at the annual meeting of the Canadian Association for Neuroscience, finds that “infantile amnesia” may be due to the rapid growth of nerve cells in the hippocampus, the brain region responsible for filing new experiences into long-term memory.

Normally youngsters do seem to remember important events for a short time after they occur, they lose these memories as time goes by.

Scientists have guessed that the hippocampus had something to do with the puzzle, says Dr. Eric Kandel, Kavli professor and director of the Kavli Institute for Brain Science at Columbia University and senior investigator at the Howard Hughes Medical Institute. But nobody really knew the mechanism of what happens in a toddler’s brain.

They did experiment to test the theory and found that it seemed like a case of overload that cause the phenomenon. The hippocampus has two jobs: to make a sort of tape recording of each event and then to file that tape recording away in long-term storage, with flags that allow the person to retrieve it. With all the energy spent making new neurons, the filing never gets done.

Ancient Plants Reawaken: Plants Exposed by Retreating Glaciers Regrowing After Centuries Entombed Under Ice

La Farge, a researcher in the Faculty of Science, and director and curator of the Cryptogamic Herbarium at the University of Alberta, has overturned a long-held assumption that all of the plant remains exposed by retreating polar glaciers are dead. Previously, any new growth of plants close to the glacier margin was considered the result of rapid colonization by modern plants surrounding the glacier.

Using radiocarbon dating, La Farge and her co-authors confirmed that the plants, which ranged from 400 to 600 years old, were entombed during the Little Ice Age that happened between 1550 and 1850. In the field, La Farge noticed that the subglacial populations were not only intact, but also in pristine condition -- with some suggesting regrowth.

In the lab, La Farge and her master's student Krista Williams selected 24 subglacial samples for culture experiments. Seven of these samples produced 11 cultures that successfully regenerated four species from the original parent material.

La Farge says the regrowth of these Little Ice Age bryophytes (such as mosses and liverworts) expands our understanding of glacier ecosystems as biological reservoirs that are becoming increasingly important with global ice retreat. "We know that bryophytes can remain dormant for many years (for example, in deserts) and then are reactivated, but nobody expected them to rejuvenate after nearly 400 years beneath a glacier.

"These simple, efficient plants, which have been around for more than 400 million years, have evolved a unique biology for optimal resilience," she adds. "Any bryophyte cell can reprogram itself to initiate the development of an entire new plant. This is equivalent to stem cells in faunal systems."

La Farge says the finding amplifies the critical role of bryophytes in polar environments and has implications for all permafrost regions of the globe.

"Bryophytes are extremophiles that can thrive where other plants don't, hence they play a vital role in the establishment, colonization and maintenance of polar ecosystems. This discovery emphasizes the importance of research that helps us understand the natural world, given how little we still know about polar ecosystems -- with applied spinoffs for understanding reclamation that we may never have anticipated."

via ScienceDaily