The Spamlist!

A model of DNA. Image: Research.gov

By Olivia Solon, Wired UK

A combined team of physicists and biologists aim to build a directional dark matter detector using strands of DNA and gold.

Dark matter is a hypothesized type of matter which accounts for much of the mass of the universe. It cannot be seen, but its existence is inferred from its gravitational influence on visible matter and the structure of the universe. Some of the most popular models of dark matter suggest that it exerts itself on galaxy clusters and surrounds the Earth like a sea as it travels around the Sun, which in turn is slowly traveling towards the constellation Cygnus as it rotates around the galactic center.

If this is the case, Earth should experience a “headwind” of dark matter in front of it (coming form the direction of Cygnus) for half of the year and a tailwind for the other half of the year, depending on where it is on its orbit around the Sun.

Many different groups are working to try and detect dark matter using expensive detectors in deep underground caverns, which protect them from radiation that could otherwise pollute the signal. They are focusing on finding the unique signature that the “sea” of dark matter supposedly produces as the Earth orbits the Sun. This should change depending on what point in the year it is and also throughout the day as the Earth rotates on its axis. A dark matter detector should be able to sense the direction change as the Earth rotates each day.

A combined team including Katherine Freese, an astrophysicist from the University of Michigan and geneticist George Church from Harvard say they can overcome challenges with detecting dark matter by using DNA to find the dark matter particles, called weakly interacting massive particles, or WIMPs.

They have created a detector using a thin gold sheet with many single strands of DNA hanging from it. The theory is that a particle of dark matter will smash into the heavy gold nucleus, pushing it out of the gold sheet and through into the DNA “forest”, knocking the strands out as it travels.

These strands fall onto a collection tray. Each of them has a unique identifier showing where they were located on the gold sheet, so researchers can reconstruct the path of the gold particle with incredible precision. The detector is made up of hundreds of thousands of these sheets placed between Mylar sheets, using around a kilogram of gold and 100g of single-strand DNA on a square-meter array.

DNA is useful in this context because its structure will separate vertically with nanometer resolution — it wills separate to the nearest nucleotide — the smallest structural units of DNA. This is many orders of magnitude better than is currently possible. Secondly, the detector can work at room temperature, rather than needing cooling. Finally, the Mylar sheets make the detector directional — each sheet should be able to absorb the gold nucleus of its energy after it has passed through the “DNA forest”. Higher energy nuclei from background radiation would pass through several of the leaves of Mylar, allowing them to be identified and excluded.

If a dark matter particle hits a gold nucleus in on direction, it will propel it into the DNA forest. If it strikes in the other direction, it will head straight into the Mylar sheet and be absorbed.

This highly unconventional approach has a number of major challenges. Firstly, it is not clear how rapidly-moving gold nuclei will interact with the DNA. The team will need to study this before building any such detector. Secondly, it will be challenging to make DNA strands long enough. At the moment, off-the-shelf DNA strands have around 250 bases. The detector would need strands consisting of at least 10,000 bases in order to absorb the energy of the gold nucleus. They would also have to hang straight down and not curl up, which would require some sort of DNA comb or “hair straightener”. One suggestion is to place a tiny magnet at the end of each strand that would allow it to be pulled downwards.

You can read about the detector in more detail in the paper, entitled New Dark Matter Detectors using DNA for Nanometer Tracking.

Source: Wired.co.uk

A little reminder that the preorder for this shirt ends Thursday, which is very soon!  Only a couple more days to guarantee this classy shirt for your body.  If you would like a different color shirt or anything like that, just lemme know!

Music Chat Corner

Welcome to the Music Chat Corner!  So, the other night I went to a Spineshank show the other night and it was great, but holy crap, the opening band was amazing!  Their name is Mureau and they are a perfect mix of everything I seem to enjoy in music these days.  Part Meshuggah, part hardcore, part metal and oh-man-so-good.

Here’s a great song by them that nicely tells the story of what Mureau is all about: California.  I talked to the singer and one of the guitarists and they are super cool dudes.  So if you like super cool dudes that write super cool metal music, then give them a listen and lemme know if you like them!

Standard VARs suggest that the effect of government spending on output lasts only as long as the government spending.

That is from Valerie Ramey.  Via Garett Jones here are her Powerpoints on the DeLong-Summers argument.

When the head cook of Viet Taste in Falls Church gets an order for a plate of Bun Cha Hanoi, he knows exactly what to do.

He has cooked the pork dish — with vermicelli noodles, greens and pickled vegetables — countless times and knows exactly how much fish sauce and fresh herbs to add.

Outside his kitchen, the customers, most of them Vietnamese, are expecting authentic Vietnamese cuisine. German Sierra, born in Honduras, makes sure they get it.

Here is more, interesting throughout.

High speed rail, especially California’s project, looks to me to be monorail economics, a costly boondoggle whose appeal lies not in rational calculation (also here) but in the desired of some politicians (and voters) to feel visionary and sexy. In theory, CA HSR  might work but the inevitable reviews, delays, lawsuits and special interest payoffs make the prospects of a beneficial project look dim, demosclerosis kills.

Slow speed rail, however, i.e. freight transport, isn’t sexy but Warren Buffett is investing in rail and maybe we should as well. In particular, there are basic infrastructure projects with potentially high payoffs. Congestion in Chicago, for example, is so bad that freight passing through Chicago often slows down to less than the pace of an electric wheel chair. Improvements are sometimes as simple as replacing 19th century technology with 20th century (not even 21st century!) technology. Even today, for example:

…engineers at some points have to get out of their cabins, walk the length of the train back to the switch — a mile or more — operate the switch, and then trudge back to their place at the head of the train before setting out again.

In a useful article Phillip Longman points out that there are choke points on the Eastern Seaboard which severely reduce the potential for rail:

…railroads can capture only 2 percent of the container traffic traveling up and down the eastern seaboard because of obscure choke points, such as the Howard Street Tunnel in downtown Baltimore. The tunnel is too small to allow double-stack container trains through, and so antiquated it’s been listed on the National Register of Historic Places since 1973. When it shut down in 2001 due to a fire, trains had to divert as far as Cincinnati to get around it. Owner CSX has big plans for capturing more truck traffic from I-95, and for creating room for more passenger trains as well, but can’t do any of this until it finds the financing to fix or bypass this tunnel and make other infrastructure improvements down the line. In 2007, it submitted a detailed plan to the U.S. Department of Transportation to build a steel wheel interstate from Washington to Miami, but no federal funding has been forthcoming.

Longman points out that:

Railroads have gone from having too much track to having not enough. Today, the nation’s rail network is just 94,942 miles, less than half of what it was in 1970, yet it is hauling 137 percent more freight, making for extreme congestion and longer shipping times.

I believe that there are valuable infrastructure projects but I am dispirited by the fact that these projects have been valuable for a long time and progress is very slow. Why haven’t the gains from better infrastructure already been taken? Why haven’t the $500 bills been picked up? It’s worrying that the bullet boondoggles get all the attention while simple things like updating 19th century technology is ignored. And it’s not just rail, sewers and the water supply are another example. Consider:

The average D.C. water pipe is 77 years old, but a great many were laid in the 19th century. Sewers are even older. Most should have been replaced decades ago.

Does that sound like the infrastructure of an advanced nation?

We need better, more trustworthy, institutions for infrastructure investment. As I said in Launching:

Our ancestors were bold and industrious–they built a significant portion of our energy and road infrastructure more than half a century ago. It would be almost impossible to build the system today. Unfortunately, we cannot rely on the infrastructure of our past to travel to our future.

Hat tip: Mark at Observation Epidemiology.

A brief piece with the title of this post recently appeared in the NYTimes, and is an example of annoying phenomenon: advertising by advance announcement in popular media with reference made to a “forthcoming” article. The points raised are interesting enough that the reader deserves access to what might be more thorough analysis and discussion. I’m thinking the correlations indicated might be quite spurious. For what it is worth, in a study involving the usual gaggle of undergraduate volunteers, the authors claim to have:

…identified several features of Internet usage that correlated with depression. In other words, we found a trend: in general, the more a participant’s score on the survey indicated depression, the more his or her Internet usage included these (rather technical-sounding) features — for instance, “p2p packets,” which indicate high levels of sharing files (like movies and music).

Our second major discovery was that there were patterns of Internet usage that were statistically high among participants with depressive symptoms compared with those without symptoms. That is, we found indicators: styles of Internet behavior that were signs of depressive people. For example, participants with depressive symptoms tended to engage in very high e-mail usage. This perhaps was to be expected: research by the psychologists Janet Morahan-Martin and Phyllis Schumacher has shown that frequent checking of e-mail may relate to high levels of anxiety, which itself correlates with depressive symptoms.

Another example: the Internet usage of depressive people tended to exhibit high “flow duration entropy” — which often occurs when there is frequent switching among Internet applications like e-mail, chat rooms and games. This may indicate difficulty concentrating. This finding, too, is consistent with the psychological literature: according to the National Institute of Mental Health, difficulty concentrating is also a sign of depressive symptoms among students…

OTHER characteristic features of “depressive” Internet behavior included increased amounts of video watching, gaming and chatting.

My column for BBC Future from last week. The original is here.

Evolution made us the ultimate learning machines, and the ultimate learning machines need to be oiled by curiosity.

I hate to disappoint you, but whatever your ambitions, whatever your long-term goals, I’m pretty sure that reading this column isn’t going to further them. It won’t stop you feeling hungry. It won’t provide any information that might save your life. It’s unlikely to make you attractive to the opposite sex.

And yet if I were to say that I will teach you a valuable lesson about your inner child, I hope you will want to carry on reading, driven by nothing more than your curiosity to find out a little more. What could be going on in your brain to make you so inquisitive?

We humans have a deeply curious nature, and more often than not it is about the minor tittle-tattle in our lives. Our curiosity has us doing utterly unproductive things like reading news about people we will never meet, learning topics we will never have use for, or exploring places we will never come back to. We just love to know the answers to things, even if there’s no obvious benefit.

From the perspective of evolution this appears to be something of a mystery. We associate evolution with ‘survival-of-the-fittest’ traits that support the essentials of day-to-day survival and reproduction. So why did we evolve to waste so much time? Shouldn’t evolution have selected for a species which was – you know – a bit more focussed?

Child’s play

The roots of our peculiar curiosity can be linked to a trait of the human species call neoteny. This is a term from evolutionary theory that means the “retention of juvenile characteristics”. It means that as a species we are more child-like than other mammals. Being relatively hairless is one physical example. A large brain relative to body size is another. Our lifelong curiosity and playfulness is a behavioural characteristic of neoteny.

Neoteny is a short-cut taken by evolution – a route that brings about a whole bundle of changes in one go, rather than selecting for them one by one. Evolution, by making us a more juvenile species, has made us weaker than our primate cousins, but it has also given us our child’s curiosity, our capacity to learn and our deep sense of attachment to each other.

And of course the lifelong capacity to learn is the reason why neoteny has worked so well for our species. Our extended childhood means we can absorb so much more from our environment, including our shared culture. Even in adulthood we can pick up new ways of doing things and new ways of thinking, allowing us to adapt to new circumstances.

Exploration bonus
In the world of artificial intelligence, computer scientists have explored how behaviour evolves when guided by different learning algorithms. An important result is that even the best learning algorithms fall down if they are not encouraged to explore a little. Without a little something to distract them from what they should be doing, these algorithms get stuck in a rut, relying on the same responses time and time again.

Computer scientists have learnt to adjust how these algorithms rate different possible actions with an ‘exploration bonus’ – that is, a reward just for trying something new. Weighted like this, the algorithms then occasionally leave the beaten track to explore. These exploratory actions cost them some opportunities, but leave them better off in the long run because they’ve gain knowledge about what they might do, even if it didn’t benefit them immediately.

The implication for the evolution of our own brain is clear. Curiosity is nature’s built-in exploration bonus. We’re evolved to leave the beaten track, to try things out, to get distracted and generally look like we’re wasting time. Maybe we are wasting time today, but the learning algorithms in our brain know that something we learnt by chance today will come in useful tomorrow.

Obviously it would be best if we knew what we needed to know, and just concentrated on that. Fortunately, in a complex world it is impossible to know what might be useful in the future. And thank goodness – otherwise we would have evolved to be a deadly-boring species which never wanted to get lost, never tried things to just see what happened or did things for the hell of it.

Evolution made us the ultimate learning machines, and the ultimate learning machines need a healthy dash of curiosity to help us take full advantage of this learning capacity.

Or, as Kurt Vonnegut said, “We are here on Earth to fart around. Don’t let anybody tell you any different.”

Given my current preoccupation with my failing 70 year old knee joints, I was drawn to a brief piece by Elizabeth Pennisi with the title of this post.  Here I give a summary graphic and a few clips of her discussion:

…a number of musculoskeletal issues are traceable to our past, in particular to the switch to walking upright more than 7 million years ago…Shifting from a four-legged support system to a two-legged one put extra stress on the legs and vertebrae. Adaptations in the feet, knees, hips, pelvis, and spine accommodate these forces, but at a cost…vertebrae that break more easily, weaker bones, and feet prone to heel spurs and sprained ankles…A brief tour of the body reveals a number of design flaws, the legacy of our past…

Spine. Back pain is the leading health complaint in the United States. In dogs, horses, and even chimpanzees, the backbone is a series of vertebrae neatly stacked and evenly spaced to form a relatively stiff, gently curving beam…the human spine… is highly flexible and can even bend backward..this flexibility creates wear and tear on joint surfaces and predisposes us to osteoarthritis…One type of break, called spondylolysis, affects about 6% of the U.S. population and is a leading cause of lower-back pain in teenage athletes. In this condition, the neural arch – a triangle of bone that surrounds the spinal cord – detaches from the rest of its vertebra, allowing the spine to slip forward relative to the back of the pelvis, pinching nerves and causing pain…the problem lies in inadequate spacing between the joints connecting the vertebrae.

Feet. To cope with the added load on just two feet, the foot evolved a shock-absorbing arch by bringing what was a grasping big toe into line with the other toes. When that arch fails to form fully, as in people with flat feet, fatigue fractures can result.

Fragile bones. The added load on two feet also caused knee and hip joints to expand, creating more surface area to absorb foot-fall forces. But the joints—and vertebrae as well—evolved to be bigger by enlarging the spongy, inner bone and thinning the hard, outer bone. As a result, human bones are less dense than those of other primates. Bone…loses mass during adulthood. With humans having ever longer life spans, bones, particularly vertebrae, may become fragile and break spontaneously.

Bipedality leaves its mark in other parts of our bodies, too, for example in the difficulty of childbirth and in our vulnerability to rotator cuff injuries of the shoulder. loses mass during adulthood. With humans having ever longer life spans, bones, particularly vertebrae, may become fragile and break spontaneously.

The amount genes and the environment contribute to our behaviour varies across the country and a new study has mapped exactly where the differences lie.

As well as an interesting finding in itself, the study also highlights an important but often misunderstood point about heritability.

The map on the right is from the study, and generated by the freely available software the research team have created. It shows the results of a large twin study that has been carried out with the help of families across the country.

Twin studies allow us to work out the amount of influence the environment and genetics has on particular trait by comparing the outcomes in identical twins, who are as close as you’ll get to being genetically identical, and non-identical twins, who share only 50% of their genes.

The map shows how much genetic contribution there is to the difference in ADHD symptoms across the UK. You’ll note that genetics makes much more of a contribution to the difference in ADHD symptoms in London than in other parts of the country.

In other words, it’s daft to give a definitive answer about ‘how genetic’ ADHD is, because the expression of genetic tendencies depends on the environment.

That’s not to say that ADHD or any other mental disorder are completely flexible with regard to their environmental and genetics bases, as there are limits and these are likely to be specific to the problem.

But it is also the case that with complex outcomes like mental illness it’s impossible to say that a particular one is solely a ‘genetic disorder’.

There’s a good write-up of the study on the King’s College London website and both the scientific paper and the software are freely available.

The software lets you map the genetic and environmental contributions to a wide number of outcomes that were measured by the study – everything from height to school performance to ADHD.
 

Link to write-up of study.

Several people have questioned my assertion in the New York Times interview that physical activity has not changed much in the past thirty years. My claim is partially based on work by Klaas Westerterp and John Speakman, who are two highly respected researchers in the field.  Klaas gave a very nice talk on the topic at a metabolism workshop at  NIMBIOS in 2011.  His slides are here.  What they basically did was to compare total daily energy expenditure (DEE) measurements to basal energy expenditure (BEE) over time.  The ratio of DEE to BEE is called the physical activity level (PAL). The higher the PAL the more of  the energy you burn every day is due to physical activity. Klaas and John showed that PAL has not changed significantly since 1980 and if you squint hard enough at the plots in the slides it looks like it may even have increased a little.  While we seem to be very sedentary now, people tend to forget that we were also very sedentary thirty years ago.