A Schooner of Science

Trojan atom

// January 27th, 2012 // No Comments » // Recent Research

What kind of control we can wield over atoms!

An electron orbiting an excited potassium atom has been confined with radio waves to mimic the movement of the Trojan asteroids of Jupiter.

The Trojan asteroids precede and follow Jupiter as it orbits the sun, like an entourage of bodyguards around royalty. Earth’s first Trojan asteroid was recently discovered, but it’s nothing to the group that Jupiter’s got, numbering over a thousand.

Resembling this comma-shaped group of asteroids, the electron was limited to a confined “wave packet”, say researchers from Rice University, Oak Ridge National Laboratory and the Vienna University of Technology.

How’d they do it? Lasers, radio waves and supersized atoms.

Here’s a video, with my explanation below it.

First they created a Rydberg atom using ultraviolet laser. That’s a highly excited atom, where the outermost electron has jumped up from its normal orbit into a much, much higher one.

As the outer shell electron jumps outwards, the atom becomes bigger. In this case, an unimaginably small potassium atom grew as large as a full stop! Say wha? I mean, that’s HUGE!!! That’s bigger than a bacteria, than a skin cell – from ONE ATOM?! Get out!

Locating that electron, even in a supersized Rydberg atom, is no easy task. Electrons, I was told at uni, wink in and out of existence. They can act as a particle or a wave. Instead of pinning down an electron, you just predict where it’s most likely to be – called a wave function. It’s a fuzzy way of looking at things.

The team could collapse the wave function with a sequence of electric field pulses, which basically limited where the electron would be. That created the comma-shaped wave packet that resembled the Trojan asteroids.

Next job – make it move! They made the localised electron move in an orbit using radio waves, which rotated the nucleus.

Brilliant!

But how can you check where the electron is, and measure your results, when you can’t see it?

The answer was to do it in snapshots. Each snapshots of the wave packet was made using another electric field pulse. Unfortunately, the process destroyed the Rydberg atom, so they had replicate the experiment tens of thousands of times to get enough data to complete the picture.

Seems like a lot of work to make something extremely tiny and wavy move like you want it, but who knows where research like this might lead. To have this kind of control over electons could lead to new types of chemistry, and quantum computing.

Mind blown.

Source: The press release and paper, published in Physical Review Letters this week.

The red queen, sex and nematode worms

// July 28th, 2011 // 1 Comment » // Recent Research, Sex and Reproduction

In Lewis Carroll’s Through the looking-glass- a whacky book if I ever read one – the laws of physics don’t really apply. Hills can become valleys, straight can become curvy, and forward is really backward.

In one scene, Alice chases after the Red Queen, both running as fast as they can, but when they stop Alice realises they are still right where they started. “Now, here, you see, it takes all the running you can do to keep in the same place” says the Red Queen.

And it might be the same with the evolution of predator and prey, host and parasite. Running doesn’t get you anywhere. So says the Red Queen Hypothesis.

As the host adapts to fight the parasite, the parasite evolves to infect the host. It’s an endless race, and extinction faces the first organism to stop running.

So what’s this got to do with sex? Sex is evolution on turbo. Mixing and matching genes increases genetic diversity, giving a species more opportunities to outlast in the ultimate game of survivor.

Field data supports the Red Queen Hypothesis as describing an adaptive advantage of sex. Models and maths support the idea that coevolving species could select for rare genes and unusual combination randomly created by sex. Direct experimentation of coevolution and nookie is tricky business.

New research, published in Science, grew several populations of nematode worms (C. elegans, roundworms) which are usually asexually, but reproduce sexually 20% of the time.

The populations were differently exposed to bacterial parasites (Serratia marcescens) as shown.

One population was given the parasites and left to their own devices. They and their bacteria could evolve together. These nematode worms increased their rate of sexual reproduction to 80-90% over time, and maintained a high level of sexy-times.

The other nematodes were given frozen stocks of bacteria every generation, so the parasites weren’t evolving as the worms did. At first, sexual reproduction increased in the worms, but then it dropped back down to 20% – the same level as nematodes which hadn’t been exposed to the bacteria at all.

Parasites on their own don’t increase sex – coevolution does.

A second experiment supported their conclusion. Nematodes mutated to be unable to reproduce sexually (asexual obligates) became extinct after 20 generations when exposed to the parasites. But mutants that always required sex to reproduce (sexual obligates) never became extinct.

When it comes to coevolution, it’s fall behind and be left behind.

Never stop running.

Morran, L. et al (2011). Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex Science, 333 (6039), 216-218 DOI: 10.1126/science.1206360
Brockhurst, M. (2011). Sex, Death, and the Red Queen Science, 333 (6039), 166-167 DOI: 10.1126/science.1209420

The electric, flashy development of tadpoles

// July 22nd, 2011 // No Comments » // Recent Research

Tufts researcher Dany Adams was filming the development of tadpole embryos, when she decided to leave the camera hooked up to a microscope going overnight. She was hoping to get some good time-lapse footage. What she got was bioelectric patterns which flashed across the developing tadpole face, outlining the future positions of eyes, nose and mouth.

“I was completely blown away.” said Dany, Ph.D, according to the Tufts press release. “I think I thought something like, ‘OK, I know what I’ll be studying for the next 20 years.” It had never been seen before, and was published in the August issue of Developmental Dynamics. Watch the video below.

“When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,” said Dany. “We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It’s a jaw dropper.”

Bioelectric signals cause cells to form patterns marked by differences in pH levels and membrane voltage, according to the researchers. The tadpoles were stained with a reporter dye that caused negatively charged areas to shine brightly while other areas look dark.

There were three bioelectric waves they saw in the footage.

First, a wave of negative ions flashed across the whole embryo at about the same time as cilia formed, tiny hairs which allow the embryo to move.

The second flash was a patterning that matched shape changes that were soon to occur in the face region. Bright areas, negative ions, show places where the surface will fold in.

Thirdly, localised regions of bright, negative areas formed, grew and disappeared without disturbing the existing pattern. At this point, the embryo began to elongate.

If bioelectric signalling is important to embryo development, you would expect development to be altered by screwing around with the signal process – and that’s exactly what happened. The researchers disrupted signalling by inhibiting a protein involved called ductin, which transports hydrogen ions. Some embryos grew two brains, others had unusual nasal or jaw development, and so on.

Interesting, I guess, but a bit sad for the baby tadpoles imho. Plus, I feel like it doesn’t take much to disrupt embryo development. Take away any protein that’s switched on at that sensitive time and development takes a detour…

All the same, bioelectricity may play a crucial role in embryo growth. Laura Vandenberg, another author on the paper, said “developmental biologists are used to thinking of sequences in which a gene produces a protein product that in turn ultimately leads to development of an eye or a mouth. But our work suggests that something else – a bioelectrical signal – is required before that can happen.”

Vandenberg, L., Morrie, R., & Adams, D. (2011). V-ATPase-dependent ectodermal voltage and ph regionalization are required for craniofacial morphogenesis Developmental Dynamics, 240 (8), 1889-1904 DOI: 10.1002/dvdy.22685

Spongiforma squarepantsii, fungus found in Borneo

// July 4th, 2011 // No Comments » // Recent Research

Absorbent and yellow and porous is he,
Spongiforma squarepantsii.

Named for the best cartoon character ever, Spongebob Squarepants, this recently discovered species is not a sponge, but a fungus.
 
Discovered in Borneo Spongiforma squarepantsii has a characteristic smell which is “vaguely fruity or strongly musty,” according to the paper published in Mycologia.

It’s a weird fungus though. Not much of a mushroom. Dennis Desjardin from San Francisco State University said “It’s just like a sponge with these big hollow holes.” (via the press release.)

“When it’s wet and moist and fresh, you can wring water out of it and it will spring back to its original size. Most mushrooms don’t do that.”

Though it looks different, Spongiforma species are related to the edible porcini mushroom. It’s ancestor would have had the traditional cap and stem fashion too, but has been lost over time.

Caps and stems are an evolutionary adaptation designed to keep spores moist and alive. A stem lifts the fungus up so spores can be dispersed better, and an umbrella-like cap keeps spores from drying out.

Spongiforma fungi are a little different. It stores water in its sponginess, and revives quickly if it dries out by absorbing moisture from humid air.
 
Finding new fungi is an adventure… I wonder if they’re looking for any volunteers? “We go to underexplored forests around the world, and we spend months at a time collecting all the mushrooms and focusing on various groups,” said Dennis.

“When we do that type of work, on average, anywhere from 25 percent to 30 percent of the species are new to science.”

And I just love Spongebob. He has just the best outlook on life and work ethic. Who else wakes up and says “I’m awake!” “I’m ready, I’m ready!” When I grow up, I want to be Spongebob.

Oh, and can someone make me these cupcakes for my birthday?

Modelling catastrophic dam collapse and natural disasters

// June 24th, 2011 // No Comments » // Recent Research, Science Communication

One of the biggest dams in the world, Geheyan Dam in China holds more water than five Sydney Harbour’s, a massive 3.12 billion cubic metres worth.

What would happen if it failed?

Australian CSIRO scientists collaborated with China’s Satellite Surveying & Mapping Application Centre (SASMAC) to model the region and apply six different dam failure scenarios.

“Our simulations show where the water would go, how fast it would reach important infrastructure such as power stations and the extent of inundation in major townships downstream,” said Dr Mahesh Prakash from CSIRO in the press release.

Dam failure is a real possibility, as many parts of China are prone to earthquakes. We’ve seen plenty of natural disasters over the past year, highlighting the need to prepare for such events.

Modelling and data visualisation can inform emergency procedure development and ensure new infrastructure is built protected areas.

“The modelling technique we developed for this work is really powerful,” Dr Prakash said. “It gives us very realistic water simulations including difficult-to-model behaviours such as wave motion, fragmentation and splashing.”

This video shows a dam failure simulation, and explains how the model was created. I enjoyed the delicious hundreds and thousands demonstration to show how water acts as a group of particles. Yummy!

The same software has been used to model other catastrophic events, including tsunamis and volcanoes. They also modeled the 1928 St Francis dam break in California. The simulation was very similar to the real event, suggesting the technique is accurate.

Genetically engineered ‘transgender’ goats makes poor reporting

// June 16th, 2011 // 2 Comments » // Recent Research, Science Communication

“Scientists genetically engineer female ‘Frankenstein’ goats in male bodies to create ‘human’ breast milk” exclaimed the Daily Mail on Tuesday.

The article leaned on a press release titled “AgResearch Transgender Goats To Be Milked” sent out by the Soil & Health Association of New Zealand last Sunday.

What follows on the Daily Mail and in blogs all over the net is extremely shoddy science reporting. Here’s a taste.

“Genetic engineers are deliberately breeding transgender goats to see if their milk is similar to that produced by humans.

“The goats being created are effectively a female trapped in a male’s body, complete with the full male anatomy.

“The company behind them wants to see if their milk contains the same proteins as human breast milk – with a view to one day possibly selling it in stores.”

And I’m not just picking on Daily Mail. Lots of blogs picked up the story.

Here’s my understanding of the situation.

First this “girl goat trapped in a boy goats body” business. Honestly, how can anyone know if a goat feels like a girl or a boy? Transgender is about self-identity. No, these goats are intersex.

Specifically, they have XX chromosomes and sterile male bodies. It’s quite common in goats. At the bottom of the article, they finally quote Dr Jimmy Suttie from AgResearch, who says “It was inadvertent. This is something which normally happens about 10 to 15 per cent of the time in this breed of goat. It just happens to be the cell line that was used.” For the 15 goats in the study, 75% were intersex.

So they aren’t “deliberately breeding transgender goats.” It was inadvertent.

The Daily Mail also says “All the ‘males’ have been sterilised to stop them breeding.” But the goats are sterile anyway because they lack a Y chromosome.

Being intersex isn’t weird or wrong, and I don’t like that the article takes a “oh noes! girlboys!” angle. Whatever! Humans can also be XX and male, or XY and female, sometimes without realising it until they are tested for fertility. Life goes on as normal.

These goats aren’t transgender. They’re just goats. End rant.

So what about the genetic engineering?

A human protein has been inserted into their genome so it will be expressed in milk, a concept called biopharming and an area AgResearch is interested in. Human proteins can be extremely useful in medicine, just take insulin as an example.

Commercial insulin to treat diabetes, was originally taken from cows and pigs after they were slaughtered for food.

Later the insulin gene was cloned into bacteria so they could make human insulin, which had fewer side effects.

More recently, the gene was cloned into safflowers to produce insulin at a reduced cost.

Proteins like insulin are long chains of amino acids, and that is exactly what a gene codes for – the order of the amino acids. But to work in the body, a protein not only needs the right order, it has to be folded to have the correct three dimensional shape to do its job. Often it also needs extra bits and pieces added to it, like a sugar chain. Sometimes it needs to be cut in certain places.

Think of it like an intricate origami with the instructions written on it. Often bacteria can’t read the instructions written on animal proteins. In that case, you need animal cells.

If the protein is made in animal cells, you then need to get it out. If you can get the protein expressed in milk, say goat milk, then you can collect it without harming the animal more than milking for food does. It’s been done before.

So the aim is to produce a human protein of medical interest in milk, so they can extract and study it. Not just sell human breast milk from goats in stores, as the Daily Mail seems to suggest.

Finally and for effect, the article threw in some outraged comments from random bloggers.

The whole thing is misleading, exaggerated and I hope it will be retracted. Plus it’s really mean about the goats, calling them unnatural and Frankensteins. Poor goaties.

There are some real concerns about biopharming, and people who are worried about it should have easy access to factual information. We can discuss the science of biopharming, the risks and benefits, how ethics approval is given, and how the goats are treated. With access to the whole story, people can draw their own conclusions rather than being spoonfed fear.

The last thing we need is a grim fairytale about Frankenstein transgender goat breast milk.

Nubia, irrigation and parasitic worms, a tale told by a Mummy

// June 8th, 2011 // No Comments » // Recent Research

A few months ago I wrote about Ancient Nubians and their antibiotic beer, delivering a dose of tetracycline in every brew.

Now bioarcheologist George Armelagos has co-authored a study showing that early irrigation channels changed how humans were affected by parasites.

I’ll describe the research at the end, but first – a story! Make yourself a cup of tea and come back to read it.

Nubia, 500AD

Since he’d taken his first wobbly steps on Nubian soil, Alara had been pulling his then insubstantial weight on the family farm. He’d pull up weeds with grubby fingers under the watchful eye of his older cousins by day. Lunch was often a paltry loaf of flat bread to share between the lot of them, supplemented with whatever local edible plant was in season, eaten hastily and followed by a brief break in which he built dirt pyramids with other children.

Now 30, Alara remembered his childhood as carefree and unplanned. His memories swam together like waves billowed out from boats on the Nile. Only small moments stood out with any clarity. A snarling dog snapping at his leg. The taste of bread warmed by the sun, seasoned with hunger. Buzzing with disbelief at the stories told by his cousins of things adult and forbidden.

A life in the sun had baked him hard and capable, and he still worked on the same farm he had as a toddler. His extended family shared the plot of land, shared the work, shared the harvest, shared the income. Shared the good years and the bad. He was a cotton farmer through and through, born and raised to the plough.

A friendly slap on the should shook Alara out of his reverie. “Wake up, brother, you are asleep on your feet! It’s time for lunch and then I need to walk to the river and check the channels. The water is not flowing as it should. Will you go with me?”

“Lunch already, Arty? I didn’t notice the sun was so high. Of course I’ll come with you.”

The midday meal of onion and lentils served with flat bread for eating with was waiting hot on the table. They ate quickly and had a weak cup of tea before walking to the Nile.

They could hear the river well before they could see it. The sound of saqiya irrigation was like music that infiltrated the whole valley, though they were so used to it they barely heard it. As they approached their saqiya, they called out a greeting to Nala who was driving the cow.

“Nala! We have brought food for you.”

“Thank you uncle,” she called back. “I’ll come down to eat.”

The saqiya was the heart of the farm, pumping the water of life from the river to the fields where it was needed. Made of wood, it consisted of cogs and a large open-spoked wheel. The cow, encouraged by young Nala, moved a wooden arm around, turning the wheels and cogs to move a pulley.

That pulley was studded with jars which dipped down into the water and lifted up to the farm’s main channel. Each jar then deposited its precious load which ran to the farm and branched out into smaller channels, delivering water for the cotton.

Alara inspected the cow and saqiya while Nala ate lunch. Despite a slightly thirsty cow, everything seemed to be working fine. The problem must lie in one of the channels.

Walking along the main channel, he stopped now and then to check the water level. Sometimes silt and aquatic plants collected at the bottom, blocking the flow of water. When he and Arty came to the first branch in the channel, they separated to cover more ground. Following his channel through several other branches, Alara found one that was a problem.

The side of the channel must have collapsed recently. Mud clogged the small stream, causing water to dam up behind it and overflow. Alara reached in and started to pull up clumps of the stuff. The water became turbulent and muddy, and he noticed more than a few of the fresh-water snails that liked to live in the slowly flowing channels. As he cleared it, the water began to run clean again and move into the farm. He spent the rest of the afternoon checking other channels, clearing several that were silting badly.

Though he didn’t know it, those snails were responsible for the troubling, itchy spots many adults had on their arms and feet. Well, it wasn’t the snails exactly, it was the tiny worms inside them.

Several species of trematode of the genus Schistosoma could infect humans. These tiny parasitic worms hatched in water and quickly found snails to infect, burrowing into their large feet. They moved through the life stages of miracidia and sporocyst inside that host, emerging as free swimming cercariae which needed a mammal host to continue to the next stages.

In contact with humans, or for some species other animals, they penetrated the skin and lost their tails, moving through the circulation as schistosomulae. In the liver they would mature into adults, pair, and migrate so the eggs they produced would be shed in stool. Those eggs would make their way to water to repeat the cycle.

Two weeks later, Alara woke in the night with a pain in his stomach which sent him running to the toilet area. By morning he was exhausted and feverish. Though the disease didn’t kill him, researchers would later find evidence of the parasitic worms in his mumified remains.

The research

Schistosomiasis, the chronic disease caused by these worms, is thought “the most important water-based disease from a global public-health perspective” in modern populations. It infects an estimated 200 million people per year. It has a low mortality rate, but causes development problems in children and damages internal organs.

Modern irrigation systems, particularly slow moving ones, boost the disease by providing habitats to the snails. But what about ancient populations?

To find out, Armelagos, Hibbs, Secor and Van Gerven studied dessicated remains (aka mummies) from two Nubian populations. Wadi Halfa (N = 46) lived in 500AD when the Nile was lower, and used saqiya irrigation on their crops. Kulubnarti (N = 191) lived 300 years later, during a time when Nile flooding was good and irrigation was less critical. They hypothesised the Wadi Halfa population would have more Schistosoma mansoni, and it would be more prevalent in children and men due to differential water contact.

One out of three ain’t bad. Indeed, Wadi Halfa people had more of the parastic worms: 26% to Kulubnarti’s 9%. However peak prevalence of infection did not occur at a younger age in the Wadi Halfa, and there was no sex difference.

Hibbs AC, Secor WE, Van Gerven D, & Armelagos G (2011). Irrigation and infection: The immunoepidemiology of schistosomiasis in ancient Nubia. American journal of physical anthropology, 145 (2), 290-8 PMID: 21469072

Note: I tried to be accurate about life in Nubia, 500AD, but please correct me in the comments

(Also, I want to be a bioarcheologist! Should I apply for one of these Graduate Programs at Emory University?

SKA – Something Kinda Awesome and a tremendous telescope

// May 12th, 2011 // No Comments » // How Things Work, Recent Research

The Australian Government just announced it will spend 40 million dollars over the next four years to support Australia’s bid to host the Square Kilometre Array (SKA.) If, like me last week, you’re not really sure what the SKA is and Google seems to think it’s some kind of music – here’s the lowdown based on the RiAus event I went to on Thursday hosted by Professor Peter Quinn.

The SKA is a radio telescope 10,000 times more powerful than any other, a single scientific instrument comprised of individual dish antennas 15 metres wide working together.

From a central, densely packed core, receiving dishes will spread outward an area of over 3,000 kilometres. Combining their signals creates a telescope with the collecting area equivalent to a single dish one square kilometre in area.

Where will this massive instrument live?

The shortlist has been whittled down to two: South Africa and Australia. If in South Africa, the dishes will reach onto islands in the Indian Ocean. If in Australia, they will extend into New Zealand.

The final decision will be announced next year. Being Australian, naturally I’m hoping we’ll get the honour.

Our bid puts the SKA core in the Western Australia desert, Murchison Shire.

From here, the dishes would spiral out in five long arms across Australia and New Zealand.

The proposed core site is a space the size of the Netherlands, it contains 110 permanent residents.

With low population comes low radio interference. CSIRO scientists are working on innovative solutions to keep the site radio-quiet.

For example, trains in the region currently communicate by radio, and there’s dialogue to come up with an alternative that will work for trains without interfering with the SKA.

What will we find out there with our powerful telescope? Well, if ET phones home within our galaxy, with the SKA, we’ll hear it. In the next post, I’ll talk more about finding first light, when the galaxies began to glow.

Here’s more about the SKA: Australian site and International site.

Sex and mosquitoes – transmitting the Zika virus

// April 8th, 2011 // 5 Comments » // Recent Research, Sex and Reproduction

When Brian Foy returned home to America from a field trip in Senegal, Africa, he didn’t know he was infected with the mosquito spread Zika virus.

But just a few days later he was sick with extreme fatigue and joint pain, and so was his wife Chilson. A new study coauthored by the pair and colleagues suggests that this is the first documented case of an insect-borne disease being transmitted sexually.

Though the paper lists the patients as Anonymous, in an interview to Science Brian revealed he was patient 1, and his wife was patient 3.

The lucky person who was patient 2 was Brian’s PhD student Kevin Kobylinski, who had been collecting mosquitoes with him as part of his malaria research. Being bitten came with the job, so they were vaccinated against some of the major disease, including Dengue fever.

The symptoms, when they arrived, seemed to suggest they had nonetheless caught Dengue fever. Headaches, torso rashes and fatigue all round lasting for a week, then muscle pains which lingered longer. They sent blood samples to the U.S. Centers for Disease Control and Prevention, who ran a number of antibody tests. The tests showed that all three had antibodies against Zika virus, which infects monkeys and humans in Africa and Asia.

But Brian’s wife, Chilson, has never travelled to Africa or Asia. The cool climate of Colorado supports different mosquito species to those tropical varieties which spread Zika. In fact, Zika had never been recorded in the Western Hemisphere.

They concluded that Zika had been transmitted human to human, and probably sexually, as their four children didn’t get the disease.

If Zika virus can be spread by sexual transmission, it could change the way the disease is prevented. Zika is considered an emerging pathogen, having infected about 70% of the people on Yap Island in the Pacific during 2007.

Foy, B. (2011). Probable Non–Vector-borne Transmission of Zika Virus, Colorado, USA Emerging Infectious Diseases DOI: 10.3201/eid1705.101939 (pdf)

Super cute kittens conceived by science

// March 18th, 2011 // No Comments » // Recent Research, Sex and Reproduction

This little kitty is a rare African black-footed cat conceived through IVF in an attempt to keep the species alive.

About 40 of these cats live in zoos worldwide, while a few wild cats live in South Africa where they are protected, but sometimes poisoned and killed by farmers.

How could you poison these little kittens, they’re so CUTE!!! Ahem. So, I have been visiting Zooborns again, it’s a serious habit.

Let’s pretend this post is about something more than just cute pictures of cats, and talk about the science that conceived them.

Audubon Center for Research of Endangered Species aim to protect seriously endangered species by creating a “frozen zoo”, banking genetic material such as eggs, sperm, embryos and tissue samples. Frozen, thawed sperm and IVF technology sparked the life of these kittens, which were really conceived six years ago and frozen as embryos.

The embryos were thawed and implanted into the surrogate mother Bijou in December last year.

It must be a bizarre experience for the mother, although I’ve heard tomcats have a barbed penis so perhaps she’s lucky to have skipped the usual event.

The frozen zoo contains frozen semen from the gorilla, Sumatran tiger, jaguar, Jabiru stork, and caracal. Other cell samples cover the African and Asian elephants, Baird’s tapir, colobus monkey, roan antelope, and black bear.

“The next step for us will be to clone the black-footed cat and transfer the embryo to a domestic cat surrogate,” said Audubon Center for Research of Endangered Species Senior Scientist Dr. C. Earle Pope in the media release.

Cloning endangered species, is that a good idea or not? I can’t tell.