Imagine walking through a neighbourhood and seeing graffiti, litter, and shopping trolleys strewn about the place. Are these problems to be solved, or petty annoyances that can be ignored in the light of more serious offences? A new study suggests that the former is right – even the most trivial of transgressions can spread and spiral because their very presence stimulates more of the same behaviour. Through a series of stunning real-world experiments, Kees Keizer and colleagues from the University of Groningen have shown that disorder breeds more disorder. The mere presence of graffiti, for example, can double the number of people who litter and steal.

Their study provides strong support for the controversial Broken Windows Theory, which suggests that signs of petty crimes, like broken windows, serve as a trigger for yet more criminal behaviour. It follows that fixing small problems can prevent the build-up of bigger ones and the gradual decay of a neighbourhood. The idea was first proposed in a magazine article published in 1982, but soon became the basis of many a social policy.

It inspired Rudy Guiliani’s Quality of Life Campaign in New York, which focused attention on seemingly trivial fixes such as removing graffiti, clearing signs of vandalism and sweeping the streets. The campaign seemed to work, which motivated other cities to try the same tactics.  But despite its popularity, the Broken Windows Theory still divides opinion, for it lacks the backing of hard evidence, it’s plagued by woolly definitions of “disorder” and critics have questioned its role in New York’s drop in crime. These are fairly hefty shortcomings for a concept that is so central to anti-crime measures and Keiser wanted to address them once and for all.

To do so, he took to the streets of Groningen and watched unknowing passers-by in real-life situations as they reacted to signs of disorder. The recurring question was this: would people exposed to inappropriate behaviour behave in a similar way themselves?

He began in an alleyway in a local shopping district, where bicycles are commonly parked and where a conspicuous red sign warned against graffiti. He attached a flyer from a fictional sportswear shop to the handlebars of parked bicycles and watched what people did as they returned to their rides. Under normal circumstances (picture on the left), most people took the flyer with them and just 33% littered by throwing it on the ground. But that all changed when Keiser covered the wall with graffiti (picture on the right). With this innocuous difference, the proportion of litterers doubled and 69% discarded their flyers on the street.

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About 18,545 years ago, give or take a few decades, a woolly mammoth died. Succumbing to causes unknown, the creature was buried in Siberian snow. Many other mammoths must have met similar fates but this one, which we now know as M4, is special. Almost 20 millennia later, its beautifully preserved remains were unearthed by scientists who have revealed both its body and its genetic code. For the first time, the genome of an extinct species has been sequenced almost to completion.

Webb Miller from Pennsylvania State University together with a large team of American and Russian scientists has just published about 70% of the full mammoth genome. Currently, about 3.3 billion of those base pairs are known and Miller’s group estimate that the full sequence would weigh in at about 4.7 billion base pairs, making it fairly… well… mammoth in size. If the estimate is right, the mammoth genome was about 40% larger than a human’s but about the same size as a modern elephant’s.

So we don’t have a complete picture yet, but it’s a major technical advance nonetheless. Sequencing ancient genomes is no easy task and just a few years ago, it would have been little more than a flight of fancy. The obstacles were numerous – traces of ancient DNA are hard to come by; when they are extracted, they are broken into tiny fragments and swamped by DNA from nearby bacteria and fungi; and the sequencing technology at the time simply wasn’t fast enough.

The first two problems were actually solved by nature thousands of years ago. While fossilisation does little for preserving DNA, the freezing process that many mammoth carcasses were subjected to was much kinder. It safeguarded their hair, a rich source of DNA that is well protected from the damaging elements and the contaminating genes of microbes.

The final technological hurdle was leapt in 2005, with the advent of a new technique called 454 sequencing that was 100 to 1,000 times faster than the favoured method of the time. In the three years since, the method has become five times faster still and can now handle billions of base pairs in a single run, allowing individual laboratories to sequence in months what international collaborations used to take years to accomplish.

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There’s a glut of awesome science coming out towards the end of this week and not much at the start, so I’m sticking the Revisited post up early (it’s usually on a Saturday) to clear the schedule later.

Imagine you are a man who has just learned, through a genetic test, that your son carried your brother’s genes instead of your own. You might well have some stern words to exchange with your partner. But if you were a marmoset, this would all be part and parcel of life.

In a striking new study, scientists from the University of Nebraska have shown that marmosets inherit genes not only from their parents, but from their monkey uncles and aunts too. Each individual is a genetic chimera.

In Greek mythology, the chimera was a monstrous mixture of lion, goat and dragon (see below). But in the world of genetics, the word has much less grotesque overtones – it simply means an animal whose body contains two or more groups of cells with distinct sets of genes.

Most species of marmoset give birth to non-identical twins. At first, each embryo is surrounded by its own protective sac ­- the chorion – but after the first month of development, these sacs fuse together.

Blood vessels connect the developing embryos and embryonic stem cells can travel between them. These swapped stem cells can eventually set up groups of cells in one twin that contain the other’s genes. So the majority of marmosets have tissues descended from the stem cells of their siblings.

Up till recently, scientists thought that this chimerism only applies to blood cells. But Corinna Ross and colleagues proved otherwise. They took DNA fingerprints of different organs from 36 twin pairs of Wied’s marmosets (Callithrix kuhlii) from fifteen different families. About three in four pairs had tissues that were genetic matches for their twins – a clear sign of chimerism.

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Many naturalists become so familiar with the animals they study that they can recognise individuals within a population using just their shapes and patterns. If that’s too difficult, animals can be ringed or tagged. These tricks give scientists the invaluable ability to track the fates of individuals, but try using them on octopuses.

Recognising shape and pattern is impossible when your subject has the ability to change the texture and colour of its already pliant body on a whim. Injured individuals are distinctive enough, but only for a short while before their remarkable healing abilities close wounds and regenerate arms. Tags, which work well for closely related animals like squid, are useless for octopuses, which have eight long and dextrous arms for pulling markers off.  And other techniques are simply either too impractical, expensive, or harmful to the creature.

This inability to track individuals in the wild has severely limited our knowledge of octopus populations, including how far their ranges extend, how many individuals live in a certain area and how long the live for. But that may change. Christine Huffard from the Monterey Bay Aquarium Institute has found a way to identify one species of octopus – the grandiosely named wonderpus – just by using the markings on its skin. 

It’s a surprising discovery for animals that are so known for their colour-changing abilities but the wonderpus has a relatively static uniform of white markings on a brown background. Huffard was studying photos of this beautiful creature (it’s scientific name is actually Wunderpus photogenicus) when she noticed that the white Rorschach-blot patterns on the back of its head differed between individuals.

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Climate change is not just about surface warming and glacial melting. The carbon dioxide that human activity is pumping into the atmosphere also dissolves in the world’s oceans, slowly increasing their acidity over time. And that spells trouble for corals.

Corals may seem like immobile rock, but these hard fortresses are home to soft-bodied animals. These creatures – the coral polyps – build their mighty reefs of calcium carbonate using carbonate ions drawn from the surrounding water. But as the water’s pH levels fall, these ions become depleted and the corals start to run out of their chemical mortar. The upshot is that in acid water, corals find it hard to build their homes.

Scientists have predicted that if carbon dioxide levels double, the reef-building powers of the world’s corals could fall by up to 80%. If they can’t rebuild quickly enough to match natural processes of decay and erosion, the reefs will start to vanish.

Now, Maoz Fine and Dan Tchernov from the Interuniversity Institute of Marine Science, Israel, have found that they have a way of coping with homelessness. They grew some fragments form two European coral species under normal Mediterrenean conditions, and others in water slightly more acidic, by a mere 0.7 pH units.

Those that spent a month in the acidic tank were quickly transformed. The skeleton dissolved and the colony split apart. The exposed and solitary polyps, looking like little sea anemones, still remained attached to rocky surfaces. When the going gets tough, the tough clearly go soft.

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When we think about cooperative behaviour, most of us would think of animals like ants, meerkats, lions or, indeed, humans. But don’t rule out yeast. The small, single-celled fungus has provided us with much of our knowledge of genetics and molecular biology and now, it’s shedding light on the evolution of cooperation too.

The budding yeast, Saccharomyces cerevisiae, is one of the most widely studied of laboratory microbes, but scientists mostly know it as a solitary species. Brewers, on the other hand, use S.cerevisiae to make beer and are all too aware of its social side. Their strains have a tendency to form large clumps, or “flocs”, which makes them easier to remove from beer once fermentation is complete. This clumping process – flocculation – has been mostly ignored by scientists because lab strains don’t do it.

Enter Scott Smukalla from Harvard University. His group found that flocculation is a great example of cooperative behaviour, for clumped cells find strength in numbers and shield each other from environmental threats. The entire process is controlled by a single and very special gene called FLO1. Switch it on, and yeast cells favour both communities and cliques – they gain the ability to stick to other cells but only associate with those that also have active FLO1.

Flo1 is what Richard Dawkins called a “green beard gene” – a gene whose bearers prefer to cooperate with carriers of the same gene. Dawkins, skilled with imagery as he is with controversy, imagined one such gene that gave individuals a green beard and favouritism for those with a green beard. It was a powerful illustration of a concept proposed by legendary biologist William Hamilton a decade earlier.

Hamilton was trying to explain why groups of cooperating individuals aren’t torn apart and taken over by cheats, who reap communal benefits while contributing nothing. It’s a problem that has occupied the thoughts of evolutionary biologists ever since Darwin. Hamilton proposed the idea of green beard genes as a possible answer to the dilemma, but he also felt that they would be extremely rare, for one gene would have to do many different things. He may or may not be right, but such genes do exist and FLO1 is one of them.

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So we’ve done koalas and cephalopods – let me actually show you something I saw in the wild. This delightful little creature is the thorny devil or moloch, names which sit uneasily with its placid nature. The spines that decorate its body are impressive and provide the lizard with a strong defence, but it’s what lies between the spines that’s really interesting. The thorny devil’s flanks are lined with grooves that are narrow enough to channel water by capillary action. The grooves end in the creature’s mouth, so the thorny devil can drink simply by standing in a puddle or waiting for the morning dew to condense on its numerous spines.

Hair, or fur, is one of the hallmarks of mammals, the group of animals to which we belong. It is an evolutionary innovation that provides us with protection and helps us to maintain our constant body temperature And while hair is a uniquely mammalian feature, its genetic building blocks are anything but. A new study has found that genes responsible for building the locks on your head have counterparts that construct the claws of lizards.

Hair is made of proteins called keratins, which interact with each other to form long, hard filaments. Keratins are widespread in the animal world but those that make up mammal hair are different to those found in scales, claws, feathers and beaks of birds and reptiles.

Until now, scientists had thought that hair keratin genes were a mammalian innovation that evolved after our ancestors split away from those of reptiles and birds, some 310 million years ago. Indeed, previous studies have failed to find such genes in species other than mammals, but a new analysis from Leopold Eckhart from the University of Vienna changes all of that.

Within the genomes of a chicken and a green anole (a type of lizard), Eckhart’s team found equivalents of human hair keratin genes – six in the anole and one in the chicken.

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Folks, I have big news…

I’ve just published a book based on this little blog. Some of you may remember me doing a quick poll about this a while back. Well since then, I’ve collected about 80 or so of my favourite posts from the last year and converted them from pixels to paper.

The book is now available through online publisher Lulu and you can order one for the tiny sum of £9.99 by clicking on these magic blue words.

It covers a wide range of biological areas – Mexican-waving bees, snow-making bacteria, viruses of viruses, the psychology of voting, the neuroscience of jazz, binge-drinkins shrews, the evolution of language, super-sharks, climate-changing beetles and more.

So… if you fancy it, please buy a copy, give some to your friends, tell other people about it, or even post about it on your own blogs. I’d appreciate any support you care to give.

Partly, that will make me happy in these economically troubled times (cue tiny violin), but more seriously, I started Not Exactly Rocket Science as a way of reaching out to people with no specialist knowledge and only a passing interest in science. The book is meant to help draw in people who don’t really read blogs so if you have any friends who are interested in science, why not tell them about it or buy them a copy in time for Christmas?

I’m really proud of it and the fact that it’s sitting on my bookshelf, all tangible and shiny. If everything goes according to plan, it should be available via Amazon and other online booksellers within a month or so although I recommend buying through Lulu because Amazon will probably charge you more and give me less.

And if you wanted more incentive, here’s what esteemed blogger and science writer Carl Zimmer had to say about it:

“Few blogs make a smooth transition from computer to paper. Not Exactly Rocket Science is one of them. Ed Yong writes elegantly yet engagingly about all manner of biology, from yawning dogs to viruses of viruses. Turn off the laptop for a while, and crack open this book. You will be pleased you did.”

Fast-food restaurants like to bedazzle consumers with choice, offering a smorgasbord of different foods and drinks with varying flavours and  sizes. And yet, these options have more in common than you might think. According to a new study, this multiplicity of choice hides the fact that the overwhelming majority of American takeaway food is actually based on a single source – corn. It provides food for the animals whose meat makes up the burgers, the oil for frying chips and the syrup that bulks out fizzy drinks.

Hope Jahren and Rebecca Kraft from the University of Hawaii discovered the omnipresence of corn by chemically analysing a variety of foods from America’s top chains – McDonald’s, Burger King and Wendy’s. At six cities across the country, the pair bought hamburgers, chicken sandwiches and orders of fries. Returning to their lab, they analysed the levels of different carbon isotopes in each.

Analyses like these have proven to be a surprisingly good way of tracing the origins of foods. Like all plants, corn gets its energy through photosynthesis, but it uses a slightly different method to other important crop plants like rice, wheat or potatoes. This difference is reflected in a plant’s ratio of two carbon isotopes – the common carbon-12 and rarer carbon-13. Corn has a signature ratio that sets it apart from other crops and by association, the meat of animals that consume it also stand out in the same telltale way.

Their results revealed that most of the cows and chickens that ended up in the burgers were fed almost exclusively on corn. Out of the 162 samples of beef they collected, only 12 came from animals that were potentially fed on other sources like grass or grains (and interestingly enough, all of these samples came from West Coast branches of Burger King). For chicken, there were no exceptions – they had corn for breakfast, lunch and dinner.

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