Tuesday, January 18, 2022

Graduate students are people

Every scientist is a person. They have a unique personality and a unique life story. Their family, friends, education, hopes, romances, cultural background, past disappointments have shaped who they are today. This past has had a significant influence on their current motivation, fears, ability to work with others, confidence, sense of identity, and manner of communication. It is important that we grapple with all this complexity if we are to appreciate and respect others, and to help them be successful. Graduate students are not slaves, robots, or all the same. Graduate students are people.

These complexities are too often overlooked. But we must engage them if we are to personally care for students and colleagues, and relate to them in a manner that helps them be successful. These issues were brought home to me recently reading the novel, Transcendent Kingdom by Yaa Gyasi. I thank my daughter for the gift, particularly as it was not the kind of book that I might normally have sought out.

The main character in the novel is Gifty, a graduate student in neuroscience at Stanford. Her parents immigrated to the U.S.A from Ghana and she grew up in Alabama, just like the author. Gifty's choice of research topic is motivated by her life experience including her brother's struggle with drug addiction. The research  described in the novel is actually based on a real scientific paper written by a friend of the author.

Molecular and Circuit-Dynamical Identification of Top-Down Neural Mechanisms for Restraint of Reward Seeking

Christina K. Kim, Li Ye, Joshua H. Jennings, Nandini Pichamoorthy, Daniel D. Tang, Ai-Chi W.Yoo, Charu Ramakrishnan, Karl Deisseroth

The novel gives an inside view of the life of a graduate student, describes experiments on mice, including the use of fluorescent proteins to image brain activity. Although science and graduate education is not the main point the novel, it may be good to give or recommend to non-scientists that you would like to understand a little of your world. The novel is easy to read and written in beautiful language.  The main character (author) is an astute observer of herself, others, and social dynamics. The novel captures some of the intensity, independence, stubbornness, and introversion of a brilliant student.


The narrative naturally engages with a wide range of issues, including the immigrant experience and the associated prejudice, racism, poverty, dislocation, and alienation that are too often encountered. It considers family relationships, particularly the bond and tensions between a mother and an adult child. It gives a picture of what it may be like to be a young woman of colour in an elite institution. Then there is sexuality, white Pentecostal churches in the USA, science and religion, mental illness, drug addiction, a personal face on the opioid crisis, the philosophy of neuroscience, including the mind-brain problem,... This does seem like a long list of issues but the author manages to engage with them in a natural and meaningful way as part of a coherent narrative.

Perhaps the only criticism I might have is that I felt that the ending was a little too quick, neat, and may betray the complexity that the rest of the novel so beautifully captured.

Here are some other reviews and articles about the novel that I found most interesting. A review in the Washington post, A review in The New York TimesThe back story of how a visit to a friends lab at Stanford led Gyasi to write the book.

Monday, December 13, 2021

This is your life: birth, sex, and death!

Symmetry breaking is integral to biology. Spatial symmetry is broken as cells differentiate and also as organs form. Time reversal symmetry is broken in the life history of the development of individuals: from birth to death, it is heading just one way.

The fourth article in The Economist, Biology briefs, is Making your way in the world: An individual’s life story is a dance to the music of time. Here is the opening paragraph.

The organs of a body are a spatial division of labour, one created by different genes being turned on in different cells. The same process serves to give individual lives a division of labour over time. Complex algae, animals, fungi and plants all have predictable life histories which separate out three basic aspects of development—the creation of an autonomous individual, growth and reproduction—and run them sequentially.

There is also a fourth stage: death!

Individual identity is tied up with sex.

A lot of the complexity here is to do with sex... Sex is clearly the start of something new: a novel individual with a novel genetic blueprint...

When a human embryo is born as a baby, it already contains almost all of the organs which that individual will ever possess. This comes about first by the repeated division of the initial, fertilised egg into many cells that have the potential to become any part of the body.

Then symmetry breaking occurs: left and right, head and tail are delineated. 

Then, around the 16th day of development, the [human] embryo folds in on itself... [and the] body plan begin to take on a physical form, defining the head and the tail (for human embryos do, indeed, have tails), the left and the right, the inner and the outer.

...a butterfly embryo develops not only the organs needed in order to be a caterpillar, but also starter packs, called imaginal discs, for the organs that will be needed in adulthood.


Plants have two separate life histories, which alternate from generation to generation—though this is rarely obvious to human observers.

These two life histories (mating and dispersal) are associated with  "two, radically different, types of body": gametophytes, the mating body type, and sporophyte the dispersal body type. The life cycle of ferns is pictured below.

Here is a beautiful video of the life cycle of a butterfly.

Aside: There is a nice discussion of symmetry breaking and pattern formation in biology in chapter 7 of Fearful Symmetry: Is God a Geometer? by Ian Stewart and Marty Golubitsky.


Thursday, December 2, 2021

The tension between efficiency, innovation, and adaptability

 If organisations are emergent can they be managed? This is the question I discussed in a previous post, stimulated by an article, The Dialogic Mindset: Leading Emergent Change in a Complex World by Gervase Bushe and Robert Marshak. They make the following claims.

To be sustainably successful, organizations have to manage learning as well as performing. This is one of the core paradoxes of management and organization theory: how to create organizations that can be simultaneously innovative and efficient; that is, how to best organize in order to learn and perform at the same time? 
The most efficient forms of organizing, like assemblyline manufacturing, are also the least able to adapt and change. Our business models for succeeding in complex, uncertain environments, like popular music or pharmaceuticals, are highly inefficient and spend lots of money on innovation hoping for one monster hit to pay it all back. Learning and performing are paradoxically related because when someone is focused on performing well, they usually are not learning anything, and vice versa.

This tension is represented in the diagram below. 


I think a good metaphor for the desired combination of efficiency, innovation, and adaptability is a jet ski. This is nicely shown in this cool video (taken about 100 km south of Brisbane). 


My choice of metaphor was inspired by discussions with a colleague who has taken a  Prince2 Agile Project Management course. To illustrate the need for a combination of efficiency and agility they use the metaphor of a jet fighter. I do not like military metaphors, because of their association with violence and the corrupt military-industrial complex. I work with people in the Majority World and such a metaphor may have a negative association. For example, a recent article in The Economist expressed concern that Nigeria is falling apart, partly due to internal insurgencies. It contains the observation
Money could come from cutting wasteful spending by the armed forces on jet fighters, which are not much use for guarding schools. 

So the challenge for real leaders (not managers) is to foster an organisational culture that balances efficiency, adaptability, and innovation. 

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. The 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 neurotransmitters 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"?