Deus Dominus Machina

Let’s do something totally unproductive today: Let`s play god.

Well, it`s going to be “playing god” if you go with the saying “Evolution is god’s way of issuing upgrades”.

For everyone else it’s going to be “Let`s play simple-laws-that-lead-to-complex-life”*.

A while back I read Richard Dawkins “The Selfish Gene” (1976) which argues that genes are the basic unit that natural selection is working on. I found the book was entertaining and it was easy to follow the arguments (even for laymen on the subject, like me). It replaced “The Science of Discworld” (Pratchett, Stewart, Cohen; 1999) as my Nr.1 popular science book. Naturally I went on reading more of Dawkins books and currently I am reading “The Blind Watchmaker”.

Fractal-Dragon-IFS-01Fig. 1: Fractal – Repetion of simple structures create a complex structure. From fractalsciencekit.

In one chapter Dawkins describes a small computer program to illustrate how evolution works. The basic principle that is used is the one of drawing a tree by using a simple algorithm. If you ever had the slightest contact with programming you`ll probably heard of that. If not you can see the basic principal here. This kind of algorithm is often used to show that complex things can arise from applying simple rules (see Fig. 1). In this case the simple rules are:

Draw a line.
After a while, split it into 2 (or 3, or 4, or 5 …) branches.
Then repeat that game with every branch.

The program in the “The Blind Watchmaker” takes the whole thing a step further:

It treads the variables in the program (e.g. “How many branches?”, “What is the angle between the branches?”, “After what distance does branching occur?”, “How often does branching occur?”) like genes that can randomly vary in their value. It also adds some more “genes” to allow for some more shapes to arise then tree-like ones. In the book the resulting figures are called Biomorphs. The program starts with a Biomorph and by randomly changing one of its variables/genes it creates “children” of this Biomorph.

And then comes the “playing god” part:
The program offers 8 children (with different variations in their “genes”) to the user and the user decides which one will be the “parent” of the next generation. Apparently it was possible to create quite complex structures using this simple program (Fig. 2). As I wanted to try the program myself I checked Google and found that there are several websites having some version of this program. Unfortunately most of them seem to be written centuries ago (meaning: in the 1990s) in a JAVA code that nowadays is mostly blocked or crashes browsers**.

Anyway, I found two versions that seem to work quite well:

1.) A pretty basic version, as far as I can tell similar to the original one described in the book.

2.) A version that seems a bit more complex and has COLOURS.

Fig. 2: Biomorphs from “The Blind Watchmaker”.

The middle square in both programs contains the “parent” which is surrounded by its “children”. To progress select one and it will become the new “parent”. You can just randomly select children to see what various forms some simple rules can create or you can put some selection pressure on the Biomorphs: Aim for a particular property (e.g. elongated, round, complex or a colour in the second program). The effect that is illustrated is breeding (evolution by selection by humans) but if you change the perspective a bit it serves as well to illustrate evolution by natural selection: Those biomorphs just “live” in an environment where it`s crucial for survival to be as colourful and as shaped as you want them to be.

Happy Evolving.

And don`t try to think too much about the possibility that we all just might be result of a slightly more complex Biomorph program – run by a procrastinating, 666-dimensional PhD-student.


*    Even though more likely to be true, this is just not such a catchy phrase as the whole Let`s-play-god-thing.

**   You could say those programs are not fit to survive in the modern day internet – it is JAVAlution.

Testing the Waters: First Experience of Research

By Rachel Kirby

Last week I completed my first seminar as a research student. I was nervous, very nervous. Not so much about standing up and presenting, but about the questions that would inevitably follow. As an Honours student it was my first experience presenting my own research project to a number of academics. Up until now presentations were based upon what we had read in the literature or smaller research assignments, and presented only to our peers and the lecturer. This was a whole new ball game.

Honours is certainly different to the coursework of the first few years of an undergraduate degree. No longer do you have constant small assessment pieces, imposed structure on your day with lectures and labs, or accountability to your lecturers. Instead it is up to you. Assessment consists of just a few large pieces, you choose what you do each day, and you are only accountable to yourself. It is a change that teaches you about self-discipline, motivation and organisation.

All this responsibility comes because you have your own project. This is probably the best thing about Honours, and why I am enjoying it so much. Working on a project that is unearthing new data, new ways of looking at a problem, and new answers is very rewarding. It is a great feeling knowing that you are adding something new and unique to the field. Progressing knowledge of an area is an exciting prospect.

So how did the presentation go? Well I survived, and I am still here at university working on my Honours project. Questions helped prompt me into where to go from here, and were a good reminder of the challenges I will face this year. Squishing a research project into less than nine months will be one of the biggest challenges, and the temptation is always to think big. Maybe a little too big in my case. However come October (when I submit my thesis) I will know how achievable my project was.

Until then I had better get back to the lab, or read some papers, or try and work out exactly how I am going to tackle this project. Seven months left… and counting!

The Amazon rainforest tipping point

By Biance

Last night I watched an interesting documentary on the Amazon rainforest dealing with the consequences of a changing climate. The documentary is part of the 6-prt TV climate series ‘Tipping points’ and investigates how the rainforest manages to deal with our shifting climate.


Parts of the forest show first signs of changes, with big trees dying and fewer growing as these trees need a lot of water to stay healthy. While the death of such huge trees causes a fair bit of destruction, new trees emerge in the gaps. However, these are smaller trees that need less water and grow less high. Together with deforestation, fires and more frequent draughts it is a first step towards an ecological tipping point where our rainforests could turn into savannahs.

Often rainforests are described as our lungs, as they remove carbon dioxide from the atmosphere and produce oxygen and keep our atmosphere in balance by doing so. Recently NASA found that the Amazon inhales more CO2 than it emits and the forest therefore reduces global warming. However, when dying the forests releases CO2 into the atmosphere, which is estimated to be 1.9 billion tons each year.

Deforestation and fires to clear forest for farmland has already changed the regional climate drastically in terms of rainfall patterns and distribution.
Furthermore, the climatic phenomenon of the El Nino Southern Oscillation is associated with dry conditions in Brazil and the northern Amazon and its frequency increased in the past years and is expected to further increase in the future.

This is a drastic change for nature and for humans as we rely on these forests to somehow keep our atmosphere in balance.
The rainforest stores an equivalent of about 15 years of human-caused emissions in its soil and biomass and a massive die-back could greatly accelerate climate change. About 2 billion tons of CO2 are taken out of the air each year by the rainforests photosynthesis, however, during draughts in 2005 and 2010 this process reversed with 3 billion tons of CO2 emitted by the Amazon. This caused a net 5 billion ton increase in CO2 to the atmosphere.
Our changing climate, fires and more frequent draughts in change with sudden floods are pushing the Amazon to a tipping point and we are closer than you would think, with large areas dying or being already dead. If we loose the rainforest, the climate will change drastically and nature will never be the same, as we know it now.

Facts and Fallacies

After finally completing my thesis and graduating I thought I’d try something a bit different, something I probably haven’t done in a long while; read a book for fun! However it was during a somewhat starry-eyed cruise through the science section at a local book retailer that I spotted something that instantly ruined the entire endeavour.

“Taxing Air: Facts and Fallacies about Climate Change”

By Bob Carter and John Spooner

Inevitably I purchased the book if only to remove it from the shelf, and to see if it had any legitimate arguments. It didn’t take long belong I stumbled across one premise that was quite troubling.

“…it has never been demonstrated that warming above today’s temperature would be harmful [to humans].”

This claim is really a trick of language, sure, we have scant evidence for the effects of warming on humans, and there is little in the way of precedent. However, we have a large body of evidence for some of the other effects from warming, and, it doesn’t take a great stretch of the imagination how these will impact humanity.

We know that warming will raise sea level through the melting of land ice and the expansion of water as it warms. Rising sea level presents a threat to the coastal infrastructure of many nations and threatens many of the smaller island nations existentially. Sea level rise could cause the displacement of millions of people from some of the poorest parts of the globe.
I could continue to cover many similar premises, but they all fall into a similar category of being implied criticisms based on ignored or cherry picked information.

The overarching reason that finding this book annoyed me is because the way arguments like this are constructed to distort people’s understanding. This problem becomes apparent when we view the discrepancy between the debates about climate change in the public and scientific sphere. This book would not be as transparent to someone who hasn’t studied climate change for the good part of their undergraduate degree.

So kudos to the people that communicate their science and the scientific communicators for their efforts in eventually drowning out the claims such as those expressed that book.

your academic writing is “slow” – some thoughts on pace

Claire K:

Brilliant piece on the importance of pace and explanation in academic writing. Well worth a read!

Originally posted on patter:

Last week I happened across a facebook post which went a little like this. “My supervisor has just told me my literature chapter was slow and tortuous. What do I do?”

This feedback is a pretty clear example of a supervisor knowing there is a problem with the writing but (a) not actually saying what writing that was ‘right” would look like, and (b) not offering any strategies for the writer to use. The PhD researcher probably had no idea what they were aiming for, nor any idea how to get there. I’m guessing they not only felt bad because what they’d done was deemed inadequate, but also pretty worried about the fact that they didn’t have a clue about what to do to rectify the situation.

Now I haven’t seen the piece of problematic writing, and I can only hazard a guess at what the problem might be. But…

View original 1,026 more words

Banana Boats

By Kate Holland

I have recently learned of the number one boating rule – bananas are not under any circumstances allowed on boats, not even scientific ones! I guess no one is ever exempt from the law…

Could it be due to their ability to stop the fish from biting once their oils are on your hands? It is their ability to harbour tarantulas, snakes or other tropical nasties? Or is it simply the age old problem of slipping on the banana peel?

No! Just No.

No! Just No.

Bananas are ominous, that’s for sure. If a ship carrying bananas happens to sink, the bananas (amongst other items) will float and leave the tell-tale sign of misfortune. This superstition dates way back to the 1700s, when ships carrying precious banana cargo from the Caribbean would have to speed across the seas to deliver the bananas in time. This was to prevent the bananas, and other fruits bananas influence with their ethylene gas by-products, from spoiling! On these journeys the crew wouldn’t catch any fish, due to their break neck speed through the seas.

Another unlucky down side to the banana is once fermented the methane gas has potential to cause some problems for the crew. And so for all the reasons above, bananas are deemed the most unlucky of all the cargo, and banned on boating vehicles. FYI, other things you probably also shouldn’t do include: killing albatross, whistling, being named Jonah, bring a suitcase, be on a boat on Friday and definitely avoid those sirens (beautiful women).

A handy sticker to tell "landlubbers' the rules.

A handy sticker to tell “landlubbers’ the rules.

The sea can be treacherous, but as long as you abide by the sea rules fish and science are attainable!

Practising Science Communication… On the radio!

I wish I had taken a picture of the studio!!

I wish I had taken a picture of the studio!!

By Claire

One of the most important jobs as a scientist is being able to communicate what you do to the people around you. Even if it’s just your mum, one day, someone without a background in your particular field of science will ask you what you do. The trick is to be able to communicate what is typically a quite complex scientific idea in simple terms.

One of my favourite things about contributing to this blog is that I get to “practice” communicating scientific ideas very simply. I am actually getting quite good (if I do say so myself), at telling people about what I am studying in my PhD.

I got an excellent chance to “practice” my science communication last week, when I was asked by the host of a community radio program called “Biodegradio” to come into their studio and record an interview on what I am studying. I was quite nervous heading into the studio, but quickly relaxed and actually had a lot of fun chatting to Alison about my work.  Continue reading