The aim of this club is to read the papers that everyone keeps citing but which few people have read. We plan to read a paper every third week for the next 20 years.
We tend to meet Wednesday mornings, and tend to announce the papers we will read ahead of time. Everyone is welcome: if a paper sounds interesting to you, please come by.
This reading group used to be organised on facebook. The old page can be found here.
- Mathematical Chemistry and Chemoinformatics, by A. Kerber et al. (summary part I and part II)
- Phylogeny: Discrete and random processes in evolution, by M. Steel (review published on SIAM News Blog: part I, part II, part III)
- Bayesian Methods in Structural Bioinformatics, edited by
T. Hamelryck, K. Mardia and J. Ferkinghoff-Borg
Phylogenetics, by C. Semple and M. A. Steel
- Protein Physics – A course of lectures, by A. V. Finkelstein and O. Ptitsyn (summary slides)
This book club is an endeavour to broaden our horizons and critically engage with good writing from across the humanities. We intend to go through a book per term, and tend to meet roughly once every 3rd week to discuss new sections of whatever book we are currently going through. Past books that we have read include:
- The General Theory of Employment, Interest and Money, by John Maynard Keynes
- The Qurʼān – A New Annoteted Translation, by Arthur J. Droge
- On Politics, by Alan Ryan
- Capital in the Twenty-First Century, by Thomas Piketty
The present version can be found here:
The author – Istvan Miklos – believes he will always be ahead of the readers in writing. We would then write a review that would be published about the same time as the book was published and we put an extended report on this page:
We also give a summarizing lecture when we have finished the book. Earlier when we did this, we met every 2nd day doing about 20 pages each time, but it can depend on the individual book. We did a similar thing to Mike Steels 2016-book, which I believe was beneficial to both authors and readers.
The ideal number of participants in such a group is 3-5. It would have to be online since I will be Israel. I like to choose a time that is either starting or ending of working day so it interpheres minimally with work. If you know somebody interested in participating in this, please tell me. If it proves a crappy book, we will stop reading, but that is not what I expect.
What did we learn at: Origins of Life Conference – ISSOL17
- written by Jotun Hein
Overall attending the conference was a very useful since I haven’t been to an Origins Conference for more than 5 years and since I have stopped teaching Origins, in general, I don’t read so much on the chemical nitty-gritty.
The was much interesting material at the conference and of course, I met some people from Oxford, that I had never seen before working on catalysis.
The first day [Monday] was mainly devoted to Exoplanets and Meteorites/Comets/Transport of Organic Matter.
The second day [Tuesday] was the physical condition on earth 4 Billion or so years ago.
The third 1/2 day [Wednesday] was dedicated to the first chemical steps towards life.
The last 2 days were on the early evolution of life and more theoretical models.
Origins of Life studies are clearly getting a lot more attention/funding now. Computational studies play a much larger role. There are much more serious attempts at synthesizing life de Novo. But I can’t say there is a single convincing scenario for planet Earth. Exoplanets clearly are very exciting, but there is no way to study the architecture of life so far away [barring SETI – that was unrepresented at ISSOL] so all one can hope for a couple of centuries is observation of convincing bio-signatures.
There seemed to have been a lot of organizational problems. I didn’t know where to go and sleep and ended up sitting all night in the airport (while paying for a room at UCSD). Another person I met had experienced something else. The conference dinner was not very different from the free dinner and there were no arrangements of where to go. Anybody going to conferences/workshops knows that many connections are made at the evening socializing.
I, William Kurdahl and possibly some from the Oxford Catalysis will give an informal orientation about the meeting Tuesday, August 29th 3 PM in the small lecture room in The Department of Statistics, Oxford.
William and I both chose 5 papers/presentations that we liked.
These are the slides in progress:
Combinatorics of Recombination: https://www.dropbox.com/s/magvyy1jkkgin63/graduate%20lecture%201.6.17%20recombi.pptx?dl=0
Research Collaboration: https://www.dropbox.com/s/gveaj5rwp0f7eok/A%20Few%20Things.pptx?dl=0
Topics – both devoted to modelling in evolution: Models of Origins of Life & Phylogenetic
Time: Friday June 9th 2.00 PM – 4.30 PM
Venue: Department of Statistics, Oxford, Large Lecture Theatre
- 2.00 PM Generality and Robustness of the SVDQuartets Method for Phylogenetic Species Tree Estimation (Swofford)
Methods for inferring evolutionary trees based on phylogenetic invariants were first proposed nearly three decades ago, but have been virtually ignored by biologists. A new invariants-based method for estimating species trees under the multispecies coalescent model was recently developed by Julia Chifman and Laura Kubatko, building on earlier work by Elizabeth Allman, John Rhodes, and Nicholas Eriksson. This method comes from algebraic statistics and uses singular value decomposition to estimate the rank of matrices of site pattern frequencies. Although the approach shows great promise, its performance on empirical and simulated data sets has not been adequately evaluated.
I will give a general introduction to the SVDQuartets method and present some results from a simulation study currently in progress (collaboration with Laura Kubatko and Colby Long) that demonstrate that SVDQuartets is potentially highly robust to deviations from the standard evolutionary models assumed by other species-tree estimation methods.
- 3.30PM Autocatalytic Sets and the Origin of Life (Hordijk)
The main paradigm in origin of life research is that of an RNA world, where the idea is that life started with one or a few self-replicating RNA molecules. However, so far nobody has been able to show that RNA can catalyze its own template-directed replication. What has been shown experimentally, though, is that certain sets of RNA molecules can mutually catalyze each other’s formation from shorter RNA fragments. In other words, rather than having each RNA molecule replicate itself, they all help each other’s formation from basic building blocks, in a self-sustaining network of molecular cooperation.
Such a cooperative molecular network is an instance of an autocatalytic set, a concept that was formalized and studied mathematically and computationally as RAF theory.This theory has shown that autocatalytic sets are highly likely to exist in simple polymer models of chemical reaction networks, and that such sets can, in principle, be evolvable due to their hierarchical structure of many autocatalytic subsets. Furthermore, the framework has been applied succesfully to study real chemical and biological examples of autocatalytic sets.
In this talk I will give a general (and gentle) introduction to RAF theory, present its main results and how they could be relevant to the origin of life, and argue that the framework could possibly also be useful beyond chemistry, such as in analyzing ecosystems or even economic systems.
WINE IN COMMON AREA AFTER TALKS
Speaker: Stephen Altschul
Title: Dirichlet Mixtures, the Dirichlet Process, and the Topography of Amino Acid Multinomial Space
Venue: Tuesday May 23rd 3.30 PM Department of Statistics, Lecture Theatre (Lower Ground)
Abstract: The Dirichlet Process is used to estimate probability distributionsthat are mixtures of an unknown and unbounded number of components.Amino acid frequencies at homologous positions within related proteins have been fruitfully modeled by Dirichlet mixtures, and we have used the Dirichlet Process to construct such distributions. The resulting mixtures describe multiple alignment data substantially better than do those previously derived. They consist of over 500 components, in contrast to fewer than 40 previously, and provide a novel perspective on protein structure. Individual protein positions should be seen not as falling into one of several categories, but rather as arrayed near probability ridges winding through amino-acid multinomial space.
The slides will be made available after the talk.
Comment: Stephen Altschul has finally proven that I can’t add 2 and 2. I have attended Altschul Dinners at my College [University College, Oxford] and never thought of connecting the two words Altschul and Altschul despite their obvious similarity. It is in honour of Stephen’s grandmother, whose brother was Arthur Lehman Goodhart and Master of UNIV 1951–63.
Today we hosted a talk by Gereon Kaiping from Leiden University. The talk went through the pipeline his group uses to go from linguistic data collected in the field to reconstructed phylogenetic trees of languages produced using mostly off-the-shelf tools. There was a lively discussion with an audience of linguists, bioinformaticians, and statisticians.
Gereon has kindly made his slides available, which can be viewed below, or downloaded.
There is a famous danish sketch called “Jarl Kakadue” from the show “Casper og Mandrilaftalen”. In the sketch, Jarl explains how he completed an iron man, but instead of running a marathon, he got a good nights sleep instead.
“But isn’t that cheating?” to host asks, to which Jarl replies “No, because such a run takes a couple of hours, but a proper nights sleep is at least 8 hours.”
As the sketch goes on, more and more of the exercise gets replaced. The full thing can be seen here: (in danish)
The concept of Extreme Reading is also a modified iron man in the following sense:
instead of swimming, we read a book.
instead of cycling, we summarise the book
instead of running a marathon, we run half a marathon (over 3 days)
So each day, we read for a couple of hours, ran 7 kilometers, read some more and then we summarized the book for each other and discussed it.
The book i question was “The origin and nature of life on earth – the emergence of the fourth biosphere” – by Eric Smith and Harold J. Morowitz
Unfortunately, the book is rather wordy and not very mathematical. The individual sections are nicely structured, but the book lacks an main message and sense of direction.
This is puzzling, since Morowitz other books are usually shorter and more precise. However, Morowitz died before the book was published, was very weak the last decade, published little in that period and was in general very short in his formulations, while this book is very long (at times lenghty). It is unclear how much Morowitz contributed to the present book.
This book is 600 pages long and consists of 8 chapters. This is a very hard topic to write a coherent book about and the chapters are quite free-standing contributions to describing or explaining the theory of life.
Eric Smith gave a talk somewhat based on the book, which can be found here: https://www.youtube.com/watch?v=0cwvj0XBKlE
The 4 geospheres are:
The point of the title is that life should be though of as a planetary property. However, the point seems more philosophical than scientific, which is the case with many of the subtle points in the book.
A longer summary will be added later.
Overall, the project was a success. We managed to run and read a lot. It is a very satisfying feeling to be both mentally and physically exhausted and we can definitely recommend similar undertakings.