Tag Archives: spectroscopy

You’re being duped with counterfeit wine — but this machine-learning approach can save you

Wine fraud — it’s a real thing. But new research from the University of Adelaide promises to offer a fast and reliable method of verifying the authenticity of any bottle out there.

Image credits Dirk Wohlrabe.

How would we ever have gone through this year if it wasn’t for trusty old wine (or any similarly inebriating drink)? But there’s a lot of counterfeit wine on the market, with the sale of such products estimated to be worth billions of dollars each year globally. The team wanted to produce a quick, cheap, and reliable method of testing the authenticity of wines, both to protect the health and interests of clients and to give wine-makers a means of building regional branding.

They successfully applied a novel technique of molecular fingerprinting using fluorescence spectroscopy to identify the geographical origins of three wine regions in Australia and the Bordeaux region of France with 100% accuracy.

Verum vino

“Wine fraud is a significant problem for the global wine industry, given a yearly economic impact within Australia alone estimated at several hundred million dollars, and globally thought to be in the billions of dollars,” says Ruchira Ranaweera, a Ph.D. student in the University’s Waite Research Institute, who conducted the research.

“Wine authentication can help to avoid any uncertainty around wine labeling according to the origin, variety, or vintage. The application of a relatively simple technique like this could be adapted for use in the supply chain as a robust method for authentication or detection of adulterated wines.”

The team compared their method to a pre-existing authentication approach, the ‘inductively coupled plasma-mass spectrometry’ (ICP-MS). ICP-MS works by measuring the ratios of different chemical components in a wine sample but is more complicated, slow, and expensive to apply than the new method.

The authors explain that the fluorescence spectroscopy technique generates a ‘fingerprint’ for each sample based on the presence of light-emitting (fluorophoric) compounds therein. This data is then fed into a data-analyzing algorithm that gauges a wine’s origin based on its chemical characteristics. Every wine they tasted this way was correctly identified by the program, but not so with the elements identified by ICP-MS, they explain.

“Other than coming up with a robust method for authenticity testing, we are hoping to use the chemical information obtained from fluorescence data to identify the molecules that are differentiating the wines from the different regions,” says Associate Professor Jeffery from the Waite Research Institute and the ARC Training Centre for Innovative Wine Production, who led the project.

“This may help with regional branding, by understanding how their wines’ characteristics are influenced by the region and how they differ from other regions.”

Ultimately, he explains, such techniques should allow us to identify the chemical markers that are characteristic to individual wine regions. Perhaps in time, they will also help us identify exactly which components give products from each winemaking region their unique personality.

The paper “Authentication of the geographical origin of Australian Cabernet Sauvignon wines using spectrofluorometric and multi-element analyses with multivariate statistical modelling” has been published in the journal Food Chemistry.

Artist's composition of a volcanic exo-Io undergoing extreme mass loss. The hidden exomoon is enshrouded in an irradiated gas cloud shining in bright orange-yellow, as would be seen with a sodium filter. Patches of sodium clouds are seen to trail the lunar orbit, possibly driven by the gas giant's magnetosphere. (© University of Bern, Illustration: Thibaut Roger)

Astronomers find clues of a volcanically active exomoon

Artist’s composition of a volcanic exo-Io undergoing extreme mass loss. The hidden exomoon is enshrouded in an irradiated gas cloud shining in bright orange-yellow, as would be seen with a sodium filter. Patches of sodium clouds are seen to trail the lunar orbit, possibly driven by the gas giant’s magnetosphere. (© University of Bern, Illustration: Thibaut Roger)

A rocky extrasolar moon brimming with lava could orbit a planet 550 light-years from Earth, astronomers led by researchers from Bern University have discovered. 

The volcanically active exomoon could be hidden in the exoplanet system WASP-49b, orbiting a hot giant planet in the inconspicuous constellation of Lepus, underneath the bright Orion constellation.

The researchers describe the exomoon as an ‘extreme’ version of Jupiter’s moon Io — the most volcanically active body in our own solar system. Thus, painting a picture of an exotic and dangerous world — an ‘exo-Io’. 

Apurva Oza, a postdoctoral fellow at the Physics Insitute of the University of Bern and associate of the NCCR PlanetS, describes the exomoon, comparing it to a famous sci-fi setting: “It would be a dangerous volcanic world with a molten surface of lava — a lunar version of close-in Super-Earths like 55 Cancri-e. 

“A place where Jedis go to die, perilously familiar to Anakin Skywalker.”

More than a grain of sodium. Uniting theory and circumstantial evidence.

Astronomers have yet to discover a moon beyond our solar system meaning that the researchers base their suspicions of the existence of this exo-Io on circumstantial evidence — namely sodium gas in WASP-49b at an unusually high-altitude. 

Oza explains: “The neutral sodium gas is so far away from the planet that it is unlikely to be emitted solely by a planetary wind.

“The sodium is right where it should be.”

Comparing this feature to observations of the Jupiter and Io system using low-mass calculations demonstrated to the team that an exo-Io could, indeed, be a plausible mechanism for sodium at WASP-49b. 

The theory that large amounts of sodium around an exoplanet could point to a hidden moon or a ring of material was advance by Bob Johnson and Patrick Huggins in 2006. Following this, researchers from the University of Virginia calculated that a three-body system comprised of a star, close giant planet and a moon could remain stable for billions of years. 

Oza took these theoretical predictions to form the basis of he and his colleagues’ work — published in the Astrophysical Journal. 

The astrophysicist explains: “The enormous tidal forces in such a system are the key to everything.

“The energy released by the tides to the planet and its moon keeps the moon’s orbit stable, simultaneously heating it up and making it volcanically active.”

The researchers also demonstrate in their study that a small rocky moon would eject more sodium and potassium into space via this extreme volcanism than a large gas planet. This would especially be the case at high altitudes. 

These emissions can then be identified by astronomers using the technique of spectroscopy. These particular elements are particularly useful to astronomers. 

Oza adds: “Sodium and potassium lines are quantum treasures to us astronomers because they are extremely bright.

“The vintage street lamps that light up our streets with yellow haze, is akin to the gas we are now detecting in the spectra of a dozen exoplanets.”

When comparing their calculations with actual observations of sodium and potassium, the team found five candidate systems where a hidden exomoon could survive thermal evaporation. In the case of WASP-49b, the best explanation for the observed data was the presence of an exo-Io. 

This isn’t the only explanation, however. As mention above, the observations of sodium at high altitudes could instead indicate the exoplanet is surrounded by a ring of material — most likely ionised gas. 

Oza admits that the team need to find more clues, and as such, are relying on future observations with both ground and space-based telescopes. Also, as a few of these exo-Ios could eventually be destroyed as a result of extreme mass-loss, the team also want to search for evidence of such destruction. 

Oza concludes: “While the current wave of research is going towards habitability and biosignatures, our signature is a signature of destruction.

“The exciting part is that we can monitor these destructive processes in real-time, like fireworks.”

Original research: https://arxiv.org/pdf/1908.10732.pdf

Physicists observe the light spectrum of antimatter for the first time

After two decades of experiments, scientists working at CERN‘s ALPHA experiment have finally visualized the light spectrum emitted by antimatter, fulfilling a long-standing goal of particle research.

Measuring the antihydrogen spectrum with high-precision offers an extraordinary new tool to test whether matter behaves differently from antimatter and thus to further test the robustness of the Standard Model (Image: Maximilien Brice/CERN)

“This represents a historic point in the decades-long efforts to create antimatter and compare its properties to those of matter,” theoretical physicist Alan Kostelecky from Indiana University, who was not involved in the study, told NPR.

“Using a laser to observe a transition in antihydrogen and comparing it to hydrogen to see if they obey the same laws of physics has always been a key goal of antimatter research,” said Jeffrey Hangst, Spokesperson of the ALPHA collaboration.

Antimatter is a strange thing. It is a material composed of anti-particles with the same mass as ordinary particles but opposite charges, lepton numbers, and baryon numbers (leptons and baryons are subatomic particles). As the name puts it, they are similar but exactly opposite to regular matter. A mirror reflection, so to speak. We know antimatter exists, we’ve seen it in the lab, but why the universe is filled with matter and virtually completely devoid of antimatter is anyone’s guess. The fact that antimatter is so hard and expensive to produce in a lab makes it even harder to study this mystery – and yet, modern particle theory predicts that every single particle in the universe has its own opposite antiparticle. This is one of the biggest unsolved problems in physics.

Antimatter spectrum

Atoms consist of electrons orbiting around a nucleus. When the electrons move, they emit and absorb light at different frequencies, representing the atom’s spectrum. Every element has its own unique spectrum, through which it could be identified, and the study of these spectra (called spectroscopy) has numerous applications in chemistry, physics, and astronomy. But what about antimatter?

The Antihydrogen Laser Physics Apparatus, or ALPHA experiment at CERN captured 14 or so antihydrogen atoms per trial and blasted them with a laser to see what kind of light they absorb. ALPHA is a unique experiment at CERN, able to produce antihydrogen atoms and hold them in a specially-designed magnetic trap, manipulating antiatoms a few at a time. Trapping antihydrogen atoms allows them to be studied using lasers or other radiation sources.

“Moving and trapping antiprotons or positrons is easy because they are charged particles,” said Hangst. “But when you combine the two you get neutral antihydrogen, which is far more difficult to trap, so we have designed a very special magnetic trap that relies on the fact that antihydrogen is a little bit magnetic.”

As expected (and hoped), the spectrum of anti-hydrogen was identical to that of hydrogen.

“It’s long been thought that antimatter is an exact reflection of matter, and we are gathering evidence to show that is indeed true,” Tim Tharp from ALPHA told Ryan F. Mandelbaum at Gizmodo.

I say “hoped” because if the spectra didn’t turn out to be identical, then it would mean that much of what we hold as true today – including the Big Bang theory and Einstein’s special relativity – wouldn’t hold up. Special relativity assumes that a single unified thing called spacetime splits differently into space and time for observers moving relative to each other. The spectra were identical, which means that the theory of relativity passed yet another difficult test. But researchers are already planning to create more antimatter and blast it with a different type of laser, to observe even more spectra.

Particle physics is a bizarre and complicated world and we are only now getting the chance to test theories proposed many decades ago.The fact that these theories are holding op, that researchers got so many things right only through theory is a testament to the brilliant mind which contributed to this field of science.


Image: SCiO

A pocket-sized gadget uses spectroscopy and tells you what’s inside food

One of the most exciting gadgets we’ve seen at CES Las Vegas this year comes from a French startup called DietSensor, which collaborated with Israeli company Consumer Physics. Their latest product called SCiO is a pocket-sized device that uses near-infrared spectroscopy to tell you how many carbs or calories are found inside your food.

Image: SCiO

Image: SCiO

Just like any spectrometer, the SCiO analyzes the chemical makeup of food and drink by working out the complex interactions between molecules and light. Basically, by analyzing the unique optical signature of the scanned material, it’s possible to determine what it’s made out of. That being said, the SCiO should work with anything: food, drink, pills, plants, dogs. The problem is it won’t be that helpful if you use it for anything other than food – heterogeneous food, to be more precise.

If you point the device on a piece of cheese or bread, it will tell you the fat content and carbs. Because it also comes with an app, all this data can be integrated so you receive custom tips like “hey stop off that cheese, because you already had 23grams already”. Those with medical conditions like diabetes who need to be very careful what they eat or drink might benefit the most from the device.

The device shines a blue light on the object you want chemically analyzed. Image: SCiO

The device shines a blue light on the object you want chemically analyzed. Image: SCiO

Now, a spectrometer isn’t that much of a big deal. They’ve been around for decades. What’s impressive about the SCiO is its size, given most spectrometers are the size of a microwave oven. At the same time, the small size should make you skeptical of its accuracy.

According to its developers, the SCiO was scaled down by handling the analysis itself externally, while the handheld gadget only takes the samples. First, the SCiO shines a light on a sample (food), and once this light is reflected  the device extracts the molecular fingerprint of that sample. The user then connects via a smartphone or tablet to the Consumer Physics’ database of physical matter and when it finds a match, it returns a result.

“SCiO is unique as it is based on a tiny spectrometer, designed from the ground up to be mass-produced at low cost with minimal compromise on the available application. This unique feature is achieved by several technology breakthroughs our team has made in the past few years, as we reinvented the spectrometer around low-cost optics and advanced signal processing algorithms,” the company writes on its website.

The SCiO scanner is available for $249. Consumer Physics has raised more than $10 million via Kickstarter, as well as a round of funding from Khosla Ventures, crowdfunding platform Ourcrowd, strategic investors, and angels.

High-resolution spectroscopy could revolutionize seawater uranium capture

New imaging techniques might revolutionize the technologies currently used to capture uranium from seawater, as researchers gain a better understanding of the way the compounds that bind the atoms interact with them.

Using high-energy X-rays, researchers discovered uranium is bound by adsorbent fibers in an unanticipated fashion.
Image via phys

A research team led by Carter Abney, Wigner Fellow at the Department of Energy’s Oak Ridge National Laboratory, used ultra-high-resolution imaging to study the polymer fibers that bind uranium from seawater. Their results, gained through collaboration with the University of Chicago and published in a paper in the journal Energy & Environmental Science, shows that these materials don’t behave the way computational models say they should.

“Despite the low concentration of uranium and the presence of many other metals extracted from seawater, we were able to investigate the local atomic environment around uranium and better understand how it is bound by the polymer fibers,” Abney said.

By looking at the polymeric absorbent materials with X-ray Absorption Fine Structure spectroscopy at the Advanced Photon Source, Argonne National Laboratory, the researchers found that the spectrum response from the polymers were very different from what they were expecting to see based on previous small molecule and computational investigations.

They concluded that for this system the approach of studying small molecule structures and assuming that they accurately represent what happens in a bulk material simply doesn’t work. What is needed is to consider the behavior of the molecules in-bulk, to take into account interactions that only start working in a large-scale setting, says Abney.

“This challenges the long-held assumption regarding the validity of using simple molecular-scale approaches to determine how these complex adsorbents bind metals,” Abney said. “Rather than interacting with just one amidoxime, we determined multiple amidoximes would have to cooperate to bind each uranium molecule and that a second metal that isn’t uranium also participates in forming this binding site.”

(Amidoximes are the chemical group attached to the polymer fibers that bind the uranium atoms.)

Armed with this knowledge, Abney and colleagues hope to develop absorbents that can efficiently harvest the vast quantities of uranium dissolved in seawater.

“Nuclear power production is anticipated to increase with a growing global population, but estimates predict only 100 years of uranium reserves in terrestrial ores,” Abney said. “There is approximately 1,000 times that amount dissolved in the ocean, which would meet global demands for the foreseeable future.”

First ringwoodite sample confirms huge quantities of water in the Earth’s mantle

The first ever terrestrial discovery of ringwoodite seems to confirm the existence of massive amounts of water hundreds of kilometers below the Earth’s surface. Let me explain how.

Under pressure

Ringwoodite is a high-pressure polymorph of olivine; it’s basically olivine, but with a different crystal structure. The mineral is thought to exist in large quantities in the so-called transition zone, 410km to 660 km deep. Judging by its properties and lab experiments, crystallographers believe that the mineral is restricted between 525 and 660 km deep.

Ringwoodite has been found in meteorites, but until now, no terrestrial sample has ever been unearthed because, well, geologists can’t go 500 km deep underground. However, a University of Alberta diamond scientist has found the first terrestrial sample. The team led by Graham Pearson, Canada Excellence Research Chair in Arctic Resources analyzed this ringwoodite sample and reported that it contains a significant amount of water – 1.5 per cent of its weight. Since this mineral is thought to be found in enormous quantities in the transition zone, that means that the equivalent of all the surface water is found inside the minerals.

“This sample really provides extremely strong confirmation that there are local wet spots deep in the Earth in this area,” said Pearson, a professor in the Faculty of Science, whose findings were published March 13 in Nature. “That particular zone in the Earth, the transition zone, might have as much water as all the world’s oceans put together.”

Interestingly enough, the mineral is notable for being able to contain water within its structure, present not as a liquid but as hydroxide ions (oxygen and hydrogen atoms bound together) . This has huge implications because ringwoodite is thought to be the most abundant mineral phase in the lower part of Earth’s transition zone, so abundant that its properties directly affect those of the mantle – so the existence of water is quite a game changer.

The sample that almost wasn’t

Pearson holding the sample. Remember that the ringwoodite inclusion is a very small part of the sample.

The sample was found in 2008 in the Juina area of Mato Grosso, Brazil, where artisan miners unearthed the host diamond from shallow river gravels. Diamonds are most often associated and brought to the surface by minerals called kimberlites – the most deeply derived of all volcanic rocks. But the discovery itself was almost accidental.

Pearson’s team was looking for something entirely different when they stumbled onto a three-millimetre-wide, dirty-looking, commercially worthless brown diamond. The ringwoodite itself is invisible to the naked eye, and hidden beneath the surface, so it’s a surprise that graduate student, John McNeill, found it in 2009.

“It’s so small, this inclusion, it’s extremely difficult to find, never mind work on,” Pearson said, “so it was a bit of a piece of luck, this discovery, as are many scientific discoveries.”

Three-dimensional confocal μXRF view of two-phase inclusion within the diamond

It took years of analysis and redoing the tests over and over again before it was finally confirmed that the sample is ringwoodite; infrared spectroscopy and X-ray diffraction confirmed this, while the critical water measurements were performed at Pearson’s Arctic Resources Geochemistry Laboratory at the U of A.

A remarkable collaboration

Aside from actually finding the sample, it’s also notable how this study came to fruition. It is a remarkable example of ome of the top leaders from various fields, including the Geoscience Institute at Goethe University, University of Padova, Durham University, University of Vienna, Trigon GeoServices and Ghent University. For Pearson, one of the world’s leading authorities in the study of deep Earth diamond host rocks, this is one of the most notable discoveries in his career, apparently confirming 50 years of theories.

Geophysicists and seismologists have long theoretized that the composition of the transition zone has to feature immense quantities of water, but that was never confirmed – until now. The existence of water in the ringwoodite in the transition zone has immense implications for volcanism and plate tectonics, affecting how rock melts, cools and shifts below the crust.

“One of the reasons the Earth is such a dynamic planet is the presence of some water in its interior,” Pearson concluded. “Water changes everything about the way a planet works.”

Journal Reference:

  1. D. G. Pearson, F. E. Brenker, F. Nestola, J. McNeill, L. Nasdala, M. T. Hutchison, S. Matveev, K. Mather, G. Silversmit, S. Schmitz, B. Vekemans, L. Vincze.Hydrous mantle transition zone indicated by ringwoodite included within diamondNature, 2014; 507 (7491): 221 DOI: 10.1038/nature13080
Hot-Jupiter exoplanet illustration. (c) NASA

Signs of water found in the atmosphere of 5 alien planets

Hot-Jupiter exoplanet illustration. (c) NASA

Hot-Jupiter exoplanet illustration. (c) NASA

Using the Hubble telescope, astronomers have identified faint signals of water in the atmosphere of five exoplanets. The alien planets, however, are classed as hot-Jupiters – huge planets with a surface temperature too hot to support life. Finding water on planets light years away from Earth is definitely of great note and marks a step forward in scientists’ quest (and whole of mankind for that matter) of discovering life supporting planets outside our solar system and alien life itself.

With the help of Hubble’s Wide Field Camera 3, NASA researchers closely followed five planets: WASP-17b, HD209458b, WASP-12b, WASP-19b and XO-1b. All of these planets are extremely far away, as you can imagine, so naturally analyzed the light absorbed by the atmosphere of these planets to see what it’s made of. Light can tell you a great deal about the chemical composition of a planet as certain wavelengths are absorbed by certain molecules only – this method is called spectroscopy.

[RELATED] Most Earth-like planet in terms of size and mass discovered

All five planets showed signs of water in their atmosphere, with the strongest signatures found in WASP-17b and HD209458b, as reported in two separate studies published by NASA researchers in the Astrophysical Journal.

“We’re very confident that we see a water signature for multiple planets,” Avi Mandell, of NASA’s Goddard Space Flight Center in Greenbelt, Md., lead author of one of the studies, said in a statement. “This work really opens the door for comparing how much water is present in atmospheres on different kinds of exoplanets — for example, hotter versus cooler ones.”

This isn’t the first time signs of water have been found in the atmosphere of distant worlds, however the two studies mark the first time researchers measured and compared profiles of the substance in detail across multiple alien worlds. For all planets, the water signature was fainter than expected, based on previous observations with Spitzer, possibly due to hazes absorbing in the NIR or non-solar compositions.

[ALSO READ] First cloud-map of an extrasolar planet

Faint or not, it’s highly likely that water is present in the air of these worlds. It’s little steps like these that might eventually help scientists refine their methods and lead to the milestone discovery we’re all waiting for.

“These studies, combined with other Hubble observations, are showing us that there are a surprisingly large number of systems for which the signal of water is either attenuated or completely absent,” Heather Knutson of the California Institute of Technology in Pasadena, a co-author on Deming’s paper, said in a statement. “This suggests that cloudy or hazy atmospheres may in fact be rather common for hot Jupiters.”

Evidence of granite found on Mars – Red Planet geology more complex than previously thought

Geologists have now found the most compelling evidence of granites on Mars – something which prompts more complex theories about the geology and tectonic activity on the Red Planet.

Granites and basalts

Basalt and Granite. Credits: Rice University.

Granites are igneous rocks, pretty common on the surface of Earth. It is often called a ‘felsic’ (white rock) – because it is very rich in so-called white minerals, such as quartz or feldspar. It is contrasted with mafic rocks (for example basalt), which are relatively richer in magnesium and iron. Now, large amounts of feldspar have been found in a Martian volcano. Interestingly enough, minerals commonly found in basalts are completely absent from that area; considering how basalts are almost ubiquitous on Mars, this initially came as a shock, but now, geologists have come up with a theory to explain this.

Granite, or its eruptive equivalent, rhyolite, is often found on Earth in tectonically active regions such as subduction zones. However, since Mars isn’t tectonically active, there are no subduction zones there, so there has to be a different cause. The team studying the case concluded that prolonged magmatic activity on Mars can also produce these granitic compositions on very large scales.

“We’re providing the most compelling evidence to date that Mars has granitic rocks,” said James Wray, an assistant professor in the School of Earth and Atmospheric Sciences at the Georgia Institute of Technology and the study’s lead author.

Red Planet geology

A 'spectral window' into the Martian geology - bright magenta outcrops have a distinctive feldspar-rich composition. (Credit: NASA/JPL/JHUAPL/MSSS)

A ‘spectral window’ into the Martian geology – bright magenta outcrops have a distinctive feldspar-rich composition. (Credit: NASA/JPL/JHUAPL/MSSS)

For many years, the geology of Mars has been considered to be very simplistic, consisting of mostly one single type of rock: basalt – a common extrusive igneous (volcanic) rock formed from the rapid cooling of basaltic lava exposed at or very near the surface. The dark rock can also be found on Earth in many volcanically active areas, such as Hawaii or Iceland for example.

But earlier this year, the Mars Curiosity started to cast some doubt on those beliefs, when it reported finding soils with a composition similar to granite. No one really knew what to make of this discovery, but since it appeared to be very localized, it was just considered a local anomaly. However, this new research analyzed things at a much larger scale, using remote sensing techniques with infrared spectroscopy to survey a large volcano on Mars that was active for billions of years. The volcano is perfect for this type of study, because it is dust free (a true rarity on Mars) – some of the fastest-moving sand dunes on Mars sweep away any would-be dust particles on this volcano.

Much to the delight of researchers, the limitations of the remote sensing technology were an advantage in this case:

“Using the kind of infrared spectroscopic technique we were using, you shouldn’t really be able to detect feldspar minerals, unless there’s really, really a lot of feldspar and very little of the dark minerals that you get in basalt,” Wray said.

Separating the white and the black

So we have an island of white feldspar amidst an ocean of black basalt – how did it form?

When you have magma in the subsurface, it cools off very, very slowly. In a tectonically inactive planet like Mars, this process can be very stable. While the magma slowly cools off, low density melt separates from high density crystals, and if the conditions are just right, this process can take place for billions of years, leading to the creation of granitic rocks, as computer simulations showed.

“We think some of the volcanoes on Mars were sporadically active for billions of years,” Wray said. “It seems plausible that in a volcano you could get enough iterations of that reprocessing that you could form something like granite.”

While we are trying to figure out the existence (or lack of it) of life on Mars, this is another wake-up call, showing just how little we understand about the geologic processes on the Red Planet – which ultimately govern the appearance of life. Anyway, the geology of Mars just got a lot more interesting.

Journal Reference:

  1. James J. Wray, Sarah T. Hansen, Josef Dufek, Gregg A. Swayze, Scott L. Murchie, Frank P. Seelos, John R. Skok, Rossman P. Irwin, Mark S. Ghiorso. Prolonged magmatic activity on Mars inferred from the detection of felsic rocksNature Geoscience, 2013; DOI: 10.1038/NGEO1994

Medical breakthrough: chemical composition of human urine determined



It may come as a shock to you to find out that the chemical make-up of human urine hasn’t been identified until now – but it shouldn’t. The study which led to this breakthrough took over seven years and involved 20 researchers; in the end, it revealed over 3.000 metabolites (small molecules resulted through metabolism). The results are expected to make a big mark in medical, nutritional and environmental testing.

The complexity of human urine took even scientist by surprize.

“Urine is an incredibly complex biofluid. We had no idea there could be so many different compounds going into our toilets,” noted David Wishart, the senior scientist on the project.

The techniques used in the study included nuclear magnetic resonance spectroscopy, gas chromatography, mass spectrometry and liquid chromatography, with the purpose being not only the identification (the ‘what’) of substances in urine, but also the quantification (the ‘how much’). They also used computer-based data mining techniques to scour more than 100 years of published scientific literature about human urine, and if you’re passionate about this subject or it has scientific interest to you, you can check their collected data base for free, online, at the Urine Metabolome Database, or UMDB. The Urine Metabolome database is a freely available electronic database containing detailed information about ~3100 small molecule metabolites found in human urine along with ~3900 concentration values. Each metabolite entry contains more than 110 data fields and many of them are hyperlinked to other databases; basically, it’s like IMDB for urine.

As one can easily guess, the chemical composition of urine is of huge interest to doctors, nutritionists, and even environmental scientists, because it offers valuable information not only about someone’s health, but also about what they’ve been eating, drinking, smoking, etc. As a matter of fact, up until the 1800s, urine’s taste and smell were the primary method for physicians to diagnose disease.

“While the human genome project certainly continues to capture most of the world’s attention, I believe that these studies on the human metabolome are already having a far more significant and immediate impact on human health.”, he added.

Now, with this complete list, we can probably expect numerous advancements and related studies in the field – especially as they have taken the correct and laudable path of sharing their results for free.

“Most medical textbooks only list 50 to 100 chemicals in urine, and most common clinical urine tests only measure six to seven compounds,” said Wishart. “Expanding the list of known chemicals in urine by a factor of 30 and improving the technology so that we can detect hundreds of urine chemicals at a time could be a real game-changer for medical testing.”

Still, it’s quite possible that even this (though extremely thorough and useful) database is not exhaustive.

“This is certainly not the final word on the chemical composition of urine,” Wishart said. “As new techniques are developed and as more sensitive instruments are produced, I am sure that hundreds more urinary compounds will be identified. In fact, new compounds are being added to the UMDB almost every day.

Journal Reference: Souhaila Bouatra, Farid Aziat, Rupasri Mandal, An Chi Guo, Michael R. Wilson, Craig Knox, Trent C. Bjorndahl, Ramanarayan Krishnamurthy, Fozia Saleem, Philip Liu, Zerihun T. Dame, Jenna Poelzer, Jessica Huynh, Faizath S. Yallou, Nick Psychogios, Edison Dong, Ralf Bogumil, Cornelia Roehring, David S. Wishart. The Human Urine Metabolome. PLoS ONE, 2013; 8 (9): e73076 DOI: 10.1371/journal.pone.0073076

What Light tells us about the Universe

I’ve written about our incredible biological ability to gather information about our environment by sensing electromagnetic radiation. As complex as our eyes are however, light holds far more information than what we are able to perceive with our eyes. Science has given us the means to determine far more than just that there is a speck of light in the night sky.

With our modern tools and understanding we can figure out how far away that light is, how old it is, and what the emission source is made of. We have a name for this science.


prism image

Spectroscopy is a big word, but it’s really not particularly complicated. It is spectral analysis, referring to the electromagnetic spectrum. You can examine the small visible section of it when you use a prism to order light into a rainbow. That rainbow is a lot more than a pretty physical effect. Rainbows are serious business! This is because different light sources produce different sets of wavelengths, which we can analyze and measure.

You can examine the light produced by a luminous object and determine what it is made of. This is especially because it isn’t limited to mere visible light. You can order radio waves, microwaves, infrared
waves, anything in the electromagnetic spectrum, to produce a signature.

Observing the Universe

Astronomy relies almost entirely on the analysis of light to learn about our universe. There are two basic different types of rainbows, or spectrums, that we can create to analyze matter: For reference, here is a full color spectrum if we had a light source that produced every wavelength.

1. Emission Spectrum: If you go gather light as it is emitted within a vacuum you will get a rainbow that shows all of the wavelengths emitted by that light source. Each element or molecule behaves differently and produces some wavelengths, and not others. For example, here is the emission spectrum of pure iron.


One iron atom can emit any one of those frequencies but not anything outside of its set. A huge collection of iron atoms, like in a chunk of iron, will have all of these frequencies present. If you heat your iron until it emits light and these are the only frequencies you get, then you know you’re looking at a pure product.

2. Absorption spectrum: Starlight only comes to us in an absorption spectrum. This happens because, while the core of a star emits every wavelength, the cooler matter that the light must pass through, as well as the star’s atmosphere, strip wavelengths out, leaving absorption lines that look like a bar code.

This allows scientists to determine the stars chemical composition. Here is the visible part of our solar spectrum.

Knowing our solar spectrum, we can use this as our baseline and use any further wavelength omissions to determine what else this starlight is passing through. For example, I’m sure you’ve heard of the ozone layer, which absorbs UV radiation. This can be used to figure out everything that light comes into contact with on its way to us.

That might seem like a tall order, but remember, those are only visible wavelengths, from 400 to 700 nanometers. A single electromagnetic wave can be infinitely small or as large as the universe itself. The effects of matter do not exist just in our tiny visible range, so a signature can pretty much always be detected if we can look in the right portion of the spectrum.

Recently, astronomers used a similar technique to show that there is a giant 288 billion mile wide cloud of methyl alcohol hanging out in space.

Redshift and Blueshift

Both of these are most easily explained with the Doppler Effect. This is something you experience every day when a car drives past you. While it drives toward you it sounds higher pitched, and while it away from you it sounds lower pitched. This is because the moving object that is emitting these sound waves is moving toward waves emitted in the direction of travel, and later away from those in the opposite direction. This causes the waves to be closer together, at a higher frequency, or at a lower frequency, and closer together respectively.

Light does the same thing. It is only noticeable when an object is moving at absurdly fast speeds, near the speed of light. Astronomers can tell that the Andromeda Galaxy is hurtling toward our Milky Way Galaxy at incredible speed because its entire spectrum is shifted. We can tell that it is shifted because the aforementioned absorption lines of the galaxy’s spectrum form a similar pattern to what we see here, but moved over a little on the spectrum.

Same story for the red shift, but moved to the right on the spectrum. Redshift is special because it tells us something else as well. All objects we can observe outside our galaxy have a redshift. This is, according to Hubble’s Law, because spacetime is expanding. In the time since the light was emitted and the time it reached us, spacetime has stretched, causing light to shift toward the red along the spectrum, more or less according to the age of the light. Because the speed of light is constant and known, we can use the discernible age of the light to calculate how far it has travelled to reach us.

By looking at absorption lines, astronomers can determine the chemical composition of the emitter. By examining the shift in those lines, we determine the age and distance of the emitter.

Daniel Harris writes for Byk Additives & Instruments, who produces color spectrometers. He is passionate about science and photophysics and enjoys writing about it.

First remote reconnaissance of another solar systems reveals unlike “any other known object in our Universe”

Researchers have for the first time conducted a remote reconnaissance of a distant planetary system with a new telescope imaging system.

Peeking at other planets


Project 1640 is a dedicated high contrast imaging program at Palomar Observatory with the goal of obtaining images and spectra of brown dwarfs and planetary mass companions to nearby stars. The solar system they analyzed is 128 light years away, and has four red exoplanets; a detailed description of the planets was published in the Astrophysical Journal, showing what an unbelievable diversity of planets our galaxy hosts.

“An image is worth a thousand words, but a spectrum is worth a million,” said lead author Ben R. Oppenheimer, associate curator and chair of the Astrophysics Department at the American Museum of Natural History.

Spectroscopic measurements

spectroscopy1Oppenheimer is the main investigator working on the project. He explained that the planets orbiting the star in case, but until now, the star’s bright light overwhelmed previous attempts to study the planets with spectroscopy. Simplistically put, spectroscopy studies how white light is split into its constituent wavelenghts, much like when it passes through a prism; it’s very useful in such studies, because every chemical element has its unique spectroscopic signature, and if the conditions allow it to be applied properly, the technique can reveal the chemical composition of a planet’s atmosphere.

“In the 19th century it was thought impossible to know the composition of stars, but the invention of astronomical spectroscopy has revealed detailed information about nearby stars and distant galaxies,” said Charles Beichman, executive director of the NASA Exoplanet Science Institute at the California Institute of Technology. “Now, with Project 1640, we are beginning to turn this tool to the investigation of neighboring exoplanets to learn about the composition, temperature, and other characteristics of their atmospheres.”

With this new system, the conditions were just right, allowing a fantastic observation of the planets orbiting HR 8799.

“It’s fantastic to nab the spectra of four planets in a single observation,” said co-author Gautam Vasisht, an astronomer at the Jet Propulsion Laboratory.

Unexpected results

spectroscopy 2

The results were very strange – unlike anything astronomers were prepared for.

“These warm, red planets are unlike any other known object in our universe. All four planets have different spectra, and all four are peculiar. The theorists have a lot of work to do now.”

The first anomaly that strikes the eye is the apparent chemical imbalance. From what we know of basic chemistry, ammonia and methane should naturally coexist in varying quantities unless they are in extremely cold or hot environments. However, at temperatures just over 700 degrees Celsius (1340 degrees Fahrenheit), which are “lukewarm” by astronomic standards, all the planets either have methane or ammonia, with little or no signs of their chemical partners.

The planets are also surprisingly red – emitting longer wavelengths of light, than celestial objects with similar temperatures. The most likely explanation for this phenomena is a patchy cloud covering all the planets.

“The spectra of these four worlds clearly show that they are far too toxic and hot to sustain life as we know it,” said co-author Ian Parry, a senior lecturer at the Institute of Astronomy, Cambridge University. “But the really exciting thing is that one day, the techniques we’ve developed will give us our first secure evidence of the existence of life on a planet outside our solar system.”

A bright future

Aside from the unquestionable value of this particular study, the system has proven its worth and now, researchers will definitely want to take a glance at other solar systems, perhaps some which are more likely to harbor life.

“Astronomers are now able to monitor cloudy skies on extrasolar planets, and for the first time, they have made such observations for four planets at once,” said Maria Womack, program director for the Division of Astronomical Sciences at the National Science Foundation. “This new ability enables astronomers to now make comparisons as they track the atmospheres, and maybe even weather patterns, on the planets.”

The fact that all these planets were different also shows that the technique works in a number of environments, bringing even more hope to the table.

“The variation in the spectra of the four planets is really intriguing,” said Didier Saumon, an astronomer at Los Alamos National Laboratory who was not involved in this study. “Perhaps this shouldn’t be too surprising, given that the four gaseous planets of the solar system are all different. The hundreds of known exoplanets have forced us to broaden our thinking, and this new data keeps pushing that envelope.”

Kawazulite conducts electricity at its surface but not in its bulk. (c) AM. CHEM. SOC.

Topological insulator super-material found in nature too

Researchers have demonstrated for the first time the existence of a naturally occurring topological insulator – an exotic class of materials that possesses the unique ability to conduct electricity and the surface, but not on the inside. Previously, topological insulators have been studied and created in labs only, however now a mineral has been found that acts as one. Moreover, this natural topological insulator is a lot better than synthesized ones since it lacks structural defects typically associated with synthetic materials.

Kawazulite conducts electricity at its surface but not in its bulk. (c) AM. CHEM. SOC.

Kawazulite conducts electricity at its surface but not in its bulk. (c) AM. CHEM. SOC.

Ordinary insulators keep electricity from flowing through out the bulk material since electrons fully occupy energy bands. In topological insulators, however, the spin-orbit interaction is so strong that the insulating energy gap is inverted — the states that should have been at high energy above the gap appear below the gap.  As a result, we have highly conducting metallic states on the surface, while the inside is completely insulated.

First predicted in 2005, scientists have since then rapidly enhanced their understanding and first synthesized a topological insulator in 2008. Just a few weeks ago, researchers demonstrated the first organic topological insulator. What makes this class of materials so exciting is its ability to boost applications of spintronics devices that work with electron spin, rather than voltage. Quantum computers that encode information in electron spin would be primarily first to benefit from the advent of topological insulators.

Pascal Gehring, a solid-state physicist at the Max Planck Institute for Solid State Research in Stuttgart, Germany along with colleagues collected samples of a peculiar mineral called  kawazulite from a gold mine in the Czech Republic. Made out of bismuth, tellurium, selenium and sulphur, the analyzed 0.7 millimetres wide crystalline sheet had electron energy and momentum distribution that matched predictions for a topological insulator.

The analysis was made using photoelectron spectroscopy, which involves measuring the properties of electrons dislodged from a material when ultraviolet light is fired at its surface. Curiously enough kawazulite was synthesized in the past, however its properties are no near as reliable as the natural occurring one, since topological insulators built in the lab always have structural defects that create unwanted conduction in the bulk.

“Surprisingly, the team’s natural sample is cleaner than synthesized samples — even though you would expect it to be more dirty,” says Feng Liu, a materials scientist at the University of Utah in Salt Lake City,. “It may turn out to be cheaper to use a natural supply of topological insulators than it is to make, process and clean them in the lab.”

The findings were reported in the journal Nature Letters.