Sunday, June 11, 2017

On Learning and the Epigenome aka. Some Cool New Work Out of My Workplace

The question of how memories are made, stored and retrieved is something that has fascinated me since my undergraduate days.
Our genetic 'recipe' is far more complex than I think any one back when the first draft human genome was finished could have predicted. There's a four letter code, followed by a layer of modifications that in themselves are numerous, and the whole thing can interact with proteins and itself in time and space. It's code + 3D structure that also responds to real time environmental changes. Yes, the genome is amazing. And now, thanks to great techniques and some scientists who think big, the dynamic thing that is our genome is being shown to be linked to memory formation and maintenance.
Many of you will have heard of the term 'epigenetics'. Epigenetics is the term for the chemical modifications that are made to DNA bases that change how the bases of DNA are used. It's an additional layer to A,C,Ts and Gs of the code. And just like the code, it can differ between people, but it's not just what you inherit, it can change depending on what a person is exposed to - it also can change in 'real time'.
Neurons in the brain with visible dendrites.
Credit: Yinghua Ma, Timothy Vartanian (The Cell Image Library)
Epigenetics is quite the buzzword, and there's been some big work around it - things like cigarette smoking being linked to changes in the epigenome - so if you smoke the way your DNA is regulated is altered. And now, well, this is where it gets really, really cool - awesome colleagues of mine have just shown that learning changes a certain type of epigenetic mark in neurons.
It gets even more interesting - this particular epigenomic mark (m6dA, a modification of the adenosine, or the A base) is associated with something called fear extinction. Fear conditioning is a learned behaviour, and works just like the famous Pavlov's dog experiment, where a stimulus is associated with an outcome - except in this case it's negative, and an individual (usually a mouse) learns to associate the stimulus with something terrible and ends up showing fear when presented only with the stimulus (it can be light, noise, something they see). The mouse is then exposed to the stimulus, but nothing happens - eventually the mouse learns that the stimulus will result in nothing negative, and doesn't get scared - their fear of the stimulus is effectively extinct.
Why is this important? Because it's good to understand memory. And what makes the brain work. And we know very little about our minds! But it may also have applications when things go wrong. A leading theory of PTSD is that the mechanisms of fear extinction are faulty, and that instead of re-conditioning to no longer have a primal fear response to a stimulus, a person with PTSD goes into the fear response with no control. If we understand how fear extinction works, it gives scientists a starting point in designing ways to treat and fix this faulty mechanism. Linking epigenetic changes to learned response and fear extinction therefore, could be a key piece in treating a terrible mental disease.
So overall - this paper is awesome - not only for the fact that Li and co. have shown that this epigenetic mark exists in neurons, not only for the cool techniques used, not because it's epigenetics but also because it's one more piece in the complex puzzle of memory and adds to our understanding of what memory is and just how we could start to think about treating conditions around memory and learned behaviour. Really neat stuff and it's awesome to see them doing this cutting-edge work every day at QBI.
And for those out there wanting to read the full paper, it's up on bioarxiv!

Thursday, January 5, 2017

The TED365 Project


As we begin a new year, I'm closing off a few projects that I undertook in 2016, and planning for what I'll be doing in 2017.

One of my projects for 2016 was to watch a TED talk a day. Many may ask why, but I was curious - what could I learn from TED? Many of the presenters are well known, but at the same time, the TED format has been criticised for providing a platform to quacks, and promoting a simplified and overly glossy and excessively motivational view of research, design and innovation (see here and here).



In some regards I agree, but feel the criticisms are extreme. Having watched 365 different talks, and even then this is only a small percentage of what's available I feel that I've gotten a good idea of what the style and content of the talks are. Not every talk was well presented, not every talk had positive or motivational themes and for some, I disagreed completely with the information being presented. But that didn't mean I dismissed the platform entirely. The great thing about TED is that often complex information is presented in an engaging way without an over-reliance on gimmicks. In some talks, otherwise boring data is presented in such a way it enthrals an audience that would normally not care for statistics. Most talks are simply a person on a stage, with a few slides or a prop or two. At the very least, TED provides great methodology training on how and how not, to present information effectively.

All sources of information have positives and negatives. It's up to the consumer of said information as to what they make of that information. One hopes that individuals have enough critical thinking ability, and enough grip on reality to understand that a 15 minute talk is going to be very focused, very simplistic and likely to present the 'best' of a topic. With this in mind, I found many great leads on TED - from research I didn't know about, to new authors, to joy in art and music to concepts I'd given very little consideration to. In some cases these concepts and ideas led me down a new avenue of study, and some of the hints and tips I picked up have found a place in my daily living.

I found the TED365 experience one that left me thinking; sometimes in favour of the material presented and sometimes not. But for me to be left with something I could find connection with, and generally could understand the topic, and leaving knowing something new, I feel was time well spent. TED has its place in the big realm of information out there; considering it is free for people to access, the talks are engaging and not overally long, it is one more source thes masses have in accessing information. And it is a source I feel that is very effective. Much of the information comes from people who have lived the experience, or experts, right through the movers, thinkers and shakers in the world, many of who otherwise the average person would never come across. If that gets people questioning, thinking, discussing and inspired then that is great.  We shouldn't criticise the platform as an attempt to vet ideas that individual presenters have that we disagree with. Instead the likes of TED should be used to initiate discussion around such topics. Overall, I recommend having a look at the vast array of information and presenters that can be found on TED, but of course, remember the style and context.

Discussion of the approach of TED aside, I must now move to what I actually watched. The array of presentations was huge and covered all aspects of the lived experience from psychology, art, music to advanced technologies, science and futurism. I was drawn to talks around my own interest in science, but also followed my interests in music, philosophy, psychology and even watched a few presentations on topics I had no idea of. And 365 talks barely scratched the surface of what is available, and new presentations are added regularly, so there's also more ideas to be shared. It's well worth checking out TED if you have an interest in a particular field - chances are there's some presentations on your interest that will help springboard further investigation. 

As the year has 12 months, I've chosen my top 12 from the year. It must be said, this was not an easy list to create as I had around 30 talks covering art, science, music, literature, design and philosophy that really stood out for me. Deciding what made a talk standout complicated the process of choosing a list - sometimes it was content, sometimes it was the speaker's style and sometimes it was the humour, passion or emotion conveyed.  

So here's my top 12, in no particular order:



If you are interested in my full TED365 list, a downloadable list is here (.pdf).

So does TED live up to it's slogan of "Ideas Worth Spreading"? I think so, from my TED365 project I learnt much, not only about various topics but also in what makes for a good presentation. I discovered many new ideas, discovered many great projects, learnt about people I'd otherwise not have encountered and had my own thoughts and conclusions challenged. TED is an incredibly valuable resource, even when presentations are about things we disagree with, as it's important not only our own worldview challenged, and ideas rationally discussed, but sources such as TED allow a place to also to address the need to discuss and contest ideas.