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Jotun gave 2 talks [31.5 1.6]
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
2 Distinguished Speakers: Wim Hordijk and Dave Swofford
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.
BREAK
- 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
Extreme Reading – status report
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
and
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:
Atmosphere (air)
Hydrosphere (water)
Lithosphere (earth)
Biosphere (life)
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.
Jotun Talk
And I will give a talk on birth-death processes and applications as well to DTC today at 4PM. If you somehow still have a choice between my and Tanja’s talk, you should go for Tanja’s talk. She know what she is talking about. I just produce sounds and metaphors.
My prelimenary slides can be found here:
https://www.dropbox.com/s/vrfxqi66nlo0skd/BD%20Multigene.DTC.9.3.17.pptx?dl=0
Interesting TALK!!
Department Seminar, Large Lecture Theatre (LG.03) Department of Statistics, Wednesday 8th March, 4.00 pm – 5.00 pm
Speaker: Professor Tanja Stadler, ETH Zürich, Switzerland
Title: A phylodynamic trip through the tree of life: From Ebola over Tuberculosis to Penguins and Murine stem cells
Abstract: Genetic sequencing data contain a fingerprint of past evolutionary and population dynamic processes. Phylogenetic methods infer evolutionary relationships — the phylogenetic tree — between individuals based on their genetic sequences. Phylodynamics aims to understand the population dynamic processes — such as epidemiological, macroevolutionary or developmental processes — giving rise to the phylogenetic tree. I will present the mathematical and computational aspects of our recently developed phylodynamic tools. Then I will focus on epidemiological applications, shedding light on the Ebola outbreak in West Africa and the spread of drug resistant Tuberculosis. Second, I will discuss a macroevolutionary study on the radiation of penguins. Last, I will explain how we recently adopted phylodynamic tools to study stem cell biology.
HEIN RESEARCH 