Archive for the ‘life’ Category

Trip to the US

October 5, 2015

Last week I visited a few places in the US. My first stop was Morgantown, West Virginia where my host was Casian Pantea. There I had a lot of discussions with Casian and Carsten Conradi on chemical reaction network theory. This synergized well with the work I have recently been doing preparing a lecture course on that subject which I will be giving in the next semester. I gave a talk on MAPK and got some feedback on that. It rained a lot and there was not much opportunity to do anything except work. One day on the way to dinner while it was relatively dry I saw a Cardinal and I fortunately did have my binoculars with me. On Wednesday afternoon I travelled to New Brunswick and spent most of Thursday talking to Eduardo Sontag at Rutgers. It was a great pleasure to talk to an excellent mathematician who also knows a lot about immunology. He and I have a lot of common interests which is in part due to the fact that I was inspired by several of his papers during the time I was getting into mathematical biology. I also had the opportunity to meet Evgeni Nikolaev who told me a variety of interesting things. They concerned bifurcation theory in general, its applications to the kinds of biological models I am interested in and his successes in applying mathematical models to understanding concrete problems in biomedical research such as the processes taking place in tuberculosis. My personal dream is to see a real coming together of mathematics and immunology and that I have the chance to make a contribution to that process.

On Friday I flew to Chicago in order to attend an AMS sectional meeting. I had been in Chicago once before but that is many years ago now. I do remember being impressed by how much Lake Michigan looks like the sea, I suppose due to the structure of the waves. This impression was even stronger this time since there were strong winds whipping up the waves. Loyola University, the site of the meeting, is right beside the lake and it felt like home for me due to the combination of wind, waves and gulls. The majority of those were Ring-Billed Gulls which made it clear which side of the Atlantic I was on. There were also some Herring Gulls and although they might have been split from those on the other side of the Atlantic by the taxonomists I did not notice any difference. It was the first time I had been at an AMS sectional meeting and my impression was that the parallel sessions were very parallel, in other words in no danger of meeting. Most of the people in our session were people I knew from the conferences I attended in Charlotte and in Copenhagen although I did make a couple of new acquaintances, improving my coverage of the reaction network community.

In a previous post I mentioned Gheorghe Craciun’s ideas about giving the deficiency of a reaction network a geometric interpretation, following a talk of his in Copenhagen. Although I asked him questions about this on that occasion I did not completely understand the idea. Correspondingly my discussion of the point here in my blog was quite incomplete. Now I talked to him again and I believe I have finally got the point. Consider first a network with a single linkage class. The complexes of the network define points in the species space whose coordinates are the stoichiometric coefficients. The reactions define oriented segments joining the educt complex to the product complex of each reaction. The stoichiometric subspace is the vector space spanned by the differences of the complexes. It can also be considered as a translate of the affine subspace spanned by the complexes themselves. This makes it clear that its dimension s is at most n-1, where n is the number of complexes. The number s is the rank of the stoichiometric matrix. The deficiency is n-1-s. At the same time s\le m. If there are several linkage classes then the whole space has dimension at most n-l, where l is the number of linkage classes. The deficiency is n-l-s. If the spaces corresponding to the individual linkage classes have the maximal dimension allowed by the number of complexes in that class and these spaces are linearly independent then the deficiency is zero. Thus we see that the deficiency is the extent to which the complexes fail to be in general position. If the species and the number of complexes have been fixed then deficiency zero is seen to be a generic condition. On the other hand fixing the species and adding more complexes will destroy the deficiency zero condition since then we are in the case n-l>m so that the possibility of general position is excluded. The advantage of having this geometric picture is that it can often be used to read off the deficiency directly from the network. It might also be used to aid in constructing networks with a desired deficiency.

Rereading ‘To the Lighthouse’

August 23, 2015

There are some statements I started to believe at a certain distant time in my life and which I have continued to accept without further examination ever since. One of these is ‘the English-language author who I admire most is Virginia Woolf’. Another is obtained by replacing ‘English-language author’ by ‘author in any language’ and ‘Virginia Woolf’ by ‘Marcel Proust’. At one point in her diary Virginia Woolf writes that she has just finished reading the latest volume of ‘A la Recherche du Temps Perdu’ which had recently been published. Then she writes (I am quoting from memory here) that she despairs of ever being able to write as well as Proust. Perhaps she was being too modest at that point. Until very recently it was a long time since I had read anything by Woolf. I was now stimulated to do so again by the fact that Eva and I were planning a trip to southern England, including a visit to St. Ives. For me that town is closely associated with Woolf and it is because of the connection to her that I was motivated to visit St. Ives when I spent some time in Cornwall several years ago. (Here I rapidly pass over the fact, without further comment, that the author with the widest popular success whose books have an association with St. Ives is Rosamunde Pilcher.) The other aspect of my first trip to Cornwall which is most distinct in my memory is missing the last bus in Land’s End and having to walk all the way back to Penzance where I was staying. We visited Land’s End again this time but since I did not want miss the bus again I did not have time to visit the ‘Shaun the Sheep Experience’ which is running there at the moment. As a consolation, during a later visit to Shaun’s birthplace, Bristol, I saw parts of the artistic event ‘Shaun in the City’ and had my photograph taken with some of the sculptures of Shaun.

When I go on a holiday trip somewhere I often like to take a book with me which has some special connection to the place I am going. Often I have little time to actually read the book during the holiday but that does not matter. For Cornwall and, in particular, St. Ives the natural choice was ‘To the Lighthouse’. That novel is set in the Isle of Skye but it is well known that the real-life setting which inspired it (and the lighthouse of the title) was in St. Ives. This lighthouse, Godrevy Lighthouse, cost a little over seven thousand pounds to build, being finished in 1859. In 1892, on one of two visits there, the ten year old Virginia signed the visitors book. The book was sold for over ten thousand pounds in 2011. So in a sense the little girl’s signature ended up being worth more money than the lighthouse she was visiting. Of course, due to inflation, this is not a fair comparison. Looking on my bookshelves at home I was surprised to find that I do not own a copy of ‘To the Lighthouse’. On those shelves I find ‘The Voyage Out’, ‘Jacob’s Room’, ‘Moments of Being’ and ‘Between the Acts’ but neither ‘To the Lighthouse’ nor ‘The Waves’. Perhaps I never owned them and only borrowed them from libraries. I have a fairly clear memory of having borrowed ‘To the Lighthouse’ from the Kirkwall public library. I do not remember why I did so. Perhaps it was just that at that time I was omnivorously consuming almost everything I found in the literature section in that library. Or perhaps it had to do with the fact that lighthouses always had a special attraction for me. An alternative explanation for the fact I do not own the book myself could be that I parted with it when I left behind the majority of the books I owned when I moved from Aberdeen to Munich after finishing my PhD. This was due the practical constraint that I only took as many belongings with me as I could carry: two large suitcases and one large rucksack. I crossed the English Channel on a ferry and I remember how hard it was to carry that luggage up the gangway due to the fact that the tide was high.

I find reading ‘To the Lighthouse’ now a very positive experience. Just a few paragraphs put me in a frame of mind I like. I have the feeling that I am a very different person than what I was the first time I read it but after more than thirty years that is hardly surprising. I also feel that I am reading it in a different way from what I did then. I find it difficult to give an objective account of what it is that I like about the book. Perhaps it is the voice of the author. I feel that if I could have had the chance to talk to her I would certainly have enjoyed it even if she was perhaps not always the easiest of people to deal with. Curiously I have the impression that although I would have found it extremely interesting to meet Proust I am not sure I would have found it pleasant. So why do I think that I may be appreciating aspects of the book now which I did not last time? A concrete example is the passage where Mrs Ramsay is thinking about two things at the same time, the story she is reading to her son and the couple who are late coming home. The possibility of this is explained wonderfully by comparing it to ‘the bass … which now and then ran up unexpectedly into the melody’. I feel, although of course I cannot prove it, that I would not have paid much attention to that passage during my first reading. The differences may also be connected to the fact that I am now married. Often when I am reading a book it is as if my wife was reading it with me, over my shoulder, and this causes me to pay more attention to things which would interest her. A contrasting example is the story about Hume getting stuck in a bog. I am sure I paid attention to that during my first reading and it now conjured up a picture of how I was then, perhaps eighteen years old and still keen on philosophy. After a little thought following the encounter with the story it occurred to me that I knew more of the story about Hume, that he was allegedly forced to say that he believed in God in order to persuade an old woman to pull him out. This extended version is also something I knew in that phase of my life, perhaps through my membership in the Aberdeen University philosophy society. On the other hand this story does come up (at least) two more times in the book and it is a little different from what I remember. What the woman forced him to do was to say the Lord’s Prayer.

I came back from England yesterday and although I did not have much time for reading the book while there I am on page 236 due to the head start I had by reading it before I went on the trip. The day we went to St. Ives started out rainy but the weather cleared up during the morning so that about one o’ clock I was able to see Godrevy lighthouse and look at it through through my binoculars. They also allowed me to enjoy good views of passing gannets and kittiwakes but I think I would have been disappointed if I had made that trip without seeing the lighthouse.

Arrival in Bretzenheim

May 1, 2015

Since I moved to Mainz two years ago my wife has remained in Berlin and we have been searching for a suitable place to live in Mainz or its surroundings. The original plan was to buy a piece of land on which we could build a house. This turned out to be much more difficult than we expected. The only land within our financial horizons was in small villages with almost no infrastructure or had other major disadvantages from our point of view. Eventually, after wasting a lot of time and effort, we stopped searching in the surroundings and looked for something in Mainz itself. Of course this was not easy but eventually we decided to buy a house (still to be built) within a small housing scheme in the district of Mainz called Bretzenheim. There is very little land available in Mainz and the scheme where we will be living is an example of the way in which the few remaining open spaces are being filled up, driven by the high property prices. The house was finished in March and I moved in on a provisional basis on 1st April, giving up my appartment, exactly two years after starting my job in Mainz. (Goodbye Jackdaws! The first birds I saw in what will be our garden were a Carrion Crow, which I am not taking as a bad omen, and a Black Redstart.) Our belongings left Berlin on 16th April and arrived in Mainz on 17th. Eva came to Mainz definitively on the 16th. So now there can be no doubt that a new era has begun for us.

The new house is conveniently situated. From there I can walk to the mathematics institute in 20 minutes and to the main train station in half an hour. It is near the end of a tram line coming from the station. Very close to where the houses have been built a Merovingian grave was found. When the garden centre a little further up the hill was being built the grave of a Merovingian warrior was found who had been buried with his horse. It is just as well for us that the archeologists did not dig too deep or we might have had to wait a long time before we could move in. Whenever you dig a hole in Mainz you are in danger of encountering a distant past and potential problems with the archeology department of the city. To show what can happen I will give an example. In the district of Gonsenheim there is a small stream, the Gonsbach. At some time when progress was fashionable the winding stream was straightened. Later an EU directive came into force which said that streams like this which had been straightened had to be made winding again, for ecological reasons, within a certain number of years. By now the deadline has been reached, or almost reached for the Gonsbach, and the city has started measures to attempt to comply with the directive. They started to dig and found … a Roman settlement. The work had to be stopped, for archeological reasons. So now, as far as I know, the archeological and ecological regulations and the city officials representing them are in deadlock.

Since I am British it is a curiosity for me that one suggested origin of the name Bretzenheim is that it is named after the Britons. It has been suggested that it could be identified with a certain vicus Brittaniae where the Roman Emperor Severus Alexander was murdered in the year 235. The evidence for this seems limited and an alternative hypothesis says that it was named after a locally important man called Bretzo. I cannot imagine what the Britons would have been doing there. Another theory is that the emperor was murdered in Britain and not in Mainz.

Hello Mainz

April 18, 2013

This post is in some sense dual to the earlier one ‘goodbye to Berlin‘. To start with I can confirm that there is no shortage of Carrion Crows (and no Hooded Crows) in Mainz. When I arrived here and was waiting for my landlord to come and let me into my flat I saw some small and intensely green spots of colour in a row of trees in front of me. I knew the source of these – they were what I could see of Ring-Necked Parakeets. I have known for a long time that these birds live wild in England but it was only relatively recently, in the course of my activity looking for jobs, that I realised they were so common in parts of Germany. While in Heidelberg for an interview I observed a big number of them making a lot of noise in a small wood opposite the main railway station. I also saw some of them when I came to Mainz for the interview which eventually led to my present job. In my old institute in Golm I often used to see Red Kites out of my office window. It occurred to me that these might be replaced by Black Kites in Mainz. During my first weekend here I was walking across the campus of the university when I saw a large and unfamiliar bird of prey approaching me. When it came closer I realised that it was a Black Kite. I enjoyed the encounter. Since that I have also seen one from my office window. The Red Kite is a beautiful bird but for some reason I feel closer to its dark relative. It gives me a feeling of the south since the first place I saw these birds many years ago was in the Camargue.

Eva and I have been using Skype to maintain contact. I feel that this big change in our life has not been without benefits for our communication with each other and when I was home last weekend it was a richer experience than many weekends in the last few years. I appreciate the warm welcome I have had from my colleagues here in Mainz and my first days here, while sometimes a bit hectic, have been rewarding. Breaking the routine of years opens up new possibilities. I assured myself that I will not completely have to do without interesting biological talks here by going to a lecture by Alexander Steinkasserer on CD83. This taught me some more about dendritic cells for which this surface molecule is an important marker.

This is the first week of lectures here and yesterday brought the first concrete example of the new direction in my academic interests influencing my teaching, with the start of my seminar on ‘ordinary differential equations in biology and chemistry’. The first talk was on Lotka-Volterra equations. The subjects to be treated by other students in later lectures include ones a lot further from classical topics.

Goodbye to Berlin

February 1, 2013

For this post I could not resist the temptation to borrow the title of Christopher Isherwood’s novel although what I am writing about here has very little to do with his book. The connection of the title to the content is that I will soon be leaving Berlin after living here more than fifteen years. I have accepted a professorship at the University of Mainz and I will move there in April. The first time I came to Berlin I landed at Tegel airport and I interpreted the Hooded Crow I saw beside the runway as a good omen. This requires some explanation. In those days the Hooded Crow (Corvus corone cornix) was a subspecies of the Carrion Crow. In the meantime it has been promoted to the rank of a species but that will not concern me here – I am not sure whether I feel I should congratulate it on receiving this honour. It differs from the nominate form (according to the old classification) by having a grey body while Corvus corone corone (Carrion Crow in the narrower sense) is all black. These two forms have the classical property of subspecies that they are allopatric. In other words they occur in more or less disjoint regions. On the boundary between the regions there is little interbreeding. The Orkney Islands where I grew up belong to the land of the Hooded Crow. Most of Great Britain and in fact most of Western Europe belong to the domain of the Carrion Crow. Even Aberdeen, where I studied and did my PhD, belongs to the land of the Carrion Crow. This helps to explain why I associate the Hooded Crow with ‘home’ and the Carrion Crow with ‘foreign parts’. It also has to do with the fact that there was a Hooded Crow which nested regularly in a garden near where I grew up in Orkney. I would climb the tree from time to time to keep an eye on the development of the brood and ring the chicks at the right moment. For these reasons the bird in Tegel seemed to tell me I was coming home. Now I am daring to venture once again (and probably for most of the rest of my life) into the land of the Carrion Crow.

When leaving a place it is natural to think about the good things which you experienced there. What were the best things about Berlin for me? The best thing of all is that Berlin was where I met my wife Eva. Eichwalde, where she lived at that time and where we both live now, has a very special feeling for me which will never go away. (Just for the record, we do not really live in Eichwalde but that is where the nearest train station is, with the result that the platform of the station there has something of the gates of Paradise for me.) Of course I cannot fail to mention the Max Planck Institute for Gravitational Physics which has provided me with a scientific home during all that time. I am grateful to the successive leaders of the mathematical group there, J├╝rgen Ehlers and Gerhard Huisken, for the working and social environment which they created and maintained. Another important thing about Berlin I will miss is the contact with its excellent research in biology and medicine. I have spent many valuable hours attending the Berlin Life Science Colloquium and I feel very attached to the Paul Ehrlich lecture hall where it usually takes place. The wooden seats are hard but the interest of the lectures was generally more than enough to make me forget that. I will also miss the stimulating atmosphere of the group of Bernold Fiedler at the Free University, which has been a source of a lot of intellectual input and a lot of pleasure.

This is perhaps the moment to say why I am leaving Berlin. Ever since I was a student I have felt a strong allegiance to mathematics. As a child I was concerned with metaphysical questions and later I got interested in physics as the most fundamental part of science. During my undergraduate study I realised that mathematics, and not physics, was the right intellectual environment for me. A key experience for me was that through my study plan I ended up doing two courses on Fourier series, a subject which was new to me, at the same time. One was in physics and one in mathematics. The contrast was like night and day. This may have had something to do with the abilities of the individual lecturers concerned but it was mainly due to essential differences between mathematics and physics. By the end of my studies I had specialized in mathematics and my commitment to that subject has remained constant ever since.

For a long time my strongest connection to mathematics concerned intrinsic aspects of the subject. The significance of applications for me was as a good source of mathematical problems. This has changed over the years and I have become increasingly fascinated by the interplay between mathematics and its applications. At the same time the focus of my interest has moved from mathematics related to fundamental physics to mathematics related to biology and medicine. This change has led to a discrepancy between the research I want to do and the research area of the institute where I work. A Max Planck Institute is by its very nature focussed on a certain restricted spectrum of subjects and this is not compatible with a major change of research direction of somebody working there. This is the reason that I started applying for jobs which fitted the directions of work where my new interests lie. The move to Mainz is the successful endpoint of this process. Moving from a Max Planck Institute to a university will naturally involve spending more time on teaching and less time on research. This does not dismay me. The most important thing is that I will be doing something I believe in. Teaching elementary mathematics and analysis, apart from establishing the basis needed for doing research, is something whose intrinsic value I am convinced of.


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