Genomics and Healthcare

On Friday afternoon I attended a seminar by Professor John Christodoulou titled “Genomic Medicine: What is its place in the Australian healthcare system?”.

One of the interesting points he brought up was how genomics had changed the ability to diagnose many genetic diseases. In the past, diagnoses would often require a three step process:

  1. Clinical evaluation
  2. Biochemical screening
  3. Biopsies, imaging, etc

This process had a number of problems:

  1. It was prolonged and expensive
  2. Many biomarkers (especially for mitochondrial diseases) could be inaccurate. e.g. blood lactate levels
  3. The more definitive tests required advanced procedures (biopsies) which required anaesthetic and its associated risks
  4. An enzymatic diagnosis could still leave you ignorant of the genetic aetiology
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How to write a conclusion

As I’ve been writing my thesis I came across a paper with such an excellent conclusion I wanted to share it. I think there are two lessons we can take from it:

  1. Use a title no-one can disagree with
  2. Quote Star Trek – I particularly like seeing Paramount in the location that you would normally see a publishing organisation such as Harvard University Press.

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Fruit flies, honeybees, and alcohol

Whilst writing my thesis, I came across an interesting paper discussing how you can get fruit flies hooked on alcohol, whilst honeybees will consistently turn their noses up to a tipple unless you literally give them nothing else to drink.

Drosophila [fruit flies] develop a preference for alcohol that increases with repeated alcohol consumption, and prefer consuming a liquid fly diet containing alcohol to a liquid diet on its own. Honey bees, on the other hand, will consume sucrose solutions with low concentrations of ethanol, but only if there are no alternatives.

As they went on to elaborate, this response makes perfect sense when you consider the fact that ethanol is often associated with decomposition. That’s perfect for a fruit fly searching for an overripe piece of fruit.

However, for the honeybee, for whom alcohol is an impairment, it would appear there is a strong selective bias towards avoiding alcohol.

It’s a good example of how important it is to understand the system (in this case the model organism) from which your data is coming from. Being aware of these differences can help you turn them into an asset, rather than a source of confounding. After all, as the authors of this paper remark:

Some animals might not be suited for studying particular aspects of drug effects with certain drugs.

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I’m going to Silicon Valley!

I’m extremely excited to announce that I was one of the 20 young Australians selected by Startup Catalyst for their Future Founders Mission to Silicon Valley at the end of the month.

As part of the trip I’ll have the opportunity to visit Stanford University, as well as multiple tech companies, including Google, Facebook, and Dropbox.

I’ll be providing regular updates on Twitter and aim to write a series of articles here distilling everything I learn on the trip.

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Sometimes working in the biology department is pretty neat
The new lord of the biology department at ANU


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Honeybees and missing data part 3: Ant search optimisation

Earlier in the year I had to reset the observation hive and sadly that process resulted in the death of a fair few bees who ended up on the ground. Now, I knew that there were large carnivorous bull ants in the area and I completely expected them to clear away the bodies within a few hours. Unexpectedly though, none of the bodies were removed.

After a couple of days, I took a closer look and noticed something interesting – the bull ants were missing, but the tiny ants* in the area had found them! I’ve circled a few of them in the image below.

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PhD Exit Seminar

On Friday afternoon I presented my exit seminar to the biology department. Things went really well, and I rather enjoyed the questions session that came after – there was a lot of great discussion about honeybee behaviour and machine learning techniques.

My focus for October is to finish writing my thesis, and once that is out of the way, I’m really excited to start regularly blogging again, and to write some articles sharing some really interesting insights into queen bee behaviour my software has been able to uncover.

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Fantastic thesis quotes page

Recently, I was reading through a thesis titled “On Honey Bee Colony Dynamics and Disease Transmission” and on page vi I came across a page of quotes. Nothing too out of the ordinary.

Then I read the second quote on the page.


Sorely tempted to do something similar with my own thesis.

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An interesting scam

I received an interesting scam email this morning from a person claiming to a representative of “Domain Registry China”. I thought I’d post it and hopefully prevent any business owners potentially falling victim to it. This is what it said:

Dear CEO,

(If you are not the person who is in charge of this, please forward this to your CEO, because this is urgent. If this email affects you, we are very sorry, please ignore this email. Thanks)

We are a Network Service Company which is the domain name registration center in China.
We received an application from Hua An Ltd on September 11 2017. They want to register “jacksimpson”, “jacksimpson”, “jacksimpson .asia” domain names, they are in China and Asia domain names. But after checking it, we find “jacksimpson” conflicts with your company. In order to deal with this matter better, so we send you email and confirm whether this company is your distributor or business partner in China or not?

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Honeybees and missing data part 2: Where do bees like to live?

This article relates to where bees prefer to build their hives. Back in the 1970s, there was a bunch of research conducted at Cornell surveying where bees build hives in the wild, and all the evidence seemed to indicate that honeybees preferred to build their hives relatively close to the ground. This finding seemed rather odd, since logically a hive built higher up would be better protected from predators.

Eventually they figured out that the answer was contained in the missing data. What had happened is that the hives which were closer to the ground were far easier to spot by the researchers! Bees do actually prefer to build a hive as high up as possible (and will do so in the majority of cases). In this case, the missing data didn’t just give the scientists more details, it changed the story entirely!

I thought this story was a great lesson for how researchers and organisations have to be careful with how they collect their data, and which data they base their decisions on, as collecting data just because it is easier to get may not just be a waste of money, it may lead you in entirely the wrong direction.

Part 1 is available here.

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