Monday, December 31, 2012

Raise your glasses (to the year that was)

It's New Year's Eve. We survived the "End of the World", Xmas madness, and now the next hurdle will be how many will feel like they'll ever survive the epic hangoverss that greet them in the morning...

In the merriment of ringing in a new year, a blank slate, a new beginning, I have to pause and think about what 2012 meant to me.

It's been a big year. A year where I made new friends, a year where things went up as fast as they went down, a year where I had new adventures and a year that when I look back on it, I think I learnt more than I ever thought possible. In fact, it's all happened in such a blur I'm not sure if it all really was just some kind of crazy dream, but then I pinch myself and realise, that well, I'm awake. Life really is short, and it seems to just get faster and faster.

So what was 2012?

2012 was the year of in the time it takes to blink everything can change. My opinions changed. The way people treated me changed, and most of all I changed. I expected to be unemployed right now but have finished my PhD. I didn't expect to be back in my hometown for years. Instead in the space of a couple of months I moved over 2000km, am now employed, but alas the thesis isn't finished (but it will be soon, I hope!)

2012 was the year I realised some people weren't meant to be my friend. I also realised that people who I considered friends, were in fact not my friends at all. That people who I thought were good, were in fact, not good at all. All in all, I learnt the hard way that assholes happen and that not everyone will like you, no matter how hard you try.

It was a year I learnt the power of my voice - that if I want to make a difference to the world, I can. It's hard work to make an impact, but I wish more people realised the power they hold as individuals, and that their dreams and goals are achievable.

I learnt the power of hard work, a kind word and how just being there for someone can make profound differences.

I saw the power science has to change the world - from the Higgs Boson, to landing on Mars to the ENCODE project I saw how science inspires others and how many people get excited by science. This has motivated me immensely to ensure to I share my passion and love of science with others.

I learnt that Rome wasn't built in a day.

2012 was a full-on year. A year of growth, of challenge, of living. It is amazing to think a year ago, there were people I talked to that now I don't, there were friendships to be made, there was knowledge I now have that I didn't then, and that I was living in a different town. A lot can happen in 365 days.

So before I ring in the New Year, and new challenges and adventures, I pause to look at the year that was and realise, that living is full of one thing - change; and even though at times I'm afraid of it, and it is hard, that at the end of the day I do welcome it. I also thank the people that in various ways have made 2012 awesome - there are those that make me laugh, made me cry, make me think, make me feel inspired and at the end of it all, made me who I am.

Happy New Year - may it be full of science, prosperity, adventure, living life to the fullest and most of all, full of wonderment.

Monday, December 24, 2012

A Christmas Tale: "The Ginger Army"

'Twas the day before Christmas, and a mad scientist planned a feat,
to make gingerbread men that would rule the street.

She mixed up spices, butter and flour;
and let the mix stew for several hours.

While working to the chants
of Josh Homme, Dave Grohl, Jack White and Robert Plant,
she carefully crafted each and every one,
Rolled, cut and baked, second to none.

Next came the bones made of icing,
The army was cooled and ready for an uprising.

Along the way a few lost arms legs or heads,
but it didn't matter, for they would still fight to the end.

The mad scientist admired her army,
and giggled in delight at her plan to take over Christmas, however it was slightly barmy!

However the mad scientist realised, there was one key issue that would lead to defeat,
for chewy gingerbread were delicious to eat!

The army ran and hid,
however, there was one small problem - they were too numerous to fit under the lid.

The scientist had a thought - maybe it would be best
and give the plan for world domination a rest.

Instead, she decided, let the gingerbread by consumed,
and rule Christmas through good food.

So the ginger army has been shared and eaten
another Christmas treat that just can't be beaten!

Monday, December 10, 2012

Excuse the Tumbleweed...

Well, that certainly went fast. One day I'm planning on updating the blog, the next it's several months later...Seriously that is exactly how it has felt. I've always said you never know where science will take you, and the last few months have demonstrated that things can be flipped around in the space of not months or weeks, but days.

While I've been sparse on blog posts, I've certainly not been sparse in living.  I've seen some major changes in my life - I've moved interstate, taken up a new job and am now finishing my PhD part-time rather than it being all consuming.

I came across the opportunity to move back to near family, and in the world of science this can be rarity. In fact, I was thinking it would be 5 years or so before I could be within 'quick visit' distance of my family.  Despite not being completely finished with the thesis, the fact I may soon be out of money was at the forefront of my thoughts and I had been applying for jobs in the hope I landed something sooner rather than later.  In many regards when it comes to finishing a PhD you are damned if you are and damned if you don't. 

In order to be able to finish your PhD thesis and walk into a job at the right time is really down to luck - luck with timing, luck with funding, and to be able to continue working on exactly what you want is even another level of luck again.  However for the majority it's one way or the other - you continue to work on the thesis full time, submit and end up unemployed or you find a good job and finish writeup in your spare time; really it's stress about money or stress about writing up, there's no in-between.

I've managed to find a job in my hometown, and even better it's in something I want to be working on - I count myself amongst the lucky (especially in the current economic climate).  And best of all, I'm happy to say I really like the new job.
 However, the relocation, the farewells, the establishment of a routine where I'm making actual progress on the thesis - some things (like this blog) were pushed aside while I dealt with the perpetual whirlwind that seemed to consume the last few months.

 So with things now settling down, it's time to breathe some life back into this blog....welcome back to paradigm of one in (almost) 7 billion.

Monday, August 20, 2012

The Short Attention Span Segment #8

Here's this week's random goodness from the web:

1. Season 3 of the Walking Dead is back soon, and there are some pretty disgusting zombies and a really cool trailer, which makes me even more excited for the return of this show: Walking Dead Season 3 

2. If you have arachnophobia don't click this link. But if you like spiders, and really cool photography then cool set of pictures is for you: Amazing Pictures of Raindrops on Spiders

3. There once as a lady who swallowed a pen, and 25 years later they found it, and it still worked: An unlikely story of a pen

4. Like documentaries? Ever wondered about evoution? Then check out this Youtube collection including Dawkins, Attenborough and one of my current favourite series called "Inside Nature's Giants". Many interesting hours of viewing to be had here: Evolution Documentary Channel

5. And for those of you that have agonised over the complex question of "what is better - cake or pie?" Here is the answer, the result of an in-depth and scientific evaluation. I do not agree with the answer however I may be biased in favour of cake. I suggest further, delicious research is needed: Hyperbole and a Half: Cake versus Pie

That's all for now, as you were...
In this case, the cake isn't a lie. In fact, it is rather delicious (and contrary to scientific evaluation, better than pie)

Thursday, August 9, 2012

Paper Dissection: A wide face may mean you are a bad boy...

On the Autopsy Table: Bad to the Bone: facial structure predicts unethical behaviour

Authors: M.P Haselhuhn and E.M. Wong

 Journal: Proceedings of the Royal Society B

Volume: 279 (2012)

The Exterior:

Essentially, if you are a male with a wide face, you are more likely to cheat and lie in controlled tests (and this could be extended to real life). This is due to the underlying genetic trait (i.e. face width) giving a sense of power to the indvidual and/or the likelihood this physical trait is perceived as aggressive to others. This study supposedly demonstrates that genetically based traits (such as face width) can be linked to behaviour. I have to admit it was difficult not to think about the days of the 'criminal' shaped head (aka. phrenology) when reading this paper. However, with all the talk of 'criminal' genes in recent times, I thought it would make for an interesting paper.

The Guts:

The researchers measured a number of people's faces both male and female, then allowed the to play a game of negotiation. The next lot of volunteers were able to enter a lottery, and were told how many chances they had to enter. However the lottery was online, and the recruits had an opportunity to cheat and enter more times than allowed.  To generate measurements for comparison, faces were measured and a width-to-height ratio was calculated (known as a WHR). The negotiation test had 192 participants and the lottery had 123.

The title pretty much sums up the results. In both cases, men with wider facers took the opportunity to act unethically. In the negotiation test men with a higher WHR would lie more often, and in the lottery, they would add more entries than told to.

The explanation that the authors supplied for the bad behaviour is actually psychological, and a result of the biological features. Men with wider faces felt more powerful, and thus this power encouraged them to cheat. It is thought that men with wider faces are seen as more aggressive and thus, can take advantage of those who sense this aggression. The authors suggest that if these men are treated like they have more power, they will probably use it to their advantage.

Would you call this man a liar to his face? And then back it up by saying he is a liar, because of his face?

The Skeleton: 
So if you have a wide face you'll lie and cheat? Not quite. Looking at the actual numbers in the study, it can be seen that the differences in WHR and cheating behaviour actually aren't large, although it is statistically significant. The authors do admit further research is needed to confirm their findings, and furthermore to confim an explanation; whether the explanation is more related to the genetic trait or a psychological phenomenon, or just due to the subjects used in this one study (it is possible that out of the entire population on earth, these researchers just ended up with a bunch of volunteers who tend to cheat and lie more often than another group).

Overall,  while this study is interesting, it doesn't quite prove that men with wider faces are unethical. What it does show is that there may be some biological predictors of how people are perceived (i.e. if you are perceived as powerful due to a strong face, your behaviour may reflect this). However, if you look around, I'm sure you'll find people with a large WHR who aren't liars, cheats or are perceived as aggressive as social and environmental influences have outweighed the biological ones. So there's a bit more research to be done before you should go treating people with wide faces as suspicious.

Tuesday, July 31, 2012

What I Read Last Week: July 23-29

One of the cool things about science is that there is always something to do, there is always something to learn and there is always something new being discovered and published. One of the big parts of being a scientist is keeping up with the trends. And how do we do that? By reading all the latest news and scientific publications. In an effort to give you an idea of the sorts of things that get published as peer review research I've started this new post - a wrap up of the scientific literature I've read this week. Most of my reading is in my area - human genetics, medical genetics, forensic science but occasionally I find other papers that are weird, wonderful or just downright interesting (yes, I do read papers for fun sometimes!) For extra kicks, I've also included what else I'm currently reading since reading could probably be considered a second profession for me.

This may be an accurate representation of actual piles of currently unread scientific papers on my desk.

The last week's reading is a little light on, because I've been trawling through my own data in the evenings rather than reading. And as you can see, it's a tad dry - lots of method and validation papers, which I've been procrastinating on reading (no guesses why). 

FYI: There's lots of talk of PCR in here - otherwise known as the Polymerase Chain Reaction. For those not playing with DNA day-to-day, here's the wiki page on PCR, which is a good one (lots of descriptions and pictures): A guide to PCR

1. Developmental Validation of the AmpFlSTR Identifiler Plus PCR Amplification Kit: An Established Multiplexed Assay with Improved Performance 
Wang et al. Journal of Forensic Sciences (2012) 57:2 

The official validation study of a new kit from Applied Biosystems which is promising better results with challenging samples. Using known DNA standards the Life Technologies team put a new DNA profiling kit through its paces to demonstrate it is robust and reliable for forensic human identification. Lots of tests were done to demonstrate the accuracy, precision and sensitivity of  the assay is and factors such as how the kit handles degraded DNA and DNA samples that contain inhibitors that make analysis difficult were explored in order to show the expected results for this kit.

2. Choosing Relatives for DNA Identification of Missing Persons
Ge et al. Journal of Forensic Sciences (2011) 56: S1

A study looking at which relatives are best for DNA identifications when only relatives can be used as a reference DNA source; usually in  cases of mass disaster or cold cases. This study gives some statistical weight to common sense - close relatives are best, and parents are more reliable than siblings.  A handy paper especially when many relatives are available and it can be hard to justify choosing or waiting for certain relatives to provide a DNA sample. While it may prove more costly, this study shows the choice of relative can yield better or easier-to-interpret results (thus saving headaches and more cost)

3. Novel Methods of molecular sex identification from skeletal tissue using the amelogenin gene
Gibbon et al. Forensic Science International: Genetics (2009) 3

A few years old now, this paper compared two PCR approaches to amplify the variable regions of the amelogenin gene (which is on both the X and Y chromosomes) for quick and cost-effective sex identification of degraded skeletal remains. Variations exist in this gene between the X and Y chromosomes, including a deletion of genetic sequence which means the same gene region of is a different size between the X and Y chromosome. This size difference and other variations can be used to identify if an individual has two X chromosomes (ie. is female) or an X and Y (ie. is male).  A good way to use DNA to confirm anthropological results especially when skeletal remains are difficult to sex (such is the case with fragmented remains). However this study also highlights the key challenge: sometimes the DNA is too degraded to get a result from PCR to analyse! 

4. Hybridization capture of microsatellites directly from genomic DNA
Refseth et al. Electrophoresis (1997) 18

In terms of modern scientific publication rates, this paper is almost vintage!  A nice easy method paper describing a method to capture microsatellites from genomic DNA. Microsatellites (or Short Tandem Repeats or STRS) are small repetitive sequences of DNA that are usually combinations of two, three, four or five nucleotides repeated a number of times eg. TCA -TCA-TCA-TCA that exist in most genomes. The number of repeats are highly variable from individual to individual, and some markers are more variable than others.  Microsatellites are key in forensic DNA biology, because it is a panel of these markers that are used for human identification. I read this paper because it describes methods to "fish" these types of sequences out of a DNA extract and analyse them without using PCR as a primary method (ie. amplifying the DNA of interest).

5. Stochastic Modeling of Polymerase Chain Rection and Related Biotechnologies
Sun et al (found online)

A short random document I found online which proposes a mathematical method for analysis of stochastic (sporadic) variation associated with amplification of DNA, using Polymerase Chain Reaction (or PCR) a very common method for analysis of DNA.

In the other pile:   The August Edition of "Australian Sky and Telescope" and "Feast' magazines. Haven't had too much of an opportunity to get really into the magazines yet, but first browse on Saturday morning with my coffee put me in a good mood - after all food and astronomy are two of my big interests in life.

Preview to next week's edition: I've started Laurence Krauss's new book, a paper comparing DNA extraction methods, some population genetics and possibly even some new research comparing new DNA sequencing technologies. 

Monday, July 16, 2012


Well that went quickly didn't it?

It's been over TWO months since my last post. Mind you, it's been a pretty trying couple of months and to be honest, I just haven't had the time or the right frame of mind to keep this blog going. However, lots has been happening on all fronts so here's an update on what I've been up to, and a short reflection on some of the recent science news.

 Of course, I can't ignore what probably will be the science breakthrough of the year, if not the decade, and for some physicists, of their lifetime: The results out of the LHC regarding that little particle. All So much has been said already by those far more qualified than I, but what I can say is that even as a biologist I can appreciate the amazing result and what it means for the standard model of particle physics.  There were the usual cries of "But what does it mean for us? How will it cure, fix, or make life better?" Science isn't just about making the world better or life easier, sometimes the beauty in science is finding out something unknown, of adding a new piece of knowledge to what we know. Where a new piece of knowledge can take us in terms of applications is really an open-ended question. It's well known in science when one answer is found, about a thousand more questions simultaneously arise and a scientists work will possibly never be done. When Einstein published the Theories of Relativity, nobody could predict it would enable us to use satellites to track locations in the form of GPS. Finding the Higgs Boson is another piece of the puzzle, and a wonderful demonstration of how global effort can be enacted to improve our understanding of the world.  I listened to the live broadcast announcement of the discovery, and I even understood little parts of it! Despite not understanding all the physics I could hear the excitement, the sheer pride of the chief scientists as they spoke of the result, and this is something that made me proud to be part of the scientific community, and inspired to keep chipping away at my own research questions. The discovery and announcement of this little particle was a wonderful day for scientists of all disciplines, and the result is a shining example of collaborative science at its finest.

I've got some great papers to review for my paper dissection posts including one on how men with wider faces tend to lie, the correlation of size and strength to human formidability and some examples of sci-fi getting real including genes that can be activiated using radiowaves and how methylation of DNA can be linked to memory.  It can be said that like New York, Science never sleeps!

Speaking of unrest, on the PhD front it's been a harrowing couple of months. I waited nine weeks to finally hear that my PhD scholarship has been extended. I didn't think waiting would actually get to me, afterall I had good grounds for an extension, but waiting that long without an answer was hard, and stressful and even at times, quite distressing. The story behind the extension is a good one - it involves a mix of an electricity cut, insurance claims, waiting for orders and a supervisor who went AWOL. Basically I was delayed, and thankfully as slow as the government was, my money was approved.   The lab work also wasn't going so well - it seemed everything I touched turned to rubbish. And I mean everything - even the most basic of procedures were either failing or turning up cruddy results. Thankfully I stuck it out and thankfully I've done the troubleshooting and things seem to be back to working (for now). I've only got three weeks of lab work left, which is pretty crazy. It's getting hard to say goodbye to things I've been doing constantly for almost three years, it is also exciting to know a new adventure is coming and I since I can see that tiny little light at the end of tunnel, the motivation to keep going is probably what will see me through the hard part i.e.finishing all the loose ends and producing a coherent document at the end of it all.

The big news is that I submitted my first paper from my thesis - it is still sitting with a sub-editor waiting to go to review. It was a great feeling to finally press submit, but there was also a touch of trepidation. I've been in the field long enough to know sometimes getting a paper published is like a lottery. Sometimes you get good reviewers, sometimes you don't, sometimes the comments are mean, sometimes they are helpful and sometimes it feels like a merry-go-round. Just when you think you've achieved something, there is a peer reviewer who will bring you right back down to ground with a resounding thump.  It does seem for every 10 steps you make, there is at least one setback - grant rejections, paper rejections, nasty comments, politics, no money, failed experiments. But all the setbacks mean when you do something great, or your paper does get published, it is all the more sweeter.  If I've learnt anything in this PhD (aside from science) is that we are all full of far more fight and passion and endurance than I ever imagined.

So stay tuned, the blog is well and truly back! And I have a new motto especially in times of stress, of which there will be several between now and when I submit the thesis:

I have a funny feeling that in order to keep calm in the next couple of months, I will be baking a lot of cakes.....

Tuesday, May 1, 2012

Does Science have an Image Problem?

In your mind, what does a scientist look like?

Chances are, you’ll think of an older man or woman in a lab coat, using big words and talking in a cold tone.  However, for someone who works with other scientists every day, I wonder if this stereotype is in fact hurting both the communication of exciting science or promoting critical and rational thinking.
Contrary to the stereotype, this is not a typical scientist.

There is a war of sorts going on – it’s a war of words, of the mind and most importantly of education. A large cohort are doing their very best to promote belief over scientific method, that thinking is effectively toxic, and that if you dare question your faith, you will give up your spot in a glorious, rose-tinted afterlife, or won’t be cured of your ailments.  The reasons as to why people promote religion over science, or ‘alternative’ therapies over actual medicine are many, but it all starts at education, usually at a young age. This agenda is about trying to push aside science in favour of promotion of non-scientific concepts as the truth. However unscientific these claims are, much of the misinformation and blind belief is touted as ‘scientific’ in order to take all the benefit of the connotations of calling something science, without it standing up to any of scrutiny of the scientific method.

But in examining the problem of the promotion woo over science, and faith over critical thought, the question of why people actually fall for the misinformation almost has been overlooked in favour of arguing that critical thinking and promotion of reason is more beneficial, and attempts to correct the misinformation.  The reason is quite simple. Think about the stereotype of the scientist, that cold factual type with who writes reports and performs meticulous experiments.  People don’t like facts, they don’t like large words and most of all, there appears to be an endemic of non-thinking going on.  The woo-meisters, the evangelists and those that peddle nonsense have a brilliant skill – the ability to appeal to emotion and to actively discourage any form of critical thought. People like emotion, they like passion, they like personable, warm words.  People also like they like the promise of a better life and rock solid promises. These are all things that delusional belief promise, whether it a God who loves you or a so-called miracle treatment for a debilitating condition.

The Creationists, the homeopaths, the psychics – they all use a language which doesn’t say much but that is warm, and people fall for it.  It is the language that promises happiness and health and therefore appeals to what people like.  However in standing up to the mis-information and personable language used to peddle nonsense, scientists tend to get angry. This response is totally understandable – scientific fact is being thrown out in favour of lies and unsupported. Scientists are under attack by those who have little understanding of the scientific method but regardless declare scientific knowledge wrong, and then peddle false claims in the place of scientific knowledge.  To have one’s credibility and life’s work dismissed is definitely worth of defence and the misinformation needs to be corrected. However, in combination with  the cold stereotype of the scientific boffin, an angry response to the warm personable language of those who peddle the misinformation and false hope may not be the most productive approach.  Take Richard Dawkins – when I hear him speak, I see him as a purveyor of fact, a promoter of science, and extremely articulate. However, quite a number of people I know find him arrogant. Is this because he is intelligent? Or that he argues from a logical and rational standpoint? Or is it because he is a scientist who has a Oxford accent? Or that he speaks in facts and is angered by misinformation? I think part of the problem is that people see scientists as being people out of touch with the ‘real’ world, and that intelligent endeavour is dangerous or should be feared.  Furthermore, based on the responses against the personable, warm language, scientists are angry, cold people who don’t understand the human condition. As for science, well science doesn’t have the miracle cure, or it is too hard, or it is too boring, therefore, people turn back to the lovely warm promises of woo and faith.

The misnomer is this – scientists are warm, they are passionate, they are friendly, some are even young, some play musical instruments, some like football and I even know a number of them who are keen about the show “Glee”. Scientists are just like anybody else; but we need the rest of the world to know this. We need to stand up, not in anger that mis-information is being spread, but rather promote that science is full of people from all walks of life and that science isn’t just for boffins in lab coats. Science affects everyone one of us everyday and scientists should be focused on the personal relationship everyone has with science.  Science is amazing, it is awe-inspiring, and most of all, we all have a relationship with it. Thinking for oneself opens up ways to looking at information in a new light, and allows people to learn how to look at the world rationally. Even with reasoning, rational thought and skepticism, the universe is still a crazy, unbelievable, majestic place.

Intelligence, critical thinking and questions should be warmly embraced, not shunned. Discussion should be based on reason, not appeals to emotion, and facts are not cold – facts come about due to the journey of discovery. This is what science is, and this is the image we should be promoting. I’ve spent many days seeing science in action – everyday scientists are making a difference, and filling in the gaps about what we know about the world as well as uncovering totally new questions to be answered.  Science evolves and it is ever changing.  Showing people this incredible side of science, and some of the wonderful and diverse individuals that have chosen the pursuit of scientific knowledge is probably one of the key ways the scientific community can polish its image.  This will hopefully help in inspiring the minds of children and adults, and allow them  to understand and even enjoy science, and in turn this will enlighten people about how interesting the scientific method actually is. The text of the message is not only important but maybe more importantly is how we deliver it. The delivery will go a long way in preventing the continued blind belief in false promises  and a very long way to winning the war on misinformation.

Monday, April 16, 2012

The Short Attention Span Segment #7

This week's picks, all quick and nasty:

1. DNA sequencing in the palm of your hand, and run by USB (yes, it is very cool!): Nature News: Oxford Nanopore

2. Possibly one of the best sites on the interwebs - full of science, art, philosophy, music, books, and great lists. Go pick the brains of the internet: Brain Pickings

3. Want to be an astronomer for a few hours (or days, or months)? Check out Galaxy Zoo, and help with characterising just what is out there: Galaxy Zoo

4. Regina Spektor releases new music - it is glorious and just a little saddening thinking of all those paintings 'imprisoned' in galleries: All the Rowboats

5. Next time you are bored, play this game. You hit cute things, and if you don't do it fast enough you literally die from boredom!  Bored to Death

Ok, you're late, you're late for a very important date! Better go focus on that....

Monday, April 2, 2012

Paper Dissection: Sorry you aren't really seeing angels, it’s all just in your mind…

On the Autopsy Table: 
There is Nothing Paranormal About Near-Death Experiences: How Neuroscience Can Explain Seeing Bright Lights, Meeting the Dead, or Being Convinced You Are One of Them”

Authors: Dean Mobbs and Caroline Watt

Journal: Trends in Cognitive Science

Volume 15, number 10 October 2011

The Exterior:
A review of neurosciences which demonstrates the scientific evidence that experiences of the afterlife are nothing more than side effects of normal neurological happenings. To put it bluntly, near-death experiences really are all in the mind. This paper is a really tidy review of what science has to say about  the experience of death and that really, there is nothing metaphysical going on.

The Guts:
The paper is a review of current research in neuroscience, which reveals the evidence that near death experiences are not paranormal. Approximately 3% of the American population declare experiencing such experiences, and I guess, will be disappointed it is not Grandma May or Aunt Tilda reaching out to them, but simply artefacts of their neurology. To begin, a short list of common features was provided, followed by the current scientific explanation for each. Here they are:

1. An Awareness of Being Dead: Out of body experiences are not limited to near death experiences.  However, this sensation can be put down to “Cotard” or “Walking Corpse” Syndrome.  It is thought that this syndrome is associated with the parietal cortex and prefrontal cortex, and has been documented during the advance stages of typhoid, multiple sclerosis and following trauma.  The syndrome can include delusions, and while a scientific explanation as to why such delusions occur is unknown, the authors suggest it may be an attempt by the individual suffering the syndrome to make sense of a strange experience.
That bright light is nothing more than tunnel vision....

2. Out of Body Experiences:  Again, this is not one confined to near death experiences. A neurosurgeon by the name of Wilder Penfield argued such experiences were based in the brain. Interestingly, the review points out that these experiences often occur when REM sleep is interrupted, resulting in paralysis but with an awareness of the external world.  The reviewers discussed a study where it was shown that out of body experiences could be artificially created by stimulating the right temporoparietal junction of the brain.  The conclusion drawn was that out-of-body experiences may result from a failure to integrate multisensory information and thus disrupt elements of self-representation.

3. Seeing a Tunnel of Light:  The experience of moving toward a bright light is synonymous with being drawn from the living to the dead. However the experience is sometimes documented by pilots flying at G-Force, a condition that is known as hypotensive syncope.  The effect of the G-force causes tunnel-like vision due to a loss of vision.  The case of near-death of experiences is not as well explained, however, it is thought that the light at the end of the tunnel is a result of oxygen supply to the eye being depleted (otherwise known as retinal ischemia).  Such tunnel vision has also been associated with fear and oxygen loss (hypoxia), both conditions associated with dying.

4. Meeting Deceased People:  Encountering the dead is an experience favoured by writers across the ages, usually to convert a less than savoury character to living a moral life because they were warned from a dead relative on the other side to pull their act together. Another commonly used plot device, is someone dying and being surrounded by angels as one departs this life, to be carried toward the bright light (that part we already have a good explanation for). Those visions of encountering long-dead Aunty Martha, are most likely hallucinations, which are thought to be caused by  compensatory mechanisms in the brain. This compensation leads to over-activation in brain structures due to stress or damage (most likely due to lack of oxygen as organs shutdown) leading to said hallucinations.  Interestingly the authors point out that similar hallucinations can be caused by lesions on the brain, macular degeneration and as a side effect ofdiseases such as Alzheimer’s. People  with all of these disorders recount vividly seeing everything from dead relatives to fairy-tale characters.   Once again, this effect can be replicated  during experiments by stimulating certain areas of the brain with electricity ; the result being patients reporting  the presence of someone standing behind them.

5. Positive Emotions: When faced with dying, people often get scared.  However upon encountering the bright light, the angels and realising is life is slipping between your fingers, many report feeling calm, even euphoric – the fear simply evaporates and is replaced by positive emotions. A compound called ketamine can be used medicinally to mimic such feelings, and at different doses can result in hallucinations, out of body experiences and the aforementioned positive emotions.  It is thought that similar neurochemical compounds are released. These pathways include mechanisms leading to opioid and dopamine release, and are thought to occur as a result of disruption of the prefrontal cortex during the process of death. A similar effect is seen in animals when under predatory attack, an example that demonstrates that similar pathways are triggered in highly traumatic events (death could be certainly be considered traumatic!).

The Skeleton:
The bare bones of the paper (excuse the pun) come down to this:  despite the fact that the underlying mechanisms for all the phenomena of near death experiences are not yet clear, the scientific evidence suggests that all aspects of near death experience have a neurological or psychological basis. The expectations of an individual who is expecting the whole ‘near death package’ may also play a role in what is experienced, if you expect to see your long dead relatives or angels, then there is a higher likelihood your brain will manifest such things. 

At the end of the day, there isn’t any paranormal activity going on when it comes to dying.  The angels you see are hallucinations, the bright light is a result of oxygen deprivation and the sensation of one’s life flashing in front of one’s eyes is due to neurotransmitters.  Near–death experiences are essentially the experienced effects of normal brain processes gone awry during the traumatic event of a body nearing death. That being said, uncovering the way the mind produces these phenomena is nothing short of fascinating. Future research will hopefully uncover some of the actual reasons that underpin the experience of dying, for it certainly isn’t anything to do with angels or long dead relatives.

Monday, March 26, 2012

From the PhD Files: A PhD is a like a Masochistic Marathon

 Well the inevitable has arrived, it is that moment that stalks every PhD student, only to jump on them usually when at their lowest – the moment when you question why you are subjecting yourself to this masochistic marathon. Melodramatic you might say but I can say from personal experience, this is not a long stretch.  The marathon – three to four years of non-stop data collection, writing, planning, reading, little sleep and no life. No endurance means no finishing this marathon.  And it’s masochistic because only someone who can take the pain, even like the pain a little will see the light of day on the other side of a complete thesis. There is no doubt about it, you need to expect and even become accustomed to pain.  The pain has many forms – rejections, criticisms, failures all put on repeat for the duration of the marathon. The pain is always there, it just depends what combination of knocks one can take before you pull up on the sideline and prepare to scream “I Quit!”

Well, that time is upon me, and you might ask what’s pushed me from determined to contribute to scientific knowledge to ready to disappear into the night looking for the nearest circus to join.  It’s a combination of things – the time has come for me to bite down, I’m finishing up in the next few months, and part of the reason I’m questioning whether to run is purely because I’m sitting at the bottom of Everest with no ice picks. The amount of work between now and handing up a coherent thesis is nearly insurmountable, and the fact that things still don’t work, I still have lab work to do and a number of experiments don’t have a guaranteed outcome.  Next is the writing – not only do the experiments have to be done, but analysed and written up into nice tidy packages. 

So rather than face the Everest of the lab, it seems easier to run.  Throw in a few weeks of failed experiments, some tense personal situations and a meeting with a supervisor who makes you feel like you aren’t working at all, and it can be seen why the circus seems a viable option. And finally on top of it, is the looming light at the end of the tunnel – what is meant to be a celebration of surviving the blisters, the sweat and tears,

So why endeavour on something inspires fear, and is full of such pain? Like any marathon, it’s the chance to take on the challenge. The opportunity to finish something that is so obstacle riddled, and survive to tell the tale is a reward that needs to be remembered at every obstacle. It is not easy for a reason because if it were easy, everyone would do it. And it’s hard for a reason – a PhD is the research apprenticeship, and research is hard. For me, in the long run, running will leave me with regret. Walking away sometimes has to be done, but in my case, it would leave me wondering what could have been, and whether my mettle would have withstood one last onslaught.

So tomorrow, I will once again down to that track and I’ll get a few more blisters.  The pages of a thesis don’t show the sweat, blood and tears, or the journey to the peak of the mountain, so at the end of the day, I’ll relish the bruises, the scratches and the knocks, because in the end they are the reminders of what the marathon took to complete.

Wednesday, February 1, 2012

The Short Attention Span Segment #6

This week's top 5:

1. Everyone from Arthur C Clarke to Ian McEwan is here. A fabulous compilation of writers discussing why the don't believe and possibly one of the best quotes from Christopher Hitchens: 30 renowned writers speak about God

2. The Sound of Nature: Trees played as records (and the music may surprise you)

3.  Geek meets Ink! Carl Zimmer at Discover Magazine has compiled the Science Tattoo Emporium

4. I usually am against an covers of Led Zeppelin's music, except for this: Trent Reznor and Karen O cover the "Immigrant Song"
5. It's Mammoth Week at Cosmos Magazine: A mammoth rundown

Monday, January 23, 2012

From the PhD Files: The death of science?

So 2012 has gotten off the ripping start. I hit the lab with great energy, I completed a draft and generally things are getting there. But the mountain remains just that, a mountain. When faced with nothing but an uphill climb, one feels like running, like pulling the quilt back up over one’s eyes and going back to sleep. Except you will wake up, and you can’t run away from this mountain.

This is the year I face the end, and it’s coming like a steam train. Whilst climbing the mountain is gradual, and I admit feels pretty good, it really is never ending. So I get all my experimental work done, I write it up, and I compile it into a nice little thesis. For a PhD candidate, submitting is a git of a nightmare. You finish and with it comes hope of an awesome position. But there’s a period of uncertainty, between submission and conferral. You don’t have the qualifications to take a post-doctoral position, but you don’t want to take a permanent position, only to have your dream research job come up and an angry boss demanding why you took a job only to be leaving a few months later. Some are lucky, they score a casual position in their lab while they write up. But then, inevitably, writing up gets pushed further and further back, and the submission date gets moved and moved again, as writing makes way for the need to pay the bills.

So one might ask, where is the university in all of this? Well, the university expects you will dot the i’s and cross the t’s but that’s about it. In fact, the pressure to take a safe option, to do the most basic of what is needed to pass a PhD is what is being put forward as the ideal model. Finish in as little time, hand in and then there is the door. At the university I attend, there is barely any support for PhD candidates in their final throws - no help with job searches, no assistance with stress and the icing on the cake really comes when you finish – often you will get emails within days of submission to clear out your desk and make way for the next number. Yes, you are a number, and yes, it seems the university really only does see dollar signs, which is a sad sign of what is becoming of once what was an honourable undertaking. The undertaking of a PhD was a process of becoming a an enlightened thinker, and someone capable of being able to synthesise ideas and then turn them into scientific results, addressing all the spectrum of challenges which arise along the way. Now, its seems it is all just a fancy exercise resulting in a few more letters after one’s name.

If it is just a case of churning out people with the correct piece of paper, what happens to the skills of the scientist? Science is about the ability to think, being creative, being able to look at things critically, and to ultimately think outside the box. Research isn't about being able to recall facts, it's about being able to use them. Simply filling out the correct forms, and doing the bare minimum to get the thesis does not make a scientist. In fact, this checkbox type approach discourages all the things that make scientists good at science. Treating a PhD like a simple exercise in producing the bare minimum without developing those necessary skills will result in many scientists who just won’t have the skills to do science. And this begs the question, with scientists who can’t live up to their namesake, what future does research have?