Monday, September 29, 2008

EndNote's Parent Company Gets Nasty

Here at the University of Sydney, we are encouraged to use EndNote citation software to manage our reference material. There isn't much discussion of competitors or alternatives to EndNote, but if you look, you'll find that there are quite a few out there. From a user's point of view, it's important that there are strong competitors to EndNote, because competition will push EndNote to try to make their software the best, to fix the problems that it has, and to add new, useful features.

Unfortunately, the parent company of EndNote seems to have decided that they will pursue a strategy of attacking their competitors, rather than trying to be the best. They've recently filed an apparently baseless suit against a new-ish competitor, Zotero.

I thought it was worth bringing this to your attention, because Zotero supports reference formats that anyone can use, while EndNote uses proprietary formats that other products can't read. Imagine if this happened with gene or protein sequence files! The Zotero strategy is far more in line with an academic needs, and they deserve our support.


Wednesday, September 24, 2008

Animal agriculture on a grand scale

The small cardboard brochure that arrived in the mail belied the spectacle that awaited me in Hanoi, Vietnam, at the 13th AAAP conference. It gathered together 1240 delegates from 36 countries and the aims were sweeping- to increase the quality of life of poor people in rural areas, and to discuss ways to reduce the disadvantage of smallholder farmers in a global economy.

The opening ceremony for the Asian – Australasian Association of Animal Production Conference, inside the soaring National Convention Centre (where APEC 2006 was held- there was even a fetching picture of John Howard in national dress on the wall), was a spectacle complete with a military band, endless floral displays, and the most enormous conference banner I have ever seen. It was a far cry from the daily lives of the people that this conference would aim to help; many smallholder farmers live on less than $2 a day.

At the ceremony, the Vietnamese Minister for Agriculture and Rural Development described the plan for Vietnam to be “industrialised by 2020”. Surely there is a hint of irony in discussing this at such a conference: What happens to the traditional smallholder farmer when he is squeezed out of the supply chain under pressure to maximise efficiency and intensify production? It is a tricky question. One cannot deny the rights of poor farmers to improved education, health and security in terms of producing enough food to live on year-round, but shouldn’t we also be aiming to preserve the culture and traditional ways of life of smallholder farmers, rather than trying to turn their farms into intensive piggeries or sterile sheds full of poultry?

Fortunately, many of the scientists at this conference are presenting interesting and inspiring research that can realistically be implemented to improve the lives of smallholder farmers without resorting to intensive non-traditional agriculture. Professor Peter Wynn (now at CSU, Australia) presented on the effects of pre- and post-natal nutrition on cow and buffalo calves, with some simple ideas to improve the growth and life-long productivity of these animals, and Dr Jean Charles Maillard (CIRAD, France) spoke about the need to preserve traditional breeds of production animal, which can be a reservoir of genetic diversity and are often more disease resistant than intensively produced breeds.

Environmental issues such as global warming and the decreasing supply of fossil fuels were not ignored, and several presenters touched on methods that can increase production or reduce greenhouse gas emissions by utilising agricultural waste. Dr Thomas Preston (Columbia) spoke about the use of a gasifier to generate electricity on small farms in Columbia (these simple machines can be fuelled by crop byproducts such as coconut shells), and Dr R.A. Leng (Australia) advocated the use of combined systems, such as farming rice with ducks to weed the paddies as a simple alternative to herbicides, and the use of grazing cattle between palm plants to increase palm oil production.

This conference has shown us many examples of this ‘back to the future’ approach, where all waste is utilised and everything is regarded as a resource. We can only hope that the recommendations from this kind of research will be implemented, as this may be the only way to ensure that smallholder farms remain viable in our increasing globalised world.

Photograph top: Red Sahiwal calf and chicken, Vietnam
Photograph bottom: Part of the foyer of the National Convention Centre, Hanoi


Tuesday, September 23, 2008

Profile: Professor John W. James

You'll find Professor John James in Room 513 of the RMC Gunn Building on most Wednesdays and Thursdays. And why would you be looking for him? Well, that bit is easy - he's a retired academic with a background in quantitative genetics, biostatistics, and computing applications, and since statistics in particular is the least favoured discipline of 99.9%* of biologists (*estimated using a thorough survey of this blog's editors), his skills and interests are very valuable.

John has retired from his post at the University of NSW, but his two days a week with us in the Vet Faculty shows that he has not been able to completely resist the siren call of academia. However, he does have other interests that keep him busy, including sport and literature.
This Renaissance Man and Fountain of Statistical Wisdom provided the following answers to our profile questions:

I was born... in 1935 at Rockhampton, the first of 7 children to 5 of whom Dad transmitted a Y chromosome. I did not pass on my copy, but my brothers have passed on 7 copies in all.

At school I... was called Jesse, after a well-known American, my resemblance to whom is, I believe, in name rather than character.

My first relationship... was begun 50 years ago and still continues.

Friends say I... like any game that involves hitting or kicking a ball.

If I wasn't me I'd like to be... Roger Federer, hitting the ball so much better than I do.

At the moment I'm reading... (as usual) several books : The Secret River by Kate Grenville, Shostakovich and His World edited by Laurel Fay, Something to Declare by Julian Barnes, and once again An Introduction to Probability Theory and Its Applications by William Feller. This old favourite provides much entertainment and instruction, and includes an account of the Galton-Watson process which can be used to model Y chromosome transmission.

My worst job was... shovelling crushed ore back on to a conveyor belt in the No. 1 Mill at Mt. Morgan mine at the points where it had fallen off. By the time we had finished at the last point it was time to go back to the first.

At the moment I'm working... not very hard,

...which is interesting because... that is also the way I worked before I retired.


Friday, September 19, 2008

Profile: Dr. Gauthami Sudhamayee Kondagari

Gauthami is one of only a few postgrad students here who has actually worked as a vet! She joined us in February, 2005, and is working on a doctoral research project, entitled "Intra thecal enzyme replacement therapy in canine fucosidosis and investigation of pathophysiology". Before coming to Australia and starting her PhD, Gauthami worked as an Assistant Professor in the Department of Physiology, College of Veterinary Science, Rajendranagar, Hyderabad, India (2002-2005). She worked as a Veterinary Surgeon from 1999 to 2002.

Gauthami has completed her Master of Veterinary Science in Physiology (M.V. Sc.) and Bachelors in Veterinary Science & Animal Husbandry (B.V.Sc. & A.H.) at the College of Veterinary Science, Acharya N. G. Ranga Agricultural University, Hyderabad, AP, India.

The story of how Gauthami came to be here with us in Australia is an interesting one. She had always been passionate about neuroscience, and loved dogs, including her family's German Shepherd, Buffy. When her husband, Ramana, found work in Australia, Gauthami started to look for roles here, and in May 2004 visited the Faculty of Veterinary Science here at the University of Sydney. She met a few potential supervisors, including Rosanne Taylor, who had a project looking at canine fucosidosis in Springer Spaniels. With such a good match for her interests, Gauthami was inspired to work on this project, and the rest is history.

Gauthami will be writing for us again soon to tell us more about living and practicing veterinary science in India. Here is her profile:

I was born... in Hyderabad, the most populous city of Andhra Pradesh which is the southern state of India.

At school I... was keen on becoming an Engineer as I was strong in Maths.

My first relationship... ended in marrying Ramana and we are blessed with 2 beautiful children.

Friends say I... am a naughty nut! "but now no more"

If I wasn't me I'd like to be... an Engineer.

At the moment I'm reading... only books related neuroscience as I am writing up my work.

My worst job was... while working as Vet in a rural area, I had to attend janmabhoomi where I was forced to attend meetings with politicians and villagers to resolve issues not relevant to my job profile.

At the moment I'm working... intra-thecal enzyme replacement therapy in canine fucosidosis

... which is interesting because... it gives encouraging information to parents whose children suffering with fucosidosis too.


Wednesday, September 17, 2008

Profile: Karma Nidup

I was born... in the cowshed nearby a beautiful lake surrounded with thick broad-leaved forest. My late brave mother was alone and while in labour she saw star through the window and named me “Kam Mindu” – meaning Northern Star. Later, my Buddhist teacher changed it to Karma Nidup which means “blessing of the stars”.

At school I… was a bit hyperactive (unusual for a northern star)

My first relationship was... that was in high school. She dumped me after few days for a guy who was a singer in the school. It is okay because even I admire singers… No grudges!

Friends say I... don’t look like 35… Keep saying it folks.

If I wasn't me I'd like to be... a television journalist or radio jockey.

At the moment I'm reading... books on genetics – well, I have to.

My worst job was... so far I have no complaint.

At the moment I'm working... on genetic diversity of Bhutanese and Nepalese pigs

... which is interesting because... these animals will change my title from Mr to Dr –hopefully, fingers crossed!


Flying pigs

Marijuana grows wild in Bhutan and only a few people, mostly poor subsistence farmers, take notice of it. But they don’t consume it- instead this wild weed is fed to the pigs to fatten them, keep them quiet at night, and restrain restless behavior during oestrous.

Perhaps this Himalayan Shangri-La Kingdom may be the only country where pigs do ‘fly’. My research involves unveiling the phylogenetics and phylogeography of these ‘flying pigs’ using FAO/ISAG-recommended microsatellite markers and partial sequences of mitochondrial DNA. My wishful thinking is that findings from this study could be useful for drawing up a program for strategic conservation and sustainable utilization of indigenous pig genetic resources in Bhutan.

By Karma Nidup

Monday, September 15, 2008

Profile: Dr. Gary Muscatello

Dr. Gary Muscatello joined the Faculty of Veterinary Science at the University of Sydney in 2008. He completed his BVSc at the University of Melbourne in 1997, after three years in practice he returned to the University of Melbourne to undertake postgraduate studies completing a PhD in Veterinary Microbiology in 2005, investigating the effects of farm management on ecology of virulent Rhodococcus equi. His work in the field of R. equi epidemiology has raised many questions regarding the method of spread of virulent R. equi on horse studs, with results suggesting an alternative contagious route of aerosol transmission.

Gary gave us some insight into his background and passions with his answers to our profile questions:

I was born... into a large immigrant Italian family in the Western suburbs of Melbourne.

At school I... was an AFL superstar in the making...

My first relationship was... in kinder with a freckled face red haired girl who lived a block from me, we were friends through to year 12 ...

Friends say I... love a challenge and don’t mind putting in the hard yards ..

If I wasn't me I'd like to be... a sports journalist.

At the moment I'm reading... Finding Nino, A sea change in Italy by Marc Llewellyn (I started reading this book at Christmas and am still on the first chapter!!).

My worst job was... haven’t had one yet!!...

At the moment I'm working... on developing new units of study in the Animal and Veterinary bioscience degree ...

... which is interesting because... it gives me the opportunity to mould young scientific minds...


Saving hundreds of foals and millions of dollars

My work on the horse lung disease called 'rattles’ could save hundreds of foals each year and the Thoroughbred industry millions of dollars.

Rattles in foal is a huge problem in the Thoroughbred industry in Australia and throughout the world with treatment and management costs alone estimated to be $5 million each year. Given that on some farms, foals that get rattles can have as low as a one in ten chance of survival and the potential million dollar price tags generated from the sale of one of these ‘well breed’ foals at yearling sales, it’s not hard to realise the significant cost of this disease on the horse breeding industry.

In my work I discovered that I could measure the microbe (virulent Rhodococcus equi) responsible for this disease in the dust on horse breeding farms. The concentration of the microbe in dust was associated with the prevalence of ‘rattles’ (i.e. high numbers of microbes = lots of rattly foals). I was also able to detect the microbe on the breath of foals that where sick, they could be seen to be breathing out the microbe and possible infecting their mob mates.

The ability to measure this microbe in the dust on farms and from the breath of foals has lead to farmers and veterinarians having a better understanding of when and where the microbe can be inhaled by the foal and cause disease. Farm managers are now better equipped to identify environmental and mob warning signs, such as dry and sandy pens and the crowding of large number of foals in small yards for a long time, that may lead to increase risk of ‘rattles’. The development of farm management strategies to reduce the impact of this disease will involve minimise the risk of foal being in danger of inhaling high concentration of the microbe. Watering paddocks, good grass coverage and making sure foals avoiding large crowds will no doubt lead to a huge reduction in the occurrence of this disease and in so slashing its economic impact.

By Dr. Gary Muscatello

Wednesday, September 10, 2008

Profile: Professor John Prescott, University Professor at Large

Professor John Prescott gave a lunchtime seminar in the Faculty of Veterinary Science on Wednesday, September 10, 2008. His talk looked at public health and zoonoses, with several attention-grabbing examples from research carried out in Canada by the Centre for Public Health at Zoonoses at the University of Guelph. Professor Prescott is in Australia for a month. This profile was sprung on him when he was least expecting it, but the results were very interesting! Let's hope other visiting professors can keep up the standard...
I was born... in a British military hospital in Libya with an identical twin brother... (evil laugh)
At school I... had a very broad education. I went to thirteen schools before I was 12. Usually when a boy changes schools they get beaten up in the playground, but that doesn't happen when you've got a twin brother.
My first relationship was... gee, I've had so many I don't remember.
Friends say I am... interesting, amusing, intelligent, handsome, good-looking...
I'm very bad at... names. People should wear name tags on their foreheads.
If I wasn't me I'd like to be... a Golden Eagle.
At the moment I'm reading... A Dance To The Music of Time, by Anthony Powell. This book was recommended by Bob Carr (Ed: recommendation is in My Reading Life: Adventures in the World of Books) as one of the best English language books in existence. It is catastrophically funny.
My worst job was... bagging barley on a back of a 3' wide combine harvester.
At the moment I'm working... in Australia on trying to improve my bacteriology teaching.
...which is interesting because... I've got quite a few new ideas.


LHC to go off with a Big Bang

Somewhere in Europe, 100 metres underground, sits a supercooled, superbig science experiment ready to recreate the early moments of the Big Bang. No, it’s not the pet project of an evil genius intent on destroying the world- it’s the world’s largest particle accelerator, set to switch on in a few hours.

It’s known as the Large Hadron Collider (LHC), a £2.6 billion, 27 kilometre tunnel loop, constructed underground at CERN on the border between Switzerland and France. Inside the vacuum of the LHC, streams of protons, steered by thousands of magnets, will make the 90 microsecond trip around the loop before being smashed together head-on. Four detectors situated in enormous underground caverns around the ring will record the results.

Physicists hope that collisions between the proton beams will produce new particles such as the elusive Higgs boson, which can explain why all other particles have mass. The data should help us to understand what is the universe is made of and how it was created in the first place- Big Questions indeed!


Thursday, September 4, 2008

Profile: Kao "no middle name" Castle

I was born... in Townsville in the 70's. My parents lived on Magnetic Island (where compasses don't work properly!).
At school I... got comments on my strange sense of humour in every report card (including kindergarten), and didn't pay much attention to my teachers.
My first relationship was... with Sam in preschool, when I tried to convince him I could fly.
Friends say I... am good at remembering birthdays. They must not know about automated reminders from electronic diaries!
If I wasn't me I'd like to be... my dog, Miles, who gets to sleep for 22 hours a day.
At the moment I'm reading... I'm not actually reading any books, but I like to check, and I love
My worst job was... temping for a security company. One client stopped paying their bills when their security system was stolen along with all of their posessions, and the security company didn't notice.
At the moment I'm working on... a bone growth disorder called osteochondrosis in Thoroughbred racehorses.
... which is interesting because... individual animals can be worth so much, and the breed as a whole is very healthy.


Wednesday, September 3, 2008

Science Fashion Tragedies Part I: The Lab Coat

Yikes!Why is lab wear white, baggy, and supremely unflattering?

I suspect it's not the fashion sense of your standard science student at fault in this situation. Instead, I'm placing the blame fair on the shoulders of lab coat manufacturers. What lack of imagination on their part blinds them to the obvious need for an Evil Genius Lab Coat, or simply the Power Lab Coat (discrete shoulder pads and high collar) for those moments when we need to come across as supremely knowledgeable?

And the colour? Why white? It's black that is slimming! Australia is currently topping the charts when it comes to the proportion of obese people in our population, so a lab coat that doesn't scream "giant white whale" would seem like a sensible proposition.

Lab coats are there to protect our skin and clothes from chance exposure to chemicals and biological fluids when we get a bit too excited with the pipette. Theoretically, you need to be able to tear the coat off when sprinting for the emergency shower after you just covered yourself with acid. But this requirement doesn't seem like much of a barrier to lab coat diversity: thanks to the miracle of press-studs (or velcro for those that are after that hypercolor 80s inspired lab coat!) we could all be stylish and safe. Personally, I think I'd opt for a classic trench-coat inspired design, feminine and flattering, that would look good with the covered shoes (to be addressed later) that are also required for lab safety.

Lab-wear manufacturers, if you think that there is not enough demand for stylish lab wear to make this work, you're wrong. If someone can make money from ties with the periodic table on them, just imagine how much you'd make from stylish lab coats... a gift that scientists would actually like to receive!


Monday, September 1, 2008

Platypuses- Dangerous when wet!

When you think of a platypus, what words come to mind? I’m thinking ‘cute’, I’m thinking ‘cuddly’, I’m thinking ‘perfect pet for my toddler/niece/nephew if only they would change those darn protected species laws’. If you thought any of those things, well, think again. I’m here to tell you that the platypus has a sting in its tail.

By now you know that male platypuses have poisonous spurs on each hind leg, which they use to inject venom into victims. Envenomation occurs when the platypus wraps both hind legs around the victim, driving the spurs into the flesh several times, and injecting venom as he does so. Unfortunate humans often need help to disengage an attacking platypus, as it is able to support its full weight by its spurs. There is even a story of one eminent platypus biologist who, when trying to untangle an angry male animal from a net, ended up with the platypus hanging from either side of his trouser fly (luckily he was wearing thick trousers and wasn’t hurt!).

I say lucky because although envenomation of humans has never reported to have been fatal, the venom produces swelling and excruciating pain- and morphine is mostly ineffective at pain relief. One victim, who had previously served in the Vietnam War, described the pain of platypus envenomation as worse than his shrapnel injuries, and it lasted for several weeks. Nausea, gastric pain, cold sweats and lymph node swelling all come with the territory too.

Yeah, yeah, you say, so they’re venomous, but they’re not all that scary. I beg to differ- have a listen to the bone-chilling growl of an angry platypus here.
So, in summary: Platypuses- get them before they get you!


Why are we blogging?

Both Camilla and Kao have entered essays in the Wellcome Trust New Scientist Essay competition. Unfortunately, neither of them received quite the award they deserved, and as a result they have been driven to publish their wonderful essays themselves.

Since they needed a website to publish these essays on, they're going all the way and publishing other things too: articles on science news, interviews with interesting scientists, profiles of the other students and academics that they work with, and horoscopes. But first of all, and most important, our (tragically non-award winning) essays are posted below.