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Alfred Russel Wallace
[ In the early 21st century, as well as in the previous century, many biologists have argued for a more informed and celebrated acknowledgement of the contributions to our understanding of evolution by the 19th century naturalist and contemporary of Charles Darwin, Alfred Russel Wallace (b. January 8, 1823; d. November 7, 1913).9
Self-organization section of life-draft for reorganizing
Self-organization
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As the wind of time blows into the sails of space, the unfolding of the universe nurtures the evolution of matter under the pressure of information. From divided to condensed and on to organized, living, and thinking matter, the path is toward an increase in complexity through self-organization.. — Jean-Marie Lehn http://www.pnas.org/cgi/doi/10.1073/pnas.072065599 |
In living systems, the order we find results to a large degree through the ability of the system to organize itself, independently of a master controller, a program director, a blueprint, a template. Self-organization 'emerges' as a spontaneous manifestation of the interactions among the systems' components, of the system with the environment embedding it, influenced by the process of natural selection. In cells, self-organization emerges in part from so-called supramolecular (non-covalent) interactions of proteins-with-proteins and proteins with other molecules.[1] [2] [3] The proteins make their appearance through a genetic transcription-translation machinery, which itself represents a self-organized molecular machine that emerges in part from the non-covalent interactions of proteins with nucleic acids and other molecules. Jean-Marie Lehn, of the Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, summarizes it in this way:
A self-organization process may be considered to involve three main stages:
- (i) molecular recognition for the selective binding of the basic components;
- (ii) growth through sequential and eventually hierarchical binding of multiple components in the correct relative disposition; it may present cooperativity and nonlinear behavior; and
- (iii) termination of the process, requiring a built-in feature, a stop signal, that specifies the end point and signifies that the process has reached completion. [1]
Molecules interact by forming and breaking strong or weak covalent bonds, and also through weaker intermolecular interactions, like hydrogen bonding and Van der Waals forces. Those supramolecular interactions self-assemble aggregates of molecules (e.g., organelles, networks), giving them the properties that enable many biological processes.[2] [4] To quote Reinhout and Crego-Calama:[5]
In chemistry, noncovalent interactions are now exploited for the synthesis in solution of large supramolecular aggregates. The aim of these syntheses is not only the creation of a particular structure, but also the introduction of specific chemical functions in these supramolecules..
Again, J-M Lehn:[6]
Starting with the investigation of the basis of molecular recognition, [supramolecular chemistry] has explored the implementation of molecular information in the programming of chemical systems towards self-organisation processes, that may occur either on the basis of design [by the chemist] or with selection of their components.
The qualifier that self-organization emerges only in part from supramolecular interactions, proteins with proteins and other molecules, reflects the involvement not only of supramolecular self-assembly but also of evolutionary mechanisms, operating on random variation through selection of molecules and networks of molecules that tend to optimize the fitness of functional self-organization — in other words, Darwinian evolution, or adaptation, operating to influence the nature of the self-organizing process.
Many workers (see: Hoelzer et al. [7]) emphasize self-organization as playing an explanatory role for the process of natural selection: "….it is clear that the process of SO represents a potential explanation for adaptive biological evolution." Hoelzer et al. discuss that in terms of the physics of self-organizing processes — the extraction of work through channeling free energy gradients — showing that a similar physics applies to the process of natural selection, rendering self-organization and natural selection complementary processes in sustaining living complex adaptive systems.
One must also invoke local real-time selective processes that confer stability and appropriate functionality to self-assembly, called homeostasis or adaptability. Thus, order emerges out of chaos.[8]
Professor of Microbiology, Franklin M. Harold, offers the following definition of self-organization:
...let me define self-organization as the emergence of supramolecular order from the interactions among numerous molecules that obey only local rules, without reference to an external template or global plan...The definition explicitly excludes order imposed by an external template, whether physical (as in a photocopier) or genetic (as in the specification of an amino acid sequence by a sequence of nucleotides)...The structure of the self-assembled complex is wholly specified by the structures of its parts and is therefore implicit in the genes that specify those parts: natural selection crafted those genes to specify parts that assemble into a functional complex.[9]
Information resides in proteins and other molecules in virtue of their structure, and through them, information flows through cells, just as energy does, and determines their organizational nature.[10]
One way to understand this self-organization is to view a living system as a 'computing device'. The inherited and acquired information base — the genome — specifies components which arrange themselves in accord with their physico-chemical properties — i.e., they 'compute' the system in a complex chemical reaction. Systems biologist, Denis Noble, incisively describes it:
Genes code for protein sequences. They do not explicitly code for the interactions between proteins and other cell molecules and organelles that generate function. Nor do they indicate which proteins are on the critical path for supporting cell and organelle function in health and disease. Much of the logic of the interactions in living systems is implicit. Wherever possible, nature leaves that to the chemical properties of the molecules themselves and to the exceedingly complex way in which these properties have been exploited during evolution. It is as though the function of the genetic code, viewed as a program, is to build the components of a computer, which then self-assembles to run programs about which the genetic code knows nothing….[11]
Yet that description under-characterizes the complexity of the system. In a multicellular organism, each cell retrieves only its own particular pieces of information from the total information base, and the selection varies with time. Each cell must perform specific computations to effect that dynamic activity. The behavior of the system's functional networks constitute those specific dynamic computations. The apparent circularity begat by adding that further characterization of the system as a 'computing device' exemplifies two-way nature of the 'computations' self-organizing the living system. With the tinkering and discovering comprising local trial-and-error and evolution’s handiwork, that 'circularity' carries out ('computes') integrative functions not explicitly encoded in the inherited and acquired information base of the system.[11]
The molecular biologist Sidney Brenner[12] expressed the 'computing device' metaphor this way:
...biological systems can be viewed as special computing devices. This view emerges from considerations of how information is stored in and retrieved from the genes. Genes can only specify the properties of the proteins they code for, and any integrative properties of the system must be 'computed' by their interactions. This provides a framework for analysis by simulation and sets practical bounds on what can be achieved by reductionist models.[13]
The structure and behavior of self-organized systems need no behind-the-scenes 'master controller', and no prepared blueprints that specify the structure and dynamics of the system. Instead, they emerge from interactions among the naturally generated and naturally selected components of a system, dictated by their physico-chemical properties, and dynamically modified by the emergent organization, which is itself modified by the environment. The single-celled zygote self-organizes into a multicellular living system as genetically encoded proteins interact, responding to changing influences from the changing environment generated by growing multicellularity — becoming a network of many cell-types working cooperatively.
That biological systems self-organize has led one prominent biologist to say they are products of a "blind watchmaker".[14]
Self-organization tends to breed greater complexity of self-organization. One important aspect of self-organization in cells rests on the tendency for lipid molecules with polar (water-loving) and non-polar (water-shunning) ends to form bilayers in an aqueous solution, each unit of the bilayer with two lipid non-polar ends mutually attracted in the center and the polar ends surrounded by water. Protein molecules can span the bilayer membrane, or selectively straddle only one or the other side of the membrane and its aqueous surrounding, according to their specific amino-acid sequence and side-groups. Those lipid-protein membranes allow cells to communicate with other cells, either in free-living cellular communities or in multicellular organisms, and those communication activities self-organize by virtue of the properties of the cells, generated by natural experiments and selected for fitness by evolutionary mechanisms, and subject to downward effects by the systems' organization and environmental influences on the systems.
Self-organization occurs at all levels of living systems. For example, the dynamics of communities, such as the feeding relationships within communities of large mammals, also reflect self-organization. The animals and components of the ecosystem embedding them self-organize, resulting in "...unitary structures with coherent properties...[that] can operate in an integrated way, which allows for the acceptance of their changes on large time-scales as evolutionary."[15]
Further elaborating the descriptions of living systems beyond the thermodynamic and evolutionary perspectives, we might say that:
A living system:
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refs
- ↑ 1.0 1.1 Lehn JM. (2002) Toward complex matter: supramolecular chemistry and self-organization. Proc Natl Acad Sci USA 99:4763-4768 PMID 11929970
- From the article: "Supramolecular chemistry has paved the way toward apprehending chemistry as an information science through the implementation of the concept of molecular information with the aim of gaining progressive control over the spatial (structural) and temporal (dynamic) features of matter and over its complexification through self-organization, the drive to life [citations]...Supramolecular chemistry has developed as the chemistry of the entities generated by intermolecular noncovalent interactions [citations]."
- ↑ 2.0 2.1 Lehn JM (2002) Toward self-organization and complex matter Science 295:2400-3 PMID 11923524
- ↑ Steed JW, Atwood JL. (2009) Supramolecular Chemistry. 2nd edition. Wiley. ISBN 978-04705112340.
- Excerpt:If we regard supramolecular chcmistry in its simplest sense as involving some kind of non-covalent binding or complexation event, we must immediately define what is doing the binding. In this context we generally consider a molecule (a 'host') binding another molecule (a 'guest') to produce a 'host-guest' complex or supermolecule. Commonly the host is a large molecule or aggregate such as an enzyme or synthetic cyclic compound possessing a sizeable, central hole or cavity. The guest may be a monatomic cation, a simple inorganic anion, an ion pair or a more sophisticated molecule such as a hormone, pheromone or neurotransmitter. More formally, the host is defined as the molecular entity possessing convergent binding sites (e.g. Lewis basic donor atoms, hydrogen bond donors, etc.). The guest possesses divergent binding sites [e.g. a spherical, Lewis acidic metal cation or hydrogen bond acceptor halide anion). In turn a binding site is defined as a region of the host or guest capable of taking part in a non-covalent interaction.
- ↑ Percec V, Ungar G, Peterca M (2006) Self-assembly in action. Science 313:55-6 PMID 16825559
- ↑ Reinhoudt DN, Crego-Calama M (2002) Synthesis beyond the molecule Science 295:2403-7 PMID 11923525
- ↑ Lehn JM (2007) From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry. Chem Soc Rev 36:151-60 PMID 17264919
- ↑ Hoelzer GA, Smith E, Pepper JW. (2006) Perspective: On the logical relationship between natural selection and self-organization. J Evol Biol. 19(6):1785-94.
- ↑ Heylighen F (2001) The Science of Self-organization and Adaptivity. In: Kiel LD (ed.) Knowledge Management, Organizational Intelligence and Learning, and Complexity: The Encyclopedia of Life Support Systems EOLSS) Oxford: Eolss
- From the Abstract: "Self-organization can be defined as the spontaneous creation of a globally coherent pattern out of local interactions…Formally, the basic mechanism underlying self-organization is the (often noise-driven) variation which explores different regions in the system’s state space until it enters an attractor. This precludes further variation outside the attractor, and thus restricts the freedom of the system’s components to behave independently. This is equivalent to the increase of coherence, or decrease of statistical entropy, that defines self-organization."
- ↑ Harold FM. (2005) Molecules into cells: specifying spatial architecture. Microbiol Mol Biol Rev 69:544-64 PMID 16339735
- Abstract: A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth.
- ↑ Loewenstein WR (1999) The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life. Oxford University Press, New York. ISBN 0-19-514057-5 Full-Text Online with Subscription
- ↑ 11.0 11.1 Noble D (2002) Modeling the heart—from genes to cells to the whole organ. Science 295:1678-82]
- ↑ Sidney Brenner’s Nobel lecture (2002) “Nature’s Gift to Science”
- ↑ Brenner S (1998) Biological computation Novartis Found Symp 213:106-11 PMID 9653718
- ↑ Dawkins R (1988) The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. New York: W.W. Norton & Company, Inc. ISBN 0393304485 Excerpt from Amazon.com review: “The title of this 1986 work, Dawkins's second book, refers to the Rev. William Paley's 1802 work, Natural Theology, which argued that, just as finding a watch would lead you to conclude that a watchmaker must exist, the complexity of living organisms proves that a Creator exists. Not so, says Dawkins: "the only watchmaker in nature is the blind forces of physics, albeit deployed in a very special way... it is the blind watchmaker." (Physics, of course, includes open-system non-equilibrium thermodynamics, pivotal to understanding how living systems fabricate and sustain themselves.)
- ↑ Mendoza M et al. (2004) Emergence of community structure in terrestrial mammal-dominated ecosystems. J Theor Biol :203-214] PMID 15302552.