Self organization - a new paradigm?

[rjw]

I’ve 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 don’t 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.



It’s this kind of work that’s 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 it’s 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.



It’s 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, I’ll describe that first paper. There are a couple of reasons for this - it’s 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 ....





 

[Paul of Eugene OR]

I’ve 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 don’t 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.



It’s this kind of work that’s 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 it’s 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.



It’s 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, I’ll describe that first paper. There are a couple of reasons for this - it’s 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 ....





Living things do manage to repair themselves . . . sounds like an enlargement of that idea in a way . . .

 

[rjw]

Living things do manage to repair themselves . . . sounds like an enlargement of that idea in a way . . .

The second paper in the OP explains it as follows. Orthodoxy tends to see the cell as a factory with lots of little machines inside of it. These little machines do things in the same kind of way that our machines do things. They use levers, gears, and other mechanical things to move around and undertake various cellular activities.

The argument here is that it's not like this at all. Those factories and machines do not exist.

Rather, these so called factories are really molecules that continually fall to pieces and self-assemble. It's in that self assembly that they do things thanks to their existence within an environment. Thus, in one case, a molecule does not move along a cellular structure via a mechanism of levers (according to one model), but rather the molecule falls to pieces in bits. As these bits self-assemble, they do so in an field of varying energies which causes the molecule to jump to a new location along the cellular structure in order to minimize its own energy.

It's that kind of thing ........ as far as I can tell.

In the orthodox scenario, the molecule is a lever that always exists. In the self-organising scenario, the molecule is continually falling apart and self-assembling. It's nothing like a lever.


I hope I have this right. I think I do.




(It's good to see you around PoE. That other forum gave you a bum steer, and was completely unfair in how it treated you. There are dark Christian forums and their are Christian Forums that are in the light, so to speak.).

 

[rjw]

The abstract of the first paper linked to in the OP reads as follows:-


Self-organization is sometimes presented as an alternative to natural selection as the primary mechanism underlying the evolution of function in biological systems. Here we argue that although self-organization is one of selection's fundamental tools, selection itself is the creative force in evolution. The basic relationship between self-organization and natural selection is that the same self-organizing processes we observe in physical systems also do much of the work in biological systems. Consequently, selection does not always construct complex mechanisms from scratch. However, selection does capture, manipulate, and control self-organizing mechanisms, which is challenging because these processes are sensitive to environmental conditions. Nevertheless, the often-inflexible principles of self-organization do strongly constrain the scope of evolutionary change. Thus, incorporating the physics of pattern-formation processes into existing evolutionary theory is a problem significant enough to perhaps warrant a new synthesis, even if it will not overturn the traditional view of natural selection.

The authors are summarizing their paper as follows:-



1. Some folk see self-organization as an alternative to natural selection as a generator of new functionality in biological systems as those systems evolve.

2. The paper argues that selection remains the fundamental creative force in evolution and it uses self-organization as one of its tools.


3. The self organization of biological systems is exactly the same self-organization seen in physical systems.



4. “... selection does not always construct complex mechanisms from scratch. However, selection does capture, manipulate, and control self-organizing mechanisms ...”. That is self-organization generates structures which selection then acts on to accept or reject.



5. Capturing and maintaining these self-organized structures is difficult because such structures are sensitive to environmental conditions. For example, such structures only come into existence within a very narrow range of environmental conditions. And so having them exist in the first place, and then continue to exist so that selection can act on them would seem to be problematical.



6. The often inflexible principles of self-organization actually constrain the scope of evolutionary change. Evolution is limited to what it can and cannot do because of these inflexible principles.



7. Given points 5 and 6, incorporating the physics of pattern formation into theories of evolution may well bring about a new evolutionary paradigm. Nevertheless, natural selection may well continue to play a central role.





To be continued ....



 

[Resha Caner]

6. The often inflexible principles of self-organization actually constrain the scope of evolutionary change. Evolution is limited to what it can and cannot do because of these inflexible principles.



Thanks for the links.

There are several interesting aspects to this, but I'll focus on #6. I've long been aware one of the principles of optimization is that after a decision is made, part of the solution space becomes unreachable. IOW, just because a solution is theoretically possible doesn't mean it can be realized. I'm glad to see some in biology begin to acknowledge that.

Also, I've always viewed this more as a process of expressing an existing structure than innovating on a blank page. For a while now I've been pondering the connection between game/graph theory and biology, so I found it intriguing that Johnson referred to this process as putting together a puzzle.

 

[rjw]

Thanks for the links.

There are several interesting aspects to this, but I'll focus on #6. I've long been aware one of the principles of optimization is that after a decision is made, part of the solution space becomes unreachable. IOW, just because a solution is theoretically possible doesn't mean it can be realized. I'm glad to see some in biology begin to acknowledge that.

Also, I've always viewed this more as a process of expressing an existing structure than innovating on a blank page. For a while now I've been pondering the connection between game/graph theory and biology, so I found it intriguing that Johnson referred to this process as putting together a puzzle.

Yes.

I found all these papers in the scientific literature. In actuality, I found one or two which, once I started reading, found myself being forced to the reference section to locate even more papers which were cited and looked to be very interesting.

The second paper I linked to is the really interesting one because it offers a really new way of considering the cell and cellular dynamics.

 

[rjw]

Before they discuss self-organization and its relationship to evolution, the paper has three sections - an introduction, a historical preface and a description of evolutionary biology as it is today, focusing mainly on selection.

Introduction

Here Johnson and Lam note that a diverse group of people in physics, mathematics and biology have argued that self-organization is at least as important as natural selection in evolution. However, most research into the mechanisms of evolution continue on along traditional lines, ignoring these calls to consider and investigate the role of self-organization.


Johnson’s and Lam’s paper is another attempt to show the importance of self-organization as a mechanism in evolution, but unlike some, demonstrate that even though it is ubiquitous and creative, it remains used by natural selection, as opposed to being complementary to it, even relegating natural selection to unimportance.



Their paper is broken into sections which aim to:-



1) Review of evolutionary theory with an emphasis on those aspects of the theory which are important to their discussion of self-organization.



2) Introduce self-organization and to do so in an intuitive manner.

3) Discuss the “intersection between natural selection and self-organization”. Here they aim to clear up the misunderstanding that self-organization “competes with natural selection as the organizing force in evolution”. And they intend to show the many ways in which the process affects evolution.

Evolution to date, has largely been about the gradual evolution of structures and functions and the authors think that the role of (any) “controlled but largely spontaneous” evolution is “the chief unanswered question of today”.


They note that many folk in the self-organization field deem that a new synthesis might be needed because evolution at the macroscopic level (the morphological level) may in fact be very different to evolution at the molecular level, where self-organization plays out. They suggest “[a]s the first modern synthesis incorporated genetics into natural selection, this new synthesis seeks to incorporate the physics of complex systems”.


Aside - a background read.



A name which often appears in these kind of papers is that of Ilya Prigogine. He won the Nobel Prize in 1977 for his work on the thermodynamics of non-equilibrium systems (living organisms are one example of such systems). Prigogine and Isabelle Stengers wrote the following book which was published in 1984:-



Order Out of Chaos






To be continued ....






 

[bhsmte]

.

 

[rjw]

A brief historical preface

In a subsection of their introduction with the above mentioned title, the authors describe why there might be a clash of perspectives within the study of evolution.

Evolution by natural selection is one of biology’s best supported theories. However, the theory was fully formed well before the era of molecular biology. Johnson and Lam make a special note of this because, they argue, the theoretical underpinnings of natural selection were developed using data at the macroscopic level. While the same principles may well apply at the molecular level, and it seems to in many cases, the principles may not universally apply, and molecular biologists may well have a point when they argue that something different is also going on at the molecular level.

And the authors conclude that evolutionary biologists should not be skeptical at the claims of the molecular biologists because “given the history, it would be surprising if a major new approach to evolution were not necessitated by data on life at the molecular level.”.


Following this, in a section titled:-



Evolutionary biology

- the authors give a sketch of evolutionary biology, particularly natural selection and those aspects of the process that are most relevant to their discussion.

I’ll not dwell too much on this section because I want to get onto self-organization, and besides evolution and natural selection are often described by various posters, so much so that even creationists should have a degree of understanding.

The authors offer an interesting definition of evolution, one that encompasses all the processes they think are relevant to the process. They define it as:-

The historical process that leads to the formation and change of biological systems.

Because their interest is in the evolution of function and selection is what gives rise to function they write that natural selection is the consequence of three properties of organisms: 1) variation, 2) differential reproduction, and 3) heritability of traits important for survival or reproduction. And much research focuses on mathematical models of these properties.

The authors intent however is to briefly discuss three consequences of 
natural selection that have fascinated biologists - adaptation, functional constraint (are all variations of a trait possible, or are variations constrained?), and the nature of evolutionary trajectories (does selection form new adaptations quickly or gradually).



Johnson and Lam spend a paragraph discussing each of these three points, and if the reader is interested, this discussion can be found at the first link in the OP.



Then the authors turn their attention to self-organization.





(Much to my sadness, I shall be absent for the next few weeks. Holidays you see. )




To be continued ....




 

[Resha Caner]

In a subsection of their introduction with the above mentioned title, the authors describe why there might be a clash of perspectives within the study of evolution.

Philosophers of science have killed entire forests writing about why these things happen. It's just part of human nature. It's hard to change ... and not necessarily because of some vicious, willful desire to avoid the truth. Sometimes a person doesn't even realize they're following a particular paradigm, and wouldn't know how to do things differently even if they did.

When I've asked, "What would the alternative be?" kinds of questions, the results tend to be rather sparse.

As I studied your links I came to realize I'm probably more interested in "self assembly" than "self organization", and the difference between those two is somewhat nebulous. But, what I find interesting is that DNA is being explored as a probabilistic computer without much attention being given to the fact that, well, DNA is a probabilistic computer - which means it doesn't necessarily need selection.

Much to my sadness, I shall be absent for the next few weeks. Holidays you see.

Rats. You realize that means the conversation is going to die.

 

[Resha Caner]

As I've been chasing this idea, I came across the following letter to Nature from 1957. Fascinating. In fact, I'm trying to figure out if I'm misinterpreting it, because I can't figure out why the phenomena related in the letter would work.

It's a short, easy read for anyone who is interested: http://cba.mit.edu/events/03.11.ASE/docs/Penrose.1.pdf

[edit] ... although it seems this paper explains why this works. Fascinating. I would never have figured out something like that.

Mapping Virtual Self-assembly Rules to Physical Systems
by Navneet Bhalla, Peter J. Bentley, and Christian Jacob

 

[rjw]

Well, the holidays are over and it’s back to reality. Get your violins out and give me a white handkerchief.


Having provided a bit of a background and introduction to evolution and the idea of self-organization, Johnson and Lam then describe the process in more detail.



Self Organization

Systems of self-organization contrast to what they label “conserved systems”. In conserved systems, energy is conserved whereas in self-organizing systems, energy is continually flowing through and being dissipated. 



Self-organization creates “dissipative structures” which can only persist as long as energy is continually being input and flowing through them. Hence a dissipative structure is not like, say, a salt crystal which persists without any input of energy once the crystal is formed. Rather a dissipative structure is like a hurricane which continually feeds off energy supplied to it by the ocean and which begins to “die” when the hurricane reaches landfall and no longer has that supply of energy. That is, a hurricane is a self-organizing system. It is a dissipative structure.

We humans are dissipative structures. We require a continual source of energy and once any energy reserves are depleted, we begin to die.



As the authors write:-



A dissipative structure is thus not a structure at all, but a metastable pattern

Our existence is stable only so long as energy is supplied to us.

They note that we are surrounded by “purely physical self-organization patterns” and in the following section introduce one such pattern, the cell, while noting that self-organization is also important in developmental and other branches of biology.

Underscoring what has just been described is the following quote by Alvin Toffler in the forward to a book by two particular metastable structures, known as Ilya Prigogine and Isabelle Stengers. They wrote a book, based largely on their work regarding these systems for which Prigogine won the 1977 Nobel Prize in chemistry. (Prigogine’s structure decayed to the point that it could no longer extract energy from the environment to maintain itself and so Prigogine returned to disorder back in 2003. On the other hand, the structure we know as “Isabell Stengers”, remains viable.) Toffler, explaining how the concept of dissipative structures contrasts with Newton’s clockwork, machine view of the universe, writes:-

Summed up and simplified, they [Prigogine and Stingers] hold that while some parts of the universe may operate like [Newton's clockwork] machines, these are closed systems, and closed systems, at best, form only a small part of the physical universe. Most phenomena of interest to us are, in fact, open systems, exchanging energy or matter (and, one might add, information) with their environment. Surely biological and social systems are open, which means that the attempt to understand them in mechanistic terms is doomed to failure.


This suggests, moreover, that most of reality, instead of being orderly, stable, and equilibrial, is seething and bubbling with change, disorder, and process.






In their next section the authors introduce the cell as a self-organizing system and in the process provide some ideas which, while very new to me, are both interesting, tantalizing and in a general sense, seemingly correct, even if, in a few cases, my mind initially balks at.





To be continued ...





 

[rjw]

As I've been chasing this idea, I came across the following letter to Nature from 1957. Fascinating. In fact, I'm trying to figure out if I'm misinterpreting it, because I can't figure out why the phenomena related in the letter would work.

It's a short, easy read for anyone who is interested: http://cba.mit.edu/events/03.11.ASE/docs/Penrose.1.pdf

[edit] ... although it seems this paper explains why this works. Fascinating. I would never have figured out something like that.

Mapping Virtual Self-assembly Rules to Physical Systems
by Navneet Bhalla, Peter J. Bentley, and Christian Jacob

Thanks for the link Resha.

That is neat.

Oddly, your specific link did not work for me, but I tracked the title of the paper down, Googled it and got a link to another copy of the article which did work. For anyone interested the title is "A Self-reproducing Analogue".

 

[SkyWriting]

Crystalization is an example of self organization.





It's not, but lets get to the paper.

"Thus, incorporating the physics of pattern-formation processes into existing evolutionary theory is a problem significant enough to perhaps warrant a new synthesis, even if it will not overturn the traditional view of natural selection."

Evidently the researcher is attempting to shoe-horn his work
into an incompatible framework of knowledge rather than letting
the investigation lead to it's own conclusions.

If anybody claims scientists have no bias, I'll send them to this paper.

 

[rjw]

Having described self-organisation, and introduced dissipative structures which, for their maintenance, require a continual flow-though of energy, the authors turn their attention to:-

The Cell: The functional unit of biology



It’s here that the article begins to get really interesting and provocative. Provocative, not because it necessarily says things that are controversial in the scientific world, but provocative in that I’d never really considered them or thought them through before.

Self-organization is, they say, “the fundamental mechanism within the cell”. From there, they claim (and are probably correct) that “the importance of the cell to evolutionary processes is usually downplayed in basic texts on evolution”.

To show how important the cell is, or should be, they write that genes don’t make cells. They don’t code for their construction. Cells are units of inheritance from a parent, just like DNA. Furthermore, the cell’s mechanisms are independent of DNA and are enormously complex. (DNA does have an important role to play in cellular mechanisms, but the authors are looking at it from a different perspective. This distinction should become clear shortly.)



These two facts have consequences for evolution. 


The cell is inherited and its processes cannot always be constructed from new via genetic instructions. But genes do control and manipulate a cell’s ongoing behaviour. The gene is the cell’s “information-storage device”, but only some information is stored there. Other information is stored within various subsystems of the cell. The basic mechanisms (these cellular subsystems and their interactions) of life are inherited as ongoing, continuous processes. They are not inherited as outcomes of DNA processes. Furthermore, if life evolved as a coupled set of interacting processes between itself and its component parts, then it has remained that way ever since.



Given all this, any evolutionary theory which focuses on the “shuffling of genes propagating through time” is necessarily a limited theory because the cell itself as well as its processes are the engines of life and these constitute far more than just the genes and their manipulations of the cell.

In short, these self-organization processes pay a large role in cellular dynamics, and that role is, or largely is independent of genes. Genetic processes have one large role to play and self-organization another large role. To be a better theory, evolution needs to consider both aspects.



To be continued ...





 

[rjw]

It's not,

Why isn't it?

Evidently the researcher is attempting to shoe-horn his work
into an incompatible framework of knowledge rather than letting
the investigation lead to it's own conclusions.

If anybody claims scientists have no bias, I'll send them to this paper.

What makes you imply that the concept of self-organisation is incompatible with evolutionary biology, specifically natural selection?

 

[rjw]

Biological examples of self-organization

In the section with the above mentioned title, the authors begin with two simple examples of self-organization. The first is the formation of the tobacco mosaic virus and the second is the formation of microtubules.

With the tobacco mosaic virus, the parts of the viral coat, under the right conditions, self assemble like a jigsaw puzzle putting itself together. Once the coat is formed, no further energy input is needed. The coat is stable. With microtubules, thin filaments that give a cell support and help it to do work, the filaments self-assemble in a similar way, except that the pieces continually come and go in a dynamic way. Here a continual input of energy is required to maintain the structure, and these kinds of organizations are called “dissipative structures”.

More complex examples of self-organization are DNA repair and transcription. Initially it was believed that these processes are undertaken by mini-machines floating around in the cytoplasm. However, when repair to a particular location of damaged DNA is required, the repair mechanism self-organizes from the cytosol. Until then, its subunits are dissolved within the cytosol.

The repair work is done and when completed, no further energy input occurs to maintain the structure and so it simply dissolves back into the cytosol.



For the repair structure to form spontaneously, an optimum concentration of subunits must be maintained in the solution. The associated molecular crowding helps maintain large numbers of random interactions, an important aspect of the self-organization process. It’s a problem the cell has to overcome, the creation and maintenance of just the right conditions so that self-organization can occur when needed.




The authors speculate on how the self-organization might be triggered. Rain “instantly” forms in clouds, saturated with water vapour above a certain threshold, providing seed particles exist. This is the principle behind cloud seeding, where large number of artificial seeding nuclei are fed to the cloud. They think something like this may be one mechanism used by the cell. Consider macro-molecules dissolved in the cell’s cytosol. The problem is to get these molecules together so that they can self-assemble. As opposed to evolving a molecule gathering machine, the cell could simply send out seed molecules and achieve the desired result, but with a very low expenditure of energy.



They offer another possibility, whereby to transport molecules around the cell, as opposed to transport machines (some of which do exist, for example, vacuoles), a cell could simply tag molecules to be sent, and tag destinations. Molecules with the right tags can be simply fished out of the stream by the destination molecules.

The authors conclude the section by pointing out that self-organizing mechanisms are the focus of intense study in biology and they provide the interested reader with the following list of articles in their reference:-



1. Murray AW, Kirschner MW. 1989. Dominoes and clocks: The union of two views of the cell-cycle. Science 246: 614–621.



2. Novak B, Tyson JJ. 2003. Modelling the controls of the eukaryotic cell cycle. Biochemical Society Transactions 31: 1526–1529

3. Glick BS. 2002. Can the Golgi form de novo?Nature Reviews Molecular Cell Biology 3: 615–619.

4. Carazo-Salas RE, Nurse P. 2006. Self-organization of interphase microtubule arrays in fission yeast. Nature Cell Biology 8: 1102–1194.

5. Misteli T. 2001. The concept of self-organization in cellular architecture. Journal of Cell Biology 155: 181–185.

6. Misteli T. 2007. Beyond the sequence: Cellular organization of genome function. Cell 128: 787–800.

7. Kurakin A. 2005. Self-organization versus watchmaker: Stochastic dynamics of cellular organization. Biological Chemistry 386: 247–254.

8. Kurakin A. 2007. Self-organization versus watchmaker: Ambiguity of molecular recognition and design charts of cellular circuitry. Journal of Molecular Recognition 20: 205–214.

9. Karsenti E. 2008. Self-organization in cell biology: A brief history. Nature Reviews Molecular Cell Biology 9: 255–262.




Many of these articles can be found online, providing you Google the title. Often you will find a PDF, or alongside the abstract will be a link to the free text. References 1, 7, and 8 are of this nature.







To be continued ....



 

[rjw]

Is self-organization an alternative to natural selection?



The authors note that some researchers see self-organization as an alternative to natural selection, thereby driving a very different evolutionary process to that generally envisaged by the mainstream of researchers. 



However, they don’t accept this, and their reasons are as follows.

There is no doubt that self-organizing systems exist within living organisms. Take the cell. The question to be addressed it this - are these self-organizing mechanisms the product of natural selection or are they simply an intrinsic properties of a cell’s physics and chemistry. If the latter then the role of natural selection is much reduced.



The authors don’t accept the latter point of view. They think that self organizing systems evolve and that the mechanisms that sustain them evolve. They describe Bernard convection cells as an example illustrating certain properties which are common to both physical and biological self-organizing systems. Bernard convection cells form rapidly and spontaneously under the right physical conditions. However, they do not form robustly, in that if the physical conditions are altered slightly, then the cells break down or fail to form. These properties appear to exist for all self-organizing processes.

Such properties are the basis for the argument that natural selection retains its importance in evolution. A cell has to do a lot of work to set up the conditions and maintain them, for self-organization of any subsystem to occur. Furthermore, finding the right elements to react with each other in a self-organizing process is not a trivial task, given all the possible components genes can make. Hence it would seem from these two points alone, if it self-organization were just an intrinsic property of the cell, then the unique processes we see and the common processes that occur amongst cells simply would not be. It’s as if some kind of “hand” is selecting certain kinds of self-organization to exist.



Furthermore, given the non-robustness of self-organizing systems mentioned above, the authors point out that cells have to go to great lengths to maintain the conditions to keep any self-organized system from falling apart as soon as it forms. They write that “Organisms are full of such regulatory procedures for maintaining homeostasis in the face of environmental perturbations, whereas self-organizing processes in isolation have no such ability”.



In short, in isolation, a self-organizing process is a product of a given circumstance and when those circumstances change (even slightly), the process breaks down. Such self organization is intrinsic. In biology however, it is different. Amongst all potentialities, only certain self-organizing systems occur, and they have to be maintained in the face of many environmental perturbations. Hence they are not spontaneous in the sense that intrinsic systems or processes are. They write that “selection has to fine-tune and control many parameters to get work out of a self-organization process. Thus, although selection does not need to construct an elaborate plan to generate complexity when self-organization is involved, it does have to drive the evolution of elaborate mechanisms for invoking self-organizing processes and controlling their dynamics. Therefore, selection should play the dominant organizing role even when much of the complexity one observes appears to be spontaneous.”




To be continued ...