RT @qikipedia: Politics is the art of looking for trouble, finding it everywhere, diagnosing it incorrectly and applying the wrong remedies… 3 days ago

The latin phrase seems apt for recent times. It has taken some time and effort to return to some equilibrium within a complex work place. This has been under-pinned by a resolute commitment to the honesty, integrity and many times nobility of the team environment (despite pernicious effects of increasingly complex interactions of personalities).

This slow but progressive resolve has been increasingly stressed and begins to erode in the face of totalitarian behaviour of the current government. The next few months will push people to the edge of a phase transition. I hope we all survive unscathed.

We are all at the banks of the Rubicon. “Alea lacta est”, we will shout (the die is cast)…it has been so difficult to discern the truth, intent and course of current negotiations. There is escalating rhetoric. The tempest is furious, the vortex accelerating…hold fast some of us may still be left but will have the energy to rebuild what has taken years to build but hours to destroy…

I received this book as a gift. I enjoyed it. The author gives a personal account of his deep and continuous involvement in the development of methodology to extract, analyse and interpret mitochondrial DNA. We inherit our mitochondrial DNA from our mother. This tool is applied to understand our genetic ancestry.

The author explains the reliable, stable and reproducible nature of mitochondrial DNA. The collaborative and adversarial/argumentative nature of scientific progress. Mitochondrial DNA analysis stood the intense scrutiny and served as valuable insight. Ultimately, through a journey including exploration of the Last Tsar of Russia, the Pacific Islands, Cheddar Man the author weaves together a complex story of the genetic network/lineage of Europe and forays into the connecting the world.

The majority (95%) modern Europeans have descending from seven clan mothers. Mitochondrial DNA can be used as a molecular clock to determine the age of these ancestors. The author…

This book is targeted to Health Sciences. It is clearly written. It covers a broad range of topics. It is committed (nicely) to the use of SI units and has many worked examples. The depth is relatively shallow but it is a good introduction, The book presents important quantification and simplifies the mathematics to algebra (no explicit calculus) from classical physics.

The authors chapter on MRI was covered in more detail and was well written. One omission in the section on Safety was the interaction with implantable electronic devices: device malfunction, induced currents in orphan leads etc.

This is a very useful book. The emphasis is on understanding concepts using visualization provided by Mathematica.

I found the second half of the book difficult. This reflects my inexperience. However, it was interesting, particularly the discussion and explorations related to neural networks.

The exercises have answers at the end of the book and I look forward to accessing the notebooks referred to in the text. The book precedes version 9 but the code updating seems relatively straightforward.

The times they are a changing indeed. Neurochemistry, time and the most precious family support (my sole unwaivering allies) are working to restore and perhaps improve my outlook. I recently experienced a spike in mood, almost elation (something I had not experienced for years). Spike have rapid declines as well as steep upstrokes and this was no exception. However, the moments of clarity and focus allowed the accumulation of some optimism, resilience perhaps.

Homo sapiens emergence, still a blip on the earth’s timescale (order of 10^{-4}), heralded the extinction of the hardy and still longer timespan neandert(h)als more than 25000 years ago. The convergence of climatic change and loss of competitive advantage appear to have precipitated this erasure (genetic data suggesting little evidence for interbreeding). The neandertals were strong, but inflexible and less adaptive than homo sapiens. They were efficient hunters but used closed range limited scope and high risk weapons. They did not modify them. They were carnivores and there is no evidence they changed their diet, despite environmental circumstances changing. In contrast, homo sapiens showed adaptive behaviours: progressive refinement of tools, collective strategies for food gathering, diversification of diet. There was a major negative population pressure (bottleneck explaining the much more limited genetic variant relative to our simian relatives) but homo sapiens endured and neandertals did not. Almost certainly random factors and other factors were important influences and this reductionist story has limitations. However, adapt or die seems to be a simple inference to contemplate.

I am, sadly, in many ways more neandertal-like, than I care to acknowledge. The climate has changed and my pattern of responses have been narrow. However, I have sensed that the social milieu (in my case solely my family), neurochemical changes and perhaps internal capacity for more adaptation give me hope.

I never watched sport as a child or a young adult. This has changed. The video is symbolic of the joy of the unexpected.

This tree has shed its leaves…it is bare but stands defiantly waiting for warmer times…and so do I.
Peace to all.

Another puzzle from the NY Times Number Play:
Wouter throws three dice.These dice look just like ordinary dice, but their faces are numbered differently.The first die has the numbers 1, 1, 2, 2, 3 and 3 on it.The second die has the numbers 2, 2, 4, 4, 6 and 6 on it.And the third die has the numbers 1, 1, 3, 3, 5 and 5 on it.He then adds up the numbers he gets from rolling the three dice.What is the probability that the resulting number is odd?

I will have the naive assumption of uniform distribution of outcomes. The second die faces are all even and the third die all odd, hence their sum is always odd. Therefore, the probability the sum of the faces of the three dice is odd=probability die 1 is even =1/3.

Simulation of 10 one thousand throws of the dice are reassuring.

I explore a puzzle about arranging a set of integers (1,2,3,…14) in a circle such that the any pair of numbers next to each have the property that their sum is prime and the absolute difference is prime. I came across this from a tweet by Professor Strogatz (the link is here).

This is the “Travelling Salesman” problem in disguise. The mindless brute force approaches of testing permutations (all the pairs) and finding gives an insight into the scalability issue of this problem. The issue of whether a solution exists for the small scale was resolved by finding it! Whether it s unique is a harder but fortunately the enormity of comparisons can be whittled down.

After a little thought, the property defines the way in which the integers are linked. It is a bipartite graph as the odd numbers must link to even numbers. This can be seen…

This book tells the story of the discovery of the Higg’s boson, what it is, what its relevance is and the intensely human nature of this endeavour. The book provided my best insight into the Standard Model and where the Higg’s field and boson fit in. The author discusses the physics but puts it in context. The people involved and their contribution is truly amazing and the author explores the limitations of attributions and prizes (Nobel) for such collaborative endeavours. This amazing discovery was the culmination of progressive systematic rigorous progress, the creativity and imagination of many many people. Solving the puzzle of a consistent theory that provides an explanation for mass of particles, esp bosons, affected by the weak force was fascinating. The importance of chirality in this was another example (to me) of the amazing universe (perhaps part of multiverse) we inhabit. This Higg’s field/mechanism/boson: the name…

This is the follow up to Guesstimation. I found the range of questions interesting. I particularly enjoyed the astronomical and materials motivated questions. This book shows how thoughtful approximation and simple arithmetic can provide insights into the world around us and the limits imposed by physical laws and our perceptions.

I enjoyed the exploration of height of mountains, feeling trees with bullets, the death by netrinos from supernova, the hazards of space travel at close to light speed, the effects of tidal forces. The exploration of posited “green” solutions and behaviours was instructive.

I rushed through “Mathematical Physiology II” and have been reading the second volume of “Mathematical Biology II”.

Mathematical Physiology II

This book was beyond my capacity. However, it is well written. The detailed descriptions of the systems covered in this book are excellent, as are the companion diagrams. The circulation, heart, blood, respiratory system, endocrine system, renal system, gastrointestinal system, vision and hearing are covered. The mathematical models and analysis form motivation for imporving my knowledge and understanding. There is (understandable) overlap with the approaches of the Murray (Mathematical Biology). The importance of nondimensionalization, linearization and linear stability analysis are discussed. These approaches are repeatedly used to illustrate features of the models.

Mathematical Biology

I am half way through this book. This is rightly a classic and I am enjoying this second volume more than the first volume. The discussion of spatial patterns in a number of contexts and exploring…