Thursday, November 25, 2021

Role of quantum nuclear motion in biomolecular systems

 Total I am giving a talk, "Effect of quantum nuclear motion on hydrogen bonds in complex molecular materials" at Light-matter Interactions from scratch: Theory and Experiments at the Border with Biology 

Here are the slides

The talk provides a concrete example of the tutorial on constructing simple model Hamiltonians for complex materials that I give before the talk. It relates to the bio theme of the meeting through work on isotopic fractionation in proteins and the recent paper below. It makes use of the simple model that I talk about.

Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems

Chi-Yun Lin and Steven G. Boxer

Tuesday, November 23, 2021

Tutorial on modelling quantum dynamics in biomolecules

This week I am giving two (virtual) talks at a meeting

Light-matter Interactions from scratch: Theory and Experiments at the Border with Biology 

supported by the ICTP (International Center for Theoretical Physics) in Trieste.

In the ICTP tradition, one talk is a tutorial and the second talk is about my research.

Here are the slides for the tutorial on Effective Model Hamiltonians for Quantum Dynamics in Complex Molecular Materials. Feedback is welcome.

The research talk is about hydrogen bonding. I will post slides for that later.




Friday, November 19, 2021

Organ music: cells self-organise into organs

Biology involves many different scales. At each scale one considers what are the essential components and how they interact with one another. 

All living beings are composed of organs which in turn are composed of biological cells. Functionality of an organ emerges from the interaction between cells. 

Part 3 of The Economist's excellent series on biology is How organisms are organised. Here are a few highlights.

The twin processes of differentiation (many different types of cell) and integration (a highly functional structure) [are] at the heart of what makes organs tick.

How are the structures of plants and animals different? Why?

... animals and plants have different relationships with time and space. These different ways of life require different sorts of flexibility. Animals move through space but, once adult, change shape comparatively little over time. Plants stay still in space but change shape a lot as they grow. 
Most animals seek the energy they need by hunting or foraging. Plants’ energy-seeking behaviour is a matter of growing roots to take in water and minerals, and flat, green surfaces to absorb the sunshine and carbon dioxide that make up the preponderance of their food.

Muscles, nerves, and bones need to grow to a pre-arranged design much more than branches, twigs, and leaves do.

A human has about 80 distinct organs. The brain is the most complicated organ. It has about 86 billion nerve cells (neurons). There are 133 types of these in the cortex of the brain. 

Neurons are the essential components. Then one needs to consider how these components interact with one another.

A single neuron may be connected to as many as 10,000 other neurons. There are more than one hundred different types of chemical neurotransmitter with which to send and/or receive messages at the points of connection between.

The figure below shows how neurons are connected to one another via axons. Electric signals travel along the axon by action potentials.

The brain is a highly complex system. There are a large number of components, of many different types, and the large connectivity between them, and a large number of ways they can interact with one another. Given this complexity is it really that surprising that brains can "think" and process complex information. Parenthetically, I think this is another simple reason why I think proposals of quantum consciousness are so fanciful. Before, invoking such speculative ideas I think proponents should first rule out a simpler hypothesis: 

Consciousness (defined in some simple computational sense, putting aside profound philosophical nuance) can emerge from purely classical processes in such a complex system.

Hopfield showed how associative memory could emerge from a model that is much simpler than an actual brain. To me, this gives confidence that it is reasonable to work with the classical hypothesis.

Saturday, November 13, 2021

If organisations are emergent can they be managed?

 Any organisation is composed of many interacting parts. For example, a university is not just composed of staff and students, but also includes collaborators, donors, employers, suppliers, parents, graduates, and trustees. Their interactions with one another are influenced by structures, such as buildings, committees, and government policy. Furthermore, a university exists in a context: political, economic, historical, and cultural. What emerges from the interactions of all these components may be new states, for good or for ill. Like all emergent phenomena these states are hard to predict. For example, what will lead to high-quality education or a diverse student body? Can desirable outcomes be managed? What is the role of leadership in large organisations? Are there some universal principles of management that are useful for a wide range of organisations, whether corporations, NGOs, universities, or government departments?

Researching, teaching, and writing about "Organisational Development" and "management" is a massive industry; from Business schools in universities to a multitude of popular books for sale in airports. A fascinating paper is

The Dialogic Mindset: Leading Emergent Change in a Complex World by Gervase Bushe and Robert Marshak.

It questions the paradigm of the "visionary leader", "command and control", and the "performance mindset" that focuses on instrumental and measurable goal setting and achievement.

To understand the limitations of this management paradigm I find it helpful to reflect on the history and context of how it emerged (!) in the USA after World War II. After the war, veterans who returned to civilian life had experienced a particular leadership and organisational culture of the military: hierarchy, authority, process, discipline, solidarity, male, mono-cultural, ...  And, it worked in the context of war!

Many war veterans, both junior and senior, took this approach and mentality into industry, and it worked well in the American post-war economic boom of assembly-line-based large-scale manufacturing. The automotive industry, centred around Detroit, was representative. Arguably, the success was based on efficiency not innovation, limited competition in a simple market, and a homogeneous workforce. Two important figures who emerged from this Detroit era were Peter Drucker and Robert McNamara. Drucker did a seminal two-year study of General Motors, during WWII, that started his trajectory towards becoming the doyen of management studies. McNamara took his strategic planning experience in the war, and applied it successfully at Ford for 15 years, rising to become President of Ford in 1960. He then became Secretary of Defense for JFK and used the same management approach for the USA's involvement in the Vietnam war. This was an unmitigated disaster, but that did not stop him from using a similar approach when President of the World Bank.

Back to Bushe and Marshak and today's world. They claim that

The “visionary leader” narrative and performance mindset that predominate in theories and practices of “Change Leadership” are no longer effective in an environment of multi-dimensional diversity marked by volatility, uncertainty, complexity, and ambiguity.

The prevailing narrative of leadership is based on the assumption that great leaders must [be strategic thinkers], have a vision, and the ability to lead followers to that vision. Leaders, followers, and commentators alike assume that being a visionary is indispensable to organizational leadership.

... a leading voice supporting an alternative paradigm is Heifetz’s (1998) leadership model that indirectly challenges the heroic, visionary orthodoxy. He divides the decision situations leaders face into technical problems, which can be defined and solved through a top-down imposition of technical rationality; and adaptive challenges, which can only be “solved” through the voluntary engagement of the people who will have to change what they do and how they think. 
In Heifetz’s alternative narrative of leadership, adaptive leaders identify challenges but instead of providing solutions, they encourage employees and other stakeholders to propose and act on their own solutions.

 A nice example is how employees shaped strategy at the New York Public Library. 

The problem with the standard narrative is that it overlooks that organisations are emergent entities where cause-effect relations are not understood and outcomes are hard to predict. This challenge is exacerbated today by the fact that any organisation is not an isolated entity but is immersed in a complex and rapidly changing environment. This puts a premium on innovation and adaptability. 

Future posts will explore what this might mean in practice. Can self-organising processes and emergence achieve desired outcomes by "changing the conversation"?

Tuesday, November 2, 2021

How to move towards doing Deep Work

"Shallow work is non-cognitive, logistical or minor duties, often performed while distracted. These efforts require little cognitive effort, tend to create little value, and are usually easy to replicate." Examples include replying to emails, browsing websites, looking at social media, filling in forms, and attending meetings.

"Deep work is the ability to focus without distraction on a cognitively demanding task. These efforts create new value, improve your skill, and are hard to replicate.”

A colleague told me that Cal Newport's book, Deep Work, revolutionised his professional life.  These two short videos give a nice summary, focusing on quite practical ways to implement the ideas. They are both based on this article by Dan Silvestre.