Science

Our ability to learn, use, and process language is something that sets us apart from other animals. Language is used for effective communication, but also allows us to express our creativity through literature, poetry, and song. However, our use of language follows strict mathematical principles as well. One of the best known of these is Zipf’s law.

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“Most scientific explanations are causal. This is also the case in evolutionary biology, where the primary goals are to explain the diversity of life and the adaptive fit between organisms and their surroundings. Yet, the nature of causation in evolutionary biology is contentious.” So starts the description of a workshop on Cause and Process in Evolution, organized by Kevin Laland and Tobias Uller. It brought together an eclectic mix of evolutionary biologists, developmental biologists, and philosophers of biology, with the aim of addressing this contention. I sat in on this workshop, like a fly on the wall, in the hope of learning a bit about the latest research and debates in evolutionary biology.

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In this day and age of the internet, where anyone can post anything, it is often difficult to know what is true and what is not. One person claims one thing, while another states the exact opposite. Who to believe among all this (sometimes deliberate) confusion? The upside, also thanks to the internet, is that you don’t need to be a professional scientist to find out at least some of the truth for yourself. With the increasing availability of public online databases and easy-to-use software, “citizen science” can go a long way at countering unsubstantiated claims.

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We’ve heard it all too many times: animal and plant species are currently going extinct at a rate that is higher than ever before. Climate change, over-pollution, and urban and agricultural encroachment all contribute to the rapid decline of our planet’s biodiversity. So much so, that there is a real danger that even within the next few decades, several major ecosystems worldwide (such as mangrove, alpine, and polar regions) will be seriously disrupted, with major consequences for us humans as well.

Thankfully, efforts are underway to try and curb some of these negative influences. But without knowing better what exactly their consequences are, it is almost like driving in the dark without the headlights on. Is there a way to estimate more accurately what the biodiversity consequences are of, e.g., a two-degree increase in global temperature? It turns out the answer is yes (at least to some extent), thanks to mathematics and computers.

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As part of a workshop at the Wissenschaftskolleg zu Berlin (Wiko), we had the pleasure of being taken on a backstage tour at the Natural History Museum in Berlin. Our private and extremely knowledgeable guide Brandon Kilbourne turned out to be a walking encyclopedia on the evolution of mammals, so we were in for a special treat. This 2.5hr tour provided many wonderful insights into amazing adaptations over millions of years of mammalian evolution, with as cherry on the cake some unique dinosaur skeletons to marvel at.

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In a post just over a year ago, I presented data on earth activity (in particular earthquakes, volcanic eruptions, and tropical storms). Given all the buzz on the internet about an increased earth activity over the past several years, I was curious to see this for myself, so I downloaded and analyzed some publicly available data. Surprisingly, though, the data showed no such increase at all. In the current post, I present the updated data for up until the end of 2016, which still shows no sign of any unusual behavior. Judge the plots below for yourself…

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Spirals are common in nature. We’ve all admired the beautiful spirals that occur on sea shells, we can find spirals in plants, and even in the arms of galaxies or weather patterns. There are also situations in which spirals aren’t a result of slow growth, but occur spontaneously in biological or chemical systems. A famous example from chemistry is the Belousov-Zhabotinsky (BZ) reaction: when several chemicals are mixed together in a petri dish, the resulting solution forms changing spiral patterns. In biology a particular slime mould, called dictyostelium discoideum, gives rise to similar patterns. Spontaneous spiral wave formation in such systems can be reproduced and studied with simple mathematical models known as cellular automata.

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Charles Darwin’s theory of evolution by natural selection is one of the most profound scientific theories to have ever been developed. However, there were several questions about evolution that Darwin himself could not answer. Not that he wasn’t smart enough (in fact, his intuition often pointed in the right direction), but the answers to those questions required sophisticated mathematical insights that were not developed far enough, or even available yet, in Darwin’s time. One such problem was the evolution of altruism. If evolution by natural selection is all about competition and survival of the fittest, how can altruistic behaviour (which, by definition, lowers the altruist’s fitness and increases the receiver’s fitness) ever evolve?

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Evolution is still all too often (but wrongly) downplayed as “just a theory” in public discussions. This is partly due to an unfortunate misunderstanding of what a theory means in science, as opposed to its common language meaning. Evolution by natural selection is much more than just a hypothesis, and is as much a valid and well-accepted scientific theory as the theory of gravitation. What Darwin did for biology is on par with what Newton did for physics — and mathematics plays an important role in both theories.

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I’ve made a short movie showing autocatalytic sets arising in a dynamical simulation of a simple polymer model. It shows how autocatalytic subsets appear, one after another, and then grow in concentration. This provides a nice visual and dynamical example of our usually more graph-theoretical analyses. Continue Reading

A key result of last year’s UN climate change conference in Paris is that we now have a new international deal to curb climate change. However, it seems primarily focused on reducing greenhouse gas emissions to limit global warming. A significant step forward, no doubt, but it does not address the more difficult, and perhaps also more relevant question of how to deal with the inevitable consequences of climate change. Are we able at all to predict what those consequences will be? And, more importantly, will we be able to do something to reduce, or even prevent, some of these consequences? When it comes to biodiversity and the distribution of species, some researchers believe this is indeed possible.

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“Please hold the line, your call is important to us.” It’s a sentence we’re all frustratingly familiar with. Just as familiar as we are with standing in line at the supermarket or post office, with the other queues seeming to move much faster than the one we happen to be in. Thankfully, mathematics can help. Queueing theory studies such situations mathematically, and tries to find solutions that minimise the average customer waiting time while also limiting the average time a queue server remains idle. This double constraint makes the problem a difficult one. An additional source of difficulty is the randomness involved. Customers usually do not arrive at regular intervals, but their arrival times are what is called a stochastic process. Coming up with a general formula that provides a solution for such stochastic problems is generally difficult, and sometimes even impossible. Recently my uncle Arie Hordijk and I studied such a queueing problem, and came up with a solution based on the movements of a ball on a billiard table…

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What is life? This question is still much debated in science. After the discovery of the structure of DNA by Watson and Crick in 1953, and the more recent advances in DNA sequencing technology, living organisms have become primarily viewed as being defined by their genes. However, there is more to life than genetics alone. In fact, a more “holistic” view is emerging in which the essence of life is considered to reside in the complex collection of chemical reactions that enable an organism to grow, repair, and reproduce itself. In other words, life as a network of self-sustaining chemical reactions. This alternative view could have important consequences for many areas of science, for example the way we might treat diseases like cancer, search for possible life on other planets or grow artificial donor organs. And now there is mathematical evidence that at least one particular living organism (the well-studied bacterium E. coli) is indeed such a self-sustaining reaction network, thus formally supporting this alternative view of life.

Read the full article on The Naked Scientists.

The internet is buzzing with claims that there has been a significant recent increase in seismic, volcanic, and atmospheric activity on our planet, and there seems to be a specific emphasis on the years 2012 and beyond. Suggested causes for such an increase include global warming having an effect on these earth activities, deliberate geo-engineering, changes in solar activity and/or cosmic radiation, and an as yet unknown or undisclosed disturbance within our solar system. However, a simple analysis of relevant and publicly available data provides surprisingly little support for such claims.  [Last update: 29 Dec 2015]

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On the night of 12-13 August, I took some friends up to the top of a small mountain to watch the annual Perseid meteor shower. This year was predicted to be particularly good, largely due to the peak of the shower being just a few days before a new moon, making for optimal (i.e., dark) viewing conditions. The weather forecast called for a clear night sky, so we were all excited to watch this show (with an expected 50-100 meteors per hour) from a high and dry vantage point away from the city lights. Continue Reading

The Living Set

Life is a self-sustaining network of chemical reactions. A living system produces its own components from basic food sources in such a way that these components maintain and regulate the very chemical network that produced them. Based on this notion of life, several models of minimal living systems were developed during the 1970s. While these models captured an essential aspect of the organization of living things, however, they could not directly explain how such systems emerged from a primordial soup of basic chemicals.

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Holland is a very flat country without any mountains or rocky areas. Yet in the northern part of this little land you will find megalithic structures with big boulders, some weighing more than 20 tons, stacked on top of each other. For a long time, the purpose of these structures and the origin of these boulders was a mystery. And even though archaeologists now have a better understanding of these dolmens, or “hunebedden” as they are called in Dutch, many of the questions surrounding them remain only partially answered.

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Evolution is just a theory.” This claim, often made by creationists, is clearly based on a confusion of the scientific meaning of the word “theory” with its meaning in common language. We can forgive confused creationists, though, as most of them unfortunately know very little about science (all the more important it is for us to explain our research in a clear way). However, when scientists themselves make such mistakes, perhaps we should be less forgiving.

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Language is something we take for granted; we use it every day and could not live without it in today’s world. However, languages are not static but, rather, evolve. While the differences between American and British English are manageable, for example, reading Shakespeare in its original form poses some challenges — and reading the original Beowulf is almost impossible. Like biological species, languages change over time and sometimes “speciate” to give rise to several descendant languages.

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[Note: This post is a modified and updated version of my earlier guest commentary on NPR 13.7 cosmos & culture]

For a long time, the origin of life was not considered a scientifically relevant problem. In fact, it was believed that life arises spontaneously all the time. Only after Louis Pasteur’s experimental demonstration that all life comes from other life, and the publication of Charles Darwin’s theory of evolution by natural selection (both around the middle of the 19th century), did the ultimate origin of life become a scientific question. However, it took (almost) another century before the first real scientific steps towards actually solving the problem were taken. Continue Reading

Standard economic theory assumes that humans behave rationally and are able to objectively calculate the value (or cost) of the different choices they are presented with. In fact, we pride ourselves on our rationality. Different from the animals, we humans have the unique capacity for logical thought and rational decision making. Or do we?

Read the full article on NPR 13.7 cosmos & culture