Wednesday, December 30, 2009

concordant zircons

f you want to accurately date a rock, you really want to grind it up and extract some grains of zircon. This mineral has several useful properties: it is very hard and chemically inert, even at quite high temperatures, so will survive relatively intact even if the rest of the rock it is surrounded by is extremely squeezed, squashed and metamorphosed.

In addition, zircon's crystal structure allows lots of uranium to be trapped within a grain when it forms, but virtually no lead. This doesn't mean that you don't find any lead within zircons if you chemically analyse them - you do. But this lead was produced within the crystal after it formed, by the radioactive decay of uranium. In fact, two different decay processes are at work: uranium 238 decays to lead 206, uranium 235 decays to lead 207. Therefore you have two ways of getting a radiometric age for the zircon: you can measure the ratio of uranium 238 to lead 206, or you can measure the ratio of uranium 235 to lead 207. This means that zircons have a built in cross-check: if you calculate the age using bothof these ratios, and they are the same within error, the age is said to be concordant, and you can have more confidence that the age you have determined reflects the original age of formation (a resetting event would affect the different ratios to a different degree, and result in discordant ages).

We're currently trying to extract some zircons - or baddeleyites, which are similarly useful for dating but more common in mafic rocks than zircons sometimes are - from the dykes I sampled in Oman last year. Of course, I could probably do with more than two, but two would be a start!

top science discoveries of 2009 and the decade

Top 20 of the Year According to

Top 10 of the Year According to NatGeo

Top 10 of the Decade According to Discovery

Retrocyclins and HIV

HIV is an elusive adversary. The virus is so good at fooling the immune system that the quest for an HIV vaccine, or even a countermeasure to resist infections, has spanned two fruitless decades. But maybe a defence has been lurking in our genomes all this time.

Nitya Venkataraman from the University of Central Florida has managed to reawaken a guardian gene that has been lying dormant in our genomes for 7 million years. These genes, known as retrocyclins, protect monkeys from HIV-like viruses. The hope is that by rousing them from their slumber, they could do the same for us. The technique is several safety tests and clinical trials away from actual use, but it's promising nonetheless.

Retrocyclins are the only circular proteins in our bodies, and are formed from a ring of 18 amino acids. They belong to a group of proteins called defensinsthat, as their name suggests, defend the body against bacteria, viruses, fungi and other foreign invaders. There are three types: alpha-, beta- and theta-defensins. The last group is the one that retrocyclins belong to. They were the last to be discovered, and have only been found in the white blood cells of macaques, baboons and orang-utans.

In previous experiments, Venkataraman's group, led by Alexander Cole, showed that retrocyclins were remarkably good at protecting cells from HIV infections. They are molecular bouncers that stop the virus from infiltrating a host cell. The trouble is that in humans, the genes that produce retrocyclins don't work. Over the course of human evolution, these genes developed a mutation that forces the protein-producing machinery of our cells to stop early. The result is an abridged and useless retrocyclin.

But aside from this lone crippling mutation, the genes are intact and 90% identical to the monkey versions. Now, Venkataraman has awakened them. She found two ways to fix the fault in human white blood cells, one involving gene transfer and the other using a simple antibiotic. Either way, she restored the cells' ability to manufacture the protective proteins. And the resurrected retrocyclins did their job well - they stopped HIV from infecting a variety of human immune cells.

Venkataraman says that we can think of retrocyclin deficiency as "an inherited disorder, albeit one with an incidence of 100%. To "cure" it, she created corrected versions of the faulty human retrocyclin genes and loaded them into white blood cells. Using glowing antibodies designed to stick to retrocyclins, she saw gleaming evidence under the microscope that the cells had made their own stock of these proteins. She even managed to purify the rekindled proteins themselves.

This clearly tells us that our cells have all the right machinery needed to actually make retrocyclins - it's just that the instructions have a typo in them. Most importantly, the restored proteins worked. They prevented HIV from infecting up to 80% of the cells, and even reduced the levels of virus in cells that had already been infected.

Obviously, gene transfer techniques like this are hardly practical for poor African nations where HIV is most rampant. For retrocyclins to really play a role in the fight against HIV, we need a cheaper and easier way of reactivating them. And Venkataraman thinks she has found one - a group of antibiotics called aminoglycosides.

In bacteria, these drugs work by blocking them from creating proteins. But in the more complex cells of animals, they do something different - they react with the protein-making machinery of our cells so that they make slightly more mistakes than usual. Normally, that would be a bad thing but for retrocyclins, it's an unexpected boon. It means that the machinery barrels straight through the mutation that causes retrocyclins to be built half-finished. It doesn't stop prematurely, and produces a full-length protein.

Venkataraman found that one of these drugs, tobramycin, was especially good at restoring retrocyclins, and did so in both white blood cells and actual vaginal tissue. The drug slashed the rate of HIV infection by about 50% - a respectable figure but clearly a smaller one compared to the sizeable benefits bestowed by the gene transfer method. On the plus side, the technique didn't seem to harm the cells in any way.

These results are promising ones indeed, and Venkataraman thinks that with more work, aminoglycoside-based creams could be used to prevent HIV infections in the real world.

HIV kills by infecting the very cells that are meant to defend us from infections and destroying them. But retrocyclins are something it hasn't encountered before. Humans lost the ability to create these guardians millions of years ago and by reawakthem, we could have a new but ancient weapon against this sneakiest of foes.

whale fetus fossil

Nine years ago, a team of fossil-hunters led by Philip Gingerich from the University of Michigan uncovered something amazing - the petrified remains of an ancient whale, but one unlike any that had been found before. Within the creature's abdomen lay a collection of similar but much smaller bones. They were the fossilised remains of a foetal whale, perfectly preserved within the belly of its mother. Gingerich says, "This is the 'Lucy' of whale evolution."
The creatures are new to science and Gingerich have called them Maiacetus inuus. The genus name is an amalgamation of the Greek words "maia" meaning "mother" and "ketos" meaning "whale", while Inuus, the Roman god of fertility, gave his name to the species.
The foetus's teeth were the first to be uncovered and only as the surrounding (and much larger) bones were revealed, did Gingerich realise what his team had found - the first ever foetal skeleton of an ancestral ancient whale (see video). Alongside the mother and calf, the group also discovered another fossil of the same species in even better condition. Its larger size and bigger teeth identified it as a male.
This trio of skeletons is so complete and well-preserved that Gingerich likens them to theRosetta Stone. They provide an unparalleled glimpse at the lifestyle of an ancient whale before the group had made the permanent transition to the seas. How it gave birth, where it lived, how it competed for mates - all these aspects of its life are revealed by these beautiful new finds.

Maiacetuswasn't quite like the whales we know and love. It was an intermediate form between the group's earliest ancestors and the fully marine versions that swim about today. For a start, still had sturdy hind legs that were good for swimming but would have allowed it to walk on land.
Another piece of evidence tells us that Maiacetus was definitely amphibious - its foetus was facing backwards in the womb. If the mother had lived long enough to give birth (and judging by the foetus's size, that wasn't far off), the infant would have greeted the world face-first. No living whale or dolphin does that - all of their young emerge backwards, leading with their tails, to minimise the risk of drowning in the event of a prolonged labour. A head-first delivery means that Maiacetus gave birth as a landlubber.
Whales are so beautifully adapted to life in the water that their relationships to other mammals aren't immediately clear. Thankfully, their evolution has been beautifully chartedby a series of "transitional fossils" documenting the change in their bodies over massive gulfs of time.
They evolved from deer-like ancestors, hoofed mammals that lived on land and occasionally ventured into the water. Early members of the family included Pakicetus, a meat-eater with long, hooved legs, a dog-like snout, and a distinctive inner ear that only whales and their kin possess. From there, the family became gradually more comfortable in the water, with later species like Ambulocetus having powerful tails and back legs that were clearly adapted for swimming.
These adaptations became even more extreme in the protocetids, a group that included species like Rodhocetus. They had seal-like bodies and possibly tail flukes like modern whale, but they still kept powerful hind legs to support their weight on land. Later whales like Basilosaurus or Dorudon were very different. Their hind legs were tiny - larger than those of modern whales, but useless for walking. Their hip bones were also disconnected from their spines. They were fully marine animals.
The newly discovered Maiacetus was a protocetid - several changes away from its original hooved ancestors, but not as thoroughly adapted of ocean life as Basilosaurus. Gingerich believes that it fed in the sea before coming ashore to rest, mate and give birth. Its teeth are suited for eating fish. Its legs were built to power swimming and support its weight on land, but they wouldn't have let it swim very far, or granted it with much terrestrial agility. These legs constrained the animal to the boundary between land and sea - jack-of-all-trades, but master of none.

The foetus was alone in the womb, which suggests that Maiacetus (like modern whales) devoted its energy to rearing a single infant during every found of breeding. As I've mentioned, the baby would have been delivered head-first while mum was safe on land. The foetus as large and its teeth were well-developed, with the growth of its permanent teeth already underway. Among mammals, advanced chompers like these are a sign that the calf would have emerged from the womb as a mobile and capable youngster - just as deer fawns can run soon after they're born.
The male skeleton was about 12% larger than the female and in the flesh, the animal would have weighed about 39% more. Compared to other marine mammals, this size difference between the two genders is actually relatively small. It suggests that males didn't have to compete too brutally for mates for those that do (like elephant seals) grow to enormous proportions that dwarf the fairer sex. These fighters hoard females in harems, and the fact that Maiacetus didn't suggests that it couldn't. Perhaps food and shelter were widely spread out commodities that were impossible to hoard and defend.
All in all, Gingerich's latest finds are among his most alluring yet. The remains of these three individuals have lasted through 48 million years of compression and today, they paint an incredibly vivid picture of the life of an ancient species. The fact that they are whales is the icing on the cake. This group's story is one of the most beautifully illustrated in the field evolution and every new discovery is a welcome one.

Octopi and coconut shells

Octopuses are masters ofcamouflagethat can change their shape, colour and texture to perfectly blend into their environment. But the soft bodies that make them such excellent con artists also make them incredibly vulnerable, should they be spotted. Some species have solved that problem with their fierce intellect, which allows them to make use of other materials that are much harder. The veined octopus, for example, dons a suit of armour made of coconut shells.
The veined octopus (Amphioctus marginatus) lives in sandy, exposed habitats that have little in the way of cover. To protect itself, it hides among the hollow husks of coconuts. It even carries its armour around with it, tucking the shell under its body, sitting on it like a bowl, and moving around on tip-tentacles.
These cumbersome hikes can last for up to 20 metres and they make the octopus look like an eight-legged stilt-walker. The octopus can even carry two shells, stacked inside each other. If danger threatens, it can quickly assemble the two halves into a protective sphere, holding them in place with its suckers.
The new discovery comes from Julian Finn, Tom Tregenza and Mark Norman, the same terrific trio who brought us the first report of the mimic octopus's amazing shape-changing abilities. They spent over 500 hours of diving across ten years, studying the behaviour of veined octopuses in Indonesian waters.
The veined octopus has hit the headlines before for coconut-related reasons. As part of its portfolio of disguises, it will often stroll across the ocean floor on two tentacles, while wrapping the other six around its head in a tight bundle. To a passing fish, it would strongly resemble a rolling coconut.
Originally, Finn suspects that the octopuses used the empty shells of dead shellfish as defence. There's no way for an octopus to crack a coconut on its own, but it has no need to do this. Coastal human settlements often use coconuts and discard the split shells. In doing so, they have provided the veined octopus with even tougher shields.
The trio suggest that the octopus uses coconut shells as bona fide tools. Many invertebrates, such as hermit crabs, shelter in shells but they do so permanently. The octopus, however, gains no protection from its shells whatsoever when it carries them around in the stilt-walking fashion. The shells' benefits lie in the fact that they can be quickly deployed as a makeshift fortress. The fact that the octopus picks up the coconuts for later use suggests a more complicated intellect at work. As Finn writes:
"The discovery of this octopus tiptoeing across the sea floor with its prized coconut shells suggests that even marine invertebrates engage in behaviours that we once thought the preserve of humans.

Amphicoelias fragillimus

While you might have heard of Supersaurus, Seimosaurusor Argentinosaurus - and perhaps even Turiasaurusand Paralititan - have you heard of... Amphicoelias fragillimus? Though described as long ago as 1878, this sauropod has remained decidedly obscure and hardly heard of until pretty recently. Naish & Martill (2001), for example, stated 'What has recently been claimed as the biggest of all sauropods and, indeed, the biggest of all land animals, is actually a specimen discovered in 1878. Based only on a single enormous vertebra, now lost, Amphicoelias fragillimus has been estimated to have reached a length of 60 m and may have attained a weight of 150 tons!' (p. 230). If these estimates are valid, then this animal was twice as long as Supersaurus andDiplodocus, and perhaps over four times heavier.
Err, gosh.

In August 1878 the famous and prolific scientist* Edward Drinker Cope (1840-1897), described a new super-sauropod, Amphicoelias fragillimus, from the Garden Park quarries of the Morrison Formation of Colorado. It was represented only by an incomplete dorsal vertebra and the distal end of a femur (contra Naish & Martill above: whoops!). A good drawing of the vertebra was provided (Cope 1878), showing that this sauropod was clearly a diplodocoid: a member of the same sauropod clade as Diplodocus, Apatosaurus and their relatives (the name Diplodocimorpha is also sometimes used for these animals: see Taylor & Naish 2005: free pdf). The big deal is how, err, big these remains were. The partial vertebra had a preserved height of 1.5 m and, when reconstructed on the basis of comparison with complete diplodocoid vertebrae, has a total height of 2.7 m. Again... gosh (or words to that effect) [Amphicoelias fragillimuscompared to a person below, from wikipedia].

* Though usually described (by palaeontologists) as a palaeontologist, Cope was also an accomplished herpetologist and ichthyologist, which explains the name of the journalCopeia.

If history were fair, we would all have grown up familiar with Cope's hyper-enormousAmphicoelias fragillimus, and we would be less impressed by Brachiosaurus andBalaenoptera, let alone with paltry little 20-m long sauropods like 'Angloposeidon' (go here). But it was not to be, and it was to sink into the morass of obscurity. In a major 1921 review of Cope's sauropods, Henry Fairfield Osborn and Charles Mook noted that they were unable to locate the immense vertebra in Cope's sauropod collection (Osborn & Mook 1921), today at the American Museum of Natural History (New York). It was lost.

-Darren Naish

Tuesday, December 29, 2009


Shevanel Take 2- I've loved you for years

My head will not rest on this pillow
As it's gripped in my arms tonight
Like reality, too tight

If a dream could last forever
I would hold you here
Time need not freeze, I need not fear

This world inside
Is a world I have longed to find

And I will not be afraid to love
I will not be afraid to lose what I once deprived myself of

My teardrops have salt-stained this pillow
As it's loosened from my weakened clutch
By the sun's light, too much

There's a hope today
That I'll find a way
This dream of life unreal to me

Sometimes I run and sometimes I crawl
Sometimes I fly and sometimes, I'm gonna fall
But this dream of mine will not change at all

hey man

first tattoo at age 50. can we be friends?

sylvia ji

love birds

away we go

chest piece

USA Today 2009 big discoveries

For a critter dead 65 million years, T. rex had a pretty good year as relatives turned up in study results almost weekly. In September, researchers led by Paul Sereno of theUniversity of Chicago reported discovery of Raptorex kriegsteini, a pocket-sized tyrannosaur from 125 million years ago. A peculiar horned tyrannosaur about 70 million years old, Alioramus altai, was announced in October. And in December, a team led by Sterling Nesbitt of theAmerican Museum of Natural History in New York unveiled Tawa hallae, a 6.5-foot-long precursor to T. rex from 215 million years ago.