Scientific Scribbles

The voice of UniMelb Science Communication students

The herbivore vs. omnivore debate rages on.

Recently I came upon this study (although it was carried out in 2008), which found a correlation between the loss of brain volume and low vitamin B12 status of elderly individuals. The news site through which I found out about this study, however, put the findings rather more bluntly, stating simply that “a vegetarian diet shrinks the brain”. A number of other news sites used equally straightforward and provocative headlines on the same study. Vitamin B12 is found in animal products, so the conclusion drawn by the news site does have factual grounding, despite its simplicity.

To me, however, the concerning element is the tone of the headline used in the article, which adds fuel to the fire of the ever-present debate between vegetarians and meat eaters regarding the health benefits of each lifestyle. This is all too evident in the somewhat spiteful comment responses to the article where one user (evidently a meat-eater) claims, “your diet is an insult to Darwin himself”. This is matched by a blunt retort from a vegetarian who asserts, “this article is bullcrap”.

A similar example that comes to mind is that of the well known advertisements that used to be on television featuring actor Sam Neill explaining the benefits of red meat consumption to an orang-utan, as this symbolised the theory that consumption of meat was crucial in our evolution from lower-order primates. These ads were met with strong criticism from animal rights groups and vegetarians.

Actor Sam Neill came under fire from some groups for his appearance in an advertisement for red meat.

By gdcgraphics, via Wikimedia Commons.

There appears to be something inherent in people to take sides on seemingly inconsequential subjects whether it be this, the use of PCs vs. Macs, shopping at Coles vs. Woolworths, etc.

Battles can seemingly erupt from the most trivial of lifestyle differences!

By Edward Percy Moran, via Wikimedia Commons.

The article outlined above takes advantage of this tendency in order to generate interest, and crafts the scientific findings to add reputability to the claims. Herein lies a stark contrast between the communication used in the scientific paper, where the study concludes that low vitamin B12 status warrants further investigation as a cause of brain atrophy, and news websites interested in generating hits. Unfortunately for the considered science papers, it is not nearly as fun for the lay person to show their friends a scientific paper and say “I told you X warrants further investigation” as it is for them to definitively declare “I was RIGHT and you were WRONG!”

Bioinformatics: the new buzz in biology

“What are you studying?”

The Holy Trinity of Bioinformatics: DNA by netalloy , Computer by plakboek.


(Pause for shock and puzzlement)

“What’s that?”

This is a conversation that I have about once a week. This post is absolutely no dis on those asking. I have had this conversation with zoologists, physicists and even biological mathematicians (and BTW I am mostly talking about Masters and PhD students as I think you guys definitely deserve the appropriate scientist label).

And it’s a valid question. Most bioinformaticians have to have a long think about it before they answer. Sometimes I fudge my answer by calling myself a computational biologist or a biological statistician, but let’s face it: that’s a cop out.

You may noticed that about 10 of your fellow bloggers are part of my bioinformatics buddies circle. We come from all over the place with undergrads in computer science, statistics and all fields of biology. We like to think of bioinformatics as the intersection of these fields. And between us we are doing all sorts of different things.

Many of us (myself included) study DNA. We sequence genomes, or bits of genomes and try to work out what makes humans, mice, bacteria etc. tick. Now the human genome for example has around 23,000 genes spread over 3.2 billion DNA bases. If you count the DNA that you inherit from both your mother and father you have almost as much DNA in one cell as there are humans on the entire planet! We bioinformaticians end up with so much data that we need big-ass super computers and fancy statistics to make sense of it all.

Now I’ve just used an example rather than a definition to represent my field. So I pose the question to my peers. What is your bioinformatics? How would you define it?

Now hopefully my next conversation to go more like:

“What are you studying?”


“Awesome! Tell me more.”

Images sourced from: DNA by netalloy , Computer by plakboek.

Wee all need to do it – or die

Wee All need to do it

‘Kidneys’ have been featuring in my life of late with a family member having kidney disease ,and it has struck me that many of the people I have talked to don’t know much about kidneys and lump ‘kidney function’ with other things down below we don’t talk about . So I’m going to talk about the wee bit I know and hope its not too wrong.

Gushing Water!
Kidneys are really clever in what they do . They act like a blood filter and remove just the right amount of waste and fluid, returning to the body what it needs. We have 2 kidneys, one on each side of the body ,and each kidney consists of about one million microscopic functional units called nephrons. Each of these act to filter our blood allowing small molecules ( water, salt, glucose etc ) in , while not allowing bigger things such as proteins and red blood cells . A nephron is a bit like a bent up tube (a tubule) – plasma ( the fluid part of blood) goes in one end (filter), and modified fluid (urine) out the other, joining the output from other nephrons, to eventually go out a bigger tube, the ureter (one per kidney), to fill up the bladder; from the bladder urine travels down the urethra (another tube) to finally end its wee journey.
Only part of the blood plasma goes on into the nephron – the rest of the blood goes on into capillaries to run beside the nephron . Our blood plasma is filtered at around 125 ml a minute, and if 125 mls per minute of urine came out, we would lose our entire blood plasma volume ( approx 2.75 litres ) in less than half an hour ! (1) Well obviously this doesn’t happen ; urine is produced , on average, at about 1 ml per minute- so water must be returned to the blood stream – and it is through the wall of the tubule(other substances too, that the body needs, are returned this way eg glucose, sodium ). Substances can also be secreted back into the tubule. So kidneys continually regulate our body’s water levels , solute levels ( eg Sodium, Potassium, hydrogen ions ), and blood pressure so that it is just right. You have no doubt noticed that your wee is a darker colour when you are dehydrated – the result of kidneys minimising the water lost from your body ; whereas a clear, pale urine is the result of the elimination of excess water.
Urine (like healthy blood) is sterile – no germs, but can become a good growth medium for bacteria if given a chance. It can easily be contaminated on exit from the body.
The urine of a healthy kidney mainly consists of unwanted water, salt, waste products of metabolism(urea, uric acid, creatinine) and foreign substances (eg drugs).
Kidney damage has many causes and appearances but where there is damage to the ‘filter’ part, then protein or red blood cells may get through to be found in the urine. Filtration rate can be reduced because of damaged nephrons and this rate can be measured using blood and urine tests. A filtration rate of ,say, 14ml per minute(my relo – much lower than 125ml/min) can give rise to a build up of waste products in the blood, and a kidney transplant/dialysis may be seriously considered depending on the type of kidney disease.
But , be aware, many people may have kidney disease and don’t even know it because outward physical symptoms don’t often appear as a warning, if at all, until the kidneys are really bad – the doctors go by blood and urine tests, looking for such things as protein in the urine ( your wee may also look foamy from this ) ,blood in the urine and elevated blood creatinine .
So, we all need to do it … or we die.
Please seek your doctor’s advice if l have worried you. Also Kidney Health Australia (2) provides an informative site .

1. Sherwood L. , Human Physiology from cells to systems, 6th ed, p506
2. Kidney Health Australia

Dropping the H-bomb, naturally.

In a lecture dedicated to academic misconduct and misleading the public, the absence of error bars in the example peer-reviewed article was, according to this esteemed academic of the University of Melbourne, deemed to be possibly a deliberate action to mislead the readers. He likened this practice to those often found in reports championing “more questionable sciences, like homeopathy”.  A snigger echoed around the auditorium triggered a word so blasphemous to modern science.

Few “medical” practices trigger such a disdainful response from the biomedical scientific community. But why? Is homeopathy the biggest con of them all?

As someone who has experienced success with acupuncture for a lower back injury and has experimented with naturopathy, I thought that perhaps homeopathy was a little misunderstood. At the point the extent of my knowledge on homeopathy was based on the explanations detailed in the wonderful fantasy-metaphysical (and fictional) novel The End of Mr. Y by English author Scarlett Thomas. Incidentally, the book neither condoned nor condemned the practice of homeopathy, rather the protagonist using a homeopathic recipe as a tool to transport to a different plane or dimension called the “Troposphere” that connects the consciousnesses of all living beings, clearly drawing inspiration from The Matrix.

As an alternative medicine, homeopathy was conceived in the late 18th Century by Samuel Hahnemann, following the observation of cinchona bark, used to treat malaria, induced symptoms similar to that of this disease. Very briefly, practitioners of homeopathy follow the philosophy of “like cures like”. Most controversially, in complete contradiction to modern pharmacological theory, homeopaths purport that the potency of homeopathic medicine is actually increased in highly diluted solutions. Responding to this, homeopaths claim that water possesses a “memory”, which that following many serial dilutions, potentiates the potency of the solution.

As a pharmacologist, the immediate reaction is to dismiss this practice as a legitimate science. What well-respected scientist would support such a claim?

Dr Luc Montagnier, the French virologist awarded the Nobel Prize for discovering the AIDS-causing human immunodeficiency virus, is perhaps the most credible supporter of homeopathy as a legitimate medicine. He is currently overseeing research into the nature and effects of “electromagnetic signals” of water molecules found in highly diluted solutions of pathogenic DNA at the Jiaotong University, Shanghai, China. “I can’t say that homeopathy is right in everything. What I can say now is that the high dilutions (used in homeopathy) are right. High dilutions of something are not nothing. They are water structures which mimic the original molecules”, quotes the Huffington Post of Montagnier. Science reported in 2010 that Montagnier “fled” France to escape “intellectual terror” he experienced by pursuing these ideas. Montagnier drew inspiration from the work of Dr. Jacques Benveniste, a once universally respected immunologist, who died in 2004. Benveniste antagonised the scientific community following the publication of a study in Nature, which examined chemicals at highly-diluted concentrations that triggered an effect in basophils.

Another Nobel Laurete, retired Cambridge University professor Brian Josephson has been a supporter of many “unorthodox” ideas. Josephson shared the Nobel prize in 1973 for the pioneering work in superconductivity, which revolutionised the efficiency of silicon chips used in computers. Josephson’s later research focussed on parapsychology, namely the possibility of telepathy (you read that correctly), which would obviously draw hostility from many scientists. Josephsen also wrote to New Scientist in support of homeopathic treatment:

“Simple-minded analysis may suggest that water, being a fluid, cannot have a structure of the kind that such a picture would demand. But cases such as that of liquid crystals, which while flowing like an ordinary fluid can maintain an ordered structure over macroscopic distances, show the limitations of such ways of thinking. There have not, to the best of my knowledge, been any refutations of homeopathy that remain valid after this particular point is taken into account.” Interestingly this letter is not available online from New Scientist and can only be found on Josephson’s website.

In The End of Mr. Y, whilst the protagonist initially requires the homeopathic solution to enter the Troposphere, she later learns to do this without the medicine, which could be interpreted as a metaphor that homeopathy does only function as a placebo. Not that a fictional work can be included as scientific evidence, of course. The point is, the placebo effect does show how positive thinking and belief in the effectiveness of a treatment, conventional or unconventional, has been associated with speedier recovery times and up-regulation of the immune system. Perhaps the best example of this response is the dismal of Vitamin C as an effective immune system booster against the various strains of influenza and rhinovirus.

Additionally many doctors encourage yoga, remedial massage, acupuncture etc. to assist in treating conditions ranging from muscle injuries to mental health issues, whilst insurance companies now provide cover for these “extras”. This shows some acknowledgement within the community that some aspects of alternative medical practices are considered beneficial, at least in providing hope and belief of regaining one’s health. But one would be hard-pressed to find a GP who would recommend homeopathy as a complimentary form of treatment.

Josephson was later asked by New Scientist how he became an advocate more unconventional theories: “I went to a conference where the French immunologist Jacques Benveniste was talking for the first time about his discovery that water has a ‘memory’ of compounds that were once dissolved in it — which might explain how homeopathy works. His findings provoked irrationally strong reactions from scientists, and I was struck by how badly he was treated”

One thing I have to make clear is that I am not advocating homeopathy, parapsychology or any of the “radical” or “unorthodox” research mentioned in this post. I remain to be convinced of the potential of homeopathy, and I highly doubt that I will be an advocate for parapsychology any time soon. Putting aside these reservations, Josephson does make one very important point though. It appears that many members of the scientific community lack open-mindedness to consider various alternative medicines.

Personally, I am convinced of the benefits of remedial massage, meditation and acupuncture. My back has never felt stronger, my body more relaxed and my mind clearer. I also don’t feel comfortable with people being critical of the various forms of alternative medicine, without having experienced the benefits for themselves. Perhaps it’s a case of Western science not yet being able to provide a biochemical explanation for each treatments mechanism of action. Montagnier, Benveniste and colleagues have attempted to provide such “Western” explanations for the mechanisms of action of homeopathic remedies. I’m not convinced…yet. What about you?

The Cruelty Behind Rodeos!!

Rodeos have been receiving some unwanted attention recently by numerous welfare groups including Animals Australia. So I thought I would post some information on the ‘sport’ and would love to hear everyone’s opinions on whether it should be banned nationally?

Rodeos are currently banned in Britain and in parts of Europe, the United States and Australia due to the pain and distress they cause to the competing animals.

A variety of competitive ‘sports’ are involved in a rodeo including bull and horse riding, calf/steer roping and steer wrestling. All of which can cause serious injury to the animal.

Many people in favour of rodeos claim that if the animal doesn’t want to buck then why would they do it? However, for cattle, and horses to a lesser extent, to perform they are often ‘encouraged’ with an electric prod, to which they are extremely sensitive to. Flank straps are also used to assist with the bucking. They are generally tightened before the animal and rider enter the ring, and to be honest, generally don’t cause extreme discomfort or harm to the animal. Many are actually lined to prevent any sort of injury, but they will cause the animal to buck unnaturally. If over-tightened to increase the animal’s performance, however, they can cause harm. Spurs are also often used on horses to initiate bucking, which if used incorrectly can cause great injury to the animal. Even the most docile horse will buck if spurred incorrectly. Numerous injuries are obtained from the bucking motion.  

‘A day at the Mareeba rodeo’ licensed under Creative Commons

Roping causes injury due to the force of lassoing and jerking the animal to a halt. It is then thrown and wrestled to the ground which can lead to tearing or stretching of ligaments, internal haemorrhaging to the thymus gland and trachea, disc rupture, broken legs and the list goes on.

The sport of steer roping, licensed under Wikimedia Commons


Steer wrestling involves the contestant jumping off the horse to grab the steer by the horns and twisting its neck in an attempt to wrestle it to the ground. The animal can receive splintered horns broken limbs and in some cases spinal injury.   

Dr. C. G. Haber, a veterinarian with 30 years experience assessing meat for the United States Department of Agriculture states ‘when rodeo animals are sent to the packing houses I have seen cattle so extensively bruised that the only areas in which the skin was attached was the head, neck, legs and belly. I have seen animals with six to eight ribs broken from the spine that at times puncture the lungs. I have seen as much as two to three gallons of free blood accumulated under detached skin.’

Now I’m not saying all rodeos are like this and every animal receives serious injury, however injuries are often and can’t be prevented even in the most organised and welfare aware rodeo.

Further Reading:

Larson, P.W. Rodeo Is A Cruel Sport

Animals Australia

ABC article: No Bull? The Great Rodeo Debate

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