The University of Aberdeen Fungal Group was awarded £5.1M to tackle fungal infections

The University of Aberdeen Fungal Group has been a awarded a Wellcome Trust Strategic Award to lead a  UK collaboration to bring fungal science closer to treating infection.

The new Medical Mycology and Fungal Immunology Consortium aims to train a new generation of scientists and clinicians but also to promote greater public awareness of fungal infections.

Professor Al Brown (right), a chair in Microbiology at the University of Aberdeen and Co-Director of this Consortium, also coordinates the FINSysB Network. 

Read more about the award on BBC or the University website.

The flash game Pandemic 2 let's YOU be the infectious disease!

To effectively fight any enemy, you have to understand it first. This is one of the most basic principles when you are trying to prevent infectious diseases. But every disease and its causative agent are different. Modes of infection, transmission, outside host survivability, symptoms and especially the underlying molecular biology is hard to pin down and explain with only one model. But there are still a couple of basic principles that are very nicely illustrated in the game Pandemic 2 below.

In this game you take on the role of an infectious disease. You can choose between being a virus, bacteria or a parasite (no fungi though, sorry). Then you are directly thrown on a world map. Congratulations, you just infected your first human in a random region of the world. Each region is characterized by a set of variables and measures taken by the government to control your disease. Many regions have ship yards and airports that are instrumental in spreading the infection. Also, national water supplies and hospitals are important factors.

While randomly occuring natural disasters helps you, governments will  hinder you by taking increasingly drastic measures.

The effectiveness of your disease depends basically on three variables. Lethality does exactly what it says on the box, a measure of how fast your disease kills an average human. Infectivity tells you how well the disease is transmitted and spreads through a population. Finally, Visibility determines how fast authorities react to your disease by closing airports, harbors, public transport and so on. For example, in the games term, the Ebola virus would have a high lethality, a medium infectivity but it would be very visible while HIV/AIDS would have a low visibility with medium infectivity and lethality. You can increase these variables by buying new traits with evolution points that are awarded for meeting certain milestones (number of infected, spread to a new region etc.).

Buying new symptoms, resistances and ways of transmission will affect the three key variables in different ways.

The game is relatively straight forward and has a good tutorial so just give it a try and see how you do. But it makes you realize how easily diseases can develop and spread. You also notice how hard the job of national and international health organizations like the WHO is to actually contain and combat a disease. So next time someone asks you what you did in your coffee break, just say you wiped out mankind. But remember, Madagaskar is always the hardest place to get. Enjoy!

Koch's Postulates

In my last post I was describing how scientists use the scientific method to keep their research objective. One of the best examples of applying the scientific method are Koch's Postulates. Robert Koch (1843-1910, left) was a german physician who was interested in how diseases are spread. He is considered the founder of modern microbiology and bacteriology together with his contemporary, Louis Pasteur (1822-1895, right).

In the course of his career, he developed countless microbial techniques that are still in use today. The Petri dish is named after his assistant. He identified the causative agents of Tuberculosis (Mycobacterium tuberculosis), Anthrax (Bacillus anthracis) and Cholera (Vibrio cholera). This earned him the Nobel prize for medicine in 1905.

One of his greatest contributions to microbiology was the formulation of the four Postulates that now carry his name. The postulates are step wise, each postulate based on the previous finding.
In order to establish that an organism causes a disease the following requirements have to be fullfilled:

Step 1: Association- The organism and the disease are observed together consistently.

Step 2: Isolation - The organism can be isolated from the diseased.

Step 3: Inoculation - The isolated organism causes the disease in a healthy individuum.

Step 4: Re-isolation - The organism can be re-isolated from the infected individuum.

Now look at each of these steps carefully and think about what they require you to do. Did you notice it? Between each of the steps the principles of the scientific method are applied. Here is a more graphic representation of the application of Koch's Postulates.

By putting clearly defined rules for what defines a disease causing organism (today referred to as a pathogenic organism or just pathogen), Koch made a major contribution to the then raging discussion about the cause and origin of diseases.

Before Kochs discovery of the Cholera bacterium, there was a heated discussion between the Contagionists and the Anticontagionists. The Anticontagionists (Max von Pettenkoffer was one of them, see also this post) argued that in their theory human-to-human transmission was only a very minor component. They were strong opponents of quarantine and disinfection because it inhibited trade and was less effective than local solutions like improved sanitation. You can read more about it here.

Koch's Postulates proved that transmissibility played an important role in epidemics and quarantines and disinfection was indeed a suitable method to counter both. In the end, everyone benefited from the discussion because it improved both local and global safety against infectious diseases. Getting scientists to agree to something is quite difficult but using the right arguments derived from proper use of the scientific method and you have a good chance of succeeding.

Next week I will write about the central dogma of molecular biology and why it is not so dogmatic anymore.

The scientific method

In my previous post I was talking about the difficulty that scientists face to keep their research objective and unbiased. Luckily, smarter people than me have developed a basic set of concepts that help do that. All these concepts are mainly based on the Aristotelian laws of logic from the third century BC. Most of the ideas that define the scientific method nowadays are already described there. The scientific method is at the heart of science as a set of rules to make research as objective as possible. It is usually described in four basic steps.

Step 1: Observation and description of a phenomenon or group of phenomena.

Step 2: Formulation of a hypothesis to explain the phenomena.

Step 3: Use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations.

Step 4: Performance of experimental tests of the predictions by several independent researchers and properly performed experiments.

Actually, people use these steps almost instinctively to predict cause and effect and adapt accordingly. For example, when you wake up in the morning, you look out of the window and see people on the street in cold weather clothing (Step 1, observation). Your hypothesis (Step 2) is that people are wearing warm clothes because it is cold outside (Step 3, prediction). To test your prediction you open a window or look at a thermometer (Step 4, Experiment). Usually the laymen abstain from enlisting independent researchers to do control experiments.

The scientific method has been refined over the centuries but the core of it is still untouched. The setup that is usually used as a checklist for adherence to the scientific method is the following:

1. Define the question
2. Gather information and resources (observe)
3. Form hypothesis
4. Perform experiment and collect data
5. Analyze data
6. Interpret data and draw conclusions serving as a starting point for new hypothesis
7. Publish results
8. Retest (frequently done by other scientists)

Notice point 6 which clearly shows that you normally refine your hypothesis based on the outcome of your first results. Most hypotheses defined by scientists continuously cycle between step 3 and 6 before they are ever published. The picture below describes the usual approach.

It is also important to note, that the scientific method doesn’t allow the absolute verification of a hypothesis. Einstein himself said: "No amount of experimentation can ever prove me right; a single experiment can prove me wrong." Especially physicists have a tendency to postulate an unknown factor, like the Higgs-Boson, to resolve issues with current theories. The current interest at the large colliders in Switzerland (Large Hadron Collider, CERN) and the US (Tevatron, Fermilab) is to experimentally proof whether or not the Higgs-Boson actually exists and has the properties that are required to make the theory behind it work.

If the Higgs-Boson could not be experimentally proven in the predicted range, most theoretical models of physics would have to be reexamined. I think that makes it slightly more understandable why there is so much money going into this kind of research because entirely rethinking physics sounds like a huge headache to me.

You can easily test what I said about the instinctive use of the scientific method. Just watch yourself and observe how your brain works and you draw conclusions about your environment. Or ask people how they arrived at the conclusion that it won’t rain today. But don’t let them get away with: “It never rains when I have an umbrella with me.” Maybe you can disprove that to them using the scientific method.

Have a nice weekend and keep on thinking!