Monday, December 26, 2011

What Hitch Taught Me


Usually when I hear that someone I admire has died, I feel sad but quickly return to usual life. With the news on December 15 of Christopher Hitchen’s death, that return to normal life has taken somewhat longer. It wasn’t unexpected news, Hitch had been ill for some time battling esophageal cancer and consequent illnesses due to both the cancer and his radiation treatment. I think the loss is felt more than usual because the world has lost one of the greats (both in mind and accomplishments); a man whose skill with words and whose passion for reason, logic and rationality, and speaking for such causes is unparalleled.

Many tributes have gone out to Hitch, from Richard Dawkins to countless people making tributes on YouTube. I know I’m far from alone, the world has been left with an intellectual gaping hole, for Hitch touched many in many different ways. So rather than just write about how great he was (Dawkins, Krauss and others have done a much better job than I ever could) I thought I’d share personally just how one man, with his acid tongue and quick wit has changed my life.


1. The 'Hitchslap': Sometimes really wish I could get straight to the point without too much fussing around. I also wish I was much better with my own native language. Well, Hitch was a master of both aspects, especially when debating – his often acidic, but wholly truthful remarks could cut someone’s argument down, often without them realizing for a moment or two. In many cases, he would barely raise his voice. This ladies and gentlemen, is the ‘Hitchslap’. If there is one thing I wish I could do, it’s a Hitchslap – a few carefully crafted words, loaded with facts and reason which will cut idiots down. The Hitchslap also demonstrates that the pen is definitely mightier than the sword. Hitch was true master of the written and spoken word, and I’m sure his comments have resonated with his opponents long after a bruise would’ve healed!


2. Don’t stand for bullshit: This applies to general discourse about history, politics and science, but has equal application in personal relations. Hitch rarely would take bullshit, in fact often he garnered much criticism for standing up against “accepted” lies, and asking questions where questions were generally not asked, such as religion. Hitch argued we should question religion, after all its long tentacles reach far and wide poisoning people’s minds – why can’t people ask for a rational explanation or question the actions taken in the name of religion? He worked to expose the frauds and hypocrisy and would fight tooth and nail to stop the bullshit. As for personal life, taking bullshit just takes up your time – time that can be spent doing better things. It is more than acceptable to question things that don’t add up, or nonsense, and to be skeptical regardless of the topic.


3. Fact, Reason and Logic are your friends: I’ve learnt the way to demonstrate a point is to know what you are talking about. Even better if you can take a statement and apply it to a situation. Again Hitch was passionate about promotion of intelligent discourse and action, not emotive arguments based on bullshit (see point 2). However he was also a master at having the evidence at hand. This is a skill I’m working on, and that if you can justify a point of view with logic and reason rather than emotion or ad hominem arguments, the conversation will be far more worthwhile.


4. Don’t be afraid to show your true feelings: Dan Dennett has written an excellent piece on how Hitch demonstrated that rudeness was sometimes called for (Dennett's essay at the Washington Post). Whilst Hitch was brilliant at using logic, he never hid his true feelings. So whilst one should use logic, reason and fact to make a point, getting passionate about it will make people listen, it will make people sit up and take notice, and furthermore, if you are angry about something (especially something as dangerous as religion) why should one hide it to be polite? Passion and a strong composure means you are serious, you mean business and aren’t going to back down without answers. Hitch was the booming voice in the room who everyone stopped to listen to.


5. Don’t let a category define you: Hitch supported the initial invasion of Iraq. This was an unusual position for someone who had always been associated with the liberal left, and it cost him friends. However he saw the justification for the invasion first hand when he visited Kuwait and saw what Saddam Hussein was doing and was capable of, something many ‘lefties’ didn’t. It didn’t matter that that this was not what the quorum was supporting, a dangerous dictator had to be brought down, and the invasion was the way to do this. Too often people associate themselves with a particular group, category or movement, and let it define them – not the other way around, when it should be defined by the members, as that is how groups evolve. Sometimes being radical and standing aside from the group is what is needed, and sometimes it’s the more reasonable thing to do. Having one’s own views, and an individual way of thinking not a pack mentality is what truly makes us individual.


6. Always make time for discussion and drink: Many of Hitch’s friends have recalled fondly as has he, the days spent taking a long lunch in which both serious discussion and frivolous fun ensued. Always make time to talk; after all we are social creatures. I can say from discussions with all sorts of people about all sorts of things I’ve been shown alternative points of view, been challenged, been inspired and learnt much. Talking to others allows me to exercise concepts, ideas and share a laugh. Drinks usually allow the shy to open up, and of course, often lead to much silliness. Hitch demonstrated that conversation can be a good way to develop one’s worldview and stretch the intellect, as well as build lifelong friendships and rivalries!


7. Don’t stop being curious: In one of the most loved Hitch comments (Check it out here on YouTube) he stated that accepting a certainty is the death for the search for truth. Unfortunately as children turn into adults, we often lose our curiousity about the world around us. This mostly can be put down to modern life, which actively discourages thinking. In some cases, such as religion, thinking is seen as bad and is actively shunned. However we all should be curious, we should all question what is put in front of us as truths. We should all think. We should all critical evaluate, and use knowledge to build our own thoughts and arguments. For me, this is something I’m increasingly doing – whether it’s the common lab “knowledge” at work, to what I read in the news to what an author thinks about a particular topic. We have to work to stay curious, we have to keep searching and never accept the status quo. All that being said however, Occam’s razor should be remembered, that the simplest explanation is usual the most reasonable (and often correct one). Keep an open mind, but don’t let your brain fall out! Hitch was in pursuit of the truth, and all of us should be too.


8. Surround yourself with intelligent people: There’s no point wasting your time with idiocy though pointing it out is important in building the case for rational process. However, in order to build on one’s knowledge, in order to have interesting discussion it’s best to be surrounded by intelligent people. Intelligent people don’t just regurgitate other’s opinions, or spout facts – that’s ROTE learning. Rather intelligent people will have their own opinions, supported by logic and evidence, and it’s from these people you can learn.

Those with irrational belief, idiots and hypocrites will often never change their stance, and often challenging such people is fruitless. At best it can point out that these people are dangerous, their beliefs are irrational and encourage an audience to think for themselves, and Hitch was known for challenging these types for this very reason. Hitch had many friends and colleagues who I see as some of the best thinkers of the 21st century: Salman Rushdie, Richard Dawkins, Martin Amis, Stephen Fry – the list goes on and on. And to revisit point number 2, there’s no point wasting better spent time on bullshit, and furthermore, people who are full of bullshit. If it’s truth, intelligence and knowledge that one wants, you need not to play a superiority game with those who are idiotic, but rather be challenged on a level playing field, it’s the only way one will grow and think more independently.


9. Being quiet won’t get you anywhere: In similar vein to point number 4, sitting down and shutting up will not get you heard.. Hitch never slunk away into the shadows, even when under fire for his contrarian ways (as was the case with the support of the Iraq war). If you want to change the world, sitting and saying nothing will not achieve it – furthermore just complaining about it will do nothing (in fact, it may be worse, as nobody likes a whinger). If you say nothing the falsehoods are able to rage on and continue to poison the minds of more people. As the saying goes “The worst atrocities are often committed when good men stand by and do nothing”. Hitch definitely took action, and continued to until his last days.


10. Stand firm: Lastly, and probably most poignantly, Hitch always stood firm. This was even in his last days, where many and in some cases vicious statements were leveled at him and his likelihood of converting to belief on his deathbed. He continued to stand firm on all issues, to promote rationality, to write, to never quit until he absolutely had to. I’ve been swayed to change my view in the past by others, to be polite, to back down in the name of not rocking the boat. If there is one lesson of all, this is the one which resonates with me the most; if you are justified in your position, then stand up for it – whilst people might disagree with you, they will respect you. When feeling like I need to keep the peace, I’ll just think of Hitch – peace means complacency, peace means acceptance, and peace means the search for truth is over, something I hope never to accept.


So there you have it, the ways in which one man changed my life – not so much an exercise in putting one person on a pedestal, but rather a demonstration of just how one person can do so much for another person. I know many intellectuals have stated they hate the way they are often levitated on a pedestal, and they are just a human like any one of us. If we all followed how Hitch lived, we could all do great things for the world, and help stop the spread of intellectual poison. We’d be more creative individuals, we’d stand up for ourselves, we’d see thinking for ourselves and being curious as a way of living, not to be shunned. And of course it would mean promotion the good things in life – intelligence, reasoning, the search for truth and the odd glass of Johnny Walker Black Label.


I was an atheist (also rather curious, and just about always questioning) before I discovered Christopher Hitchens, but he has helped me rediscover old passions, learn new things and improve the way I think about the world. He wasn’t a scientist, in fact he was the only one of the “Four Horsemen of the Apocalypse” who wasn’t, but he would rival many scientists in his ability to apply logic and reason. The world is a lesser place without Hitch, but is a greater place due to his writing, his speeches, and his fight against the irrational, hypocritical and stupid. I hope that like Shakespeare, Hitch will have many come to know him through his works, for despite no longer being here in the flesh, his words are immortal.


Thursday, December 22, 2011

Falling by the wayside (Again)

This blogging thing is harder than I thought. I was hoping to be a bit more regular (at least weekly), but alas life has gotten in the way again, namely in the form of my PhD. I can make time for the gym, so I can make time to keep this thing updated. Now I'm on Christmas holidays, I've started writing for the blog again, so stay tuned!

Tuesday, November 15, 2011

The Short Attention Span Segment #5

1. Because governments make scientific funding a near impossbility, scientists are looking to crowd funding (aka. public donations) to get small projects off the ground. A great idea, but it really shouldn't be necessary: The SciFund Challenge

2. Where bad science and the underbelly of research is exposed: Retraction Watch

3. Telling it like it is and reviewing games for what they are (and hopefully revealing the harsh truth to the fans of Halo): Zero Punctuation

4. Some songs actually sound better as classical arrangements, and some songs become more awesome as classical arrangements: The Vitamin String Quartet cover Muse and Bruce Springsteen

5. Saw a great documentary on this team and how they are analysing dinosaur footprints to determine dinosaur behaviour: Australian Age of Dinosaurs

Tuesday, November 1, 2011

Book Review: "Solar" by Ian McEwan


It's time for a new (and hopefully fairly regular) post in the form of book reviews. I read quite a bit, and some ago was part of a great bookclub. I miss the bookclub very much, and as I can't share my reviews with them, thought I'd post them here....and if you happen to be looking for something new to read, well, maybe I'll be able to help!

I've just read Solar by Ian McEwan. McEwan is an award winning author, and penned a book called "Atonement" which was consequently turned into a beautifully shot film starring Kiera Knightly and James McEvoy. One of his other books, titled "Amsterdam" did win the Man Booker prize in 1998, but I do know of at least one person who would argue that the award for that book was definitely not justified.

So what about "Solar"? Well, I picked up the novel with no idea as to what to expect. It was a library loan, so it didn't even have a dust jacket with a blurb. I came across the book via the recent RiAus Great Science Reads where people nominated their favourite science books, and "Solar" just happened to be on that list.

For a start, Solar isn't your typical science book. Rather than the traditional science fiction books which often deal with some sort of cause and effect of a scientific discovery, or are futuristic time-travel robotic imaginings of the future, this book focuses on the scientist. And boy, does that scientist have an interesting story to tell.

The entire book revolves the character of Michael Beard, Physicist and Nobel Laureate. And for a protagnist, Beard is completely repulsive. He's a cheater, a liar, overweight and selfish. Beard sells out on his career to become an expert for hire, using his name in the field of physics to secure a lucrative position heading a group in the hot topic of the minute - climate change. Add to this that his fifth wife has just left him, and you quickly realise, if you had to work with this man, you'd probably wish you could stab his eyeballs out.

But it's what Beard represents that makes this book so interesting - the pompous greed of those who wish nothing more that to keep their name up in lights at whatever cost. Beard represents all that can be wrong with science - the jealously, the backstabbing, the win-at-all costs...and in the end, it doesn't end up going so well. It's a commentary on intersection of science and the public over big issues, of which climate change is the headlining act. And McEwan uses satire to maximum effect, illustrating all that is wrong with both public and scientific attitudes in the pursuit of furthering human endeavour, especially when that pursuit is for all the wrong reasons.

All in all, I ended really enjoying this book - it was an unexpected story, and I ended up hooked on finding out what was going to happen next, as I really wanted Beard to get his comeuppance. It's not often a protagonist is someone you end up loathing, and McEwan does a brilliant job of highlighting what's wrong with the world of science, all in the form of a fat, selfish man. A very different commentary on the scientific world, and one that I'd recommend.

Monday, October 31, 2011

The Short Attention Span Segment #4

Ok, here we go, this week's top five for those who don't want to pay attention for too long:

1. NASA Astronomy image of the day, for absolutely breathtaking images of the universe, I can stare at these for hours: Today's Image (31st October)

2. Getting into the spirit of Halloween, with some amazing pumpkin carving: Halloween Pumpkin-Palooza

3. Because Ezio is the ultimate assassin: Penny Arcade

4. The Atheist Experience, a fab radio/web streaming show: Atheist Experience Homepage

5. Australian scientists Mike Lee and Trevor Worthy argue the case for Archaeopteryx being a primitive bird (and not a raptor as argued by Chinese researchers in July 2011): Cosmos Magazine News and Original Publication

Tuesday, October 18, 2011

Picture of the Week: The Bedside of Awesome

My bedside to-be-read pile of recent purchases/borrowings. From top to bottom: "Cosmos" by Carl Sagan, "Pandora's Seed" by Spencer Wells, "The Magic of Reality" by Richard Dawkins, "Arguably" Essays by Christopher Hitchens and last, but by no means least "The Philosopher's Breakfast Club" by Laura J. Snyder.

Absent is "Warm Bodies" by Isaac Marion, my latest purchase for the zombie fiction collection. It's was absent as it's currently on my desk.

Some epic reading ahead - I cannot wait to get stuck in, trouble is, I don't know which one to go for first! Too bad I can't have a week off work with bad weather.

Monday, October 17, 2011


2012 Global Atheist Convention

The Short Attention Span Segment #3

This week’s top five:


1. Richard Dawkins’ new book “The Magic of Reality”. Aimed at all ages, and it is one of the most beautifully illustrated books I’ve ever seen. A gorgeous book which shows that true magic is really all around us: The Magic of Reality at RD.net


2. After a few months absence, Hitch back on his feet – still full of sharp wit and all kinds of awesome. He was at the Texas Freethought Convention receiving the Dawkins Award from Richard himself: Geoff Bang's Blogpost on the event and Videos : Part 1 and Part 2


3. The Dropkick Murphys are in town (and yes, I’ve got tickets): State of Massachusetts


4. T-Rex just got even more scary: Science Daily


5. I somehow don’t think this will mean we can give up the gym: Cosmos Magazine

Monday, October 10, 2011

From The Phd Files: You can't always get what you want....

Last Friday I attended the opening of the Adelaide Festival Ideas. As well getting to see a personal hero in the flesh, it also sparked much discussion and thought amongst the attendees. In case you are wondering, my personal hero who was in attendance is Professor Peter Doherty, Nobel Laureate, immunologist and champion of science communication. Alongside Peter was Phillip Adams (another fave of mine), Barbara Hardy and Professor Penny Sackett, the former Chief Scientist of Australia. Penny gave the keynote address of the festival entitled "Science and Uncertainty", in which she talked about the uncertainty of the measurements of science, the importance of a transparent scientific process, and just how perfection is impossible. She also argued we really need to use the evidence we have on which to base our actions, and as the wheels of science keep turning, we can build and improve on the evidence in the never ending process of research and understanding. What followed was a great discussion between the audience, Phillip, Peter, Penny and Barbara, and I walked away feeling honoured that I'm part of the machinery which furthers our understanding of the world, and how science and knowledge and knowledge in all its amazing forms make me feel inspired to be part of humanity.

On a personal level, the concept of uncertainty really hit hard in the last few weeks. Whilst the evening at the festival of ideas made me feel inspired, of late I've been feeling anything but. It's a well known fact that the process of obtaining a PhD is like a rollercoaster - full of the highest of the highs, and the lowest of the lows. The moment of elation when that experiment works cannot be compared to anything else, but the drudgery it can take to get there can just about break the strongest of wills. And PhDs are full of uncertainty - uncertainty about how the research will pan out, where the money will come from, whether you'll get the paperwork done in time, if you'll have a job next year or whether tomorrow you'll log in to your email to find someone has just beat you to the punch and published your scoop, thus downgrading your hard work and revelationary findings to a much lesser journal. This is the nature of the beast that is science, and a PhD is a the baptism of fire into probably one of the most uncertain, but most rewarding careers.

Anyway, a case in point happened to me recently. I went away for a bit over a week - an escape from the lab to refresh, get my head around some statistical analyses I needed to master, and catch up with the family - a working holiday of sorts. Three days in, and just as I'm undoing all the stress and craziness of the last few months, and getting into the swing of country pace, I get a email and a phone call. Turns out, the contractors the university employ are incapable of reading - they shut down the power to the cleanroom, which involved entering said cleanroom in their dirty work gear, pulling all the plugs and leaving. No power for a weekend means no fridge and no freezer keeping things chilled. I got the phone call when my colleague rang me - they had arrived Monday morning to a lab which was akin to a swimming pool. As for the reagents? Written off - enzymes don't like room temp! And even so, it's often not worth bothering with sub-par reagents. If things don't work how does one know that it's the experiment or the thawed out dodgy enzymes?

It turns out the university had forgotten to notify us of the power outage, as they had forgotten we had a laboratory in the building. But they did have insurance - now comes the painstaking task of reordering all the ruined stock and waiting, and dealing with a new ordering system to boot makes this not the most pleasant of tasks. The kicker of the situation was that some of my reagents had just been bought prior to going away, they were unopened, and ready and waiting for the flurry of productivity I was going to launch into when I got back....but as my title tells, you can't always get what you want. Very rarely in science do things go the way you want or plan, but as the song goes, you sometimes get what you need, and in the process you get more interesting results and learn a few lessons which will make you a better scientist.

So in light of Friday's lecture and discussion, it got me thinking - we have scientific uncertainty in the form of the experimental measure, we have uncertainty about where the next paycheck is coming from, we have uncertainty about whether we can get that publication accepted, uncertainty about the results, and to add to all this uncertainty, whether we can do our experiments at all. Day in and day out, there's uncertainty on all levels in science, and it can drag you down. When I read a paper, I can now appreciate not only the data collection, the analysis but the day to day dealings that have had to be overcome to enabled that paper to get to publication. There's a lot of blood, sweat and tears in a few pages of scientific results, and now I'm living it day to day I've got a another whole level of respect for those authors.

So would I trade the roller coaster of research for some sort of certainty? Never! The thrill of not knowing what results will reveal, of not knowing what each day will bring, or what the next challenge is, that mystery is part of what makes science so great, and why I love what I do. In spite of losing all my reagents, and of the delays, the payoffs in spite all those types of scientific uncertainty are immense - the potential to contribute to the understanding of the world around us, to be part of the scientific machinery, to feel that elation when your paper is published or you see those bands on a gel far out ways the failures, the stress, the tedious moments and the downers. After all, how boring would life be if everything was certain?

Tuesday, October 4, 2011

Citizen Science: How People Power Is Helping to Solve Scientific Riddles


Science was once seen as off limits to the average person, to be only to be conducted by nerdy types in white coats, who speak in strange terms and don’t have much of a life. Well, that stereotype is well and truly toppled with the recent news regarding the use of a program called FoldIt, a group of gamers and the unravelling of a protein which is found in virus family known as retroviruses, which include the likes of HIV.

With recent technological developments, scientists are producing an ever-increasing amount of data, more data they can possibly hope to analyse in their lifetimes. On the opposite side of the spectrum, many people have computers, Xboxes and Playstations that don’t utilise their full processing power. In 2008, a group of Washington University researchers saw the potential to harness people’s technology in its downtime and FoldIt was the result.


FoldIt is just one example of a program that utilises either people or their technology (or in some cases both) to further scientific research. In the case of FoldIt, participants download the program, and then set about playing a ‘game’ against one another to determine a folding pattern for a particular protein. However in this case, this game doesn’t result in a high score, it results in contributing to scientific knowledge. Humans still outdo computers when it comes to complex pattern recognition and FoldIt harnesses our inner problem-solving capabilities to elucidate structures within a competitive gaming environment which makes the science fun! In regards to the protein mentioned earlier, FoldIt participants solved the structure of a protease whose structure had been baffling researchers for 15 years. Proteases are cutting enzymes and are important in the complex formation of retroviruses such as HIV. According to the FoldIt website, it took gamers just 3 weeks to sort out the predicted structure for the protein.


The results were published in the journal Nature Structural and Molecular Biology with both researchers and gamers listed as authors. And the implications? A 3D structure is vital for scientists not only to study a protein and its interactions, but for finding new drug targets and designing new therapies. The combination of the citizen scientist and experts may mean the development of new drugs not only for HIV, but the likes of Alzheimer’s disease, cancer and other diseases.

From the smallest of viruses to the largest of the galaxies, the involvement of volunteers in science is making a big impact.


But the involvement of the community does not end there. Whilst one computer’s processing power may not seem like much, the combination of thousands of participant’s computers certainly adds up, and enables a lifetime’s worth of searching and analysis to be performed in a matter of days. A number of other research groups have applied people (and computing) power including in the field of astronomy. In August 2010, a paper was published in the prestigious journal Science, and was co-authored by a couple who were credited with discovering a new radio pulsar named PSR J2007+2722-. Radio pulsars are a signal of a neutron star. The couple were not researchers, but had downloaded Einstein@Home, a program which analyses gravitational wave sources, in the search for neutron stars, and were using their spare computing power to analyse masses of astronomical data. Neutron stars are what is left after a supernova, and thus can provide information about not only the lifecycle of a star but improve understanding about the workings of the universe.


The most famous use of voluntary computing resources is probably SETI@Home, which is the use of processing power to search for radio signals that may indicate the presence of intelligent life in the universe (aside from us, of course!). Established in 1999 by researchers the University of California Berkley, SETI@Home was the first use of home computer users, and currently there are over 5.2 million participants worldwide, who have logged over two million years worth of computing time – a massive feat, which may not have turned up ET but has demonstrated the need for people-power and how citizen scientists are turning up some great discoveries, which otherwise would just not be possible.


For further information on how you can get involved through your CPU to unravel HIV, search for neutron stars or search for extra-terrestrial life check out the homepages of the programs:

FoldIt

Einstein@Home

SETI@Home

Rosetta@Home

Folding@Home


And you never know, it may be your Playstation or computer which provides the next big discovery and helps scientists understand the world around us. Science is no longer just in the hands of the folk in white coats, it is in the hands of anyone who wants to get involved.


References:

Scientific American, September 20 2011 - Foldit Gamers Solve Riddle of HIV Enzyme within 3 Weeks

Science Daily, August 12 2010 - Citizen Scientists Discover Rotating Pulsar

Wednesday, September 28, 2011

Hiatus...

Well, this blog has been rather neglected, but suffice to say I'm well and truly aware of this problem. Late August and September have been incredibly busy! I've been to an international conference, and then straight onto visiting family. However I'm back, and from next week the blog will resume regular posting. So stay tuned, as I have quite a number of PhD tales to tell, some new photography and of course, epic science!!

Monday, August 15, 2011

The Short Attention Span Segment #2

My top 5 - music, websites, science - whatever is catching my short-term fancy!!

This week's top five from around the block:

1. Hubble captures pretty pictures of the Necklace Nebula: Science Daily
2. X-level solar flares last week on the Sun - a sign of things to come?: Scientific American
3. Cowboys and Aliens! Trailer
4. Parasites and the art of manipulation: Saturday Morning Breakfast Cereal
5. The big one of this week - nucleobases, aka. parts of DNA have been found in meteorites - well, we are all made of stardust! But this could indicate that DNA could be abundant in the universe: Cosmos Magazine

From the PhD Files: Ego and the Douchebags of Science


During my short time in the field of science, I’ve met some interesting folk - many people from many walks of life, with very different personalities who converge in the lab on a daily basis.
It makes for an interesting workplace, but one trend I have noticed, is that scientific research and ego are very closely linked. I guess it is because science is one field where to get anywhere, you pour your soul into your work, you want to be proud of what you publish, and your reputation is EVERYTHING.

When some anonymous reviewer rips you apart, your supervisor is not happy with your work after months of data collection and you get knocked back from a job or funding for the 1000th time, you tend to become thick-skinned. This can been seen as confidence, or in some cases, arrogance. However for the most part it’s a demeanour, built up to protect oneself from the constant onslaught of criticism. Finally achieving that elusive scientific success can breed arrogance, and when you are at the top of your game, a touch of arrogance is actually acceptable – you’ve made it, you are an expert and you have the publications to prove it! But what is more worrying is just the lure of a career in science can attract folk who have a point to prove. Some people are attracted to the field because of the image it portrays, that the moment you say you are a scientist people comment with “oh it takes brains to do that”. Scientists are put on their own pillar in society, of being knowledgeable, and the field is shrouded in a type of secrecy – people in white coats scurrying around, talking in their own terms, working on everything from DNA to galaxies.


In reality, science is mainly about hard work, with a touch good luck and whilst you do have to have brains, getting into science to promote the fact you are somehow smarter than everyone is not an approach that generally confers success. This is where ego and science actually clash – it’s a career of dedication, and those who get in it just for the glory don’t usually go anywhere. In my own personal experience, I’ve encountered a few of these types, and I can say, I’ve moved on pretty quickly, usually because I’ve got an experiment on the boil which needs attending to. I don’t have time for these people, because I’ve found like in most fields, a PhD doesn’t prove you are smart, it doesn’t prove you are a good person, and furthermore I’ve found some of the most intelligent people have never set foot on university campus. PhD can mean respected, it can mean intelligent, but it also can mean douchebag.


Lucky, it’s not hard to spot these types. Usually they are the ones who are all style and no substance – often talking up whatever it is they are working on, bragging to their friends who aren’t in the field that they work on this that and the other. They are rarely seen in the lab, and when they are, they are sponging off the people who actually know their stuff because they would rather be talking up their project than actually doing science and researching things for themselves. Unfortunately my work crosses two fields which seem to attract these types – forensic biology and ancient DNA. Forensic science attracts the douches because they think they are then next Gil Grissom, and ancient DNA because well, it is freakin’ cool to say you work on ancient Romans, mammoths, Neanderthals or any other awesome long-dead or extinct being. What isn’t exposed in either of these fields is how difficult they are – forensic science must meet legal scrutiny which poses its own sets of challenges and limitations, and in ancient DNA, the field is tiny so if you annoy anyone, you are blacklisted EVERYWHERE. Furthermore for every success in ancient DNA there are about 1000 failures – samples are hard to come by, DNA is sometimes too degraded, and sample sizes are always small, making analysis difficult.


What the douchebags don’t seem to realise is their holier than thou attitude actually is damaging to the field. Because egos are inflated, self-worth often takes precedence over actual science, and as the big ego is the one who has to be in charge, collaboration is often difficult. Cutting down students to make yourself feel better is not the sign of a good supervisor, and can quickly turn the best student against any further career in research. Criticism is essential, but simply trashing something to enforce a sense of superiority will ensure the best minds get out of the field. Furthermore, these types play into the image of the stereotypical image of the arrogant intellectual. In an age where promotion of science against false information and woo is critical, the last thing the field needs is egos perpetuating an image of arrogance and superiority to the general public. The egotistical scientist is looking for the easiest way to get up their name up in lights, to solve the case and to be deemed the hero of the day. So grant proposals go nowhere, the science is often not the best it could be, and who really wants to support or work with someone like that?


The interaction of people and ego manifests itself in different ways. Aside from the usual egotistical douches, there is also the realisation that when you start a PhD, you go from knowing everything to knowing nothing. The best way to deal with this daunting task is to get stuck in. Afterall, the sooner you read, the sooner you do lab work, then the sooner you can start to know something. However, in my time as a student, I’ve come across a more emotive response. And my thoughts are that it’s linked to the type of person who is doing science to prove a point and to feed their own belief they are somehow smarter than the rest of the world.


I believe in collaboration, in sharing ideas and knowledge – we all have troubles in the lab, and the times I’ve come across people who have solved my problems and saved me weeks of pain. I've noticed in my short time in the sciences, that this seems to be the most successful approach for getting the most out of funding and collaboration and getting the best science out of often limited resources. If I can share something I know which saves one other person time and bashing one’s head against the brick wall, then talking about my experiences, piping up in lab meetings and putting forward suggestions is worth it. However it has a downside – that when an ego who maybe is new to the PhD game hears it, it unsettles them. Rather than do the hard work and learn, they feel threatened.


I’m sure the psychology behind this is fascinating, but I find this type of confrontation hilarious. Rather than work on getting hold of knowledge or doing actual science they attack the people who have knowledge. The funniest has to be the name calling; usually it’s something ad hominem, that you think you’re the boss, that you’re better than all of us etc. etc. Of course it’s nonsense, and for a person of any sort of substance, it just makes them shrug and move onto the next experiment or paper that needs writing. This childish name-calling comes from that insecure person’s ego, because it challenges their notion that just because you’ve gotten to studying for toward a PhD, you’ve made it. The reality is quite far from this, and another person who is supposedly on the same level but actually is about the science is so unsettling, and so threatening to their superficial notions they have to call names. It doesn’t matter this person may have been there longer, or farther into their candidature, or has put the hard yards in. The saddest thing is, the egotistical individual refuses to accept that science is about the effort, and those hard yards, and the image of intellectual grandeur is just an illusion.

Hey at least the hat is cute.


At the end of the day, substance threatens superficial. And there is always someone better than you, either in your field, in your department or your lab group. Rather than trying to prove to the world that you are a ‘scientist’ it’s far better to be a decent person, to help, to be approachable and to work your backside off – for the more knowledge and experience you have, the closer you are to getting published, and if you are lucky, a bit of recognition. There are bad apples in all walks of life, and science is no exception. We have the talented, the inspiring and of course, the douchebags. But one thing is for sure; science really is a career where you get out exactly what you put in.

Sunday, August 7, 2011

The Short Attention Span Segment

My top 5 - music, websites, science - whatever is catching my short-term fancy!!

This week's top five from around the block:

1. NASA releases results about the potential for water on Mars: at ScienceDaily
2. The tale of your ancestors (and the fortuitous evolution which has lead to your existence) in comic form: AbstruseGoose
3.Anti-oxidants are not exactly scientifically proven to be beneficial : The Doctor and the Pomegranate
4. "Wonders of the Universe" hosted by the amazing Brian Cox currently on the ABC: ABC preview
5. Hit the Road Jack: Ray Charles

Not Quite Gattaca: Part 3: The Ethics


So, the technology exists to for studying DNA, and this has applications to everything from medicine to agriculture. The next question is – should we? What should we do with the knowledge? Is there potential for mistakes which could be detrimental?

One cannot deny the amazing things science has allowed humanity to achieve. Daily living has changed drastically – cars, mobile phones, computers and on the large scale – the Mars Rover, deep sea exploration, piecing together T-Rex and evolutionary theory, all products of science, and all things which have furthered our knowledge of the world around us.

But science has its dark side. Often it is not the science itself which has negative results, but rather the application of the knowledge. Robert Oppenheimer famously quoted 'Now I am become Death, the destroyer of worlds' at the detonation of Hiroshima bomb. It was thought to be an indication of his regret of his genius part in the development of the atomic technology, but in fact, was his reflection on the destruction his science had left behind.


Thalidomide is considered one of the worst medical disasters of the 21st century. But that hasn’t stopped science, and the ongoing progress of medical research. What an event like the exposure of the toxicity of thalidomide has done is ensured certain checks and balances are enforced, and led to the public questioning the science. However, what is key with any new method, knowledge or treatment is that those questions arise not due to hysteria, hype or misinformation, and that criticism of a scientific outcome is based on the same rigours and tenants of science itself.


So for genetics, what are the ethical issues? The short answer is that there are many. For example in the case of medical genetics, should we allow people to have tests to determine the likelihood of them developing a particular condition? What would insurance companies do with such knowledge? And what about the addressing the requirement to ensure people are adequately educated about said tests and their results before making drastic decisions about their future? And who owns the genetic code? Should corporations be able to take ownership of genes they find confer benefits to humanity? Or is our genetic code our own?


And it is not just the use of human genetics that is raising big questions. The modification of plants has generated much debate and even hysteria in regards to not only their safety for consumption, but also the possible effects on the environment. Otherwise known as GM crops, the use of genetic modification to make plants more tolerant to drought, more productive or nutritious may seem as ideal and a boon to humanity, but massive questions have been raised about the thoroughness of the science and the long-term effects. It seems the general public has indeed learnt from science’s darkest hours, but at what cost?


Humanity likes to take advantage of the great developments in science, but will rapidly question areas of contention perpetuated by mass media. The classic example is animal testing. What the media never portrays is that most scientists would love to see an end put to animal testing and use of animals in experiments – it’s not ideal as animals are bred purely for testing, is very costly and furthermore requires large a time investment from the scientists to care and maintain their animals. I’ve never heard of intentional cruelty to animals by scientists, when in fact, most scientists care very much for the animals which they have invested much time into, and which often are the underpinning thing to their results.


The media doesn’t explain this side of the story and furthermore don’t tend to highlight the work some scientists are doing to develop alternatives to the use of animals. In some cases, this is already done, through the use of cell cultures such as HeLa – cell lines are much cheaper to store and care for, but still have limitations. However, one should be very aware that scientists fully acknowledge the animal sacrifice that occurs in their research and do their best to use alternatives or to care for the animals that give them their results.


Without animal testing or the use of animals in experiments, our knowledge about the way genes function would be drastically cut, and we’d be setting medical treatments up for failure. Animal testing is the one method scientists have to test a new treatment, and whilst this may have negative results and animals may be sacrificed, the question has to be asked about the long term benefit. Is it better to test on animals or humans? This is an ethical question both in regards to the value of life, and also in how science is perceived. In light of all these ethical issues, science is all about knowledge, and utilising that knowledge to further the journey of humanity, to improve the lives of all animals and plants and understand our place in the universe. However, in some cases, the use of science may be misused or misunderstood, and it is hoped active debate about the ethics behind the science can both educate the public about the limits of science and also prevent mistakes as much as possible. It does have to be remembered that scientists are human too!


In the end, all these questions will all need to be discussed, and the limits established. Already much discussion is taking place, and debate about the use of genetic technology is incredibly vigorous. Opinions from scientists, ethicists, animal rights groups, politicians, philosophers and of course, the public all weigh in as to how handle genetic ownership, education and use. What is important is that the opinions around the ethics of genetic knowledge and technology are built not on media mongering, clever marketing or hysteria. The foundation for decisions about the use of genetics needs to built on the scientific observation, reason and rationality. It is only through this approach can the complete picture be pieced together, and the greatest benefits from genetic science can be provided to humanity.

Thursday, August 4, 2011

Not Quite Gattaca: Part 2 - The Reason



In my last post, I discussed some of the major technological breakthroughs in the last few years that have enabled DNA sequencing to become faster and cheaper. But the next question is why?

Well, the cliché answer is the pursuit of knowledge. By gathering DNA and RNA sequence from many organisms, and also understanding variation between a population of organisms scientists learn more about the world around us, and of course, what makes people different, and the genetic code in both health and disease.


I mentioned RNA or as it’s known in its full form - ribonucleic acid. In the simplest of terms, RNA functions as the messenger between DNA and protein, it's even known as messenger RNA or mRNA for short. DNA consists of two major parts – introns and exons. Exons are encoded into proteins which build our cells and regulate everything from cell metabolism to cell death. However RNA can influence DNA by intereacting with it, and the overall behaviour of the central dogma of molecular biology (Figure 1) is far more complex than turning DNA into a product. Add to this the effect of the environment on the genetic code, and the system is one of massive complexity.


Figure 1. The central dogma of molecular biology, now understood to be less than straightforward.


Not long ago it was thought the genetic code would read much like a book, however this is rapidly being overturned as researchers began pulling apart the human genome. Whilst the draft of the human genome was published in 2000, the 6 billion base pairs sequenced is the tip of the iceberg. Understanding the obvious outcome of genetic mutations in disease, as well as the more complex traits arising from that interaction of environment has proven to be anything other than straightforward.


But cheaper, large scale DNA technology doesn’t end with human genetics. The study of plants and animals has been revolutionised through new technology. This not only includes the living animals, but also extinct animals. In 2008, the woolly mammoth genome was published – the first extinct animal to have its genome decoded. This was possible due to new sequencing technology, which as well as being able to generate sequence for millions of bases of DNA per run, but also is far more sensitive. This sensitivity is ideal for sequencing the small, degraded fragments of ancient DNA, and the large coverage enables endogenous sequence to be sequenced against the high background often seen in ancient DNA samples. Since the first Neanderthal DNA sequences, we’ve seen the entire Neanderthal genome published, DNA from cave bears, extinct equine species and even the giant moas of New Zealand. And it’s not just extinct animals that of interest; understanding population dynamics of currently extant populations is important. From understanding previous human migrations, to the effects of climate change on different animal populations, to domestication events on plants and animals large scale DNA sequencing has allowed for an improved understanding of evolution, the impact of human interaction on animal and plant species and the impact of large climatic events on ecosystems.


New sequencing technology has opened many doors – from medical genetics to conservation to evolutionary biology. It’s a great time to be a biologist, and all this new technology is giving us improved methods to understanding the basis of life - the genetic code. And as it has been realised, the genetic code isn’t a straight forward page turner, it’s more like a choose your own adventure book – not to be read from front to back, but rather backwards, forwards and under the influence of the environment around it. Thus all these tools have come at an ideal time for we are firmly in the era of the genome in all its wonderful and varied complexity.

Tuesday, July 12, 2011

Not Quite Gattaca: Part 1 - Technology

So for my triumphant return, I’d thought I’d tackle one of the hottest topics in modern science – that of human genetics, and its r applications to modern life. We aren’t quite at the way life is portrayed in Gattaca, but there’s been some great developments since the publication of the draft human genome in 2000, and alongside greater understanding about human genetics, comes greater questions about how to be ethical with such knowledge.


It’s a huge area, and I’m hoping to break it down into some key areas over the next few blog posts – the first is one of my favourites - the technology.


In any part of science, one picks up lingo particular to the field, it’s almost like a second vocabulary, and when it comes to current DNA analysis methods, one almost needs an encyclopedia. We’ve seen a technological revolution in the last 5 years akin to what happened to computers in the last 20 years – things have been effectively turned on their head, and what took years and costs millions is now a simple single day procedure. There are machines for doing massive amounts of DNA sequencing, machines for targeting specific pieces of the genome which might be of interest and of course, there’s a machine for making coffee which keeps all the grad students going long into the night!


What has happened is an increase in power – the human genome is 6 billion base pairs long. Broken down, this works out approximately 3 billion base pairs for each set of chromosomes. As well as the chromosomes contained in the nuclei of the cell, each cell contains a second DNA strand – the DNA contained within mitochondria, which reside in the cell, and have several functions, including acting as the producers of chemical energy for the cell. Whilst our chromosomal DNA is a mixture from both of our parents, our mitochondria usually are inherited only from our mother and doesn’t recombine between generations – hence why ancestry studies of mitochondrial DNA have been able to trace deep genealogies into the human past.


So what does sequencing the human genome or human mitochondria tell us? And why bother with fancy machines which can generate tonnes of data? Well, when the draft human genome was produced, many thought it would be the beginning of the end – that by reading the DNA sequence like a book we could unlock all the mysteries of not only our genes, but why diseases such as cancer arise.


Unfortunately, science is often a complicated thing – what was found is that the human genome varies much more that expected, is much more complex than expected, and environmental influences over our lifetime have a huge impact on how the genetic code translates to proteins and cellular responses. Having a single human genome just wasn’t going to cut it. So scientists starting targeting bits of the genome which were known to be linked to cancer or other diseases looking for mutations. An example of this is the BRCA genes associated with breast cancers – mutations arising in this gene have been linked to risk factors associated with breast cancer.


The human genome varies from person to person and from disease to disease. Some of the variances can be used for tracing ancestry, some for identification such as DNA profiling, and of course for identifying genetic basis of disease. Just as many mutations may give rise to one cancer, there are many types of cancers. Furthermore, whilst some disorders and disease have clear mutations such as the BRCA mutations, Huntington’s disease or Down Syndrome, many don’t. Many are a complex mixture of both multiple mutations and environmental influences. These are the challenging disorders and are very hard to understand and include things such as cancer, schizophrenia and even how much genetics is behind the way we look.


So with the first human genome, scientists were just getting started, and the demand for cheaper, faster tools for generating genetic data was needed. The original draft of the human genome took several years, and about a billion dollars – to understand variance of different populations of people, of differences in health and disease, cheaper and quicker methods were desperately needed. And hence a revolution began. And now in 2011, we have sequencers capable of not only targeting small pieces of the human genome but also for generating entire genomes for analysis. One platform, the illumina HiSeq is capable of generating 600gigabses of DNA sequence per run. This takes several days, but this amount of data is equivalent to 100 human genomes. So considering that it took several years to sequence the first human genome, scientists have the capability to generate several human genomes for a few thousand dollars, and in a few days.


The illumina HiSeq: It may be just a large fancy looking box, but this machine can sequence

your genome several times over in a matter of days .


And this is just the beginning – whilst the $1000 genome is still a little while off, the cost is dropping rapidly. These technologies also have much greater sensitivity, which means that samples long archived, samples which have degraded and samples which were beyond the reach of tradtional analysis are now able to be studied and analysed. This opens up fields including ancient DNA, and allows greater information to be gained from the smallest and most degraded sources of DNA.

These new technologies pose their own unique challenges – scientists have to learn to manipulate massive amounts of data and this is a long way from the single DNA reads produced by traditional sequencing technology. Increasingly computer science is being utilised to not only utilise the large amounts of data generated by these platforms but also to assess the data and ensure it is reliable and accurate prior to it being analysed. This is incredibly important as whilst large amounts of data is great, it needs to be accurate if it is to be used to understand the human genome, and for future clinical diagnostics.


This new array of tools opens the door for scientists to gain a further understanding of what is now realised to be incredibly complex – the human genome in both health and disease. By reducing costs, improving output and addressing the need for genetic information which is quick to produce and reliable, we are on the way to understanding our origins, our fundamental genetic constitution and also building knowledge for the future. It’s not quite Gattaca, but these new tools are starting to reveal just who we are.

Well as they say, absence makes the heart grow fonder…

I’ve been terribly slack in keeping this blog going, I seriously thought I would’ve been a bit more prompt in updating it. However as the title suggests, it hasn’t been far from my mind and well, I’m finally back. There are many reasons (not excuses!) for me not updating, but I’ve finally got the schedule sorted, so no more reasons for not updating!!

Tuesday, May 10, 2011

If Tony Soprano was the Boss of a Lab (instead of a mafia family)

So of late I’ve been watching the Sopranos, season to season, back to back. I know I’m a few years behind, but at least I can watch it without ads and in my own time. The series is amazing and epic and well I can see why it has such a cult following.

But it got me thinking, what if a research lab was run by Tony? Here for a bit of fun are some things I think would apply if Tony got out of the ‘waste management’ business and moved into the lab:

· If your PCR or any equipment didn’t work you could just shoot it

· Sales reps who sold dodgy products could be dealt with swiftly using a metal pipe to the knee caps.

· Trade in black market and unused reagents would be encouraged. And I bet it would be still cheaper than buying from Applied Biosystems

· Lab meetings and journal club would be accompanied by gravy (the tomato version) and pasta and deli rolls

· Post Docs could be called Captain. Postgraduate students could take on term I think is much more suited to their position and workload – soldiers

· Lab staff who didn’t pull their weight and replace stock could be dealt with by a quick centrifuge lid to the knuckles

· When other staff tried make life difficult or give you more work it would be perfectly acceptable to shout “MUTHAF#$A” and tip over chairs, throw phones at the wall and stomp out

· If you have a difficult or awkward situation, the mood can immediately lifted by saying “I’m just breaking your balls”

· Lab coats would be replaced by leather jackets or white terry towel bathrobes

· Everyone would have nicknames such as Paulie, Vito, and Junior

· Big overworked hair, excess makeup, long nails, gum chewing and platform shoes would be required PPE for the women in the lab.

· The lab stereo would permanently set to play a mixture of The Doors, AC/DC, Led Zeppelin, Deep Purple and other rock classics, with the occasional Dean Martin song thrown in

· Pipettes would be referred to as “pieces”

· Acceptable adjectives in research articles would include “a$#hole” and “f*$#kin” and “oooh”

· Rather than being in the waste management industry, Tony’s kids would tell their friends their Dad is in the ‘Biotech Industry’

· Long meetings would be accompanied by a quality scotch on the rocks

· The air in the meeting room and offices must be thick with cigar smoke at all times

· A singing fish would be mandatory on the boss’s desk

· Food would be the answer to all problems

· Ethics approvals would be a thing of the past

· Gambling and other ‘business’ would be legitimate methods to funding research


So there you have it. If Tony Soprano ran a lab, I think it would be a very interesting place to work, not that labs aren't interesting now! Well now it's back to "The Sopranos", only three episodes left before the marathon ends.....