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# Category Archives: Science

## Skype Book Discussion Group in “Computational Complexity of Sampling”

The present version can be found here:

http://renyi.hu/~miklosi/CCC/ComputationalComplexityOfCountingAndSampling.pdf

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:

https://heingroupoxford.com/learning-resources/lectures/

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.

## 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.

## Penrose is Great

We have started a reading Roger Penrose: The Road to Reality which so far is a subperp book. Normally we Skype-meet Tuesday morning AM 6.30 for 60-90 minutes. We normally cover 20-40 pages per session. In coming week we will have done 5 chapters:

**1 The roots of science **

**2 An ancient theorem and a modern question **

**3 Kinds of number in the physical world **

**4 Magical complex numbers **

**5 Geometry of logarithms, powers, and roots **

In Jotun’s view the book is great balance for formulas, intuitive explanations and historical backgrounds.

## About the Science Book Club

*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 byT. 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)

## Graph Grammar Library

Summary of the paper “The Graph Grammar Library – a generic framework for chemical graph rewrite systems” by Flamm et al.

The paper explains how a C++ package works, which implements graph grammar rewriting rules for chemical reaction networks. There are some other chem(o)informatics stuff in the package as well.

The main story of the paper is that Yadav et al. requested a package like GGL, which is now available.

Most of it seems quite logical/intuitive based on the what it tries to do.

The software translates to/from SMILES at the beginning and end, but everything is done using graphs.

For more information and guides on how to use the software, see: http://www.tbi.univie.ac.at/software/GGL/

## Mathematical Chemistry and ChemoInformatics part II

Jotun Hein and William Kurdahl will review two books: Leach and Gillet (2010) Introduction to Chemoinformatics and chapters from Faulon Handbook of Chemoinformatics Algorithms (2007). Additionally briefly summarize key papers on Graph Grammars, Reaction prediction and related topics. The talk ends with an attempt to identify projects in chemoinformatics that would be worth it to work on.

The slides can be found here: http://tinyurl.com/j28y67s

Thursday December 8th 10AM to noon LG Department of Statistics

## EVOLUTION of PROTEIN STRUCTURE

Michael Golden has worked on an angle (psi,phi) diffusion model of protein evolution and it has turned out well. The first paper was submitted yesterday and a talk is given on Thursday December 1st 3.30Pm in The Department of Statistics.

Preliminary slides can be found here: http://tinyurl.com/PhiPsiEvolution