Until a few years ago, it was known that one of the principle chemical processes of epigenetics was to add a small chemical modification to genes. The process is called methylation, which adds a cluster (group) of methyl (an organic carbon, CH2) to the DNA base cytosine. The chemical name is 5-methylcytosine – 5mC. Adding 5mC to a gene turns it off; removing it turns the gene on. This is fundamental to the way cells dynamically alter the expression of DNA to adapt to the environment.

Just a few years ago it was discovered that there is another form of methylation, this time including a water-like molecule known as hydroxyl (OH). The name for this is 5-hydroxymethl-cytosine, the 5-hmC mentioned above. The take-home here isn’t the names or even the chemistry, but the fact this second form of methylation has been shown to be very important in how cells differentiate into different types. This is especially true for stem cells, which to various degrees are ‘blanks’ that epigenetic factors – likely through 5-hmC – are guided to differentiate into adult types of cells such as muscle or nerves.

While it required three paragraphs of preamble to get back to 5-mC and 5-hmC here is the real news: While scientists were aware of these two types of methylation, they had great difficulty in separating them within the cell and on DNA. That’s where the discovery of a new method for distinguishing both types during the sequencing of DNA comes in. The technique was developed in a collaboration between scientists at Cambridge University (Cambridge, UK) and Babraham Institute (Cambridge, UK), and published in the journal Science [26 April 2012, paywalled, Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution]. This work represents an important advance of genetic sequencing technology into the realm of epigenetics. By analogy, it is something like creating a new way of using a microscope through which the unknown is penetrated by a different perspective. While in one sense this tehcnique, which has the unmemorable name of oxidative bisulfite sequencing, is not ‘big news’ for the wider world, it could very well be one of those ‘keystone’ techniques that makes it possible to (eventually) answer questions such as “How do stem cells become adult cells?” or “How does the genetics of cancer cells go off the rails?” The field of epigenetics is in its infancy, this kind of advance in technique and technology gives it a lot more room to grow.

The race to put a man on the Moon between the United States and the Soviet Union is long over. NASA got there first, national glory was achieved and then NASA and the American public lost interest in the Moon. The Russians’ all out space effort collapsed with the Soviet Union and is slowly rebuilding with intermittently successful commercial rocketry. In the follow-up to the Moon as the Next Big Thing, the International Space Station (ISS) is ‘completed’ and doing far less science, or anything else, than was expected. The NASA shuttle craft that were to establish healthy trade between Earth and the ISS – are finished, history, already on their way to becoming museum pieces. These days, the squabbles over mission priorities and budgets at NASA are tawdry and dispiriting. Budgets for space are riddled with cuts and complex politics in most of the other countries that have a presence in space – except China. China appears to be gung ho about space (if the right expression is gung ho, which in the original Chinese are the two words, ‘work’ and ‘together’); but strangely there’s hardly any reaction to China’s space achievements from governments, the media or otherwise. It appears there will be no space race with China. It’s as if we – the professionals, enthusiasts and the non-space engaged public – have mostly lost interest.

What seems to be missing is motivation, a real and powerful motivation to once again garner the attention and interest of the public in exploring space. With the exception of the Chinese, national pride seems to be out of the picture. Science, for all its true value, has never produced much general passion. There is always economics, but so far the exploration of space is a massive loss operation – as if it had any serious economic intention to begin with. Now that could change, perhaps in a big way.

Enter these gentlemen, multi-multi-millionaires and billionaires all: Larry Page, K. Ram Shiram, and Eric Schmidt (Google), James Cameron (film director), Ross Perot Jr. (Perot Systems), Charles Simonyi, Paul Allen (Microsoft), Peter Diamandis (X-Prize), Burt Rutan (aerospace engineer), Eric Anderson (Space Adventures). They have aligned with a company called Planetary Resources, Inc. that has the express purpose of exploring about 1,500 of the 9,000 or so Near-Earth Asteroids (NEA) with the intention of extracting from them valuable resources such as water and platinum. The company predicts that the value of such extraction will be measured in trillions (dollars, presumably).

Although the company was founded in 2009 by Peter Diamandis (a key figure in the personal space flight industry) and Eric C. Anderson (co-founded Space Adventures with Diamandis), the public launch was a rather eagerly anticipated formal announcement made from the home base in Seattle (Washington, USA) on April 24, 2012. In the years since 2009, the company’s narrative has been developed and more importantly the impressive list of names was added to the support roster. The announcement made a relatively big splash in the news for a company that as yet has far more plans than product. So, what have we here?

First, a disclaimer: Three years ago I wrote a novel precisely about the subject of commercial resource extraction from Near-Earth Asteroids, which means I’ve done some homework and have a bias in the direction of thinking the company’s plans are reasonable and feasible. That said, I’m aware that Planetary Resource’s notion of ‘mining asteroids’ is borderline fodder for late-night comedy. Some say it is crazy; et cetera.

I would say that for most people the idea of mining asteroids is brand new, and I use the word ‘brand’ intentionally. As a rule of thumb, most people know about exploring the Moon; most people are aware of plans to reach Mars – but the asteroids? The notion of reaching asteroids with orbits in the neighborhood of Earth has been a fringe idea. There is an important exception: In 2009, a report by the NASA commissioned blue-ribbon committee, the so-called Augustine Report, examined the future of the American humans in space program and recommended that NASA make reaching an NEA a priority. The recommendation was generally disregarded. The choice of a mission to reach an NEA, compared to return to the Moon or a major deep-space mission to Mars has had little or no constituency. However, some of the people involved with Planetary Resources noticed the Augustine Report recommendation.

To explain all the comparative reasoning behind an NEA versus other missions would require a book; I won’t attempt much here except some key points.

Ease of access: Some of the asteroids that have orbits approaching Earth are at their nearest point relatively as close to Earth as the Moon. Although the navigation is more complicated, reaching these asteroids is not much more difficult or time consuming than reaching the Moon. The major factor is that asteroids have no significant gravity. Unlike the Moon, which has one-sixth the gravity of Earth, there is no gravity well to fight on the way onto or off an asteroid. This is a huge savings in energy and simplifies local maneuvering.

Resources: There are many kinds of asteroids, three are the most common. Some are composed primarily of metals (M-type), mostly nickel-iron, mixed with stone and other metals and minerals. Others are composed mostly of carbon-based materials (C-type) including complex hydrocarbons (e.g. methane, ethane, etc.) and materials containing water. More than 75% of asteroids are C-type. Then there are asteroids composed mainly of stony material, often high in silicon mixed with a wide range of minerals. All types of asteroids contain material of commercial-industrial value, but the two materials that are singled out are water and precious metals. Water is arguably the most important because of its potential as a source of rocket fuel (hydrogen and oxygen), and oh yes, life requires it. Water is unfortunately quite heavy, and lifting it off the Earth’s surface is very expensive. The Moon has some water in deep polar craters, but from what we know; it is not available in industrial quantities and would still have to be lifted out of the Moon’s gravity well.

Precious metals – gold, silver, platinum, palladium, ruthenium, rhodium, osmium, and iridium – are of high commercial value, relatively compact for value, and are present in asteroids in what are believed to be accessible conditions. That is, unlike the Moon, the concentrations are relatively high – possibly high-grade ores – that can be extracted and potentially processed on site. Of course the big draw here is these metals are of extreme value on Earth for cosmetic or industrial uses. A thousand kilos of platinum is worth about $50 million at today’s spot price. Lifting quantities such as that from an asteroid for transportation back to Earth is feasible and potentially profitable.

That’s where Planetary Resources, Inc. comes into the picture.

A single 500-meter platinum-rich asteroid contains the equivalent of all the Platinum Group Metals mined in history. “Many of the scarce metals and minerals on Earth are in near-infinite quantities in space. As access to these materials increases, not only will the cost of everything from microelectronics to energy storage be reduced, but new applications for these abundant elements will result in important and novel applications.”
[Source: Planetary Resources press release]

In short, extracting water especially for rocket fuel and human environment supply and mining of valuable ores is the core of Planetary Resource’s plans. Sounds pretty good, but of course how this is to be done – that’s the thing isn’t it? The good news here, which you would expect from people who are both visionary and carefully rich, is that the company isn’t planning a gold rush. Contrary to some of the gushing media coverage, the program spans many years, perhaps decades, and takes everything step-by-step. The first step is to select, explore and analyze candidate NEAs for their commercial value. This will be done by robotic probes – asteroid prospectors. Planetary Resources is already building the first of these probes called the Arkyd-100 Series, which will orbit Earth and participate in the study of NEA candidates. A follow-up series, Arkyd-300, will journey to the target asteroids to conduct on-site exploration. Launch of the first robotics will be in 2013-2014 aboard various rockets.

Common intuition would caution not to minimize the technical difficulty of what Planetary Resources proposes to do. Launching expensive probes is never a sure thing. Getting them to their targets is not trivial. The technology for gathering the appropriate information, especially material samples, is still largely experimental. Returning samples to the Earth is also difficult. Then there comes the whole business of seriously extracting material from the asteroids – the technology for which exists only in Earth-based experience and the imagination of engineers. Let’s put it another way, the path to profitability is very long and uncertain. Why then are the quite intelligent and successful people who support Planetary Resources willing to put up their name and their cash?

Some of them have spoken about it, but I’ll summarize and extrapolate. In a nutshell: The vision of mining asteroids combines some of the romance of space exploration and development of the human race with the notion of making a great deal of money. It replaces the fading motivations of nationalism, the semi-obscure goals of science, and the abstract ideas about building things for Earth in space with something tangible and lucrative. I suppose one could kvetch about greed and profit motive as a mass motivator for developing our solar system, but few who have thought about it would argue that it would, sooner or later, become the ongoing driver.

Meanwhile, the Planetary Resources program will probably have a couple of important effects: It will provide a continuing story that can be followed by the media and the public. It will also require – and put pressure on – governments and space agencies to collaborate with and support the effort. It’s no secret that Planetary Resources will need to work with the science, technology, expertise and funding of academic and government sources. These folks may be rich, but not that rich. So, the effort to reach the asteroids and develop extraction techniques will be a massive joint effort – or it won’t work at all.

I have no idea whether this will happen. I hope so. In a sense, Planetary Resources, Inc. represents the human race getting off its collective butt and once again trying to do something really ‘out there’ – difficult, challenging, and at least in the long run exciting. There’s no need to romanticize the development of space to make it exciting, making a lot of money will do.

This new type of DNA is, for one thing, distinguished by existing outside the chromosome. Finding bits and pieces of DNA separated from the chromosome, in itself, isn’t too surprising. It’s a bit like finding flotsam along the shoreline; you expect some loose bits of material to be floating around in the cell. However, what scientists now call an extra-chromosomal circular DNA (eccDNA) may be something more significant.

One type of eccDNA, dubbed microDNA and recently discovered by scientists at the University of Virginia (USA) and the University of North Carolina (USA), is found in great numbers of relatively short strands (200-400 base pairs – the combinations of Guanine-Cytosine and Adenine-Thymine) in non-repeating sequences. Their finding has just been published in Science [08 March 2012, paywalled, Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues]. Where these ‘pieces’ of DNA come from has not been verified, but geneticists think it could be from cutting bits of chromosomal DNA (excision), replication of short DNA sequences, or reverse transcription of certain RNA. The research tends to show that microDNA mostly comes from deletions, which would indicate they are part of the repair and maintenance process for DNA.

The big question is what – if anything – are microDNA pieces for? Do they play an active role in the repair process, or are they the result (detritus) of that process? They do seem to be associated with gene variation between different types of cells. So far the researchers have found microDNA in human and mouse cells, but it may not be universal. At this point there are more questions than answers, although the pattern in genetic discovery tends to lead from the simple toward the complex. It is possible that microDNA and other eccDNAs have an important role in the genome – or not. It’s these kinds of questions that keep geneticists on their toes.

Google calls it Project Glass. You may call it futuristic, fantastic or just let’s wait and see. These highly sophisticated computerized specs are intended to receive and process information from the Web and display it to one eye. It’s called augmented reality. For example, using voice commands, you can ‘ask the glasses’ to locate a nearby French restaurant, say in New York City. The glasses will more or less instantly show a list of restaurant names. You call out one of them, and a map to the restaurant, based on your present location, will appear. Or something like that. Since nobody except Google employees have actually used these glasses, the details are unknown. What is known is that the glasses will be able to operate like a phone, send video (from a built-in camera), and do – Google searches. Much depends on the reliability of voice control, the quality of the image on the glass (under various lighting conditions), and whether people can get used to having wearable computers participate in their reality. It’s a fascinating concept, very sci-fi of course, until it isn’t sci-fi anymore, which may be relatively soon. Imagine half the population running around with this kind of phone/computer and nobody knowing whose recording what while talking to somebody on the street…

As is often the case with a medical advance surrounded with hype, there are doubts and concerns. A major new study by Johns Hopkins medical research in Science Translational Medicine [02 April 2012, paywalled, The Predictive Capacity of Personal Genome Sequencing] involving thousands of identical twins is outspoken about the failure of personal genomic analysis to identify a person’s risk for most common diseases. In fact, it flat out warns people not to uncritically accept negative genome test results.

Since the personal genome sequencing business is turning into a major growth industry and the stake of research on the links between genes and disease is enormous, this study is bound to be not only something of a knowledge-bomb, but also instantly controversial.

The basis of the study is recorded data on thousands of identical twins in the registries of Sweden, Denmark, Finland, and Norway along with the Twins Registry of the American National Academy of Science. Because identical twins are thought to share identical genomes, it should follow that if one twin presents a genetic based disease, statistics should indicate a prevalence of the same disease in the identical twin. The researchers used information on 24 diseases (cancer, autoimmune, cardiovascular, genitourinary, neurological and obesity-associated). Statistical models were created to predict the risk of each disease based on typical doctors’ diagnosis.

The results need a careful reading: A whole genome sequencing could indicate an increased risk of at least one disease, but most people would get negative test results for the majority of diseases in the study. Put another way, even for diseases with links to a genetic foundation, the presence of those genes in one individual is not a satisfactory predictor for another individual. Statistically, for example, if 2% of women show a genetic predisposition for ovarian cancer, it does not mean that the other 98% who test negative for the gene won’t get ovarian cancer.

You may have noticed that this is not a blanket denial of genomic analysis. The researchers are careful to say that genomic information can be very helpful for people with families who have a strong history of a particular disease. In addition, certain diseases that are shown to be particularly related to genetic variation such as coronary heart disease in men, thyroid autoimmunity, type 1 diabetes and Alzheimer’s disease are more likely to be accurately predicted by genomic analysis. This list is likely to grow as medical research advances.

However, in the broader perspective the ability of genomic analysis to predict a limited set of diseases leaves most people and most diseases unpredictable by this method. For example, while some hereditary cancers are gene influenced, hereditary cancer is rare. Most cancer is caused by genetic mutations acquired by environmental exposure, lifestyle choices (like smoking) and random errors in genes that occur during cell division. As one of the lead researchers, Bert Vogelstein of Johns Hopkins Kimmel Cancer Center (Maryland, USA) puts it:

We believe that genomic tests will not be substitutes for current disease prevention strategies. Prudent screening, early diagnosis and prevention strategies, such as not smoking and removing early cancers, will be the keys to cutting disease death rates.
[Source: EurekAlert]

If you’ve had any exposure to how the brain and nervous system works, you probably know about synapses – the juncture where the end of one neuron almost meets the beginning of another neuron. The synapse is two neurons and the gap between them, the point where either chemical neurotransmitters or gap junctions for electrical current carry a nerve signal from one neuron to another. I’m simplifying here in order to get at something that significantly complicates the notion of a synapse. The traditional picture of a synapse tends to obscure the fact that the ‘gap’ (synaptic cleft) between neurons isn’t self contained – it’s part of something outside the neurons. And what is that ‘something’ outside the neurons? Again, traditionally, this has been pictured as the realm of glia, the ‘other’ cells of the brain and nervous system. There are seven kinds of glia and they’ve been considered for a long time to be mainly structural (holding the neurons in place) or supportive (providing nutrients and other housekeeping activity for neurons). In general, the various glia were considered not very interesting compared to the neurons and certainly were not important to the signaling operation of the nervous system. That evaluation is changing and may profoundly affect how we believe the nervous system works.

It’s been known for some time that there are roughly as many glia cells in the brain as there are neurons. Few thought this was significant, although in general, where there is a lot of some material, Nature tends to put it to multiple uses. It was roughly during the 1990’s that researchers began to discover other functions for glia, the most significant was arguably that instead having a passive role in neurotransmission, some forms of glia – astrocytes in particular – have an intimate relationship with neurons in the role of modulating neurotransmission. One of the leaders in these discoveries is Miaken Nedergaard, professor of neurosurgery at the University of Rochester Medical Center (New York, USA). Her pioneering work demonstrated that astrocytes participate in communication with neurons, albeit in a passive role.

The basic idea for astrocytes’ role in the synapse is to regulate the concentration of potassium ions in the synaptic cleft – translated: A signal travelling from one neuron to the other across a synapse may use chemical ions (electrons), including those of potassium and calcium, to transfer the signal. When this happens, astrocytes perform the function of withdrawing ions (potassium) so that the signal will stop, in preparation for the next signal. It was originally assumed that the stopping was controlled by the neurons. The Nedergaard team’s newest research indicates that astrocytes can actively (that is, on their own) stop the signal by withdrawing ions. In a recent paper to be published by Nature Signaling [ April 2012, paywalled, ] the indication is that astrocytes in some way orchestrate the synaptic firing of neurons so that ‘noise’ (random or unwanted neuron activity) is minimized. Neuroscientists call this ‘maintaining synaptic fidelity’ (something like a noise filter on a hi-fi system).

How astrocytes do this ‘orchestration’ and how this all fits together in terms of functioning synapses – to say nothing of how all this fits with general brain and nervous system activity – remains to be seen. As Nedergaard puts it, “Astrocytes are integral to the most sophisticated brain processes.” Indeed, if her team’s findings are corroborated, it implies that the functioning of synapses is more complicated than was already thought. It adds to the notion that there is a ‘third partner’ in the operation of synapses, the astrocytes. What that brings to the party, and why, leaves open questions of potentially high impact. Neuroscientists have already coined a term for this model of neuron activity back around 2006: the tripartite synapse, consisting of the presynapse (axon neuron), postsynapse (dendritic neuron) and glia (astrocytes). Since then, research such as Nedergaard’s continues to show more involvement by astrocytes in modulating how synapses work.

One of the biggest unknowns in neuroscience, especially for the working of the human brain, is how the all-important connections (the synapses) in the neural system (the network of neurons) are organized and cooperate. It appears that the formerly ignored glia may be part of the answer, but the answer, whatever it is, will be yet more complicated. There may be a reason why two of the most complicated intelligences on the planet – humans and elephants – also have the greatest percentage of glia in the brain.

The key to the Envia technology is a solution to the efficiency (or inefficiency) of the battery’s cathode and anode components. In simple terms, batteries work by the generation of electrical ions, in this case lithium ions, which move from the anode (negative) side of the battery to the cathode (positive) side, providing a stream of electricity. The cathode and the materials used to make it were one part of the problem. Earlier research found that incorporating manganese into the materials of the cathode increased the efficiency – called energy density – of the battery. The Envia team uses that improvement and turned their attention to the anode and the Argonne Lab research. Here they found that by blending silicon into the typical graphite material of the anode increased the efficiency, but there was a problem – silicon in battery fluid ‘swells.’ The result was a battery that could only be recycled (recharged) at most ten times. The solution was to coat the silicon in carbon and mix that with carbon fibers. This protects the electrical properties of the silicon while increasing the recharging cycles up to 400 times (so far).

The result of these changes, according to the company and testing by the U.S. Naval Surface Warfare Center (Crane, Indiana), is an energy density of 400 watt-hours per kilogram at a cost of about $150 per kilowatt-hour. Most current lithium-ion battery packs used in electric cars run about 120 watt-hours per kilogram. The higher energy density allows for smaller and less heavy battery packs, which also makes cooling more efficient. (Lithium-ion batteries are notorious for ‘thermal runaway’ – bursting into flame.)

This all sounds very promising. It certainly adds some spice to the competition. The fact that a major car manufacturer and the U.S. government have a hand in seeing this innovation to market lends credibility. As ever, however, the technology is still several years of testing and manufacturing process development away from appearing in new model cars. It’s appropriate to be enthusiastic about this technological fix, but not ecstatic.

In the moderately successful Steven Spielberg film Minority Report the hero of the story is seen walking down a street where the advertising signs recognize his face and change their ad message accordingly. That scene won’t be science fiction much longer. Hitachi has already recognized that its prime market for the new system will be ‘suitable for customers that have a relatively large-scale surveillance system, such as railways, power companies, law enforcement and large stores.’ Face recognition has been an important research area for many decades; it was only a matter of time as the capability and accuracy rates increased to a point where systems like Hitachi’s could be used commercially.

As with all security surveillance systems, the applications can have an impact in many directions. One is obviously security, keeping the bad guys out. Of course, much depends on who is classified as a bad guy. Another direction is keeping the good guys in line, as in watching protest crowds or other group activities and using this technology to identify the participants. In countries where the courts and legislators are reasonably fair, this sort of massive increase in the effectiveness of surveillance will probably result in legal challenges based on false recognition, invasion of privacy and illegitimate application. Elsewhere, and anywhere unless detected, this adds to the sensor arsenal of those with the money and authority to survey anything.

Actually, the whole incident goes deeper than that. It shows how modern science is conducted, warts and all. The original blockbuster announcement was indicative of the pressure on scientists to make an impact with the media. Funding, reputation and institutional positioning all play a role in how such highly unusual and likely very controversial discoveries are handled. In this case, the OPERA organization tried to say that its findings were preliminary, but that was mostly obscured by the explosive coverage – which was predictable. Once the announcement was made, two other aspects of normal scientific procedure kicked in – criticism and skepticism were voiced, and new experiments were planned and carried out. The new experiments, some of them conducted by the OPERA team, failed to validate the faster-than-light speed of neutrinos. Then, under internal audit looking for causes of a potential misreading of data, the faulty cable connection was discovered. Finally, under censure from a majority of the members of the OPERA consortium, ‘heads rolled.’ It wasn’t a unanimous vote of no-confidence, but sufficiently clear to indicate the necessity of resignation by the two men who were the public face of the original announcement.

Sometimes the ‘self correcting’ mechanisms of science work well. For the exciting but unfortunately erroneous case of the faster-than-light neutrinos, this seems to be true.

Back then I learned, “You can never get enough disk space.” I’m not sure that’s true even now, and with 10 terabyte disks in the next few years, there’s a distinct probability that more people will simply load whatever they want on their disks and forget about storage space. Unless they are professional media artists, our normal but trivial usage will hardly burn through a single disk.

Speaking of burning, the new Seagate technology achieves these mind-boggling storage capacities by using a very sophisticated laser arrangement to heat the metal of the disk just prior to the magnetic imprinting of the data. It’s called heat-assisted magnetic recording (HAMR) and was based on the finding that if the metal is pre-heated, it is much more reliably magnetized and is much less apt to flip bits in the presence of normal operating temperatures. The laser used is very tiny, small enough to heat an area of only 100 nanometers, but the area heated needs to be about 25 nanometers. So the engineers got busy and devised a tiny parabolic mirror to focus the laser beam and further tightened it with a miniscule gold antenna that produces a final heating spot of 30 nanometers. So, in a way, the technology is back to ‘burning disks.’ However it’s done, we definitely seem to be heading toward the day when the question is not ‘How many angels can dance on the head of a pin?’ but ‘How small a device can hold all of human knowledge?’ Seriously.