If you think about fossils, you probably picture a piece of bone or shell, turned to stone and buried in the ground. You visit them in museums; some of you may even have found some. But your closest fossils are inside you, scattered throughout your genome. They are the remains of ancient viruses, which shoved their genes among those of our ancestors. There they remained, turning into genetic fossils that still lurk in our genomes to this day.
We’ve known about our viral ancestors for 40 years, but a new study shows that their genetic infiltration was far more extensive than anyone had realised. The viral roots of our family tree have just become a lot bigger.
In the brain of a baby, developing in her mother’s womb, a horde of DNA is on the move. They copy themselves and paste the duplicates into different parts of the genome. They are legion. They have been released from the shackles that normally bind them. And in a year’s time, the baby that they’re running amok in will develop the classic symptoms of the debilitating brain disorder known as Rett syndrome.
Children with Rett syndrome – they’re almost all girls – appear normal for about a year before their development is spectacularly derailed. The neurons in their brain fail to develop properly. They lose control of their hands. Most will never speak and at least half cannot walk on their own. Digestive problems, breathing difficulties and seizure are common. They will depend on their loved ones for the rest of their lives.
In most cases, this panoply of problems are all caused by faults in a single gene called MECP2, nestled within the X chromosome. MECP2 is a genetic gag – it silences other genes in a way that’s essential for producing healthy, mature neurons. But Alysson Muotri and Maria Carol Marchetto – a husband and wife team – have found that MECP2 also has another role. It acts like a warden, restraining a mafia of mobile genes called LINE-1 sequences or L1.
It’s time for bed, and what better way to ensure a comfortable sleep than snuggling into a cocoon of your own mucus?
Humans could probably think of some alternatives, but for many coral reef fish, mucus sleeping bags are all part of a good night’s rest. Many species of parrotfish and wrasse belch out their own cocoons every night, covering themselves in under an hour. And Alexandra Grutter from the University of Queensland thinks she knows why – the mucus deters vampires.
In the 18th century, Europe started sending boatloads of white settlers to Australia. But unbeknownst to these colonists, Australia had sent its own white contingent to set up colonies in Europe, around 450,000 years earlier. These migrants were sharks – great white sharks.
When Chrysoula Gubili from the University of Aberdeen compared the DNA of white sharks from around the world, she found a big surprise. The great white is the most genetically diverse shark studied so far but the Mediterranean fish are only distantly related to nearby populations in the North-West Atlantic, or even in South Africa. Their closest kin actually live half a world away in the Indo-Pacific waters of Australia and New Zealand.
Welcome to Humanville, a lively metropolis of over a hundred trillion bacteria living in and around your body. Like many cities, most of Humanville’s denizens live in its centre – the bowels – although a sizeable population have set up shop in the surrounding suburbs of the skin. The residents of Humanville, collectively known as the microbiome, are model citizens. They’re the unseen force that processes much of the city’s food supply, regulates its defences against invaders, and keeps it working like a healthy, well-oiled machine.
Humanville isn’t alone. It is one of many similar bacterial conurbations, each thriving in the body of a different animal. Those that live in humans have understandably received the most scientific attention. But Howard Ochman from the University of Arizona wanted to go further afield to study at the locals who live in neighbouring cities – Gorillaville, Chimpville, Bonoboville and so on.
He found that the evolution of these microbes mirrors those of their hosts to a remarkable degree. As an example, the bacteria found in two species of gorilla are more closely related to each other than either one is to the inhabitants of Humanville. The bottom line: you could reconstruct the evolution of the apes, simply by comparing the bacteria in their bowels (provided you used the right methods; more on this later).
They look innocuous: a set of small cuts, scratches and dents made in some animal bones. But these marks, recovered from Dikika, Ethiopia, have launched a controversial debate about nothing less than when human ancestors started using tools. It’s an argument that shows no signs of abating.
The debate revolves around when and how the marks were made. Shannon McPherron, who led the team that discovered the bones, thinks that they’re the handiwork of stone tools, wielded by prehistoric butchers at least 3.39 million years ago. That predates the evolution of modern humans, meaning that the tool-users probably belonged to one of our ancestral species, Australopithecus afarensis (such as the famous ‘Lucy’). The timing also pushed back the earliest estimates of tool use in our family tree by 800,000 years.
McPherron’s game-changing conclusions were published earlier this year in the journal Nature and unsurprisingly, they stirred controversy. Now, another team led by Manuel Dominguez-Rodrigo has hit back with a rebuttal paper published in PNAS.
In 2004, evolution itself served as a witness for the prosecution in the case of the State of Washington versus Anthony Eugene Whitfield. Whitfield contracted HIV in an Oklahoma prison, and first learned about his infection in 1992. After his release in 1995, he had more than a thousand sexual encounters with 17 different women, even fathering children with three of them. He rarely wore a condom, never told any of his partners about his infection and flatly denied it when asked.
However, Whitfield did confess to various people that if he had HIV, he would give it to as many people as possible. He got his wish – five of his 17 partners became HIV-positive. Whitfield was finally arrested in 2004 and convicted on 17 counts of first-degree assault with sexual motivation, among other offences. His total sentence came to 178 years and a month.
To demonstrate Whitfield’s guilt, the prosecution had to show that he had wilfully exposed women to HIV, that his five HIV-positive partners contracted their infections from him. Fortunately, David Hillis from the University of Texas and Michael Metzker from Baylor College of Medicine knew exactly how to do that. They had evolutionary biology on their side.
There are two weeks left to submit entries to Open Laboratory 2010, a collection of the best science blog posts from the last year.
If any Not Exactly Rocket Science posts particularly took your fancy, do submit them for consideration here. If you need to jog your memories, here’s a full list of all the posts on the blog. Only those from 2010 are eligible.