Category: Justin Byrne

By Justin Byrne

In my PhD, I compare ancient British woodlands with younger ones in an effort to describe how microbial biodiversity, and the associated ecological processes, change over time. Scientific endeavours like this focus on building generalisations, but what is the use of a generalisation if, in the real world, things are always atypical?

Biodiversity, the breadth of variation in the living components of an environment, tends to increase over time. Below is a picture of some tanks of standing water in our office, initially these tanks were used to age water for our aquarium. When spring began, the water would quickly fill with algae so we stopped using it. Instead of throwing it away, we left it, occasionally topping it up with wastewater from aquarium water changes. When we put a few plants in there things really kicked off and now the tanks teem with life. Water boatmen, snails, water fleas and no doubt plenty of other microscopic inhabitants have colonised the tank. Nature is the same but slower.

In natural systems we generally expect environments to go through a series of successional stages. First, colonisers arrive, generally fast growing, with high dispersal and plenty of offspring. At a time it was popular to refer to these species as r-selected species (r for high growth rate). These reshape their environments with their activity, waste, and their death, providing altered environments for other species to colonise. As more species arrive, they continue to change their environment until long living species generally crowd out and dominate, forming a climax community. These, were once popularly referred to as k-selected species (k for Kapazitätsgrenze, the German word for carrying capacity – the stable population limit of the environment). This is succession, a conceptual model of how ecosystems behave. British woodlands are the basis of my work and have an extensive history of management, not unlike my water tanks. The Ancient British woodlands used in my research have not yet reached a climax community, the theorised final state of succession. They do not conform to the model. Perhaps the post-glacial wildwood reached climax over the thousands of years of succession it experienced before humans reshaped the British Isles.  Perhaps chaotic processes within it prevented it reaching that point. Despite having good generalisations about how the environment should shape itself, in reality things are more messy.

We base our models of how ecosystems work on imperfect individuals. I attempt to look past the individuality of woods with a carefully designed study with lots of replicates. Generally, I might find that the diversity of microbes in woodlands increases over time. Alternatively, “middle aged” woodlands might be most diverse. Statistics gives me an idea of how trustworthy this generalisation is. However, it remains impossible to say what a certain wood will be like in a few decades or centuries. Whatever relationships I find, individual woods may entirely buck the trend. The strength of scientific theories is in their ability to predict general trends. Their weakness will always be in predicting individual events.

Any understanding of the mechanisms behind observed results is going to be a generalisation, and for that we sacrifice certainty. I think that is why many have come to doubt the advice of experts; those who can tell you what should happen, but never what will happen. Developing scientists have to become comfortable with uncertainty, while striving to increase the confidence of their assertions. Offering assurance is not a natural part of this skill set, which can be troublesome when a scientist is called upon to explain an item of news or a development (see the ongoing climate debate). There are two clear responses to this; either science, being uncertain, is a poor arbiter of truth, or certainty is a western virtue that should be valued less highly. To see the downsides of each worldview, one need not look far.

By Justin Byrne

Currently the School of Natural and Environmental Sciences is assimilating what was my school – the School of Biology. Changes will come with the new super school, but hopefully along with increased opportunities for collaboration. It may seem perfectly natural to bring together related schools into a single body, but each discipline uses different equipment, jargon, methods, analyses, and philosophical approaches. Reconciling these differences presents a challenge and I wonder whether it is something that is either possible or desirable. Concerns of this nature are central to the philosophy of science, relating to the concept of the unity of science, and have their roots in the very beginnings of western thought. Now seems like the perfect time to explore unification as a concept and perceived scientific ideal.

“Knowledge also is surely one, but each part of it that commands a certain field is marked off and given a special name proper to itself.” – Plato, Sophist, 257c.

Even before Plato expressed this, the idea of a unified theory of knowledge was discussed and revered. This ideal was passed on by great thinkers, such as Wilhem Dilthey, who first introduced distinctions between the natural and social sciences, building himself upon work by Kant. It is in this way (container unity) that we now tend to approach natural science as a unified concept, separate to social and cultural studies and distinct from pseudoscience and religion. However the age and tenacity of these ideas does not guarantee their validity. Indeed, certain pluralistic views of science would argue against this “one”-ness, rejecting the view of science as a collection of related disciplines that together strive towards a single, correct understanding of nature. This kind of unification of disciplines within science is referred to as connective unity. Pluralists might argue that the differences between certain disciplines in thought, vision, or method, are sometimes irreconcilable. As such, they must be viewed and treated as separate projects, perhaps with similar themes.

All of this is to say that, when bringing the schools together, difficulties of integration should be expected. How we view the concept of unity in science will affect how we attempt to solve potential problems. One scientist (whether they know it or not) may be a reductionist, perhaps believing in a pyramid of knowledge built up from the foundation of physics and mathematics, with each subsequent level reducible to concepts of the previous. When disagreements arise between fields they might be inclined to side with the more fundamental or “hard” science. Reductionism attempts to unify disciplines along lineages, where more fundamental disciplines underlie the principles of the others, but this is not without criticism.

Within the scientific community there is broad acceptance of the unity of science. It underlies scientific principles of hypothesis formation, falsifiability (as an improvement over verifiability), and empirical evidence. However its critics have described it as overly dogmatic, restrictive, and ultimately unrealistic in describing the chaotic history of how theories have emerged and reached acceptance. Scientists work on a variety of tasks that go beyond basic empirical methods, such as collaboration with artists and media outlets, discussions with other scientists, and interdisciplinary work outside of the natural sciences. A narrow definition of science that ignores the way modern science is conducted is not useful, and may mean that the separation between the natural sciences and other disciplines is exaggerated.

Whether the sciences are distinct or not, we still need to resolve differences within our new school. I am predisposed to a live and let live attitude. Believers in the concept of emergence in science might argue that in increasingly complex subjects, new concepts, tools, rules and principles form that are irreducible, and cannot be deduced from more “fundamental” studies. Due to my own interest in complex systems and dynamic networks, I must admit that I am personally inclined to this view. As the research areas within the new school touch upon social, economic, biological, and political research, this incredible complexity may require a more sophisticated approach.

Finally, Otto Neurath once imagined science as an old boat at sea, undergoing constant repair without a stable foundation. The workers constantly reconstruct it with the best available components, reusing some and discarding others. In doing so he was rejecting the primacy of physics as the foundation of science, instead arguing for a united effort, allied for practical reasons. Cooperative, separate efforts, all attempting to produce good predictions and enable control of the natural world requires the sharing of tools and ideas. Unity in science was a tool for cooperation in his post-war landscape with cultural, political, and economic ramifications. Though I am inclined to disagree with those who would unify natural sciences by reducing its many principles to expressions of physics and chemistry, I find this kind of unity compelling. As we move forward and shape our new school Neurath’s views on the unity of science are perhaps the most important; how can we work together to produce a more peaceful, cooperative and prosperous future.

By Justin Byrne

My PhD focuses on the use of ecological networks (like food webs) to study biological communities, so I spend a lot of time thinking about what a “healthy” community might look like. Perhaps spending too much time thinking about one topic leads you to try and apply that thinking to everything else. Let me give you an example.

To study the microbial communities I will focus on, I have had to educate myself on a developing field in biology that may offer an alternative way to identify species: DNA barcodes. This method allows us to identify organisms based upon a small snippet of their DNA that is unique (more or less) to that species. Specifically, I will be working with large numbers of species, mixing all their DNA together and extracting all the “barcodes” at once. Using the wonders of new DNA sequencing technology, I will then be able to read all of these short DNA sequences and produce a list of everything present. This complicated process is called “DNA metabarcoding”.

If that all sounds complicated, that’s how I felt too. Especially for an ecologist who spent the last year looking at birds and running computer models. While learning about this, I have been surprised by the number of researchers at Newcastle who are using DNA barcoding. Some have been using these methods to look at historical trends in species DNA (a field called paleoecology) to verify archaeological farming records. Others, myself included, have been investigating questions of conservation and ecology. Across the university, researchers are being pulled together due to common interests and are discussing collaborative efforts. This is all an essential part of the academic process, perhaps these links between researchers are an indicator of community health?

My research will look at characterising the fungi and bacteria present in various woodland soils. I’d like to add to our understanding of ancient woodland soil communities. As the project involves fieldwork with woodland soil, lab work with DNA and computer analysis of large amounts of data, it helps to be part of a broad research community that can offer guidance on multiple issues. Both community health research and healthy research communities are important at Newcastle, which is a good sign. What’s not a good sign is that I seem to have taken to simplifying every aspect of my life to network representations of real things. Send help, preferably in the form of Eigen vectors that transform me out of this state.