Emergence (biology): Difference between revisions

From Citizendium
Jump to navigation Jump to search
imported>John R. Brews
(→‎Supervenience: reword to be less strident)
imported>John R. Brews
(→‎Supervenience: miswording)
Line 31: Line 31:
</ref>  
</ref>  


Supervenience is a deceptive descriptor. For example, consider the relations between a microscopic theory like [[kinetic theory]] based upon specific interactions, a mesoscopic theory like [[statistical mechanics]] largely independent of the specifics of interactions, and a macroscopic theory like [[thermodynamics]] where microscopic considerations about interactions are not considered.  According to the definition above, statistical mechanics is not supervenient of the microscopic theory, because many different systems have the same thermodynamic description. On the other hand, a change in temperature is a key element in thermodynamics, related to microscopic theory by statistical mechanics. So it appears that a macroscopic theory is supervenient of a more microscopic theory that explains the macroscopic theory on a more fundamental level. Although strictly within a thermodynamic description it may be correct to say that a change in temperature ''causes'' a [[Phase (chemistry)|phase]] change, say from ice to water, the microscopic theory provides a deeper understanding of phase changes entirely in terms of the fundamental atomic interactions.<ref name=caveat>
Supervenience is a deceptive descriptor. For example, consider the relations between a microscopic theory like [[kinetic theory]] based upon specific interactions, a mesoscopic theory like [[statistical mechanics]] largely independent of the specifics of interactions, and a macroscopic theory like [[thermodynamics]] where microscopic considerations about interactions are not considered.  According to the definition above, thermodynamics is not supervenient of the microscopic theory, because many different systems have the same thermodynamic description. On the other hand, a change in temperature is a key element in thermodynamics, related to microscopic theory by statistical mechanics. So it appears that a macroscopic theory is supervenient of a more microscopic theory that explains the macroscopic theory on a more fundamental level. Although strictly within a thermodynamic description it may be correct to say that a change in temperature ''causes'' a [[Phase (chemistry)|phase]] change, say from ice to water, the microscopic theory provides a deeper understanding of phase changes entirely in terms of the fundamental atomic interactions.<ref name=caveat>


This view must be tempered by the observation that application of statistical methods to complex systems often imposes statistical assumptions that are not obvious from the microscopic viewpoint.</ref>  
This view must be tempered by the observation that application of statistical methods to complex systems often imposes statistical assumptions that are not obvious from the microscopic viewpoint.</ref>  

Revision as of 08:19, 29 August 2012

This article is developing and not approved.
 Main Article
 Discussion
Related Articles  [?]
Bibliography  [?]
External Links  [?]
Citable Version  [?]
 
https://en.citizendium.org/wiki/index.php?title=Emergence_(biology)&printable=yes
This editable Main Article is under development and subject to a disclaimer.

Systems biologists and theoretical biologists study, among other things, the phenomenon of emergence, the exhibition of new properties related to the complexity of organization.[1] These properties are viewed by some as inexplicably unpredicted novel properties, functions and behaviors, ones not observed in the system's subsystems and their components, and not explainable or predictable from complete understanding the components' properties/functions/behaviors considered in isolation from the system that embeds them. Others take the view that these novel properties are the outcome of interactions between the constituents understandable from microscopic behavior, but more readily envisioned by introduction of novel organizational concepts.

Every cellular system in biology exhibits emergent behaviors. Emergent behaviors of living systems include such things as locomotion, sexual display, flocking, and conscious experiencing. Even the biological components of living cells, such as mitochondria and other organelles, exhibit emergent properties.

This article will explore emergence as a concept with a long history, differing interpretations, and much controversy.

Water as an example

For an example of emergence in a non-living thing: We can say that the properties we associate with liquid water, its transparency, its wetness, its ability to flow, etc., 'emerge' from the properties of oxygen and hydrogen and their organizational dynamics. Consider these questions:

  • Would we expect that oxygen and hydrogen interacting in accord with their known properties, enabling them to self-assemble into a self-organized dynamic, to result in a fluid with the characteristics of a bowlful of water as we observe them with our native senses?
  • Would we need to know thoroughly the characteristics/dynamics of the environment — to see how they might co-determine the behavior of hydrogen and oxygen, known to behave differently under different environmental conditions — in order to approach the task of visualizing water from its particulate/energetic components, hydrogen and oxygen?
  • Would constructing a computer requiring the resources of the entire universe provide sufficient information processing capability to explain the look and feel, and the chemistry, of water as medium for living systems and their systems?
  • Wouldn't the computer need the ability to compute water molecule interactions with every other compound/ion in the system.

Supervenience

A concept often used in discussing emergence is supervenience, often mistakenly taken to indicate what controls what. State A is supervenient of state B if and only if every change in A requires a change in B.[2]

Supervenience is a deceptive descriptor. For example, consider the relations between a microscopic theory like kinetic theory based upon specific interactions, a mesoscopic theory like statistical mechanics largely independent of the specifics of interactions, and a macroscopic theory like thermodynamics where microscopic considerations about interactions are not considered. According to the definition above, thermodynamics is not supervenient of the microscopic theory, because many different systems have the same thermodynamic description. On the other hand, a change in temperature is a key element in thermodynamics, related to microscopic theory by statistical mechanics. So it appears that a macroscopic theory is supervenient of a more microscopic theory that explains the macroscopic theory on a more fundamental level. Although strictly within a thermodynamic description it may be correct to say that a change in temperature causes a phase change, say from ice to water, the microscopic theory provides a deeper understanding of phase changes entirely in terms of the fundamental atomic interactions.[3]

In a similar vein, the notions of chemical bonding, valence, and so forth are used directly in molecular physics and chemistry to explain how atoms engage with one another, and one might say a particular molecule is the result of such factors, which supervene atomic behavior. But the explanation of these factors lies within quantum mechanics, which does not use the term "bond" at all, and describes all chemistry in terms of electron behavior and electromagnetic interactions.

One may well assert the "poverty of the supervenience relation".[2]

Emergence in biology as materialistic vitalism

Emergence relates to phenomena that arise from and depend on some more basic phenomena yet are simultaneously autonomous from that base.[4]


Given emergence, some biologists might find it tempting to see a type of 'vitalism', or 'life force', in living systems. What physico-chemical mechanisms explain emergence, they ask? What explains the behavior of an organism fleeing from a predator if studying all the subsystems does not visualize the predator-prey phenomenon? The answer: to see the emergent phenomenon one must study the organized behavior of those subsystems and the dynamics of that organized behavior and consider the novelty of the system's behaviors that organized interacting subsystems would engender, and that natural selection would operate on its variations.[5]

Because biologists and their co-scientists can explain emergent properties/phenomena, if only sometimes in principle, by mechanisms that do not transcend interactions of matter and energy, any ‘vitalism’ position properly can credit only a ‘materialistic vitalism’, which gives 'vitalism' a new sense. A new sense that incorporates the mystery of how does emergence-generating organization arise. The mystery dispels in biology by the realization that organisms organize themselves, having developed their pattern of behavior by trial and error and natural selection. The rest is history, a history that leads to the mystery of the origin of life.

Whatever the origin of life, incidentally, if evolution-based biological emergence can lead to cognition capable of wondering how living systems originated, what possible more complex cognition might emerge through continued trial-and-error and natural selection? Global brains, group minds? What limits to the capacity and properties of evolving emergent cognition exist, if any? Can a galactic-wide living system emerge and if so, can we imagine its physiological cognitive parameters? Scientists of philosophic bent, and philosophers of science, like to consider those kinds of interesting meta-science questions.

Emergence in biology, the new now-materialistic vitalism, appears spontaneously through energy expenditure from an external source working on matter particles, the various patterns of biological emergence persisting to the extent their organization has the ability to retain its materialistic vitality. The real mystery: the origin of matter and energy. The non-materialistic vitalist can retreat to that mystery to argue for old-time vitalism, if cannot have faith in science.

Examples of emergence

One example of emergence: When the components of signaling pathway, one that enable between-cell communication, interact to form a functional network of signaling systems, novel properties/behaviors can arise — such as a self-sustaining feedback loop and generation of the signals themselves; signal integration across multiple time scales; and, generation of distinct outputs depending on input strength and duration.[6] One cannot explain or predict those novelties from combined knowledge of the individuated properties of the separate components of the network system. Such networks produce emergent phenomena.

For another example, in studying a protein separated from the cellular system that embeds it in a cell, one can observe many of its chemical and physical properties, but with increasing knowledge of those properties one approaches no closer to explaining any of the properties it has only in the context of the system that embeds it, such as the operation of catalyzing a biochemical reaction, or of binding to other proteins to form a protein complex that generates novel behavior. Those behaviors of the protein emerge in the context of the protein’s environment — how it interacts in the context of the system as a whole. Moreover, those emergent properties may result in effects within the system that, in a feedback way, further alters the emergent behavior of the protein in the system, as when a reaction product alters the catalytic ability of the protein.

Emergent processes have been recognised as, for example, contributing to understanding:

  • subcellular morphology[7],
  • developmental biology[8],
  • metabolic networks[9],
  • proteomics[10] [11]
  • evolution of complexity in living things

Emergent phenomena appear even in non-biological physical systems.[12] Emergent phenomena attract the attention of cellular neuroscientists;[13]  and cognitive scientists[14]. Emergent properties manifest in the behaviour of ant colonies and in swarm intelligence.[15] Systems scientists have simulated emergent phenomena.[16]  Emergent phenomena in human societies has also received attention. [17]. Biologists even explain the biosphere itself as emergent.[18]

Why emergence

Why do not all of the properties/behaviors of a living system predictably result from the properties of its components? After all, the reductionist paradigm that dominated the Scientific method in the 20th century operated on the assumption that they could. One reason: the intrinsic properties of a system’s components cannot themselves determine those of the whole system; rather, their 'organizational dynamics' does — how the components interact coordinately in time and space. Those organizational dynamics include not only the interrelations among the components themselves, but also interactions among the many different organizational units in the system. [19] Secondly, the living system always operates in a certain context (its external environment, or surroundings), and those surroundings, in turn, always affect the properties of the system-as-a-whole. For example, nutrient gradients in its environment influence the direction a bacterium’s locomotion. The impact of environmental context affects the dynamic organization of the components within the system — a 'downward causation'. [20] For another example, environmental signals can activate or suppress a metabolic pathway, reorganizing cellular activity[21] One cannot simply take a living system apart and predict how it will behave in its natural environment.

As Gilbert and Sarkar[5] puts it: “Thus, when we try to explain how the whole system behaves, we have to talk about its parts the context of the whole and cannot get away talking only about the parts.”

Philosopher of science D.M. Walsh puts it this way: "The constituent parts and processes of a living thing are related to the organism as a whole by a kind of 'reciprocal causation'."[22] In other words, the organization of the components determine the behavior of the system, but that organization arises from more than the set of its internal components. How the whole system behaves as it interacts with its environment determines how those components organize themselves, and so novel properties of the system 'emerge' that characterize neither the environment nor that set of internal components.

For example, the behavior of a human kidney cell depends not only on its cellular physiology, but also on all the properties of the organ (kidney) which constitutes its environment. The kidney's overall structure and function influence the cell’s structure and behavior (e.g., by physical confinement and by cell-to-cell signaling), which in turn influence the organization of its intracellular components. The kidney in turn responds to its environment, namely the individual body that it lives in, and that body responds to its environment, which includes such factors as the availability of particular food items, fresh water, and ambient temperature and humidity. Systems biologists regard emergent properties as arising from a combination of bottom-up and top-down effects — Walsh's 'reciprocal causation'. The "top" consists in the effects of the system's interactions with its environments. The "bottom", the effects of the interactions of the system's components.

Using the example of termites out of whose combined individual behaviors without outside management emerge complex colony mounds, a recent National Research Council report on the role of theory in advancing 21st century biology commented on emergent behavior as follows:[23]

A reasonable way of thinking about emergent behavior might be to focus on the level or scale at which the rules reside. If the rules are specified at a low level, for example, the individual termites, and the patterns and structures, like termite mounds, emerge at a scale where there are no rules specified, we may call this emergent behavior.[23]

Other examples of rule-free emergent behavior for which the 'rules' appear specified at a lower level than the emergent behavior itself include the flocking behavior of birds, and the folding of amino acid polymers into catalytic proteins.

Emergence and complexity

Emergent systems always display what we recognize as ‘complexity’, a feature we have a difficult time precisely defining. Complex systems appear to require more bits of information (words, sentences, lines of computer code, etc.) to describe than the bits of information in the system itself. [24]  The operation of the system itself supplies its own most economical model.

According the paleontologist and origin of life researcher, Robert Hazen, four basic complexity elements underpin emergence in a system: [25]

  • a sufficiently large ‘density’ of components, with increasing complexity as the concentration increases, up to a point;
  • sufficient interconnectivity of the components, with increasing complexity with greater and more varied types of interconnectivity, up to a point;
  • a sufficient energy flow through the system to enable the system’s components to perform the work of interacting in the self-organized way characteristic of the energized system;
  • flow of energy through the system in a cyclic manner, presumably facilitating the spatiotemporal patterning characteristic of organized systems.

Coherent entities and coherence detectors

We can think of emergence as the appearance of a novel 'coherent entity', coherent in the sense of the entity behaving in a functionally consistent manner, and an entity in virtue of that functionally consistent behavior. Perhaps the human circulatory system exemplifies functionally consistent behavior, and qualifies as a coherent entity. But to see it, we need a way to detect the existence, properties, and behaviors of the circulatory system — a coherence detector. Physiology and systems biology predominately study emergent phenomena, coherent entities exhibiting unexpected behavior produced by dynamic physico-chemical processes of great complexity. The emergent behaviors they study depend on their resources of coherence detectors, making observer-dependence a property of emergence. In biology, emergent systems abound, suggesting greater abundance as coherence detection advances in sensitivity and power.


References

Citations and notes

  1. ↑ Bernard Feltz, Marc Crommelinck, Philippe Goujon (2006). “Introduction”, Bernard Feltz, Marc Crommelinck, Philippe Goujon, eds: Self-organization and Emergence in Life Sciences. Springer. ISBN 1402039166. 
  2. ↑ 2.0 2.1 Cliff A. Hooker (2011). “Conceptualizing reduction, emergence, and self-organization in complex dynamical systems”, Cliff A. Hooker, ed: Philosophy of Complex Systems. Elsevier, p. 212. ISBN 0444520767. 
  3. ↑ This view must be tempered by the observation that application of statistical methods to complex systems often imposes statistical assumptions that are not obvious from the microscopic viewpoint.
  4. ↑ Bedau MA, Humphreys P. (editors) (2008) Emergence: contemporary readings in philosophy and science. A Bradford book." ISBN 978-0-262-02621-5 (hc), ISBN 978-0-262-52475-9 (pbk)
    • From publisher´s description:  This reader collects...classic writings on emergence from contemporary philosophy and science...three sections ("Philosophical Perspectives," "Scientific Perspectives," and "Background and Polemics")...A bibliography lists more specialized material, and an associated website (http://mitpress.mit.edu/emergence) links to downloadable software and to other sites and publications about emergence.
    • Contributors:  P. W. Anderson, Andrew Assad, Nils A. Baas, Mark A. Bedau, Mathieu S. Capcarrère, David Chalmers, James P. Crutchfield, Daniel C. Dennett, J. Doyne Farmer, Jerry Fodor, Carl Hempel, Paul Humphreys, Jaegwon Kim, Robert B. Laughlin, Bernd Mayer, Brian P. McLaughlin, Ernest Nagel, Martin Nillson, Paul Oppenheim, Norman H. Packard, David Pines, Steen Rasmussen, Edmund M. A. Ronald, Thomas Schelling, John Searle, Robert S. Shaw, Herbert Simon, Moshe Sipper, Stephen Weinberg, William Wimsatt, and Stephen Wolfram
    • About the Editors:  Mark A. Bedau is Professor of Philosophy and Humanities at Reed College in Portland, Oregon. He is the coeditor of Emergence: Contemporary Readings in Science and Philosophy and Protocells: Bridging Nonliving and Living Matter, both published by the MIT Press in 2008….Paul Humphreys is Professor of Philosophy at the University of Virginia.
    • Table of Contents and Downloadable Sample Chapters.
  5. ↑ 5.0 5.1 Gilbert SF, Sarkar S. (2000) Embracing complexity: organicism for the 21st century. Dev. Dyn 219:1-9 PMID 10974666
    • Abstract: Organicism (materialistic holism) has provided the philosophical underpinnings for embryology since the time of Kant. It had influenced the founders of developmental mechanics, and the importance of organicism to embryology was explicitly recognized by such figures as O. Hertwig, H. Spemann, R. Harrison, A. M. Dalq, J. Needham, and C. H. Waddington. Many of the principles of organicism remain in contemporary developmental biology, but they are rarely defined as such. A combination of genetic reductionism and the adoption of holism by unscientific communities has led to the devaluation of organicism as a fruitful heuristic for research. This essay attempts to define organicism, provide a brief history of its importance to experimental embryology, outline some sociologically based reasons for its decline, and document its value in contemporary developmental biology. Based on principles or organicism, developmental biology should become a science of emerging complexity. However, this does mean that some of us will have to learn calculus.
  6. ↑ Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283:381-387 PMID 9888852
    • Abstract: Many distinct signaling pathways allow the cell to receive, process, and respond to information. Often, components of different pathways interact, resulting in signaling networks. Biochemical signaling networks were constructed with experimentally obtained constants and analyzed by computational methods to understand their role in complex biological processes. These networks exhibit emergent properties such as integration of signals across multiple time scales, generation of distinct outputs depending on input strength and duration, and self-sustaining feedback loops. Feedback can result in bistable behavior with discrete steady-state activities, well-defined input thresholds for transition between states and prolonged signal output, and signal modulation in response to transient stimuli. These properties of signaling networks raise the possibility that information for "learned behavior" of biological systems may be stored within intracellular biochemical reactions that comprise signaling pathways.
  7. ↑ Tabony J (2006) Microtubules viewed as molecular ant colonies. Biol Cell 98:603-17 PMID 16968217
  8. ↑ Theise ND, d'Inverno M (2004) Understanding cell lineages as complex adaptive systems. Blood Cells Mol Dis 32:17-20 PMID 14757407 and Ruiz i Altaba A et al. (2003) The emergent design of the neural tube: prepattern, SHH morphogen and GLI code. Curr Opin Genet Dev 13:513-21 PMID 14550418
  9. ↑ Jeong H et al.(2000) The large scale organisation of metabolic networks. Nature 407:651-4
  10. ↑ e.g. Grindrod P, Kibble M (2004) Review of uses of network and graph theory concepts within proteomics. Expert Rev Proteomics 1:229-38 PMID 15966817
  11. ↑ Ye X et al.(2005) Multi-scale methodology: a key to deciphering systems biology. Front Biosci 10:961-5 PMID 15569634
  12. ↑ Cho YS et al. (2005) Self-organization of bidisperse colloids in water droplets. J Am Chem Soc 127:15968-75 PMID 16277541
  13. ↑ see e.g. Burak Y, Fiete I (2006) Do we understand the emergent dynamics of grid cell activity? J Neurosci 26:9352-4 PMID 16977716
  14. ↑ e.g. Courtney SM (2004) Attention and cognitive control as emergent properties of information representation in working memory. Cogn Affect Behav Neurosci 4:501-16 PMID 15849893
  15. ↑ Theraulaz G et al (2002) Spatial patterns in ant colonies. Proc Natl Acad Sci USA 99:9645-9 PMID 12114538
  16. ↑ Theraulaz G, Bonabeau E (1999)A brief history of stigmergy. Artif Life 5:97-116 PMID 10633572
  17. ↑ Bonabeau E, Meyer C (2001) Swarm intelligence. A whole new way to think about business. Harv Bus Rev 79:106-14 PMID 11345907
  18. ↑ Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 281:237-40.
  19. ↑ Note: For example, physical chemists cannot predict the properties of water from knowledge of its components, hydrogen and oxygen. The way hydrogen and water interact to form H2O, and the way H2O molecules interact, enables the properties of water to 'emerge'.
  20. ↑ Note: Following up on the example of water, the properties of its environment (e.g., temperature, pressure) affect the way the H2O molecules organize themselves, as ice, or liquid, or steam
  21. ↑ Note: In relation to downward causation, the environment’s effect can sometimes reach down to the genetic database with molecular signals, altering its expression and consequently the characteristics of the cells without altering the database itself — so-called 'epigenetic' effects. When epigenetic alterations of gene expression occur in the reproductive organs, the system changes can be transmitted to the next generation. See
    • Jablonka E, Lamb MJ (2005) Evolution in Four Dimension: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge: MIT Press
    • Gorelick R (2004) Neo-Lamarckian medicine. Med Hypotheses 62:299-303 PMID 14962644
  22. ↑ Walsh DM (2006) Organisms as natural purposes: the contemporary evolutionary perspective. Stud Hist Philos Biol Biomed Sci 37: 771-91
  23. ↑ 23.0 23.1 Committee on Defining and Advancing the Conceptual Basis of Biological Sciences in the 21st Century, National Research Council. (2008) The Role of Theory in Advancing 21st Century Biology: Catalyzing Transformative Research. Board on Life Sciences, Division on Earth and Life Studies, National Research Council of the National Academies. The National Academies Press, Washington, D.C. ISBN 978-0-309-11249-9.
  24. ↑ (1991) Zurek WJ (ed) Complexity, Entropy, and the Physics of Information: The Proceedings of the Workshop on the Complexity, Entropy, and the Physics of Information May-June, 1989, Santa Fe, New Mexico. Addison-Wesley Publishing Company, The Advanced Book Program, Redwood City. ISBN 0201515091
  25. ↑ Hazen RM (2005) Genesis: The Scientific Quest for Life's Origin. Joseph Henry Press, Washington DC. ISBN 0309094321
Retrieved from "https://citizendium.org/wiki/index.php?title=Emergence_(biology)&oldid=359882"