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.