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==Self-organization==
==test==
{|align="right" cellpadding="10" style="background-color:lightyellow; width:40%; border: 1px solid #aaa; margin:1px; font-size: 85%;"
Thomas Jefferson National Accelerator Facility.
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[http://education.jlab.org/itselemental/index.html The Periodic Table of Elements.]
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
* Clicking on an element brings up a page containing a wealth of information about that element. For example, clicking on 'V' (vanadium) bring up [http://education.jlab.org/itselemental/ele023.html this page], maintained by Steve Gagnon (last accessed 27-Sep-2009), reproduced below (with formatting changes):
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** The Element Vanadium ([http://education.jlab.org/itselemental/iso023.html Click for Isotope Data])<br>
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.<ref name=lehn2002pnas>Lehn JM. (2002) [http://www.pnas.org/cgi/doi/10.1073/pnas.072065599 Toward complex matter: supramolecular chemistry and self-organization.] ''Proc Natl Acad Sci USA'' 99:4763-4768 PMID 11929970
** '''Atomic Number''': 23<br>
:*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]."</ref>&nbsp;<ref name=lehn02>Lehn JM (2002) [http://dx.doi.org/10.1126/science.1071063 Toward self-organization and complex matter] ''Science'' 295:2400-3 PMID 11923524</ref>&nbsp;<ref name=steed2009>Steed JW, Atwood JL. (2009) Supramolecular Chemistry. 2nd edition. Wiley. ISBN 978-04705112340.
** '''Atomic Weight''': 50.9415<br>
* '''<u>Excerpt:</u>'''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.</ref> 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:
** '''Melting Point''': 2183 K (1910°C or 3470°F)<br>
 
** '''Boiling Point''': 3680 K (3407°C or 6165°F)<br>
<blockquote>
** '''Density''': 6.0 grams per cubic centimeter<br>
<p style="margin-left:2.0%; margin-right:6%;font-size:0.95em;"><font face="Comic San MS, Trebuchet MS, Consolas">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.</font> <ref name=lehn2002pnas/></p>
** '''Phase at Room Temperature''': Solid<br>
</blockquote>
** '''Element Classification''': Metal<br>
 
** '''Period Number''': 4    '''Group Number''': 5    '''Group Name''': none<br>
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.<ref name=lehn02/> <ref>Percec V, Ungar G, Peterca M (2006) [http://dx.doi.org/10.1126/science.1129512 Self-assembly in action.] ''Science'' 313:55-6 PMID 16825559</ref>&nbsp;To quote Reinhout and Crego-Calama:<ref>Reinhoudt DN, Crego-Calama M (2002) [http://dx.doi.org/10.1126/science.1069197 Synthesis beyond the molecule] ''Science'' 295:2403-7 PMID 11923525</ref>
** '''What's in a name?''' Named for the Scandinavian goddess Vanadis.<br>
 
** '''Say what?''' Vanadium is pronounced as veh-NAY-di-em.<br>
<blockquote>
** '''History and Uses''':<br>
<p style="margin-left:2.0%; margin-right:6%;font-size:0.95em;"><font face="Comic San MS, Trebuchet MS, Consolas">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..</font></p>
*** Vanadium was discovered by Andrés Manuel del Rio, a Mexican chemist, in 1801. Rio sent samples of vanadium ore and a letter describing his methods to the Institute de France in Paris, France, for analysis and confirmation. Unfortunately for Rio, his letter was lost in a shipwreck and the Institute only received his samples, which contained a brief note describing how much this new element, which Rio had named erythronium, resembled chromium. Rio withdrew his claim when he received a letter from Paris disputing his discovery. Vanadium was rediscovered by Nils Gabriel Sefstrôm, a Swedish chemist, in 1830 while analyzing samples of iron from a mine in Sweden. Vanadium was isolated by Sir Henry Enfield Roscoe, an English chemist, in 1867 by combining vanadium trichloride (VCl3) with hydrogen gas (H2). Today, vanadium is primarily obtained from the minerals vanadinite (Pb5(VO)3Cl) and carnotite (K2(UO2)2VO4•1-3H2O) by heating crushed ore in the presence of carbon and chlorine to produce vanadium trichloride. The vanadium trichloride is then heated with magnesium in an argon atmosphere.<br>
</blockquote>
*** Vanadium is corrosion resistant and is sometimes used to make special tubes and pipes for the chemical industry. Vanadium also does not easily absorb neutrons and has some applications in the nuclear power industry. A thin layer of vanadium is used to bond titanium to steel.<br>
 
*** Nearly 80% of the vanadium produced is used to make ferrovanadium or as an additive to steel. Ferrovanadium is a strong, shock resistant and corrosion resistant alloy of iron containing between 1% and 6% vanadium. Ferrovanadium and vanadium-steel alloys are used to make such things as axles, crankshafts and gears for cars, parts of jet engines, springs and cutting tools.<br>
Again, J-M Lehn:<ref name=lehn07>Lehn JM (2007) [http://dx.doi.org/10.1039/b616752g From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry.] ''Chem Soc Rev'' 36:151-60 PMID 17264919</ref>
*** Vanadium pentoxide (V2O5) is perhaps vanadium's most useful compound. It is used as a mordant, a material which permanently fixes dyes to fabrics. Vanadium pentoxide is also used as a catalyst in certain chemical reactions and in the manufacture of ceramics. Vanadium pentoxide can also be mixed with gallium to form superconductive magnets.<br>
 
** '''Estimated Crustal Abundance''': 1.20×102 milligrams per kilogram<br>
<blockquote>
** '''Estimated Oceanic Abundance''': 2.5×10-3 milligrams per liter<br>
<p style="margin-left:2.0%; margin-right:6%;font-size:0.95em;"><font face="Comic San MS, Trebuchet MS, Consolas">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.</font></p>
** '''Number of Stable Isotopes''': 1  ([http://education.jlab.org/itselemental/iso023.html View all isotope data])<br>
</blockquote>
** '''Ionization Energy''': 6.746 eV<br>
 
** '''Oxidation States''': +5, +4, +3, +2
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.
** '''Electron Shell Configuration''': 1s2 2s2 2p6 3s2 3p6 3d3 4s2
 
Many workers (see: Hoelzer et al. <ref name=hoelzer2006>Hoelzer GA, Smith E, Pepper JW. (2006) [http://dx.doi.org/10.1111/j.1420-9101.2006.01177.x Perspective: On the logical relationship between natural selection and self-organization.] ''J Evol Biol.'' 19(6):1785-94.</ref>) 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 &mdash; the extraction of work through channeling free energy gradients &mdash; 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 (Biology)|homeostasis]] or adaptability. Thus, order emerges out of chaos.<ref>Heylighen F (2001) [http://209.85.173.104/search?q=cache:yKBZk1ta9UsJ:pespmc1.vub.ac.be/Papers/EOLSS-Self-Organiz.pdf+heylighen+%22the+science+of+self-organization+and+adaptivity%22&hl=en&ct=clnk&cd=3&gl=us  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."</ref>
 
Professor of Microbiology, Franklin M. Harold, offers the following definition of self-organization:
 
<blockquote>
<p style="margin-left:2.0%; margin-right:6%;font-size:0.95em;"><font face="Comic San MS, Trebuchet MS, Consolas">...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.</font><ref name=harold05>Harold FM. (2005) [http://dx.doi.org/10.1128/MMBR.69.4.544-564.2005 Molecules into cells: specifying spatial architecture.] ''Microbiol Mol Biol Rev'' 69:544-64 PMID 16339735
* <b><u>Abstract:</u></b>&nbsp;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.</ref></p>
</blockquote>
 
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.<ref name=loewenstein1999>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 [http://www.questia.com/read/62414230# Full-Text Online with Subscription]</ref>
 
One way to understand this self-organization is to view a living system as a 'computing device'. The inherited and acquired information base &mdash; the genome &mdash; specifies components which arrange themselves in accord with their physico-chemical properties &mdash; i.e., they 'compute' the system in a complex chemical reaction.  Systems biologist, Denis Noble, incisively describes it:
 
<blockquote>
<p style="margin-left:2.0%; margin-right:6%;font-size:0.95em;"><font face="Comic San MS, Trebuchet MS, Consolas">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….</font><ref name=noble02>Noble D (2002) [http://dx.doi.org/10.1126/science.1069881 Modeling the heart—from genes to cells to the whole organ.] ''Science'' 295:1678-82]</ref></p>
</blockquote>
 
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.<ref name=noble02>Noble D (2002) [http://dx.doi.org/10.1126/science.1069881 Modeling the heart—from genes to cells to the whole organ.] ''Science'' 295:1678-82]</ref>
 
The molecular biologist [[Sidney Brenner]]<ref>Sidney Brenner’s Nobel lecture (2002) [http://nobelprize.org/nobel_prizes/medicine/laureates/2002/brenner-lecture.html “Nature’s Gift to Science”]</ref> expressed the 'computing device' metaphor this way:
 
<blockquote>
<p style="margin-left:2.0%; margin-right:6%;font-size:0.95em;"><font face="Comic San MS, Trebuchet MS, Consolas">...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.</font><ref>Brenner S (1998) [http://www3.interscience.wiley.com/cgi-bin/bookhome/114294640/ Biological computation] ''Novartis Found Symp'' 213:106-11 PMID 9653718</ref></p>
</blockquote>
 
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 &mdash; 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".<ref>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.)</ref>
 
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."<ref>Mendoza M ''et al.'' (2004)  [http://dx.doi.org/10.1016/j.jtbi.2004.05.002230 Emergence of community structure in terrestrial mammal-dominated ecosystems.] ''J Theor Biol'' :203-214] PMID 15302552.</ref>
 
Further elaborating the descriptions of living systems beyond the thermodynamic and evolutionary perspectives, we might say that:
 
{|cellpadding=10 align=center style="width:80%; border: solid 1px #4682b4; background:lightblue"
|A living system:
:*Organizes ''itself'' into a spatio-temporal dynamic system
:*Such self-organization happens as a spontaneous manifestation of the physico-chemical interactions among the system's components, influenced by the larger system embedding it, and by that systems interactions with its environment
|}
<br>
 
===refs===
<references/>

Revision as of 19:27, 27 September 2009

test

Thomas Jefferson National Accelerator Facility. The Periodic Table of Elements.

  • Clicking on an element brings up a page containing a wealth of information about that element. For example, clicking on 'V' (vanadium) bring up this page, maintained by Steve Gagnon (last accessed 27-Sep-2009), reproduced below (with formatting changes):
    • The Element Vanadium (Click for Isotope Data)
    • Atomic Number: 23
    • Atomic Weight: 50.9415
    • Melting Point: 2183 K (1910°C or 3470°F)
    • Boiling Point: 3680 K (3407°C or 6165°F)
    • Density: 6.0 grams per cubic centimeter
    • Phase at Room Temperature: Solid
    • Element Classification: Metal
    • Period Number: 4 Group Number: 5 Group Name: none
    • What's in a name? Named for the Scandinavian goddess Vanadis.
    • Say what? Vanadium is pronounced as veh-NAY-di-em.
    • History and Uses:
      • Vanadium was discovered by Andrés Manuel del Rio, a Mexican chemist, in 1801. Rio sent samples of vanadium ore and a letter describing his methods to the Institute de France in Paris, France, for analysis and confirmation. Unfortunately for Rio, his letter was lost in a shipwreck and the Institute only received his samples, which contained a brief note describing how much this new element, which Rio had named erythronium, resembled chromium. Rio withdrew his claim when he received a letter from Paris disputing his discovery. Vanadium was rediscovered by Nils Gabriel Sefstrôm, a Swedish chemist, in 1830 while analyzing samples of iron from a mine in Sweden. Vanadium was isolated by Sir Henry Enfield Roscoe, an English chemist, in 1867 by combining vanadium trichloride (VCl3) with hydrogen gas (H2). Today, vanadium is primarily obtained from the minerals vanadinite (Pb5(VO)3Cl) and carnotite (K2(UO2)2VO4•1-3H2O) by heating crushed ore in the presence of carbon and chlorine to produce vanadium trichloride. The vanadium trichloride is then heated with magnesium in an argon atmosphere.
      • Vanadium is corrosion resistant and is sometimes used to make special tubes and pipes for the chemical industry. Vanadium also does not easily absorb neutrons and has some applications in the nuclear power industry. A thin layer of vanadium is used to bond titanium to steel.
      • Nearly 80% of the vanadium produced is used to make ferrovanadium or as an additive to steel. Ferrovanadium is a strong, shock resistant and corrosion resistant alloy of iron containing between 1% and 6% vanadium. Ferrovanadium and vanadium-steel alloys are used to make such things as axles, crankshafts and gears for cars, parts of jet engines, springs and cutting tools.
      • Vanadium pentoxide (V2O5) is perhaps vanadium's most useful compound. It is used as a mordant, a material which permanently fixes dyes to fabrics. Vanadium pentoxide is also used as a catalyst in certain chemical reactions and in the manufacture of ceramics. Vanadium pentoxide can also be mixed with gallium to form superconductive magnets.
    • Estimated Crustal Abundance: 1.20×102 milligrams per kilogram
    • Estimated Oceanic Abundance: 2.5×10-3 milligrams per liter
    • Number of Stable Isotopes: 1 (View all isotope data)
    • Ionization Energy: 6.746 eV
    • Oxidation States: +5, +4, +3, +2
    • Electron Shell Configuration: 1s2 2s2 2p6 3s2 3p6 3d3 4s2
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