From Code to Cognition: The Computational Future of Neuroscience

Lily Li

Lily Li is a second year BSc (Adv Maths) student at Sydney university and a resident at the Women’s College. She is hoping to pursue a double major in pure mathematics and physics. Meanwhile, she is channeling her passion for science communication to work as a demonstrator for the Kickstart program run by the School of Physics.

Imagine a future where highly accurate and efficient neurological tests can be performed at the comfort of your couch and coffee table, on your trusty 13-inch MacBook Pro. Thanks to the ongoing efforts of physicists, mathematicians, computer scientists and neuroscientists over the past few decades, that future is more tangible than ever. Amalgamating knowledge and techniques from this diverse array of scientific disciplines, an emerging field known as “Computational Neuroscience” has come to being.

“How do our brains function?” has been a question of philosophical, theological, and scientific debate over a good chunk of civilised human history. Driven by the fascination with this unanswered question, and the fast-paced advancements in computational technologies, scientists have been looking beyond biochemical orientated areas of study in search for an answer.

In the late 1940’s Alan Turing investigated what were called “unorganised networks”, and sought to simulate neural networks with a digital computer. Since Turing’s time, scientists have come to the realisation that the computer’s ability to perform detailed calculations on a large scale renders it the most powerful tool for studying systems that can’t be explained by a unifying general principle. Complex biological systems like the brain would be considered such a system.

Luckily, many biomolecular mechanisms in the nervous system can be approximated with mathematical equations. Once we map out some of these basic mechanisms for neuronal behaviour, we can piece them together to form a network. This network can then model a region, or even the entirety of the brain. In the past few years, several networks that model roughly as many neurons as that of a real mammalian brain have been published.

In the second semester of 2015, I was lucky enough to take part in a research project in the field of computational neuroscience, as a part of the School of Physics’ Talented Student Program. My project focused on manipulating a “simple” network of a few thousand neurons that were able to recreate brain waves characteristic of Parkinson’s Disease, and looked at how we could utilise this neural network in conjunction with a computerised arm model in order to simulate physical movement.

To initiate the perpetuation of interactions between neurons, the network requires input from “other parts of the brain”. Our project took advantage of this very particular aspect of neural network modelling, by investigating the way our model responded to changes in the background input. This allowed us to implement background activity modelled on a Parkinson’s affected brain, and to compare the sensorimotor outputs (e.g. movements created by the arm models) to that of a network driven by healthy activity.

Naturally, there are many ways to form a neural network, by choosing different connection metrics or with different sets of approximation equations. This means that an important theme underpinning all research in the field is the continuous search for models that are more computationally efficient and biologically realistic. The study of computational neuroscience is a reflection of everything we know behind the intricate workings of the complex machinery that is our brain. Apart from creating the opportunity for a non-invasive, cost-efficient future of neurological studies, the billions of tiny circuits and transistors allowing you to read this article might soon shed some light on the very nature of cognition.

 

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Beethoven vs. Einstein: The balancing act of two crazy-haired careers

Chelsea

Chelsea Witham is a second year Bachelor of Psychology student at The University of Sydney, and intends to complete post-graduate qualifications in Clinical Psychology. She has previously completed her Bachelor of Music majoring in Flute Performance at the Conservatorium of Sydney, and continues to perform regularly as a casual musician with the Australian Opera and Ballet Orchestra. She is currently a Resident Assistant at The Women’s College.

Upon leaving school, I never imagined I would study anything but music. Although I had considered pursuing a health-related discipline while at school, my dream of becoming a classical musician always seemed to crowd out everything else. After successfully auditioning to study at the Conservatorium of Music, I dedicated myself wholeheartedly to becoming an orchestral flautist.

In my third year of study, I successfully auditioned to be part of the Sydney Symphony Fellowship program. Through this opportunity I was lucky enough to perform as a professional flautist with the orchestra. My first ever performance was playing Beethoven’s famous Fifth Symphony in the Opera House as second flute, which will forever remain as one of the most incredible experiences of my life!

After playing in a few concerts with the SSO I started to gain a feel for what kind of life I would have as an orchestral musician. Despite loving every minute, I have always also been incredibly passionate about medicine and health, and began to feel that that limiting myself to only being a musician was not what I wanted for my life. I was equally excited to gain expertise in a health-related field where I could expand my knowledge, my opportunities for work, and ability to undertake research. After speaking to various medical and psychology professionals, I fell in love with the idea of becoming a psychologist.

Upon the completion of my music degree, I applied to study psychology at Sydney University and was overjoyed to be accepted into my second Bachelor degree. The transition to Psychology from music certainly hasn’t been easy. The performance-based nature of my previous study meant that I was not used to writing essays or studying in the traditional sense. Additionally, I was starting study in a field I had absolutely no experience in! Science was very foreign to me, and the introduction of statistics, validity, experiments and report writing was quite overwhelming at first. However, I remained positive and asked questions wherever I could, and am now very comfortable studying a science degree.

Despite its challenges, I wouldn’t change my decision for anything. I have also never felt that I couldn’t pursue both of my careers simultaneously – one certainly doesn’t cancel out the other. In my first year of studying Psychology I also auditioned successfully for a casual position with the Australian Opera and Ballet Orchestra, which has meant that I still can perform professionally while I study.

My advice is not to let people tell you how you should structure your life, because only you can make those decisions for yourself. Ask questions, pursue opportunities, and don’t be afraid to back yourself. If you’re passionate enough, you can make it work – even from one crazy-haired career to another!

Freefalling into First Year

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Angie Lu is a 1st year student completing a Bachelor of Science and Bachelor of Arts. With aspirations to teach high school students and explore the education system, she loves residing at the Women’s College and constantly learning from others.

My transition into university was a freefall into an abyss of newfound responsibilities and academic experiences. Never would I have anticipated such a steep learning curve but I couldn’t be more inspired by what’s happened so far.

The structure of my double Arts/Science degree means my first year timetable is mostly comprised of science units. Introductory mathematics courses are compulsory. However, by virtue of this fact (and the abundance of science students), you’ll never fail to find a study buddy or friend to bemoan the horrors of differential calculus. This kind of bonding and solidarity spawned relationships and academic experiences I now value very highly.

I was relieved upon discovering that 45% of the people in my biology lecture hadn’t completed a HSC Biology equivalent either. Thus, the beauty of first year biology is two fold. Firstly, the department constructs the course knowing exactly this fact. Secondly, the subject still accommodates for a spread of student abilities with challenging and achievable assessments. My academic results benefited from these understandings as well as the fantastic extra tutorials provided at the Women’s College.

I also had the opportunity to enroll in a unit of bioethics and was excited to explore the morality of scientific research and procedures. I utilised literacy skills even though thought processes were firmly grounded within the logic and factual realms of science. Structuring essays from this perspective was eye-opening and thoroughly enjoyable.

I’ve continued my mathematics and biology for semester 2 but have replaced bioethics with a unit of logic. Studying the laws of truth is looking promising with unusual but interesting content. However, being able to complete another philosophy perfectly marries my love for the arts and sciences. In particular, the sciences at The University of Sydney reiterate the importance of discipline and hard work. The support I’ve received from the Women’s College has provided both balance and guidance. This made it possible for me to push myself but enjoy my first year so far. As such, I genuinely look forward to the challenges and experiences to come.

Myths and legends: In defence of general chemistry

 

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Elisabeth Tondl is in the second year of her PhD at the University of Sydney, investigating selective delivery of chemotherapeutics to prostate cancer. She holds two Teaching Fellowships, at The University of Sydney and The Women’s College, and is insatiably curious about the world.

There are some pretty crazy ideas on the interwebs about chemicals and how they can make you (and the environment) sick. So, as a researcher in chemistry, I’m going to contribute my 2 cents’ worth by combating some common misconceptions.
“Pure H2O is the healthiest”

This attractive legend is thoroughly undermined by an understanding of osmotic pressure. In our blood, we have lots of different molecules – proteins, sugars, enzymes and so on. For every litre of our blood, there’s a certain amount of those molecules in there (known as concentration), just as the liquid in our cells has a certain concentration.
The principles of osmotic flow tell us that water flows towards the region of highest concentration – this means, if we dilute our blood by drinking pure H2O, water will rush from our watered down blood into our very concentrated cells. Such a sudden influx causes the cells to burst and die. Next time you buy bottled water, take a look at the label telling you how much magnesium, chloride and other stuff there is in your H2O, and be glad to have averted the slaughter of your cells.
“Natural sugars are better than synthetic sugars”

This myth springs from a misunderstanding of the chemical structures of sugars, which are short-chain carbohydrates. There are lots of different kinds of sugars in our bodies and in our environment, and you’re most probably familiar with glucose (diabetics have harmfully high levels in their blood) and sucrose (edible table sugar). The point is, these sugar molecules have defined chemical structures – sucrose is the same, whether you get it from a plant, or eat it in a muffin.
Given that the chemical structures are the same, it’s really not logical to claim that “natural sucrose” from plants is any different to the white crystalline sugar you buy from the shops, or the sucrose I can make in the lab. The only difference is in whatever accompanies the sucrose molecules – other molecules that are removed in the refining process, to give you pure sucrose to stir in your coffee or tea.
“I have a chemical-free diet”

No, you don’t, unless you are living in a vacuum and never breathing, eating, or drinking anything at all (and then your body would still be making chemicals, until you died, and then it would make some more chemicals when your body decomposed). When people say this, they commonly mean that they are avoiding preservatives or foods containing compounds they know to have been synthesised in a lab (see comments on the previous myth). But I just had to mention this misconception, because as a chemist it hurts me physically to hear it, and I will go about contradicting it until I die and decompose.

Science and A World of Opportunities

Maryam Eghtedari is a third year Bachelor of Advanced Science and Doctor of Medicine student with majors in Neuroscience and Anatomy. Maryam founded SciMed at The Women's College in August 2014.

Maryam Eghtedari is a third year Bachelor of Advanced Science (Neuroscience and Anatomy) and Doctor of Medicine student at the University of Sydney. 

Through our National Science Week Blog at SciMed, we aimed to showcase some of the opportunities available during or soon after completing a science degree. Our young female scientists have shared their stories, passions and experiences on the blog, with a hope to encourage younger students to consider similar opportunities, and to make the most of their journey at university.

The structure of a science degree entails developing essential practical and communicative skills. Teamwork and leadership are also important traits of a scientist, which are highly encouraged through the assessments and laboratory work during the degree. It is worth noting that outside of the classroom, there are many opportunities to practice these skills: it could be through studying abroad in Europe or Asia, or taking part in a group project such as iGEM.

Participating in research is also a fantastic way to apply skills learned in the classroom to real-world problems. There are many ways to take part in a research project: it could be through summer scholarships, the Talented Student Program or by completing Honours. Alternatively, if you are interested in a particular area, find a supervisor in that field and ask for an opportunity to work with them. Academics are usually willing to support enthusiastic undergraduate students, and to provide them with a chance to participate in research.

There is a range of career options open to science graduates, and indeed trained scientists are equipped to tackle the world’s most challenging problems! As our members have written, it could be as rewarding as teaching science or as exciting as completing a PhD or studying medicine.

In addition to the academic aspects of the degree, the social aspects and the extracurricular activities open to students throughout their studies are incredibly valuable during and after university. There are many opportunities to meet and network with peers and academics in science, including through tutorial sessions, seminars and clubs at university and College – such as SciMed!

In conclusion, on behalf of SciMed, I would like to thank our authors for contributing to the National Science Week Blog. We hope that we have played some small part in inspiring our younger students to pursue the opportunities available in science, and we hope to welcome more scientists to SciMed and The Women’s College in the future.

Hidden Gem: A Unique Undergraduate Research Opportunity

Gaia Herrmann is in her 3rd year of a Bachelor of Science (immunology and biochemistry). She is a member of this year's Sydney University team in the iGEM competition.

Gaia Herrmann is in her 3rd year of a Bachelor of Science (immunology and biochemistry). She is a member of this year’s Sydney University team in the iGEM competition.

The International Genetically Engineered Machine Competition or iGEM for short is a prestigious and unique competition open to undergraduate students interested in the field of synthetic biology. Being a member of this team involves creating and carrying out individual research projects that are aimed at solving real world problems using novel genetic techniques.

Being able to direct our own research is a truly unique experience for undergraduates. In 2015 there will be over 200 teams competing from across the world including some iGEM powerhouses such as MIT, Oxford, Helenski, and Cambridge. All teams compete against each other at the Giant Jamboree held in Boston during September. The University of Sydney Team is in it’s third year of competition. We are attempting to optimise the expression of an enzyme in a bacteria found in your gut called E. Coli. If successful then this bacteria and enzyme has some really interesting and useful applications.

One such application is bioremediation in which the enzyme can change chloroalkanes are common ground water pollutants into something that is sufficiently less toxic for humans and animals. It can also perform biocatalysis reactions producing drug precursors. Most of these precursors can only be chemically synthesised which is incredibly expensive and toxic, so if we can perform this same process through an enzyme then it will be cheaper and more efficient. Our experimental process involves cloning, and gene design.

Having the ability to conduct novel research in such a rapidly advancing field has not only been incredibly exciting, but has opened my eyes to the multitude of opportunities that a research career has to offer.

The first chapter of a science degree

The Clock Tower entrance of The Quadrangle at The University of Sydney 

The Clock Tower entrance of The Quadrangle at The University of Sydney

Emma Castle is a 1st year Bachelor of Science student at the University of Sydney and a resident at The Women’s College. Emma hopes to major in Neuroscience.


After 13 years of schooling, a hectic HSC year and 3 months of holidays. I was ready to head into the “real” world. University. A place of uncharted territory and I was diving in headfirst.

During my last years of school I told my parents that I wanted to study science at university. They both had studied economics degrees at Sydney University and their only words were “ you know that is a lot of hours,” and boy did they mean it. In my first semester I had 23 contact hours a week and that certainly kept me busy with lectures, labs and tutorials. The style of learning at university is very self motivated and was quite different to the structure of high school, so it was a difficult at first to adjust. By the time I got into the swing of things, semester was over and exams were approaching.

Doing a first year science degree I do a variety of different science subjects such as maths, chemistry, biology and even psychology to have a basic foundation for my second and third year studies. I like how university shows the collaboration of the different sciences, explaining how that each science isn’t actually pigeonholed into one area but rather it all interacts. I also like the problem solving aspect of the course, where you learn to think for yourself compared to school where you are spoon fed information.

Since moving into The Women’s College, it has made the transition to university so much easier. I have met so many people through various college activities such as O-Week, choir and basketball. I have many friends doing science degrees at college, which form such a great support base when it comes to understanding content as well as venting about a subject.

I’m looking forward to this semester so I can keep building on my base of knowledge from first semester. I’m also excited for second year where I can finally delve into my areas of study for my major.