Saturday, 13 June 2009

Questions for Dr Karl, part IV

Our bodies are composed of a large amount of water and each day we are required to replace the water that is lost to maintain healthy bodily function. We consume water in drinking and eating, and lose water in urinating, sweating and breathing. If we are to sufficiently replace lost water, why is that we excrete so much of it, apart from the reason of removing toxins from the body. Here is an example: If you drink a large quantity of water in one go, most (if not all) will be excreted in urine soon after. If water was so vital for the body, wouldn’t the body have developed a way to harbour the excess water or even utilise it rather than excrete it at once. I know for a fact that I don’t drink enough water and as a result my body is dehydrated. If I drink a large volume of water, most of it is excreted in urine. Why isn’t my body designed to use that water even though I know that I am often dehydrated? Is that part of the imperfection of the human body?

The light at the end of the tunnel….

Two weeks ago (1st June) was the third anniversary of me starting my PhD. For the past two years, I have blogged (here and here), about my PhD and its progress (sort of) at each anniversary and have even celebrated by bringing in cake to share with my lab mates. Sadly, this third anniversary may be the last I will ever celebrate if things go according to plan. I should be happy because it means that my PhD will soon be complete and I will enter a new period of my life and not have the burden of lab work/thesis writing or ‘feelings of guilt for not being in the lab or not reading a manuscript’ hanging over my shoulder. A few weeks ago I prepared an application to extend my candidature and scholarship for another six months. Part of this application required a detailed ‘time line’ of my plans for the extra six months of time and funding I was asking for. In it I had to state what I was doing month-by-month until the end of the year and this included submitting my thesis in early January 2010. The main reason I feel a little sadness over completing is because, unlike most PhD students, I have enjoyed every step of my PhD. I immersed myself in university life as much as I could and feel I have received as much back as a result. Thankfully, I haven’t encountered too many obstacles from my PhD and this also has contributed to an enjoyable candidature. Anyway, I won’t go into detail about my candidature but my point is, the time during my PhD has been the best few years of my life – academically, socially, personally. And to think that these enjoyable years are now coming to an end is a little sad. On a happy note, I’m so not going according to that timeline I prepared so this PhD thing may go on a little longer than proposed.

Sunday, 10 May 2009

When three is a crowd….

I’ve often heard the term ‘a third nipple’ but I've never looked into it until today. Whilst preparing for a demonstrating session about mammary glands, I came across the term ‘polymastia’ and ‘polythelia’, otherwise known as an extra breast and an extra nipple, respectively. Immediately intrigued by this, I googled it and found images of these breasts and nipples. One particular case that caught my attention was a breast and nipple on the sole of a woman’s foot! A 22-year old woman sought medical attention for a lesion which she had on her left foot since birth (see picture below). The lesion was identified as a pseudomamma: incomplete breast tissue and a nipple. Further histological examination (examining tissue under a microscope) of the lesion confirmed the diagnosis as class 5 pseudomamma based on the Kajava classification system. The presence of fat, a nipple, an areola, and the absence of glandular tissue classified the lesion as a pseudomamma. This was the first known diagnosis of a pseudomamma on the sole of a foot. The patient eventually had the pseudomamma removed.
Pseudomamma on the foot

In further readings, I discovered that the phenomenon of extra breast tissue (either nipple or breast) was a lot more common than thought. Approximately 1-5% of the population present with this, although it occurs more commonly on the back, shoulders, face (yikes!) and thighs. Additionally, I discovered that extra breast tissue, when containing glandular tissue, is susceptible to diseases of normal breasts (cancer) and even monthly cyclical alterations of breasts induced by hormones ie. swelling, pain and sometimes even milk secretion. Fortunatley for the woman in this case, her pseudomamma was asymptomatic (ie. showing no symptoms). Imagine having to walk on a breast at certain times of the month. Ouch!

(1) Conde DM, Kashimoto E, Torresan RZ and Alvarenga M (2006) Pseudomamma on the foot: An unusual presentation of supernumerary breast tissue. Dermatology Journal Online. 12(4).
(3) Fleurs des Champs image: Wikimedia Commons

Friday, 8 May 2009

Questions for Dr. Karl, part III

I was listening to a radio interview a few nights ago where the interviewer was interviewing a blind person whose sight had slowly deteriorated over-time through his life, eventually leaving him fully blind. I found the interview fascinating as the interviewee was describing many facets of life for the blind which i had not previously thought about. Soon after i found myself wondering what blind people see in their dreams. If you are blind from birth, what do you dream? Will you see images, pictures, colours, etc. If you lose your sight later on in life, will you continue to see images in your dreams as had done before you lost your sight? Or will your dreams eventually become similar to someone who has been blind from birth?

Monday, 6 April 2009

Fashionably scientific

For the hard-core fashionable scientists out there, this one is for you....

Science T-shirts
Made with molecules

I absolutely love it!

The benefits of hugging

What prompted me to write this blog post was a small article I read in the paper on the weekend about an artist named Keeta Dean Dixon who designed an interactive piece called ‘The Hug Wall’. Attached to long fleece gloves is a wall made from stretch of tarp. The movable gloves allow the ‘hugger’ to extend their arms through the wall and hug a ‘hugee’ without any skin-to-skin contact and visual identification. This ideas has apparently been well-received.

So if you didn’t know it already, human touch is essential for development and growth in babies and young children. Human touch is also beneficial in adults. Touching can take various forms but the form I will write about today is the act of hugging. A hug can indicate love and affection towards another or it can be a physical way of expressing support. A 2005 study examined the effects of ‘warm contact*’ on individuals in relationships by assessing their levels of cortisol (a ‘stress’ hormone), sympathetic activity by measuring norepinephrine (another ‘stress’ hormone), oxytocin (a feel-good hormone) and blood pressure both before and after ‘warm contact’. The results of the study found that levels of oxytocin were increased in both men and women after the period of partner support (ie. warm contact) compared to levels measured prior to partner support. Interestingly, results showed that only women presented a link between greater levels of oxytocin and lower levels of sympathetic activity and blood pressure suggesting warm contact/partner support was cardio-protective for women.
So there you have it girls. I’m sure you knew that a hug made you feel better but now you can be assured that it decreases your chances of acquiring heart disease at the same time.

*‘Warm contact’ was defined by couples sitting close together in a love-seat which was followed by couples talking about their closeness, watching a romantic video seen previously (non-pornographic) and finally concluded with a lingering hug.

(1) Grewen KM, Girdler SS, Amico J and Light KC (2005) Effects of partner support on resting oxytocin, cortisol, norepinephrine, and blood pressure before and after warm partner contact. Psychosomatic Medicine. 67. p.531-538.
(2) Image:

Saturday, 28 March 2009

Suprising wild animal instincts

Earlier this year, the state of Victoria in Australia was ravaged by several bush fires. The devastation caused by the bush fires was described as Australia's worst natural disaster. Up to 300 lives were lost and 5000 people were displaced from their homes. In addition to the toll on human lives, thousands of animals were injured and even perished from the infernos. In amongst the chaos, which last for many weeks, several stories of bravery, survival and courage came forth including this heart-warming story about the Australian fire-fighter who gave a wild koala a drink from a bottle of water. This story made headlines around the world and video footage was taken during this moment.

Edit: It seems that the Koala, affectionately known as Sam, has attracted alot of popularity since her debut (

Video: Youtube

Another recent incidence of 'suprising wild animals instincts' came from Borneo in Malaysia. A mother organutan and her baby were reportedly stranded on a tree for several days trying to escape from a flood. Since orangutans are known to be afraid of water, it came as a shock to rescuers when they threw her a rope in an effort to pull her to through the water onto land. The mother reached for the rope and held onto it as she was pulled across ensuring that her and her baby's head remained above water.


These two examples of survival instincts shows the display of intelligence by wild animals which are often over-looked or underestimated by humans. It also shows the level of trust offered by animals in times of desperation especially when a baby is involved.

Friday, 27 March 2009

Check me out…..

I just wanted to indulge in a little bit of self-promotion of my new blog. Welcome to my so-called “right brain”.

Interesting architecture

A friend of mine sent me an email today with the subject 'The top 40 unusual buildings'. Unusual and amazing they were. I have displayed two of my favourite amazing feats of architecture.

The first is a building is in Pigeon Forge, Tennessee, USA. This building houses a science amusement centre and is named ‘WonderWorks’.


The second building is called ‘Stone house’ in Guimares, Portugal. Unfortunately I couldn’t find any literature on this house.


Sunday, 8 February 2009

Facebook for dogs

The other day, I came across an Australian Facebook-like site for dogs named DogBook. Although various pet applications exist within Facebook - the popular human social networking site, where a Facebook user can add a pet application - this website is the only site where you have to register independently of your Facebook account. How cute is that?

Wednesday, 28 January 2009

Scientists identify the molecule responsible for the wrinkly Shar-pei

As cute as they look, Chinese Shar-pei dogs are afflicted with a potentially dangerous skin disorder which causes mild to severe wrinkling and thickening of the skin. Severe wrinkling can lead to bacterial infection in the skin and entropion (the inward folding of eyelids which can cause eyelashes to rub against the cornea). Scientists recently identified the molecule primarily responsible for this skin condition and its cause. The technical term for this type of skin wrinkling is cutaneous mucinosis, where cutaneous refers to the skin and mucinosis refers to deposits of mucin in the skin. Mucin is a clear jelly-like substance and the main component of mucin is hyaluronic acid (yes, the dermal filler). The researchers hypothesised that the accumulation of hyaluronic acid in the dermis caused mucinosis in the Shar-pei. By examining the correlation between mucinosis and the levels of blood hyaluronic acid, the researchers identified that the accumulation of hyaluronic acid was responsible for the mucinosis. The results of the study showed a strong and clear correlation between the severity of mucinosis and levels of blood hyaluronic acid ie. dogs with greater wrinkling had higher levels of hyaluronic acid in their blood.

(1) Zanna G, Fondevila D, Bardagi M, Docampo MJ, Bassols A and Ferrer L (2008) Cutaneous mucinosis in shar-pei dogs is due to hyaluronic acid deposition and is associated with high levels of hyaluronic acid in serum. Veterinary Dermatology. 19. p.314-318.
(3) Image: Wikimedia Commons

Let’s look to the stars

2009 is the International Year of Astronomy (IYA). Celebrations in Australia were officially launched today by Australia’s chief scientist, Professor Penny Sackett. Australia will play a part in the IYA by raising awareness about astronomy and promoting the science. There will many events held throughout the year where the general public can get involved.

For more information, visit:
The Australian IYA site -
The International IYA site -

(2) Image: International Astronomical Union (

Friday, 23 January 2009

Attention contact lens wearers!

Have you ever wondered how your contact lens (CL) solution rates in anti-bacterial effectivity when compared to other CL solutions? Or whether the silver impregnation of a CL case enhances the anti-bacterial effectivity of the case? If you have then read on...
All CL wearers are vulnerable to contaminating bacteria regardless of rigorous CL cleaning practices. To minimise the time and tediousness of cleaning CLs, manufacturers of CL solutions have experimented with the ingredients of their solutions and other factors such as composition of CL cases, cleaning techniques and time required to soak CLs in CL solutions. A 2008 study examined the killing effectivity of three multi-purpose CL solutions, and the effectivity of silver impregnations in CL cases. Details of solutions used in this study were given, including their shelf name, manufacturer and active ingredients. However, to make this blog-post non-discriminatory against the different CL solutions on the market, and as you can never be fully certain whether published studies testing products from pharmaceutical companies provide unbiased results, I decided to re-name the CL solutions but include their respective active ingredients. This way you can check to see whether the CL solution you use contains the important active ingredients.

Three different CL solutions (see table below) were tested for their anti-bacterial effectivity. Biofilms (a layer of bacteria which forms on the surface of an object) of bacteria* were grown on CL cases and incubated with each CL solution and 0.9% sodium chloride (a control). Similarly, planktonic bacteria* (bacteria floating freely in solution) were tested by suspending the bacteria in each CL solution. The killing effectivity of both types of bacterial forms were tested. Additionally, the numbers of live and dead bacteria transmitted from CL solution to lens were measured using both bacterial counts and microscopy (fluorescence). The effectivity of silver impregnated CL cases was also tested.

Summary of results: The results showed that:
(1) Solution A had the highest killing effectivity for both biofilm and planktonic bacteria.

(2) The silver impregnation of CL cases with added CL solution increased the killing effectivity of one type of bacteria (Pseudomonas aeruginosa) but not the other.

(3) Solution A transmitted the lowest number of bacteria from solution to CL and silver impregnation of the CL case did not make any difference when solution A was used.

Conclusions: Solution A has the most effective anti-bacterial effectivity as seen in this study. Silver impregnation of CL cases is useful in enhancing anti-bacterial effectivity but is redundant if solution A is used. According to the paper, other researchers have found opposing results however these studies were not carried out in “real-life” conditions ie. other studies carried out their incubations of CLs in CL solution for 7 days as opposed to over-night which is more realistic of a CL wearer.

* Bacteria tested include Staphylococcus aureus and Pseudomonas aeruginosa.

(1) Vermeltfoort PBJ, Hooymans JMM, Busscher HJ and Van der mei HC (2008) Bacterial transmission from lens storage cases to contact lenses - Effects of lens care solutions and silver impregnation of cases. Journal of Biomedical Materials Research part B 87(1) p.237-243.
(2) Image: Wikimedia Commons

Friday, 16 January 2009

Nature pooh-poohs?

Readers, did you know that 'pooh-pooh' was a legitimate word? I didn’t, and was completely shocked to read the word nonchalantly used (see below) in an article (Squint of the fossil flatfish) in the prominent science journal ‘Nature’.

"On occasion, this property has been pooh-poohed, even by palaeontologists who have considered that fossils can help in refining relationships already inferred from living species, but tell us little about the process of evolutionary character transformation."

Sure, I was aware of the term ‘poo-poo’ meaning faeces but not ‘pooh-pooh’?!?! When did pooh-pooh become a word? The definition of ‘pooh-pooh’ is ‘to express disdain or contempt for’ or ‘dismiss lightly’.

Can anyone empathise with me? Please let me know whether you knew 'pooh-pooh' was a word by participating in the poll on the RHS panel near the top of the page.

(1) Janvier P (2008) Squint of the fossil flatfish. Nature. 454. p169-170.
(3) Image:

Seeing ‘eye-to-eye’

The flatfish (namely the sole, plaice and halibut), named for the shape of its body, is a remarkable fish I only recently heard about. What is so interesting about this creature is that the young flatfish starts off ‘normal’ with its eyes placed on both sides of its body (think of a typical looking fish) and a symmetrical skull. But, as the fish rapidly develops into an adult, one eye migrates from one side of its body close to the other eye and the skull becomes asymmetrical! At this point, the body of the flatfish remains the same but both eyes are on one side – named the ‘eyed’ side, as opposed to the ‘blind’ side. For a long time, evolutionary biologists speculated the origin and asymmetrical nature of the flatfish but with no conclusive evidence. Some biologists proposed the asymmetrical flatfish arose through natural section whilst others proposed the fish arose through evolutionary leaps - a process known as 'saltation'. However in 2008, Dr Matt Friedman became the first scientist to provide the most conclusive evidence of the origin of the asymmetrical nature of the flatfish. Dr Friedman was given permission to study 45 million year-old fish fossils using computer tomography imaging which lead to the finding of an ‘intermediate’ fish which had an eye on either side of its body but with an asymmetrical skull. This was the ‘intermediate’ fish which all evolutionary biologists had been looking for. Interestingly, one eye of this intermediate fish was found to be normal whilst the other eye was a squinting eye.
A good image of a flatfish can be found here. An explanation for the migration of the flatfish eye (from an evolutionary point-of-view) is presented by Richard Dawkins in the YouTube clip here.

(1) Janvier P (2008) Squint of the fossil flatfish. Nature. 454. p169-170.

Wednesday, 14 January 2009

Male face preferences during the menstural cycle

Oooh la la, Tyson Beckford - I must be in the follicular phase of my menstrual cycle :) Image: Wikimedia Commons.

Hormones - chemicals released by the endocrine organs in our body - are important molecules which have control over many of our bodily functions. It has been known for sometime that a woman’s preference for male traits (including but not limited to facial features, depth of the voice, behaviour, height, odour and body shape) changes according to the different phases in her menstrual cycle. Hormonal influence is one of many factors that is able to dictate a woman's preference for a male during a particular phase of her menstrual cycle. Several studies since the late 1990s up until now have examined the relationship between timing during the menstrual cycle and male trait preferences, with all studies having small variations in research method. I thought I would closely examine and summarise the findings of one of the early studies that looked at the relationship between the menstrual cycle and male face preference. This particular study employed Japanese women who had regular menstrual cycles and were not on the pill. The women were asked to select computer generated-faces which they considered physically attractive. The faces were a mix of five Caucasian and five Japanese men. The findings of this study strongly indicated that the women preferred male faces that were more masculine in the follicular phase of the menstrual cycle – the phase prior to ovulation/end of menses which allows the greatest chance of conception. During the luteal phase (post-ovulation, pre-menses), the women preferred men with feminised male faces. The reasoning behind this preference is as follows….Women prefer masculine facial features during the follicular phase because masculinity is supposedly thought of as an indicator of high quality males (although this relationship is controversial). During the follicular phase, a woman wants a “masculine” man – one with a strong immune system, one that is able to provide quality children and one that is able to confer resistance to disease. During the luteal phase, women prefer feminised male features which is thought to be an indicator of a man’s potential investment as a long-term partner ie. a man with a feminine face supposedly indicates cooperation in parental care and one that is unlikely to cheat.

Other studies examining the relationship between the menstrual cycle and male traits have reported vocal masculinity, dominant behaviour, taller men, facial symmetry, masculine body shapes as preferable during the follicular phase.

This may explain my preference for more feminised male features in an on-line experiment I participated in last year. After taking the test, I came up preferring feminised male faces. I may have been in the luteal phase of my menstrual cycle.

Reference: Penton-Voak IS, Perrett DI, Castles DL, Kobayashi T, Burt DM, Murray LK and Minamisawa R (1999) Menstrual cycle alters face preference. Nature 399 p. 741-742.

Tuesday, 6 January 2009

12 random facts about the author….

I have to give credit to my friend Li for inspiring this blog post. I thought it would add a personal touch to my blog in which I endeavour to protect my identity. So here are some random snippets about the Afro Scientress…

1. I love people who can make me laugh alot. I don’t mean this in a sexual way but personality-wise. It applies to guys and gals.

2. My favourite colour is orange.

3. I love taking photos and being creative when taking photos. My next camera purchase will hopefully be a SLR or something more professional than the digital camera I use now.

4. I hate it when people say things they don’t mean.

5. I have only 24 teeth in my mouth as opposed to the standard 32.

6. The older I get, the more I fear the future. Ironically, I look forward to change.

7. I love nearly everything about summer.

8. In high school I was voted ‘nicest person’ and ‘person with the best smile’ – how things have changed.

9. I drink a banana milkshake on most mornings. One whole banana, half a cup of milk, a teaspoon of honey and a sprinkle of cinnamon. Blend.

10. I would hate to be famous.

11. 2008 will be considered as one of the best years of my life. It was a year that was filled with opportunities and experience. I had several opportunities for personal and uni-related interstate and overseas travel. I had wonderful and not-so-wonderful experiences in personal relationships all of which I have taken something away from. I turned a hobby into something that provided me with an additional income. I did some teaching/demonstrating, which is something I have wanted to try for a long time. I learned to appreciate the beautiful state I live in: Western Australia. Edit: A couple of things i forgot to mention because i was too consumed in personal matters include our prime-minister, Kevin Rudd, delivering a formal aplogy to the stolen generation, and the election of Barack Obama. These things, although not personal, made 2008 an even better year.
It’s only a week in to the new-year but unfortunately 2009 is not a year I am looking forward to. It started off fine but quickly went down-hill in my personal life and I can sense that this trend is set to continue. I have been dreading this year mainly because I know I have to finish most of my PhD. My supervisor has asked me to do additional lab work on top of the lab work of my own project which means longer hours in the lab on top of writing a thesis. As an incentive, my supervisor has agreed to give me a top-up on my scholarship. In my circle of friends, most of my closest friends are either getting hitched, moving away or both whereas I am still single and have no plans to move away for at least two years. To top it off, 2009 has quite literally hit me in the face a week into the new year. True story: I was half asleep in bed this morning when all of a sudden my annual calendar slid down the wall behind my bed, rebounded off my bed-head and fell smack-bang right onto my face. The really scary thing was the hook on the wall hadn’t come off nor did the hook holding the calendar to the wall. I think 2009 is trying to tell me something. I recently came across a 2008 website which I think appropriately describes my 2009 so far.

And finally…

12. The next blog post will be science-related :)

Tuesday, 16 December 2008

A sudden urge of inspiration

I have been pretty slack with my blog lately, largely due the science journalism taking up my writing time. I’m about six months into the journalism and so far it has been greatly rewarding and so enjoyable. I have met so many new people and learnt about many disciplines of research and science going on in Western Australia, which I would never have encountered otherwise.
But back to the blog…Over the past couple of weeks my inspiration for my blog has been slowly accumulating so with great gusto I decided to stop beating around the proverbial bush (I’ll throw a shoe at it instead LOL) and just write something to get the ball rolling. So, I hope this is the start I need. Unfortunately an unavoidable hurdle lies in the way which means I won’t be able to write again until the new year. Hopefully this won’t stop the blog-ball rolling and I will be able to come back in 2009 with built-up enthusiasm for science. On that note, I would like to wish all my readers (a grand total of 2, if that LOL) a lovely Christmas and a safe new year.
PS: I have updated my blog roll with a couple of exciting blogs so please check them out.

Thursday, 25 September 2008

Launch of National Breast Cancer Foundation campaign turns Australia pink!

To officially launch the National Breast Cancer Foundation (NBCF) pink ribbon campaign, cities around Australia have turned their lights on to light up important landmarks. Breast cancer month is inaugurated annually in October to raise funds for research and raise awareness of breast cancer, which can affect 1 in 8 women and also the lives of their families and friends. Each capital city and a few additional cities in Australia will participate by lighting up notable landmarks in pink – the official NBCF campaign colour. Perth will play a part by lighting up several major landmarks including Winthrop hall at the University of Western Australia. As I was driving home today, I caught a magnificent view of Winthrop hall and just had to stop to takes some pictures.


Government-funded research to be made freely available to public

It's about bloody time, i say. I read the following article today (a recommended read) which got me quite excited. In short, Australia is looking to make publicly-funded research findings freely available to all. I think this is a great idea and something that should have been implemented long ago. Some of the reasons as to why research findings should be accessible to all are outlined in this old post.

For extra information:

Wednesday, 27 August 2008

New age conference posters

It was brought to my attention today that conferences are now resorting to a new style of conference posters which are printed on cloth! Conventional conference posters are usually printed on thick laminated paper. Posters are then rolled up and carried around awkwardly in poster tubes to conferences whether it be local, national or international. If attending a national or international conference, posters are often too large or bulky to be considered as ‘carry-on luggage’ and have to be thrown in with baggage. Amongst other things, large posters can be difficult to pin up on poster boards, difficult to roll up and a pain to carry around. So, when I was shown a cloth poster today, I was excited to hear about it. The person who presented the cloth poster was also in support of them. He suggested that these posters could be scrunched up and thrown into luggage, or even worn as a scarf. Now you can truly match your attire to your conference poster and integrate fashion and learning at the same time :)

Monday, 25 August 2008

How do you react to faces?

The New York Times recently published an article on the best online psychology tests (initially reviewed by PsychCentral). In an attempt to learn more about myself, I tried all six tests that were recommended and found the 5th one (Faceresearch) to be most interesting and stimulating.

I participated in Faceresearch’s test for ‘facial attractiveness’. This test required the participant to rate which face was more attractive out of two almost-identical faces (which included both men and women). The differences between the two faces were initially hard to pick up on at first glance but did become apparent after studying the faces for a few seconds. While I was doing the test, I noticed that a trend was developing in my selection: I preferred those with a slim face, groomed eyebrows, cheek colouring and non-droopy eyelids. After analysing 40 faces, the feedback according to my selection stated that:

“On average, people preferred the more feminine women 80% of the time and the more feminine men 54% of the time. You preferred feminine women 90% of the time and feminine men 85% of the time.”

Being heterosexual, I have no idea what this means apart from the fact that I find feminine features more attractive in the opposite sex.

Faceresearch has a bunch of other interesting facial reaction tests. I recommend this website if you have some time to spare.

BRIEFING: Japanese scientists ‘crack’ stem cells from wisdom teeth.

Scientists in Japan have been able to extract stem cells from the dental pulp of wisdom teeth of a 10-year old girl. These cells have been tested and have been identified as being similar to embryonically-derived stem cells. This is an advancement in the stem cells field as this method provides a quick and less invasive way to extract these cells and most importantly, there are no ethical concerns.

If wisdom teeth stem cells are able to successfully differentiate into other cells, the tooth fairy might have to give up his/her day job LOL.


Saturday, 16 August 2008

Put your safety googles on, grab a pipette and don a lab coat

Because it’s that time of year again where the scientists of the land take over to celebrate National Science Week (NSW). Running from 16-24 of August this year, the organisers of NSW have a number of events lined up to inspire the scientist in all of us. Each state is running a number of presentations, shows, seminars and forums for people of all ages and all walks of life. Some of the events include ‘Scinema’ which is a science film festival; ‘shopping trolley science’ which provides interactive science demonstrations at local shopping centres; and various lectures on pseudoscience, plants, bacteria, astronomy and sustainable gardening. There’s plenty more to see and hear during NSW which runs until the end of August.

For more information, visit

Sunday, 27 July 2008

Gija Jumulu

Kings Park in Western Australia was gifted a 750 year old Boab tree from the Gija Aboriginals of Australia last week. The Jumulu (meaning ‘Boab’) was transported from the Kimberley region in an overt operation on the back of a large open truck. Settled in its new home at Two Rivers lookout in Kings Park, the tree stands at approximately 14 m in height and just over 2 m in width. Since its arrival, visitors have flocked to view the tree as it protrudes from its enclosure, surrounded by Eucalypts.


Saturday, 26 July 2008

R.I.P Randy Pausch

Randy Pausch, a well-known computer scientist from Carnegie Mellon University (CMU) in Pennsylvania, sadly passed away on July 25th 2008 after a long battle with pancreatic cancer. Regarded as a prominent scientist in the field of computer science, he was thrust into the public spotlight after delivering an inspirational presentation titled ‘The Last Lecture: Really achieving your childhood dreams’, which was delivered to a full house at CMU in September 2007. In his speech he described his childhood ambitions (one which included ‘being Captain Kirk’), the ways in which he achieved them and advised the audience on how to reach their dreams. This humourous yet profound speech, which touched many people around the world, conveyed his positive outlook on life and strong, brave spirit despite his circumstances. His ‘Last Lecture’ speech was released as a book in early 2008.

Below are a couple of quotes delivered in his "Last Lecture" speech:

"The brick walls are there for a reason. The brick walls are not there to keep us out; the brick walls are there to give us a chance to show how badly we want something. The brick walls are there to stop the people who don't want it badly enough. They are there to stop the other people!"

“Experience is what you get when you didn't get what you wanted."

- Randy Pausch

Thursday, 24 July 2008

The Acacia and the Ant

There are many symbiotic relationships in nature. Some relationships are visible: For example, cleaner fish remove parasites/dead skin from other fish and in doing so, provide a meal for themselves and clean the surface of the other fish. Other relationships are not so visible. One such invisible relationship occurs between the Bullhorn acacia and the ant. The Bullhorn acacia gets its name from the thorn-like structures on its branches, which resemble horns of a male bull. Unlike most acacias, the Bullhorn acacia lacks the bitter alkaloid which would normally protect the tree from attack by insects or grazing livestock. To compensate for the lack of this defence mechanism, the Bullhorn acacia produces protein-lipid nodules (Beltian bodies) which are used as a food source by ants living on the tree. These ants, which are harboured in the thorns of the Acacia, use the protein-lipid nodules to produce and secrete pheromones which are picked up as a deterrent by other insects and grazing animals. Furthermore, the ants are capable of a nasty sting which acts as an additional deterrent.

(2) Image: Dan L. Perlman ( /Ant,Bullhorn_Acacia,thorn,Pseudomyrmex,EL_DP162.jpg)

Saturday, 19 July 2008

Look ma, I’m a freelance science journalist!

Well, I don’t know at which point I can call myself this but late last week I scored a job writing articles as a freelance science journalist for an on-line science newsletter. My first article was published on Friday after a hectic but exciting week. My week involved pitching a story, tracking down a voice recorder, attending a seminar to capture the main point of my story, liaising with media officers, conducting an interview, writing the article and then nervously waiting to hear the editor's opinion after submission of the article. I would describe this new experience as an exciting adventure that spiced up what would normally be a relatively mundane week for a laboratory scientist.

Saturday, 12 July 2008

Dance like nobody's watching (Warning: Tear-jerking video clip)

Here’s another New York Times (NYT)-inspired blog post. No extra words are needed to describe this article and video (below) which featured in the NYT on July 10th 2008. Please watch the video clip, read the article and then the numerous comments that follow :-)

Where the Hell is Matt? (2008) from Matthew Harding on Vimeo.


Monday, 7 July 2008

JAMA poetry

I have to give credit (and a plug) to the New York Times (NYT) for initiating this blog post. A few days ago I read an article in the NYT (which may I add is one of my favourite publications right now) which brought my attention to the Journal of the American Medical Association’s poetry publications written by patients, researchers and doctors. While perusing the JAMA, the name it is commonly referred to in medical research circles, I realised that the journal does not limit itself to just scientific publications and poetry, it also publishes book and media reviews (of medical relevance) and short literary pieces describing experiences of doctors (in “a piece of my mind”), among other things. In addition, the cover of the journal (journals have covers?....just kidding) features beautiful artworks of prominent and less prominent artists. I guess this is one of pitfalls of having literature that is easily accessible on-line - we never get in touch with the real thing. Anyway, although JAMA is not related to my field of research, i know that I will appreciate this medical journal for being a bit different to most journals I read.
Below I have posted two profound poems from the “poetry and medicine” section of JAMA.

The Suit
When the time comes to donate your clothes
i will leave the gray check suit in your closet for the foreseeable future.
I'm not so foolish to think that you're coming back and will need it again
rather, i want some tangible item other than pictures documents and death certificates glossy flat and thin.
With your suit i am able to
put my hand into its sleeve
roll my arm in the pant leg
puff out the jacket and feel your silken space.
There's something so substantial in its emptiness
that i need now after five months
when the memories are still strong
but your reality is slowly eroding.

- Frank DeCicco MD

Everything is nervous here, vibrating
to the hum of air conditioning.
Outside, the palms are never still.
Inside, palms sweat in high anxiety.
Even the indifferent chameleon
sunning on the hot veranda
blows his red sac as a warning.
On the Gulf a tropical depression
brews a hurricane. Depression
in this place is deeper still,
this space where hopes die,
wishes fail, silent waiting ends
as the next white-coated person
speaks of trying everything.
And the coldness that comes then
makes the heat of anger welcome,
like the coming storm.

- Robert L Jones

(1) The NYT:
(2) DeCicco F (2008) The Suit. The Journal of the American Medical Association 229(12): 1404
(3) Jones RL (2008) Thermostat. The Journal of the American Medical Association 299(16): 1878
(4) Cover image (2006) The Journal of the American Medical Association 295(9): cover. This cover features a painting by Henri Matisse (1869–1954), La méditation: après le bain (the Meditation: After the Bath), 1920, French. Oil on canvas.

Saturday, 5 July 2008


No, this is not a form of medieval torture nor is it a social/political movement; it is in fact a common medical condition afflicting many people. Bruxism (pronounced brucks-ism) is a physical condition where a person grinds their teeth and clenches their jaw during sleep.

Sufferers of bruxism can often feel the effects of a night of good teeth grinding the following day by presenting with symptoms including headaches, jaw pain, tooth chipping and fractures, and even tooth loss! If symptoms of the condition are not immediate, then overtime-bruxism-sufferers will notice tooth wear. Alternatively some people will not present with any symptoms at all unless the wear and tear is picked up by a dentist. Bruxism sufferers can often be made aware of their suffering by partners and family members as teeth grinding can be forceful and consequently audible.

The cause of bruxism is questionable but it is diagnosed to be a result of a number of ailments including, but not limited to, stress and anxiety, disturbed sleep, sleep disorders, an abnormal bite, large consumption of stimulants (eg. coffee), digestive problems and consumption of drugs/stimulants.

Bruxism is most commonly controlled with the aid of a custom-made splint or mouth guard. This uncomfortable-to-wear guard is made of durable plastic moulded from a sufferer’s teeth/gum impression and stops wear and tear of teeth. Various forms of relaxation (eg. meditation) before bedtime are recommended for sufferers if stress/anxiety is thought to be the cause. Sore mouth/jaw muscles often manifests as a result of teeth grinding so Botox has been proven as a successful form of treatment as it relaxes the muscles in the area and prevents further muscle contraction.


Wednesday, 2 July 2008

Conversations with proteins

Olga Kuchment is a researcher in the Kuriyan laboratory in the Department of Molecular and Cell Biology & Department of Chemistry at the University of California, Berkeley. The Kuriyan laboratory study the mechanism of Src activation at the molecular level. To find out more about the Src proteins, Olga decided to interview the v-Src protein. With Olga’s permission I have posted the transcript of this entertaining and ingenious interview (which i highly recommend reading) as it appears in “The Scientist” (Proteins gone wild, 26th June 2008).

The Src protein helped teach the world about the molecular basis of cancer. The animal Src protein, c-Src, was first discovered because its mutant, v-Src, was spread among chickens by the tumor-causing Rous Sarcoma Virus. Both proteins are tyrosine kinases, cell signaling enzymes that activate other enzymes by moving a phosphate from ATP to a tyrosine amino acid. Animals require c-Src activity for proper bone development and T-cell development and activation, among other things. c-Src is only active when it receives specific cellular signals, but v-Src is less inhibited and much more active.

The two faces of Src (adapted from Young et. al., 2001.)

My lab mates and I here at the University of California, Berkeley, study the mechanism of Src activation at the molecular level. Unable to reach c-Src for this interview, I invited v-Src, a very dynamic molecule, for a drink at our local pub. The protein got a little tipsy, and it was waving its phosphorylated activation loop like mad.

v-Src: You know, I'm the most important molecule in a Rous Sarcoma Virus infected cell. I help cells ignore signals to die, or help them divide uncontrollably and invade healthy tissue.

Kuchment: That is impressive! One type of rogue molecule can cause incredible damage. I know the DNA that codes for you has some mutations, which is why you always misbehave. But what causes the overall genetic instability in the infected cells, making them accumulate more and more mutations in various cell signaling proteins?

v-Src: That's not very interesting. Let's talk about me.

At this point, we were unexpectedly joined by c-Src. Not noticing that v-Src was there, it came directly toward me. c-Src takes extreme care in its appearance; not a single loop was out of place. Its SH2 and SH3 domains were docked neatly behind its kinase domain.

c-Src: Kuchment, I've been looking for you. I am outraged. People have no appreciation for the good work my family and I do. We work toward cell proliferation, differentiation, survival, and when necessary, cell death. All I ever hear is that I'm a target for cancer drug design!

Kuchment: I apprec...

c-Src: The name "Src" is just a throwback to "sarcoma." I have nothing to do with it. For every one of us that gets out of control due to a couple of mutations, there are millions that do their jobs carefully. Just because v-Src was the first to be studied doesn't mean it's representative of all of us!

Kuchment: I agree, and I'm a big fan of your work. I've been studying your regulation for several years, as you know.

A pregnant pause.

c-Src: Thank you, that means a lot. But I can't stress it enough: I am not affiliated with v-Src. At first we were the same, but when the Rous Sarcoma Virus stole a copy of the src gene from a chicken cell, it cut off the tail and made several other mutations. As a result, v-Src is completely unregulated. It phosphorylates its substrates always, without paying attention to signals from proteins like Csk. Oh, v-Src! I didn't see you there.

v-Src: Are you jealous of the way I live? I'm free, and you're just a tool. You live your life in the service of the cell. And you spend most of it sitting around with your tail in your SH2 domain.

c-Src: Leisure is underrated.

v-Src: Your regulatory domains hold you back! Your SH2 is bound to the phospho-tyrosine in your tail, your SH3 is bound to the SH2-kinase domain linker, your kinase domain is inactive, and stuck that way!

c-Src: That's simply because I'm waiting for a signal from someone like a growth factor receptor tyrosine kinase. Once the regulatory domains are bound by the right ligand, they release, then my activation loop is more likely to get phosphorylated so that my kinase domain can become more active. You wouldn't understand.

v-Src: Give me your activation loop! I'll phosphorylate it, and...

c-Src: Sorry, maybe some other time. My activation loop is tied up right now.

v-Src: Then I'm leaving. But I'll get you later!

Kuchment: c-Src, as you know, I've been studying how you move from the inactive state to the active. Could I see it?

c-Src: Ah... No, I really can't stay. I have to catch a vesicle to the cell membrane.

Kuchment: Wait! Let me see! What happens to the SH2 and SH3 domains, how do you move the alphaC-helix in, and what do you do with the activation loop? Oh, darn.

So it went. Maybe the pub wasn't the best place to get serious answers from tyrosine kinases. I decided to finish my drink and go back to the bench.

Source: The Scientist, Proteins gone wild, 26th June 2008

Sunday, 29 June 2008

UWA delivers flexible learning to students by featuring lectures on iTunesU

Various lectures, tutorials and publications from the University of Western Australia (UWA) have now been made available for free downloading on iTunes under the “iTunesU” subsection. This service will enhance the conventional iLecture (Lectopia) service provided by UWA for its students. The service will also cater for UWA students with additional interests and for non-UWA students aswell. Currently, the iTunesU – UWA service provides free educational content to anyone who has access to iTunes and includes modules on self-development, sample lectures in various disciplines and recordings of invited speakers. UWA is the first western Australian university to participate in this initiative following the trends of other Australian universities including the University of Melbourne, Australian National University and Swinburne University of Technology (Melbourne).

Follow the links below in iTunes to reach the UWA - iTunes site:
iTunes store --> iTunesU (located under iTunes STORE in a LHS panel) --> Universities & Colleges (located under Find education providers --> The University of Western Australia (located under the T subheading).


Saturday, 28 June 2008

ENDO 2008

I recently returned from the 2008 ENDO meeting in beautiful San Francisco where I was given the opportunity to present my PhD results to date in a poster presentation. The meeting in its 90th year was held at Moscone Center and attracted over 7000 attendees, which was a record for ENDO. Held over four days the meeting showcased scientific sessions ranging from plenary talks, oral and poster sessions, workshops, conversations with researchers, debates, symposias and the dozens of pharmaceutical/biotechnology sponsorship booths. I was pleasantly surprised as the meeting really did offer something for everyone including presentations which were left of centre eg. Art in endocrinology. Although most presentations were intensely focused there were several which targeted the lay audience and many that were indirectly applicable and crossed-over with my work. The meeting, while attracting a couple of the big names in my field, did not pull in as many experts as I had hoped for. Nevertheless it was a great opportunity to meet with these experts, receive their feedback, establish contact and put a face to a name.
Whilst in San Francisco, I also had a chance to do some sightseeing and discover what the city had to offer. Below are some pictures from my trip (for more pics see my Flickr website).

The Moscone Center, San Francisco, where ENDO 2008 was held.

The relaxation station for ENDO attendees....a necessity for ENDO as the abstract book alone weighed 1.5 kg!(How do i know this? The abstract book tipped my luggage over the 20 kg baggage allowance limit).

My feet being massaged while waiting in line to get my back massaged at the relaxation station.

One of San Francisco's ridiculously steep streets. This one is so steep that the sidewalks had to be made into steps!

One of many beautiful murals in Berkeley.

San Francisco as seen through one of the arched windows of Coit tower. Do you see the Golden Gate bridge in the horizon?

The current political landscape in the USA.

A tram on Market Street in downtown San Francisco.

A rainbow flag flying high and proud over the Castro district in San Francisco. June 17th 2008 marked the first full day that gay and lesbian couples could get married in the state of California. The city will put on the 38th annual gay pride festival parade this weekend (29th June). The theme for Sunday's pride parade is "United by Pride, Bound for Equality".

Thursday, 29 May 2008

ASMR Medical Research Week ®, June 2-8th 2008

The Australian Society for Medical Research (ASMR) Medical Research Week® begins next week. The week long affair will be celebrated in each state with events including scientific symposiums, out-reach programmes, career development days, celebratory dinners and science in the cinema events aimed at targeting primary, secondary and tertiary students and the general public.

For more info, visit

Second year blues…no more

June 1st 2008 marks the end of the second year of my PhD and the start of the third year. It felt like yesterday when I was wrote the post which marked the end of my first year (see here). Time has flown by so quickly. Anyway, to keep to “old” traditions, I celebrated (or commiserated) with my fellow lab mates and with the help of a famous Swiss patisserie, once again.

Wednesday, 14 May 2008

Demonstrating dilemmas

I had an interesting experience whilst demonstrating yesterday. One of the students came up to me at the end of the lab class to get his book signed; below is the dialogue which took place between him and myself:

Student: "What's a cute little thing like you doing in a lab like this?"

Me (gob-smacked): "What was that supposed to mean?"

Student: "Just exactly what i said."

Me (turning beet-red): "Errr...demonstrating...and...err....earning money."


Federal budget outcomes for university students and researchers

The government released the 2008-2009 federal budget yesterday. Below are the outcomes for higher education and research.

Education Investment Fund (EIF)
"The Government will invest $5 billion to establish the EIF. The EIF will absorb and extend the Higher Education Endowment Fund, bringing total funding to around $11 billion. The EIF will fund capital expenditure in Australia's higher education institutions" (1).

(a) Higher education
"To help universities upgrade and maintain teaching, research and other student facilities, the Government will provide $500 million by 30 June 2008. The Government will also spend $626 million to reduce the cost of studying maths and science at university and to reduce HECS HELP repayments for science and maths graduates who undertake work in a related field.
The Higher Education Review, due later this year, will shape the next steps in the Education Revolution for universities"

Full fee-paying places have been scrapped and students will only be accepted into university courses based on merit.

(b) Support for research
"To strengthen the link between research and innovation, the Government will boost Australia's research capacity by providing: $326 million over four years to fund four year Future Fellowships valued at up to $140,000 a year for 1,000 of Australia's top mid career researchers. $209 million over four years to double the number of Australian Postgraduate Awards for PhD or Masters by Research students" (1).

The Council of Australian Postgraduate Associations (CAPA) is a non-profit body representing Australian post-graduate students. CAPA is the only organisation that advocates issues concerning post-graduate students at the federal level. Since the reign of the new federal government at the end of last year, CAPA has attempted to negotiate many issues relevant to post-graduate students. A few of these include:

1. Stipend award rates and duration of awards - In 2008, CAPA predicted that the stipend payed to those holding APA/UPA scholarships would fall under the poverty line by the end of the year. CAPA has advocated for a 30% increase to stipends in addition to the extension of the duration of the awards to match the four year candidature allowed for post-graduate PhDs.
2. Abolishing voluntary student unionism (VSU).
3. Exemption of tax on part-time scholarships.

Unfortunately, the above items were dismissed in this year’s budget.


Tuesday, 13 May 2008

Siamese fruit

I came across this Siamese mango today which I thought I would add to my blog for amusement. I call it mango booty ha ha. Check out this subsection of the Museum of Food Anomalies for other conjoined food. My favourite are the loving carrots on page 2. How sweet are they?

Monday, 12 May 2008

The benefits of imagery

The bulk and most significant part of my PhD examines signalling pathways within the cell. Alot of these pathways are complex and intertwined, and the molecules involved often have more than one name, can be a part of more than one pathway and often have more than one purpose. The reason for this post is to reinforce the benefits of imagery to simplify and retain ideas, theories, notions, concepts, whatever, and in my case, signalling pathways. During my readings today, I used Microsoft PowerPoint to construct one complex pathway which I had struggled with for sometime. In the past when I had read about this pathway, I had just read the relationship of the molecules involved, envisioned an image in my head and then put the paper aside. By the following week, I had forgotten what I had read. The PowerPoint image I created today simplified a concept which I had struggled to retain, and put it into an understandable and recallable format. It has been etched into my mind and I believe I would be able to later recall the relationship of these molecules and their appropriate positions in the pathway. The concept of using images or diagrams to remember detail is not new but often overlooked or forgotten. Try it yourself.

PS. The above image is not the signalling pathway i created today but it does resemble the complexities of cellular signalling i have to deal with on a daily basis.

Thursday, 8 May 2008

SURVEY: Perceptions in health and medical research careers

The Australian Society for Medical Research (ASMR) is a body which broadly represents registered health and medical researchers of Australia and also researchers in numerous affiliated associations. ASMR credits itself by acknowledging that it has a role in public, political and scientific advocacy. In late 2006, the ASMR commissioned a workforce survey which aimed to understand and improve the perceptions of researchers (registered ASMR members) in the health and medical field with an emphasis on job satisfaction, workplace conditions, brain drain/gain and the attitudes towards health and medical research in Australia.

The survey targeted 1258 registered ASMR members however only managed to recruit a total of 379 (30%) respondents. The paper acknowledged the limitations of the cohort size especially when it came to factors such as career progress (eg. student or worker), qualifications (eg. honours, PhD or post-doctoral researcher), work place (eg. university or hospital) and field of research but ensured the reader that the cohort was a close representation of a whole population on demographic variables such as sex and age.

The results of the survey were divided into four sections of which I will briefly outline the main findings:

Question 1: To what extent has each of the following factors had an impact on your career over the past 15 years
The top factors which were considered to create a negative impact on careers in health and medical research included the lack of security in employment, general lack of financial support for research and shortness of funding time frames relative to project development needs. Other options, all of which rated as having a negative impact but not as negative as the above three factors (ie. more positive) included inadequate infrastructure for research, time required to prepare grant applications, lack of managerial support and uncertainty about what funding agencies expect.

Question 2: If you have left, or have considered leaving health and medical research, how important in your decision were the following factors
The factors which were considered important to very important with this question included the shortage of funding in health and medical research, lack of career development opportunities, poor financial rewards as a health and medical researcher, shortage of work opportunities in health and medical research and availability of better employment opportunities elsewhere. The two factors which were not considered as important with this question included needing time off due to family responsibilities and the changed nature of health and medical research.

Question 3: To what extent did the following reasons have an impact on your decision to leave health and medical research in Australia to seek health and medical research employment overseas (this question was relevant to 165 respondents who indicated that they had worked or were currently working overseas)
The factors which were considered important with this question included broadening your scientific experience, collaborating with other researchers, researching new techniques, access to equipment & physical infrastructure and greater opportunities to do research. Factors which were considered important but not as important as the above mentioned included better project funding, personal interest in living outside Australia and increased quality of working environment.

Question 4: If you have returned to or are planning to return to Australia after working in health and medical research overseas, indicate your agreement with the following statements in terms of their influence on why you have returned or why you will return to Australia (this question was relevant to 165 respondents who indicated that they had worked or were currently working overseas)
The general consensus generated from this question was that in comparison to overseas employment (ie. the country where the respondent had worked or was working), 50% of respondents believed that Australia had fewer career opportunities and fewer university positions. Close to 40% of respondents believed that Australian health and medical researchers were paid less, had lower job security and had less support in comparison to overseas employment.

The results of this survey paints a poor picture of the Australian health and medical research sector but is reflective of workers’ attitudes. The main concerns of Australian health and medical researchers, as seen by this survey, are employment uncertainty and funding security and this is reinforced a number of times throughout this survey. The paper acknowledged the limitations of the study and stated that the issues may be understated because of the survey population. Although this survey only represented a very small proportion of health and medical researchers in Australia, the views and sentiments shared by this cohort, in my opinion, would be accurate if extrapolated to a larger scale. Having been in the medical research field for close to ten years, I have heard similar complaints to the responses this survey has generated and I have even faced similar difficulties myself. Securing funding (which often equates to employment security) is probably the biggest burden for researchers and is becoming increasingly difficult and more competitive as governmental budgets fail to increase proportionally to the number of postgraduate researchers produced by universities, which has increased over the years. Additionally, I believe that the nature of health & medical research has unfortunately created and perpetuated an environment where research is not being thoroughly thought through because everyone is in a mad rush to generate results, publish papers and subsequently secure funding. As a result, a lot of waste is created, money is spent unnecessarily, experiments are left incomplete due to poor design. All these factors could contribute to a loss of funding.
Speaking about a loss of funding, I read a very interesting article today in “The Scientist”, an on-line publication, titled “Losing your lab” (volume 22, issue 5, page 32) which provided examples of people who have had to shut shop and discussed the outcomes they faced and options for those in similar circumstances. In the US, the major governmental funding body, the National Institutes of Health (NIH), provides bridge-funding awards to grant applicants who score well but are unable to secure major grants. This sort of funding is also provided by several US research institutions. This practice allows researchers to continue their post and gives them a second chance at securing funding the following year, and as described by the article, nurtures a scientist and sees them as investments for institutes that are not worth losing. I am not sure whether this practice is prevalent in Australia but it sounds like a great idea.
As to outcomes from this survey, the paper suggests “a review of current policies affecting research careers and health & medical people support in broader terms may be timely if Australia is to retain its reputation for research excellence and leadership”. The paper goes on to say that “the fact that a large proportion of respondents have considered leaving active health & medical research in Australia highlights the need for a coordinated multi-streamed approach to ensure the long-term viability of the sector. Any significant loss of Australia's highly trained health and medical research workforce represents a potential erosion of its intellectual capacity and future preparedness. To maintain Australia's competitive edge, it will be necessary to provide a career path that captures, nurtures and retains talented minds and provides fertile career opportunities” (2).

(2) Kavallaris M, Meachem SJ, Hulett, MD, West CM, Pitt RE, Chesters JJ, Laffan WS, Boreham PR and Khachigian LM (2008). Perceptions in health and medical research careers: the Australian Society for Medical Research Workforce Survey. Medical Journal of Australia. 188 (9). p520-524.
(3) McCook A (2008). Losing your lab. The Scientist. 22(5). p32

Tuesday, 6 May 2008

Large Hadron Collider

The large hadron* collider (LHC) is due to begin operation this month in Geneva, Switzerland. Located on the Swiss-French border at the world's largest particle physics laboratory named the European Organization for Nuclear Research (abbreviated to CERN, the out-dated acronym is still used today but initially it stood for European Council for Nuclear Research), the LHC was built in a circular tunnel with a circumference of 27 km and is situated 50-175 m underground. Loosely speaking, the LHC is a particle accelerator or an atom smasher. In layman’s terms, the LHC consists of two beams of particles which travel in opposite directions in a vacuum and are accelerated close to 99.99% of speed of light at high energies. The orbits of these particles are controlled by strong magnetic fields created by 9300 magnets (to be precise) which are cooled to temperatures as low as -271 degrees Celsius. The magnets tightly control the orbits of the particle beams right up to collision which takes place at four places (particle detectors) around the accelerator ring. It is estimated that approximately 600 million collisions will take place every second! The LHC was designed to answer some of the fundamental and unresolved questions in particle physics such as the origin and composition of mass; the composition of dark matter and dark energy; what happened immediately after the big bang; and the existence of other dimensions.

*A hadron is a strongly interacting subatomic particle


Wednesday, 9 April 2008

Air Zoo

This story made me smile when I saw it on the news today. No, it’s not your typical New York street trash but a clever idea sparked by fine arts student, Joshua Harris. The creator of Air Zoo, Harris, had the idea of bringing nature back into the city. Normally lying motionless and limp, the constructed garbage bag animals are suddenly injected with life and vigour as air from the underground subway rushes up through street air vents changing the street-scape and giving passers by something light-hearted and entertaining to gaze upon. Once the train has passed, the animals collapse into a random and lifeless heap until the next train is due. His first garbage bag animal creation was a white polar bear (see YouTube video). Only a few days ago, he displayed a 6-foot giraffe. His idea has been received positively by passers-by.


Micro-organisms munching on antibiotics

Recent and alarming news from the world of microbiology is the finding that bacteria are able to utilise antibiotics as their sole carbon source. On top of the pre-existing problem of antibiotic resistance in medicine, this study has been widely publicised and given much hype due to the potential of antibiotic resistance becoming much more prevalent. Although the phenomenon of bacteria thriving on antibiotics has been previously reported in the medical literature, the cases were limited to a small number of micro-organisms and antibiotics. This study is the first of its kind to establish the level of resistance amongst a wide range of micro-organisms.

Methods: The researchers examined 18 different antibiotics ranging from natural, semi-synthetic to synthetic which could target a wide range of bacterial families and included ciprofloxacin, penicillin and kanamycin which are some of the more commonly prescribed antibiotics in medicine. Seventy-five bacterial samples were isolated from 11 diverse soil samples ranging from farm soil (cornfields fertilised with manure from cows fed with antibiotics), urban soil and pristine soil (untouched forest areas). This method ensured that the bacteria were isolated from areas with varying degrees of exposure to human-made antibiotics. More than half of the samples included bacteria from the phylogenetic order of Burkholderiales and Pseudomonadales, both capable of inflicting disease in humans. Two antibiotic concentrations (20 mg/L and 1 g/L) were tested with one concentration (1 g/L) being 50 times greater than standard antibiotic resistance concentrations.

Some of the alarming results: As there was no break-down on which phylogenetic order each of the 75 individual samples came from, the results when examined as a whole showed that 32 of the 75 bacterial samples (42%) were resistant to almost 100% of the antibiotics at 1 g/L and 17 of the 75 bacterial samples (22%) were resistant to over 50% of the antibiotics at 1 g/L. Ciprofloxacin, penicillin and kanamycin at 1 g/L, which get notable mentions for their widespread use in medicine, had 34, 73 and 54 of the 75 bacterial samples, respectively, come up resistant.

The findings of this study are a cause for concern because: (1) the wide range of bacterial families examined are closely related to clinically-relevant bacteria and (2) the antibiotic classes examined are commonly used in medicine and the occurrence of lateral transfer of genes between distantly related bacteria is highly possible which could potentially lead to greater levels of antibiotic resistance. Although disconcerting, these findings remind us of the capabilities of these microscopic organisms that go unnoticed and consequences when antibiotics are misused.

(1) Dantas G. et al. (2008) Bacteria Subsisting on Antibiotics. Science. 320: p100-103.
(2) Leslie M. (2008) Germs Take a Bite Out of Antibiotics. Science. 320: p 33.

For more information:

Tuesday, 1 April 2008

Acts of God?

Earlier today, I was reading through the ‘terms and conditions’ of a competition I was about to enter and as I skim read through the standard wording I came across the following:

In the case of the intervention of any outside agent or event which naturally changes the result or prevents or hinders its determination, including but not limited to vandalism, power failures, tempests, natural disasters, acts of God, civil unrest, strikes; the Promoter may in its absolute discretion cancel the competition and recommence it from the start on the same conditions.“

I have never come across “acts of God” in the wording for terms and conditions of any competition I have ever entered. Is this a common occurrence? Can this clause be used in the legal system or is this a huge misinterpretation on my part? I'm not an atheist and I don’t mean to offend anyone but I find this unusual and almost comical in this context.

Wednesday, 12 March 2008

Hello, San Francisco.....Oh, we finally get a chance to meet

I received news today about the acceptance of an abstract I submitted for a conference in San Francisco. I was so delighted to hear this. This will be my first international conference and will hopefully give me the opportunity to meet with many of the experts within my field whose works I have been reading about for the past two years.

Inter-species refloating technique

I heard a heart-warming story today: On Monday, a resident dolphin off Mahia Beach on New Zealand’s North Island helped two beached whales swim back into the sea preventing potential death. Two Pygmy Sperm whales (mother and calf) became stranded on-shore and failed to return to the water after several rescue attempts made by volunteers. Conservation workers believed that the two whales would have been euthanised if it had not been for the efforts of the dolphin. A bottlenose dolphin, named Moko, detected the distress signals from the Pygmy Sperm whales (mother and calf) and intervened after volunteers had tried for an hour to coax the whales back into the water. A volunteer rescuer described the heroic efforts of the dolphin as it pushed its way between the humans and whales and guided the whales through a channel back into the sea. The whales were not seen after the rescue however the dolphin returned to the shore to play with local residents. What a beautiful story.

Just in case you were wondering, Ta Moko which is also known as Moko, is the permanent body and face markings used byindigenous people of New Zealand who are known as Maoris. It was used in the 19th and 20th centuries for several reasons including the display of rank or status; attracting the opposite sex and signifying the transition from childhood to adulthood. Today, Moko is more commonly used to signify Maori cultural identity.


Saturday, 8 March 2008

My first demonstrating job

I start my first job demonstrating practicals for undergraduate students next week. Although I have done a bit before, it wasn’t professional and it was only a couple of practicals in a laboratory that I worked in. This will be an on-going thing for the entire semester. I am really excited but also quite nervous.

Friday, 22 February 2008

Pilobolus' symbiotic performance

I only discovered the TED website tonight which i am absolutely loving and have added to my favourites. While browsing TED, i came across this act which i thought was indescribably beautiful. The fluid performance is subject to interpretation but is described by TED as "Pilobolus dance company members Otis Cook and Jennifer Macavinta perform the sensuous duet "Symbiosis". Does it trace the birth of a human relationship, or the co-evolution of a pair of symbiotic species? That's left for you to decide. Gorgeous, organic choreography blurs the boundaries between the two performers, who use the body's own geometry to lift, move and combine".

One of the comments left by a viewer described the performance perfectly as "beautiful physical poetry".

Getting in touch with nature

A recent radio broadcast titled “Greening the psyche” relayed the importance of nature to the mind and covered a number of ideas which I found enlightening. The blurb for the programme read:

Intuitively we sense that nature relaxes us - even small pockets of green in the concrete urban jungle seem to make a difference. But finding good scientific evidence for how and why has been more difficult - until now. Crime rates, academic performance, aggression and even ADHD. Could a bit of greening make all the difference? And, ecology on the couch - a self described 'ecotherapist' with novel techniques.”

The point of this post is to just randomly highlight some of the ideas expressed in the programme. However, I will start with personal experience to attest the idea of greening the psyche. I can understand why people love gardening and its idea of getting in touch with nature literally and metaphorically. The main reason why I stay out of the garden is my ridiculous fear of certain insects, particularly insects which fly without direction and no consideration for the human face. Besides this and my lack of time, I have thoroughly enjoyed the few gardening experiences I have had, which have included weeding, watering and the occasional planting. Each time I have attempted to appreciate the greenness in my yard, I have left feeling grounded, calm and relaxed. Now to another profound experience which shocked me a little by how immediate its effects were. I recently visited a friend’s house; prior to the visit I had been feeling extremely anxious. After roughly ten minutes of being at my friend’s house, I was overcome by a peaceful and once again, relaxed feeling. Apart from the presence of my friend, I would attribute this change in feelings to the in-door water feature in the house. The trickle of the water was loud and soothing, and within minutes, all my anxieties had disappeared and I was able to remain in this state of mind for the whole duration of my visit. These are just two experiences which I am able to reflect back on and would recognise as contributing to “greening my psyche”. Another common scenario or experience where nature has a calming effect on the mind is while watching a sun set or in my case, being within a pseudo-rainforest in the middle of an urban setting (see image).

Now back to the radio programme…The broadcast briefly mentioned the idea of the Biophilia hypothesis, which is something new to me. First introduced by Erich Fromm and made popular by Edward Wilson, Wikipedia describes Biophilia as:

An instinctive bond between humans beings and other living systems.”

Wikipedia goes onto to say:
The term "biophilia" literally means "love of life or living systems." It was first used by Erich Fromm to describe a psychological orientation of being attracted to all that is alive and vital. Wilson uses the term in the same sense when he suggests that biophilia describes "the connections that human beings subconsciously seek with the rest of life.” He proposed the possibility that the deep affiliations humans have with nature are rooted in our biology. Unlike phobias, which are the aversions and fears that people have of things in the natural world, philias are the attractions and positive feelings that people have toward certain habitats, activities, and objects in their natural surroundings.”

While researching the Biophilia hypothesis, I discovered the connections between Biophilia and Biomimicracy. Biomimicracy was introduced in 1997 by Janine Benyus who argued that “human beings should consciously emulate nature's genius in their designs”. Many of those who supported the notion of Biophilia also had a strong belief in biomimicracy (including Lynn Margulis, a scientist mentioned in a previous post (Architecture mimicking nature and Gaia) who co-authored a book called “God, Gaia and Biophilia”). Biomimicracy is another newish term to me. Although I had heard of it before I had never taken a keen interest in it. Interestingly, this is exactly what I wrote about in the above mentioned post but I did not realise it had a name! Janine Benyus gives a truly fantastic and inspirational talk on Biomimicracy called "12 sustainable design ideas from nature", which i highly recommend watching (

Once again to get back to the interview….one of the interviewees on the programme was Frances E. Kuo. Frances supervises a landscape and human health laboratory at the University of Illinois ( The lab’s overall interest is described as “a multidisciplinary research laboratory dedicated to studying the connection between greenery and human health”. Some of the group’s most recent work includes using green activity settings to reduce ADHD symptoms; using view of trees from houses to improve girls’ self-discipline; using trees near houses to boost concentration and coping mechanisms; and residential landscaping to discourage crime, domestic violence and strengthen communities. Their work has been published in peer-reviewed journals showing the positive results of nature on human psyche.

Just to end this post, below are a couple quotes I took away from this programme, which I thought were beautifully described:

Community living rooms - the spaces between buildings”.
- Frances E. Kuo

Nurturing nature gives you something that humanity can’t; helping people feel part of a bigger whole”.
- Ambra Burls, an ecotherapist, who uses nature as co-therapy

(1) “Greening the psyche”, All in the Mind, ABC Radio National (16th February 2008)