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# Category Archives: Science

## 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

## Theory, Modelling and Simulation in Origins of Life Studies

“Theory, Modelling and Simulation in Origins of Life Studies”

By Peter V. Coveney, Jacob B. Swadling, Jonathan A. D. Wattisb and H. Christopher Greenwell

Gives a brief summary of the history of the fields and the major hypothesis out there and some of the current work being done. The most famous experiment being the Urey-Miller experiment, which is still relevant. Possibilities for life arising consist of the pre-biotic soup, black smokers, alkaline vents and “outer space origin”.

The article describes the RNA world and homochiralization, as well as gives a brief comparison between the modelling methods of Quantum Mechanics (typically density functional theory) and classical Molecular dynamics.

Two quotes from the review:

“In particular, whilst symmetry-breaking is exhibited by the hexamer model, it is not possible within the tetramer model. This serves as a warning to theoreticians who wish to deduce the properties of a complex model simply by analysing a significantly reduced version.”

“The intrinsic value of modelling cannot be overstated”

Overall, the article contains a lot of references to further reading but also emphasises some chemical research whose relation to OoL is unclear to this reader.

The paper comes with a slideshow presentation covering the same material using different graphics etc.