This article appeared in the Spring 2014 issue of Current Exchange Magazine.

So specialized are reef organisms to their particular ecological niche that merely a decade ago, it was nearly impossible for a person to recapitulate the delicate and awesome beauty of a reef in their own home. Today, things are different. A dedicated community of hobbyists has generated a vast amount of information about the care and maintenance of captive reef ecosystems, thanks in no small part to the advent of the Internet. I have been a reef enthusiast since I was 13 years old, and I grew up in online message boards such as Reef Central (reefcentral.com) and in monthly reef meetings scattered across Long Island. The truth is, everyone who keeps a coral reef aquarium becomes a little bit of a fanatic so today, and in future issues of Current Exchange, I will attempt to explain why. Who knows—maybe you’ll find that you’re a bit of a fanatic yourself.

What are corals?

The first and perhaps most astonishing fact about corals is that they are metazoans, or animals. More specifically they are cnidarians, a phylum that also includes sea anemones and jellyfish. An easy way to think of corals is to imagine them as upside-down jellyfish. A mouth, set in a central disc, is surrounded by a ring of 6 or 8 tentacles. This simple organism is a coral polyp, and the corals that most people are familiar with are actually colonies composed of many hundreds or even thousands of polyps.

Soft corals can exist as free-living single polyps, or in colonies. This is a diverse and hardy group of corals, united in their distaste for CaCO3 secretion. Pictured: A few tiny green star polyps (Briarium) will rapidly grow into a “lawn” of colonial polyps, whereas the red mushroom polyp (Discosoma) will divide slowly to produce large individual polyps capable of relocation. A hermit crab (unidentified) examines the scene. Bonus fact: Red Discosoma corals were the source of dsRed (a form of RFP).

Many coral colonies also secrete a calcium carbonate “skeleton,” which eventually contributes to the overall structure and substrate of the reef. Many corals have a symbiotic relationship with photosynthetic dinoflagellates called Zooxanthellae, which are the source of the many astonishing colors of corals. Zooxanthellae live inside the clear bodies of coral polyps, and produce sugars to nourish the corals in exchange for a safe place to live. Coral bleaching, which occurs when a coral is severely stressed, occurs when Zooxanthellae “jump ship” and abandon the dying coral. Today, mass coral bleaching is occurring at an ever-accelerating pace due to human disruption of the ocean environment. It is sobering to imagine that, one day, corals may only live on in the aquaria of reef enthusiasts.

Types of Corals

It is important to limit the number of fish in a reef aquarium, as they produce a lot of waste and may snack on corals or other invertebrates. Pictured: Clownfish (Amphiprion ocellaris) are among the safest fish for a reef aquarium. These juvenile clowns are presently male, but in time the dominant fish will grow larger and adopt different coloration as it morphs into a female.

Hobbyists typically describe corals as belonging to one of three groups, based on polyp morphology and the presence of a calcium carbonate skeleton. Small polyp stony corals (or SPS) have intricate and often branching skeletons, bright colors, and tiny polyps. They are both the most immediately recognizable corals and the most difficult to grow successfully, requiring tremendous amounts of light and current and pristine water conditions to truly thrive.

Small polyp stony corals (SPS) secrete calcium carbonate skeletons with intricate branching patterns, and require large amounts of light and current in order to thrive. Pictured: Montipora and Acropora species, with red Gracilaria macroalgae in background.

Large polyp stony corals (LPS) tend to be easier to maintain, and their large polyps with long “sweeper tentacles” are able to catch a meal to supplement their diet. Care must be exercised in positioning these corals, as their long tentacles can sting and kill nearby corals overnight.

Large polyp stony corals (LPS) also secrete a CaCO3 skeleton, but their polyps are larger and extra tissue is apparent. LPS corals can supplement their diet with food captured via their long “sweeper tentacles.”. Pictured: Red Chalice coral, Echinophyllia sp.

Soft corals are by far the easiest to maintain in captivity. As their name suggests, these corals do not secrete a skeleton, and they can be found in colonies or as free-living polyps. Most reef hobbyists start out keeping soft corals, and then move on to their more finicky stony brethren.

Well over a trillion tablets later, aspirin remains the biggest-selling drug ever created, and whilst it is no longer the recommended treatment for birth pain its uses have grown beyond just rheumatism to all kinds of ills, from hangover cure to reducing fevers and inflammation, preventing heart disease and stroke, and even reducing the incidence of various cancers – a wonder drug if there ever was one.

Felix Hoffmann started out his career as a pharmacist, but became so fascinated by the drugs he handled that he retrained as a chemist, getting a job as a research chemist with Bayer, Germany’s leading chemical company. Soon afterwards, and in the space of just two weeks, he synthesised both aspirin and heroin. He was not actually the discoverer of either drug, but he was the first to recognise the pain-relieving and fever-reducing properties of aspirin (initially by using his long-suffering father as a guinea-pig), and his employers were extremely quick to make it into a commercial success. Despite being arguably the most commercially successful synthetic chemist of all time, Hoffmann never received any royalties on his immensely valuable discoveries, although he had a long and profitable career with Bayer and eventually retired to live out his old age in Switzerland.

Pre-1904 Bayer advertisement for Aspirin and Heroin

Bayer aggressively marketed the drug and it became a commercial success within two years. Going from discovery to commercial production in such a short time would be impossible now, but in those days the head of the pharmaceutical department simply tested it for toxicity on himself, noticed no ill effects, and proceeded with trials on a ward-full of patients in a nearby hospital, before sanctioning production.

Interestingly the same easy-going approach to commercialisation was also applied to Hoffmann’s other discovery of the month, heroin. Heroin (actually acetylated morphine, discovered some 25 years previously by the English chemist C.R.A. Wright), was also commercialised by Bayer and marketed as a pain-relieving drug for childbirth and as a cough suppressant, of all things. It was not for some years until its extreme addictiveness was recognised, and it was almost 30 years before its use made illegal. It would be interesting to know which drug has proved most profitable over the years.

By patenting the synthesis of aspirin, Bayer had prevented others from manufacturing it, and so had a monopoly on the market. The first world war stopped the export of the drug from Germany, so the British Government offered a prize for anyone who could find a way of making it, since Bayer had also kept this secret. Within a year an Australian, George Nicholas, succeeded, naming his version ‘Aspro’; ironically, whilst Hoffmann did not benefit commercially, Nicholas did, to the tune of the £20,000 prize.

After the war, aspirin quickly became the world’s leading painkiller, and when Bayer’s patent expired in 1930, generic versions spread its use even wider. New uses of the drug were far from over though: in the late forties a Californian doctor named Laurence Craven noticed that it might be effective in reducing heart attacks, a suspicion confirmed by more extensive studies in the 1970s. Today, far more aspirin tablets are taken to prevent heart disease than to relieve pain.

In the last decade a number of studies have demonstrated that aspirin can also reduce the onset of various forms of cancer. It has been shown to reduce the likelihood of pancreatic cancer, and it has been estimated that regular use could prevent as many as 43 per cent of cases in women. Another study has shown that it can reduce the onset of polyps associated with colorectal cancer by a similar amount. Yet another recent study demonstrated that taking aspirin reduces the risk of contracting cancers of the mouth, throat and oesophagus by two-thirds.

Little could Herr Hoffmann Senior have foreseen the consequences of complaining to his chemist son about his rheumatism. And a good job he tried the aspirin and not the heroin.

Digging up bones for DNA
Although researchers cannot directly study deadly bacteria that existed thousands of years ago, they can unearth and study the remains of victims of age-old bacterial outbreaks. The scientists who do this type of work (called paleopathologists) are able to sequence the bacterial genes preserved within human bones and teeth. Analyses of ancient microbial DNA are providing crucial information about the origins and evolution of lethal human bacteria, and are changing our view of some of most devastating pandemics in history, such as the Black Death.

How old is the plague?
In the past two thousand years there have been three well-documented outbreaks of the bubonic plague: the Plague of Justinian (6th century), the Black Death (14th century), and the so-called “third plague pandemic” (19th and 20th centuries). Yersinia pestis is the causative agent – the bacterial bad guy – in all three of these pandemics, but there’s been some debate as to whether or not the Justinian Plague and the Black Death came from the same strain of Y. pestis. In other words, are they different pests or the same pestis?

Researchers recently studied two 1,500-year old skeletons in Germany, from a cemetery that is home to victims of the Plague of Justinian. Y. pestis DNA was sequenced from the skeletons and the analysis showed that the strain of the bacterium present in the 6th century (during the Plague of Justinian) differs from the strain that caused the Black Death. The fact that different strains caused these two pandemics, suggests that new deadly strains could emerge in the future.

Despite a long and sordid history of killing large numbers of people, Y. pestis is neither the oldest nor the most deadly human pathogen; that award just might belong to Mycobacterium tuberculosis, which, as the name implies, causes tuberculosis.

Is tuberculosis our oldest enemy?
Tuberculosis, which is caused by M. tuberculosis, is a disease that primarily affects the lungs, although other parts of the body can also be infected. Despite the potential to be fatal, most infections are asymptomatic, resulting in a latent form of tuberculosis. Of these infections, about 10% will eventually progress into an active, and potentially deadly form of the disease.

In 2008, paleopathologists studied 9,000-year old skeletons exhumed from an abandoned village in Israel. The researchers were amazed to see signs of tuberculosis on the skeletons (lesions on the bones) and were ultimately able to identify tuberculosis DNA within the remains. This indicates that tuberculosis has been active for 9,000 years – and it continues to infect new individuals daily. But does that mean it is the oldest human-specific pathogen? Although nine millennia is a long run for any disease, the bacteria that cause leprosy (Mycobacterium leprae and Mycobacterium lepromatosis) may be even older.

What is leprosy?
Leprosy causes a loss of feeling on the surface of your skin, the severity of which varies depending on the number of M. leprae or M. lepromatosis bacteria in the body. Feeling no pain may not sound too bad, but it can lead to reoccurring accidental injuries – burning, cutting, bruising, etc. – eventually causing permanent disfigurement. Today, the majority of the world’s population is immune to leprosy, but the disease was highly prevalent in Europe up until the 16th century, when infection rates suddenly dropped. Although M. leprae and M. lepromatosis were not discovered until 1873 and 2008, respectively, there have been accounts of the disease over the millennia. Most historical documentation shows a stigmatization of leprosy, with lepers being ostracized and isolated from the general population.

The age of leprosy
The age of an organism is often difficult to determine, but new research managed to identify the DNA of skeletons and used genetic techniques to figure out additional information. By studying the genes of leprosy-causing bacteria trapped in human remains, scientists estimate that a leprosy-causing ancestor existed as far back as 20 million years ago, and the DNA hasn’t significantly changed in comparison to modern strains. Unlike tuberculosis, where evidence only dates back 9,000 years, leprosy was infecting the early ancestors of modern humans, making it the oldest infection discovered thus far. But why did the leprosy rates suddenly decline in the 16th century?

How we adapted to beat leprosy
Humans – their genome and immune system – change over time. In the present day population, 95% of people are immune to leprosy and numerous changes in our DNA have resulted in genes that contribute resistance to leprosy. The burden of this disease over the years has induced mutations on the human race, and it’s likely that this genetic selection is what accounts for the sudden drop in leprosy rates in Europe. With leprosy-resistant mutations on our side, most people in the world will never have to worry about getting hauled off to a leper colony anytime soon.

With the looming age of antibiotic-resistant bacteria and other infections, it’s easy to understand why we fear these ancient microbes. Many concerning reports have recently surfaced about the Ebola virus, MERS in the Middle East, and MRSA in our hospitals, but we don’t hear often enough about the victories on the microbiological battlefield. The World Health Organization is committed to increasing access to medication. Hygienic practices are being improved and regulated on a larger scale. It’s no longer common to see rodents infesting urban streets. Although there are many dangers out there, we have made so many advances that our oldest parasites – causing the plague, tuberculosis, and leprosy – might just have to find some other hosts.

Tirthankar Ray is a third-year undergraduate in Biology and Microbiology and Immunology at Western University. He attended the 2013/14 fall-semester biology seminar series as a science communications project with Dr. David Smith from the Biology Department. David Smith is an assistant professor in the Biology Department at Western University. You can find him online at www.arrogantgenome.com and @arrogantgenome.

The Rosetta project has been 21 years in the making and the probe itself has spent over ten years merely getting to comet 67P/Churyumov-Gerasimenko, culminating in some incredibly intricate and complicated manoeuvres to place the probe in orbit around the comet. The reason it’s so important is that comets are believed to be remnants from the dawn of the solar system, formed about 4 billion years ago, so by closely observing 67P we can see what comets and by inference the earliest planets were made of. But it’s a risky project – as the comet heats up either the lander or Rosetta or both could be knocked out by erupting jets of material. Closest approach to the sun will be on 15 August 2015 and the mission is due to run until December 2015, so armchair astronomers are in for an exciting year as the comet approaches the Sun.

The next date on the celestial calendar is April 2015 when NASA’s Dawn probe will visit the biggest asteroid, Ceres, almost half the size of Pluto. Dawn has already visited the second largest asteroid, Vesta, where it made the important discovery that there was water locked in minerals beneath the surface, and which appeared to periodically erupt outwards from pits up to 200 metres deep.

Comet 67P seen from Rosetta (ESA)

In July 2015 we reach what will perhaps be the celestial highlight of the year when the New Horizons probe flies past Pluto, hopefully avoiding the small crowd of satellites that have been discovered around Pluto in recent years. What will Pluto look like? And where will New Horizons go next? The plan is for a Kuiper Belt Object, but it depends a lot on what objects are within reach.

Then in July 2016, NASA’s Juno probe will reach and go into orbit around the gas giant Jupiter, the first craft to spend time at the planet since the NASA-ESA probe Cassini was there over a decade before. Juno will focus on investigating Jupiter’s composition, atmosphere and magnetic field, aiming to distinguish between prevailing theories of its formation in the solar system as well as to understand its internal dynamics better.

Montage of Juno probe and Jupiter (NASA)

We shouldn’t forget the veritable party going on at Mars though, with seven active missions in progress this year. On the surface, the Curiosity and Opportunity rovers are trundling around investigating its geology and looking for signs of past water, and above them are the Odyssey, Express and Reconnaissance orbiters, joined just last month by NASA’s MAVEN craft and the Indian Space Agency’s Mars Orbiter Mission (also known as Mangalyaan).

Mangalyaan in particular is a huge technical triumph, making India only the fourth country or country-group to have successfully sent a probe to Mars, and most remarkably doing so successfully at the first attempt, something that not even the US or Russia achieved. It is also the start of a minor flurry of missions next year by the newer space nations with China, India and Russia all planning to land probes on the Moon.

Further out the story gets even more interesting with not just India and China entering the planetary exploration game, but private enterprise too. In 2018 Inspiration Mars plans to launch two people on a 500 day return trip to Mars, and in 2023 Mars One aims to land the first human settlers on Mars. Now that really will be something to watch.

The instrument used by Cavendish was fabricated by the geologist John Michell. The torsion balance, introduced by Michell, was an important progress in gravitation experiments. Unfortunately, Mitchell died before he could complete his instrument and his apparatus was handed to Cavendish who improved it further by minimizing the effects of the induced air and temperature differences.

The apparatus consists of a fine torsion metal fiber that supports a dumbbell-shaped structure consisting of a wooden arm and the two small lead spheres. The gravitational force between the two large, stationary spheres and the two small spheres can be measured from the twist of the fiber since the arm with the two smaller spheres rotates until it is in equilibrium, that is, when the torque due to the force of gravitation is equal to the elastic torque due to the fiber. Cavendish used the period of oscillation of Michell’s torsion balance to compute the gravitational attraction between the spheres, which he then applied to compute the Earth’s density to an astonishing degree of accuracy. Cavendish’s work paved way for an accurate calculation of G, the gravitational constant, and the mass of the Earth.

Cavendish’s setup was remarkable in many ways. Before Cavendish’s experiment, there were efforts to demonstrate gravitation by measuring the influence of gravitational force on a pendulum due to a mountain in order to measure the density of the Earth; this phenomenon was known as the ‘Attraction of the Mountains’ and the experiment that used this effect to find the Earth’s mean density was known as the Schiehallion experiment. However, the Cavendish experiment was much more accurate and straightforward. Also, being able to probe the world from his home laboratory rather than out in the open was probably more favorable to his shy and agoraphobic personality, an aspect that is best described by Christa Jungnickel and Russell McCormmach in their book, Cavendish:

“With it [his setup of lead spheres instead of mountains] he did not need to go out into the world to know it; he could know it and know it more precisely by staying home and manipulating his apparatus and reasoning from universal principles. The world came to Cavendish. (Another way of viewing it is that Henry Cavendish was a Cavendish, and the Cavendishes liked to stay home and let the world come to them.) Cavendish stayed at home, inside of a building, looking inside of a room and through a slit in a case inside of which was the world – his world, on his terms.

It has been noted that while there is much talk about the effect of the scientist’s personality on science, there is little of the other, perhaps more profound, effect of science on the personality. In Cavendish we see both effects, mutually reinforcing. From the beginning Cavendish turned away from what he found difficult, ordinary society, and toward nature and its understanding through science, and through science he came into a society he found, if not comfortable, to his liking.

[...]

The experiment on the density of the earth is arguably not Cavendish’s most important experiment, but if it is looked at for what it reveals about the experimenter – as if it were a diary, which he did not keep, or a formal portrait, which he did not allow – it is the most expressive of his experiments.”

Finally, it was during the time of Cavendish that precision measurement emerged as an important factor in science. Cavendish often worked with instrument makers and attempted to improve their inventions. This is what he did with Michell’s setup; he also published a paper on how to improve astronomical instruments for better accuracy. His work was celebrated for its carefulness and exactness.

Michell’s setup, for example, modified and used by Cavendish, continues to be remembered because it was able to measure the delicate force of gravity between the two lead balls, only 1/50,000,000 of their weight! He achieved it by removing all factors and sources of error that might have affected the precision of his experiment. The estimate of the Earth’s density computed by Cavendish lies within 1 percent of the value that is accepted at present!

Further Reading
Cavendish: The Experimental Life, by Christa Jungnickel and Russell McCormmach

This article appeared in the Spring 2013 issue of Current Exchange Magazine.

In May of 2010, a group of researchers led by Svante Pääbo of the Max-Planck Institute for Evolutionary Anthropology in Leipzig, Germany published 60% of the Neanderthal genome. The genome was reconstructed from three female Neanderthal bone samples found in the Vindija Cave in Croatia.

Researchers compared the human and Neanderthal genomes to identify genes unique to modern humans. Some of the genes found only in humans are important for skin development, metabolism, and cognitive abilities. Specifically, differences in the RUNX2 gene may explain morphological differences in the brain and the upper body between humans and Neanderthals.

For many years, the question of whether modern humans and Neanderthals mated has been intensely debated. Coming as a surprise to the researchers, portions of the human genome resemble parts of the Neanderthal genome. In particular, sequences from humans of non-African descent (European, Asian, Papaun) are found to be more similar to Neanderthals than to Africans.

Recently, Sriram Sankararaman and David Reich of the Department of Genetics at Harvard Medical School in Boston, Massachusetts and co-author Pääbo published a study estimating that the last interbreeding events between Europeans and Neanderthals most likely occurred 47,000–65,000 years ago. This recent time frame counters the hypothesis that the sequences shared between non-Africans and Neanderthals may have come from a more ancient ancestor.

With advances in sequencing and analyzing ancient DNA, more studies will address the question of interbreeding between modern humans and Neanderthals and elucidate the genes that make humans unique.

In fact, many of the familiar coastlines and estuaries of the world that we know have only existed for about 10,000 years. All the indications are that then, as now, about a third of the world’s population lived less than one hundred metres above the high-water mark, roughly the same amount by which sea levels rose at the end of the last ice age. Consequently many of the places our early ancestors lived are now inaccessible, submerged hundreds of feet beneath the waves – leaving large gaps in our knowledge of our past.

Investigating large areas of the sea bed on a scale fine enough to find human artifacts and settlements by traditional diving is an almost hopeless task. However, over the past decade, archaeologists have made enormous progress in developing other methods to uncover mankind’s history in areas now covered by the North Sea, the Arabian Gulf, and the Bering Strait, which were key population centres for our ancestors during the last ice age.

These discoveries are changing our understanding of our species’ development at a key period around 10,000 years ago when we started to become ‘civilised’, moving from hunter-gather lifestyles to begin to build and live in cities, supported by agriculture in fixed perennial locations. Here are a couple of examples.

Doggerland: the lost heart of Europe

One of the first submerged areas to be successfully investigated has been the southern North Sea between Britain and Europe. This large shallow area is known to fishermen as Dogger Bank, and trawlers have been bringing up Mesolithic artifacts up in their nets for around a hundred years – artifacts such as mammoth tusks, lumps of peat whose pollen indicates a woodland environment, and even antler points which have been worked by humans into harpoons – clear evidence that humans once lived there.

Fortunately, the area has been extensively surveyed by the oil industry, and archaeologists have been able to use the resulting seismic data to reveal the original land surface 10,000 to 8,000 years ago – now lying beneath about fifty metres of water and layers of sediment – and to map its rivers and valleys and even make 3D landscape models. Pollen samples from marine cores have then been used to add vegetation information to create a remarkably complete and vivid picture of this lost land, which archaeologists have now dubbed Doggerland.

Knowing better where to look, marine archaeologists have since dredged all kinds of man-made artifacts from the sea bed, giving an extensive picture of a human population who lived and hunted on Doggerland at the end of the ice age, what kind of animals they hunted and even their belief systems from artwork carved in bones and tusks. The people of Doggerland must have seen their island steadily shrinking as the ice sheets melted and sea levels rose, some gradually drifting away to drier lands – until one day it just wasn’t there at all.

The Garden of Eden: the ultimate archaeological site?

Arguably the place where humans have been most dramatically effected by past sea level rise has been the Arabian Gulf. Today`s Gulf is actually a very recent feature, only formed between 14,000 and 6,000 years ago by the same sea level rise that drowned Doggerland.

Prior to that, the Arabian Gulf Oasis, as it is usually referred to before the Gulf flooded, was a major human population centre for a very long time. When our ancestors first left Africa, one of their major exit routes was across the southern end of the Red Sea and southern Arabia, and then up into the Arabian Gulf Oasis. This fertile valley of over 250,000 sq km became a major population centre for humans for tens of thousands of years.

It was from here that our ancestors were to continue their global trek west into Europe, east to South East Asia and Australia, and north through Asia into Russia and China, from where they crossed the Bering land bridge into the Americas.

The Arabian Gulf Oasis is also the strongest candidate for a real-world location of the Garden of Eden, something that is supported by multiple evidence sources such as the description of rivers flowing through the Garden given in the Bible and the Quran, the locations where the legend was first recorded in ancient texts such as the Legend of Etana and the Epic of Gilgamesh, and the description of the flood in the Sumerian King List.

Human artifacts proving Mesolithic settlement have yet to be found beneath the Gulf in the same way as at Doggerland, but convincing evidence that it was once a regional centre of human development has come from another source. In 2010, Dr. Jeffrey Rose of the University of Birmingham mapped the occurrence around the Gulf of pottery and artifacts known as Ubaid style belonging to a relatively sophisticated people, all dated to around 8000 years ago. As Rose put it: ‘These settlements boasted well-built, perma¬nent stone houses, long-distance trade networks, elaborately decorated pottery, domesticated animals, and even evidence for one of the oldest boats in the world.’

The curious thing was, they were all found along the present day coastline of the Gulf, and they all appeared more or less out of nowhere, in areas with no previous history of fixed human settlement or those specific types of artifact. He concluded that the only explanation was that the people that made them had all come from a common origin, and that that origin had to be the Arabian Gulf Oasis. So the settlements and artifacts we find along the coast could only have been made by people from the Gulf.

The descendants of these Ubaid people went on to found the world’s first cities such as Ur and Uruk in present-day Iraq, invent writing, and develop civilizations. Marine archaeologists are now starting systematic sea bed searches for settlement remains similar to those found on land in an attempt to locate the earliest settlements in the Gulf Oasis.

In North America, another area of active research interest is the Bering land bridge between Alaska and Russia, which was a broad ice-free area during the ice age, and is now known to have been inhabited by humans for tens of thousands of years before rising sea levels engulfed it. Other signs of ice age human settlement have been found offshore Haida Gwaii on Canada’s west coast (the route which humans are believed to have taken as they migrated down into the Americas), and beneath Lake Huron stone structures for herding buffalo were recently discovered, built by the earliest First Nations people shortly after the ice sheets retreated.

Finally, these advances don’t merely fill in some of the blanks in our knowledge of our earliest human history. They also have a particular relevance for us today given concerns about the coming impact of rising sea levels caused by global warming; the difference is that back then humans were nomadic and could easily move to higher ground. With hundreds of millions of people living in large coastal cities with inflexible infrastructures, it will be much harder for us to adapt to such events in the future.

David Millar is a science writer with an interest in climate change past and present. He is the author of Beyond Dubai: Seeking Lost Cities in the Emirates which tells the tales of several Arabian lost cities abandoned through past climate change, as well as the story of man’s migration from the flooded Arabian Gulf Oasis towards surrounding lands to create the world’s first civilizations.

This article appeared in the Spring 2013 issue of Current Exchange Magazine.

Household examples are Android, Firefox and Linux. Slightly more obscure examples are Apache (a common web server that effectively runs the majority of the Internet), MySQL (a database platform that powers commercial and consumer information systems), and Python (a powerful, intuitive programming language). Open source software is found everywhere from the phone in your pocket to the critical computers that power nuclear submarines for the US department of defense. It is ubiquitous because it is too good to be true – it is powerful, transparent, often brilliantly engineered, and free.

While almost fifteen years have proven that open source software can actually be sensible for business, a three year old legal definition applying the same principles of open source to entire electronic devices remains largely untested. Open Source Hardware (OSH), in general terms, are any electronic devices whose design files and firmware are free and licensed in the public domain. A paper definition contributes a sense of identity, but what has really propelled open source hardware into being is the advent of open source microcontroller and computing platforms like Arduino, Beagleboard and LeafLabs. As a person not educated in the intricacies of assembly language (very few people on Earth are), these technologies allow someone with rudimentary programming skills to use a microcontroller – a programmable computer on a chip – to intelligently control something they design for as little as $3. These game changing platforms have found their initial niche powering commercial hobby products – for example, 3d printers (MakerBot), thermocyclers (Open PCR) and submarines (OpenROV), but have been largely absent from business and academic research. What is missing is a precedent to generate trust.

Behavioral Systems Neuroscience, the field of research seeking to understand how a live brain functions at the circuit level to produce behavior, is a natural candidate for testing the reach of Open Source Hardware. It is a tinkerer’s science by necessity, a Cell Biology waiting for its electron microscope. Three key applications in this field necessitate rapidly evolving electronic devices which are often proprietary and very expensive: 1. acquiring weak electrical or optical signals from the brain and storing them to disk, 2. electrically or optically manipulating brain activity, and 3. precisely controlling and capturing aspects of the subject’s environment. Signals acquired from the brain are aligned to the record of the environment, and decrypted to determine what information they contain about manipulations and behavioral events. Using this strategy, the codes used by the brain to represent faces, places, sounds, judgement errors, movements and visual scenes to name a few, have been at least partially solved.

An open hardware toolset in Behavioral Systems Neuroscience would provide flexibility in experimental design – since the process of changing how the equipment functions under the hood (or knowing this information at all) begins as simply as looking up the design files in a public repository. With technological sophistication, our era has heavily delegated the task of reimagining bioscience methods that depend on electronics to commercial bioscience engineers who generally keep their innovations secret, and enormous potential for bench-side innovation by bioscience researchers goes unrealized. Though it is arguable that this division is necessary for either professional to achieve expertise, perhaps it has gone too far. With some well-funded and forward thinking laboratories being the exception, it is generally the case that when the answer to an idea is to hire a consulting engineer, good ideas end up going unexplored.

Thankfully, development of an open source toolset for Systems Neuroscience is already well underway, and the initial results are quite promising. The Open Ephys project was spearheaded by graduate student co-founders Josh Siegle and Jakob Voigts in the Picower Institute for Learning and Memory at MIT. The Open Ephys team has engineered a full-featured electrophysiology acquisition system that has been validated on awake, behaving mice. In plain terms, their instrument amplifies up to 128 weak electrical signals captured from brain probes (often only tens of microvolts in amplitude), converts them to a digital format that a computer can read, filters parts of the signals that are useful for analysis, and stores the processed data to disk – and it does this for each of its 128 channels 30,000 times per second. A comparable instrument from leading commercial vendors (e.g. Neuralynx, Tucker Davis Technologies, Blackrock Microsystems) typically costs well over $80,000, while Open Ephys weighs in at well less than a twentieth of that price if assembled in-house. The development time course of Open Ephys was greatly accelerated by the decision to use bioamplifier chips from Intan Technologies, a company that has been very supportive of the team’s goal of keeping the design completely open. In the past month, the team has upgraded their original design to include an embedded accelerometer for recording head motion – a sensible innovation that simply isn’t available in commercial alternatives. Cost and hardware advantages aside, where Open Ephys really outshines commercial instruments is in its software. The Open Ephys application takes stylistic cues from pro audio processing suites like Ableton Live and Reason, providing the ability to define a sequence of digital processing steps for each channel by dragging and dropping configurable filters onto a visual pipeline. Unlike commercial alternatives which sometimes still rely on configuring cryptic text files for configuration, the experience is rife with elegant visualizations, feels intuitive and makes the behavior of the instrument explicit. These categorical improvements upon existing methods illustrate the power of a tool that is actively curated in the same setting where it is used for research. Though its inception required the design of an open source instrument from scratch, since the design files and software are in the public domain, the barrier for researchers to add similar-minded improvements as their needs arise is now much, much lower.

While Open Ephys has done a spectacular job open-sourcing the process of acquiring data from the brain, a complementary project to develop open-source hardware for orchestrating brain manipulation and stimulus control has taken root here at Cold Spring Harbor Laboratory. The instrument is called Pulse Pal, and it presently powers almost a dozen ongoing research projects by controlling lasers and generating simple psychoacoustic waveforms. Pulse Pal can be assembled at a soldering bench in under one hour, costs less than $200 in common electronic parts, and improves upon the functionality of commercial instruments costing thousands (eg. AMPI Master8). The project is in the final preparation stages for its public debut, and a more sophisticated derivative work based on newer surface mount technology is slated to converge with the Open Ephys project.

So far, both initiatives have been graduate student side projects – but graduate students eventually graduate. These projects are different from open source software tools which can often still do useful work out of the box if they are perfected and released without further active support. Even with thorough documentation, the assembly process in low quantity orders (as is almost always the case in an academic setting) requires expertise, and people willing to dedicate their time to learn the ropes. Finding these technically minded researchers is less difficult in institutions that foster an engineering culture like at MIT, where Open Ephys got its start – and a much taller order for institutions that specialize in non-engineering disciplines. The instruments could be produced commercially, but it remains an open question whether a business model based on open source scientific instruments can survive on its profits alone. Regardless of whether they are actually produced, the availability of transparent, quality instrument designs in the public domain has the potential to transform what possibilities researchers think to entertain, and how well they understand the black-boxes that empower their research. The public availability of these designs will also encourage commercial instrument designers to innovate more quickly to stay above the bar.

Behavioral systems neuroscience research is critical to understanding how the brain functions in health and in disease; yet as a field, it is especially throttled by the sophistication of its instruments. Perhaps, a family of rapidly evolving open source tools can leverage good ideas contributed by the research community at large, allow more ambitious research to proceed in settings with tight funding, and generally bridge disciplines to un-throttle our rate of progress along several fronts in the quest to understand the brain.

Natural pearls are extracted from oysters, a form of bivalves. Diving for pearls and capturing the unsuspecting oyster used to be the predominant industry in some regions, such as the Persian Gulf. However, not every oyster houses a pearl. This is because pearls first begin as a useful layer to protect an oyster; the formation results from a biological process, which starts when an oyster encounters a foreign particle.

The inner layer of a two-part shell of an oyster (kept open by a ligament so that the oyster can eat) is made from a substance called nacre. This material is produced by a vital organ called the mantle. If a foreign particle manages to enter the oyster, it can irritate¬ the mantle; this is the beginning of a natural pearl. The oyster reacts, and its man¬tle covers the foreign substance with coatings of nacre, which ultimately shapes into a pearl.

A pearl is then an obtrusive, foreign particle coated with several layers of nacre, or mother-of-pearl, which is responsible for its luster. Often, pearls have an irregular shape and are known as baroque pearls. But it is the perfectly rounded pearls that are the most valued. There is a claim that it acquires a round shape because of a turning movement, resulting in an even deposition of nacre on its surface. The surface of a pearl has been examined under a scanning electron microscope, and a saw-tooth texture has been observed that perhaps helps the pearl to rotate as it develops, resulting in the prized sphere.

So not all pearls are round and not all oysters have pearls. In the earlier days, they were not manufactured artificially either, and the natural pearls were not cut, faceted or polished. These organic jewels were also delicate to handle because their soft structures are not protected once extracted from the oyster. Nicely rounded pearls were therefore rare, and pearls in general, were quite expensive. They also had a human price; the pearl divers had to endure many hardships, spend months at sea surrounded by hostile sea creatures with no fresh water to rinse their malnourished bodies. They suffered from frequent, often fatal, illnesses. During colonial times, many of them were treated inhumanely, several died, and the ones that survived had to accept low wages.

Now, of course, we have mastered the art of tricking oysters. Pearl harvesters are able to produce cultured pearls by opening the shell of an oyster, creating a small slit in the mantle tissue, and introducing irritants that nucleate into lustrous pearls. Manufacturing them has crippled their value because they are no longer rare. However, overharvesting has caused a severe decline in oyster beds.

Formation of pearls is an interesting phenomenon, physically and biologically, because some of these organic items display dazzling spherical symmetry. And yet, chemically, pearls take on an unarresting personality of aragonite calcium carbonate, water, and an organic binding material. These simple ingredients combine when an oyster starts to feel uneasy due to a foreign object inside its shell. And this is the key: the oyster has to be annoyed else you will only get a hollow shell. Perhaps the Shakespearen phrase should be reworded to ‘the world is your inconvenienced oyster’.

Each country’s tax treaty is slightly different, but a good example of a treaty provision that creates a tax exemption for some foreign scientists can be found in the U.S.-Spain tax treaty. Article 22(1)(a) of the treaty states:

In plain English, this means that Spanish researchers who come to the U.S. for the purpose of: (1) studying; (2) training; or (3) engaging in research (if that research is paid by a grant or fellowship from a government agency or not-for-profit institution); are entitled to an exemption from taxation for all or some of their income. The amount of the exemption is equal to: (a) the full extent of any payments made to the scientist from abroad for the purpose of her maintenance; (b) the full extent of the grant or fellowship she receives; or (c) $5,000 for any income based on personal services that is not covered by an exempt grant, fellowship or payments from abroad.

IRS interpretation

A word of caution: the U.S. Internal Revenue Service (IRS) frequently examines, or audits, individuals who claim treaty-based tax exemptions on their tax forms. IRS examiners often interpret the treaty provisions very narrowly. For example, IRS examiners sometimes take the position that Spanish researchers are only entitled to a $5,000 exemption, even if they receive a fellowship from a not-for-profit institution. This position is based on a common misunderstanding among IRS examiners, in which they assume that the $5,000 limitation on the exemption for personal services is also a limitation on the exemption for fellowship income. This interpretation is not supported by the language of the treaty, or by the IRS’s own interpretation as set forth in IRS Publication 901 regarding U.S. tax treaties. When confronted with legal arguments regarding the language of the treaty and IRS publications, IRS examiners often concede that the $5,000 limitation on the exemption for personal services does not apply to the exemption regarding fellowships.

W2 vs. 1042s

Exempt income should be reported by the hosting institution on IRS Form 1042s instead of on the scientist’s W2. Scientists should be careful to consult with their institution’s payroll department immediately if they believe that some or all of their income has been reported on the wrong form. IRS examiners generally give substantial weight to a hosting institution’s decision to report a scientist’s income on the W2 instead of 1042s, even though it is well known that these institutions (like other employers) often inadvertently misclassify their researchers’ income on tax forms. In many cases, the institution’s payroll department might make an honest mistake in determining that a researcher is not entitled to an exemption. These kinds of mistakes can cost a scientist dearly if the IRS denies the exemption on the sole basis that the fellowship income was reported on the scientist’s W2 instead of 1042s. Attorneys have successfully argued that fellowship income should be exempt even if it was misclassified on the scientist’s W2, but IRS examiners in some cases may demand that the hosting institution issue a formal correction in order for an exemption to be granted.

Get a Second Opinion

As discussed above, several countries’ tax treaties with the U.S. contain similar provisions, but each treaty is slightly different. Scientists should carefully review their country’s treaty and consult with an attorney or accountant if they are interested in exploring whether they qualify for the exemption. Even if a representative of the hosting institution��s payroll department argues that the scientist’s fellowship income is not exempt based on her home country’s tax treaty, she should consult with an outside professional if she believes she has a good faith argument for an exemption. If faced with an IRS examination, scientists should be sure to consult with an accountant or attorney who has direct experience dealing with tax exemptions for fellowship income, in order to avoid any missteps in responding to the audit.