Ive come across a series of fascinating articles which to an extent looks at evolution in a different way, and most certainly looks at the cell and cellular processes in a new way.


The articles deal with a process familiar to physicists, called self-organization.


Self organization is a process whereby some kind of structure or process pops into existence, doing so thanks to local interactions between components of a system that was initially disordered. Its a spontaneous process, requiring no controlling agent either inside or outside of the system. Crystalization is an example of self organization. Convection patterns in a liquid heated from below is another example. Self-organization is, to use that cliche, order out of chaos.


Two papers in particular make for an interesting read:-

Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software



Self-Organization versus Watchmaker: stochasticity and determinism in molecular and cell biology



Both papers are quite readable although the second of the two is more global in scope. The first looks at the process of self-organization in the context of evolution, particularly the role of natural selection. The second looks at self-organization in the context of the cell and cellular components and perhaps makes for a more interesting read. This is so because it challenges so much of what we think we know and understand about the cell and the processes which occur inside of it.


Basically the second paper blames Newton and Descartes for setting us up with a reductionist, mechanistic, clockwork view of the universe. The problem with this has been that once scientists came to grips with the notions of the cell, ribosomes, DNA, and genes, so they interpreted their experiments in the light of this mechanistic clockwork paradigm. And when electron microscopes and other devices were invented such that the cell and its subsystems could be observed, so scientists continued to interpret what they saw, using this paradigm. Thus the cell and its various subsystems were seen as mini-factories. Proteins and other molecules moved around thanks to systems of levers and cogs.
However, the second paper argues, this is really a deception. At the level of the cell and its various components, these mini-factories and systems of levers and cogs simply dont exist. What is being viewed are molecules and conformations that are continually falling apart and reforming, and its this that allows these subsystems to do work and to evolve, thereby allowing an organism to live and organisms to change over time.


Its this kind of work thats behind the occasional claims that evolutionary biology needs a rework, that the current paradigm is anything from totally inadequate to adequate, but in need of retuning and reconceptualizing at its most fundamental level.


I found both papers to be a thrill to read.


I am not qualified to judge them to be right or wrong, but I do understand them enough to find their ideas very interesting.


Next time you read a text book on molecular biology, the cell, genetics or evolution, these papers will make you ponder as to what is really happening at the deepest physical level. They will certainly sit in the back of my mind at least.


They remind me a bit of quantum mechanics and its relationship to classical physics. In our world, we see levers, gears, and cogs doing things and moving things. In the world of quantum mechanics, this simply does not happen. Virtual particles pop in and out of existence. Particles can be here and there, lacking a discrete existence.
And its like that here. Proteins might look like levers in some cases, levers that mechanically move along some part of a cellular structure, thanks to the mechanical forces of classical physics as used by engineers. But, say these scientists, that is not what is happening. Rather the proteins continually fall apart and self-organize and because this happens in the context of a surrounding environment, this is what causes the protein to move, as it reassembles itself in part or in total.


Its like hopping in a car to drive from Adelaide to Sydney, and the car moves, not because of levers causing wheels to turn, but the car moves because its wheels continually fall apart and reassemble, and in the process moves the car on its journey.

 This movement occurs because, during the reassembly, the components interact with an environment which brings about this motion.
And they claim to have the experiments to support this new way of looking at life.



Over the next set of posts, Ill describe that first paper. There are a couple of reasons for this - its shorter, deals only with one topic - evolution, and was easier to understand.


My war in reorganizing the back yard continues, and in a few days I go away on holidays. So there may be breaks in posting.




To be continued ....




The articles deal with a process familiar to physicists, called self-organization.


Self organization is a process whereby some kind of structure or process pops into existence, doing so thanks to local interactions between components of a system that was initially disordered. Its a spontaneous process, requiring no controlling agent either inside or outside of the system. Crystalization is an example of self organization. Convection patterns in a liquid heated from below is another example. Self-organization is, to use that cliche, order out of chaos.


Two papers in particular make for an interesting read:-

Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software



Self-Organization versus Watchmaker: stochasticity and determinism in molecular and cell biology



Both papers are quite readable although the second of the two is more global in scope. The first looks at the process of self-organization in the context of evolution, particularly the role of natural selection. The second looks at self-organization in the context of the cell and cellular components and perhaps makes for a more interesting read. This is so because it challenges so much of what we think we know and understand about the cell and the processes which occur inside of it.


Basically the second paper blames Newton and Descartes for setting us up with a reductionist, mechanistic, clockwork view of the universe. The problem with this has been that once scientists came to grips with the notions of the cell, ribosomes, DNA, and genes, so they interpreted their experiments in the light of this mechanistic clockwork paradigm. And when electron microscopes and other devices were invented such that the cell and its subsystems could be observed, so scientists continued to interpret what they saw, using this paradigm. Thus the cell and its various subsystems were seen as mini-factories. Proteins and other molecules moved around thanks to systems of levers and cogs.
However, the second paper argues, this is really a deception. At the level of the cell and its various components, these mini-factories and systems of levers and cogs simply dont exist. What is being viewed are molecules and conformations that are continually falling apart and reforming, and its this that allows these subsystems to do work and to evolve, thereby allowing an organism to live and organisms to change over time.


Its this kind of work thats behind the occasional claims that evolutionary biology needs a rework, that the current paradigm is anything from totally inadequate to adequate, but in need of retuning and reconceptualizing at its most fundamental level.


I found both papers to be a thrill to read.


I am not qualified to judge them to be right or wrong, but I do understand them enough to find their ideas very interesting.


Next time you read a text book on molecular biology, the cell, genetics or evolution, these papers will make you ponder as to what is really happening at the deepest physical level. They will certainly sit in the back of my mind at least.


They remind me a bit of quantum mechanics and its relationship to classical physics. In our world, we see levers, gears, and cogs doing things and moving things. In the world of quantum mechanics, this simply does not happen. Virtual particles pop in and out of existence. Particles can be here and there, lacking a discrete existence.
And its like that here. Proteins might look like levers in some cases, levers that mechanically move along some part of a cellular structure, thanks to the mechanical forces of classical physics as used by engineers. But, say these scientists, that is not what is happening. Rather the proteins continually fall apart and self-organize and because this happens in the context of a surrounding environment, this is what causes the protein to move, as it reassembles itself in part or in total.


Its like hopping in a car to drive from Adelaide to Sydney, and the car moves, not because of levers causing wheels to turn, but the car moves because its wheels continually fall apart and reassemble, and in the process moves the car on its journey.

 This movement occurs because, during the reassembly, the components interact with an environment which brings about this motion.
And they claim to have the experiments to support this new way of looking at life.



Over the next set of posts, Ill describe that first paper. There are a couple of reasons for this - its shorter, deals only with one topic - evolution, and was easier to understand.


My war in reorganizing the back yard continues, and in a few days I go away on holidays. So there may be breaks in posting.




To be continued ....