We might be remiss if we did not mention the major methodical nemesis of reductionism, holism. In some ways holism might be thought of as the opposite of reductionism: often summarized as “the whole is greater than the sum of its parts,” the relation of the parts to the whole is such that the individual parts do not explain the state of the whole. This includes aspects of emergent properties that can’t be reduced to the parts that produce it. This latter formulation is the Cousin of holism, nonseperablity. This is the idea that the state of the parts do not explain the state of the whole. Holism as a mythodological thesis can best be understood as the idea that “the best way to study the behavior of a complex system is to treat it as a whole.” Holism may also be a metaphysical thesis. In that sense it’s about the relation of the whole to laws that govern it and the independence of the law from the individual parts. There are three types of metaphysical holism:
Ontological Holism: Some objects are not wholly composed of basic physical parts.
Property Holism: Some objects have properties that are not determined by physical properties of their basic physical parts.
Nomological Holism: Some objects obey laws that are not determined by fundamental physical laws governing the structure and behavior of their basic physical parts.
Apparently most physicists are holists in methodological terms, but there are notable exceptions. Both methodological and metaphysical versions of holism and reductionism are assumed in different ways among physicists.
It is surprisingly difficult to find methodological reductionists among physicists. The elementary particle physicist Steven Weinberg, for example, is an avowed reductionist. He believes that by asking any sequence of deeper and deeper why-questions one will arrive ultimately at the same fundamental laws of physics. But this explanatory reductionism is metaphysical in so far as he takes explanation to be an ontic rather than a pragmatic category. On this view, it is not physicists but the fundamental laws themselves that explain why “higher level” scientific principles are the way they are. Weinberg (1992) explicitly distinguishes his view from methodological reductionism by saying that there is no reason to suppose that the convergence of scientific explanations must lead to a convergence of scientific methods.
Carl Popper rejected holism because it has a long standing relationship with totalitarian thinking. In social terms the individual is determined by the whole, social groupings play out on a massive scale. According to the social holist individuals are formed by the social groupings to which they belong. Popper was critical of holism for this reason, this doesn’t mean that physicist using holism as a methodological tool think in a totalitarian fashion. It’s a matter of how you look at it. The reductionst reducing everything to one thing is totalitarian. The reductionist move of losing phenomena of religious experience and categorizing such experiences which they have never had is totalitarian.
We clearly see philosophical implications and repercussions in these matters. In physics science interfaces with philosophy to such a degree its hard to tell where one ends and the other begins. It would seem that what is needed a sharper focus on the use of reductionism/holism as a methodology and better fences between philosophy and physics. The problem the spreading ideology of scientism, that seems to detract from any respect for philosophy, while ransacking its territory. One commentator and blogger wrties:
I don’t know what’s the matter with physicists these days. It used to be that they were an intellectually sophisticated bunch, with the likes of Einstein and Bohr doing not only brilliant scientific research, but also interested, respectful of, and conversant in other branches of knowledge, particularly philosophy. These days it is much more likely to encounter physicists like Steven Weinberg or Stephen Hawking, who merrily go about dismissing philosophy for the wrong reasons, and quite obviously out of a combination of profound ignorance and hubris (the two often go together, as I’m sure Plato would happily point out). The latest such bore is Lawrence Krauss, of Arizona State University.
This is no mystery but what we’ve been observing. There is a tendency even among “regular science” or shall we say “real science” to infuse scientific work with philosophical assumptions. The scientistic/reductionist mentality has fomented the notion that science is the only form of knowledge. Those who take his credo seriously are assaulting real philosophy to clear it out of the way so they can make room for their ideology. If this is the only form of knowledge it’s proponents are clearing away all the non knowledge. The only problem this only knowledge is made up of different approaches to philosophy and other disciplines.
This is by no means an exhaustive account of holism. It’s very complex and just doesn’t allow for streamlined summary. There’s just too much there to justice to the topic. I would be remiss if I didn’t discuss briefly one upshot of holism which is downward causation.
Systems theory has been construed as anti-reductionism. In this stance it says “the whole is greater than the sum of the parts.” Reductionism says that we can know the nature of the whole by knowing the nature of the parts, because the whole is nothing else but the sum of the parts and can be reduced to the parts. The basic assumption of systems theory in its anti-reductionist stance is that because the whole has emergent properties it is more than the sum of its parts thus it can’t be reduced to the parts. This means that mind can’t be reduced to brain. “Emergence” is sometimes a veg idea thus some thinkers prefer to call it “downward causation.” Downward causation is the opposite of the reductionist premise: “The behavior of the parts is determined by the behavior of the whole.” “Top-down causation refers to the effects on components of organized systems that cannot be fully analyzed in terms of component-level behavior but instead requires reference to the higher-level system itself.”
There are five types of downward causation or “top-down” causation: (1) Algorithmic top down causation; (2) Non adaptive information control; (3) adaptive selection; (4) adaptive information control; (5) Intelligent top down. Random processes allow all of these forms of causation to work at the same time without negating other causal processes. Each of these five forms of causation takes place in the human brain. As an explanation of number one, (1) Algorithmic: Ellis tells us that “physics is the basic science underlying physical reality, characterized by mathematical descriptions that allow predictions of physical behavior.” He raises the question are other forms of causation merely epiphenomenal grounded in purely physical causation? This is the view of strong reductionsits. He argues that the other forms of causation do exist in the real world and that they are acting within the framework provided by Aristotle of the four kinds of causes. He gives a table that provides a simplified scheme of hierarchy of levels of reality. “Each lower level underlies what happens at each higher level in terms of causation.” Level 1: particle physics, level 2: atomic physics, level 3: chemistry, Level 4: Biochemistry, level 5:, cell biology, level 6:, physiology, level 7: psychology. Level 8: Sociology/Economics/politics.
Downward Causation also contains
But downward causation does not assert that the only direction of causation is downward. There is causation both ways; the whole is to some extent limited to the parts and vice versa. The example that Heylighen uses is that of a snow flake. Snow flakes all contain a six point similarity but within that similarity, which is the whole because it’s universally found, each crystal contains it’s totally individual shape. The shape is the result of the chemical composition of water molecules but the shape is confined to the whole.
The appearance of this "two way causation" can be explained in the following way. Imagine a complex dynamic system. The trajectories of the system through its state space are constrained by the "laws" of the dynamics. These dynamics in general determine a set of "attractors": regions in the state space the system can enter but not leave. However, the initial state of the system, and thus the attractor the system will eventually reach is not determined. The smallest fluctuations can push the system either in the one attractor regime or the other. However, once an attractor is reached, the system loses its freedom to go outside the attractor, and its state is strongly constrained.
Now equate the dynamics with the rules governing the molecules, and the attractor with the eventual crystal shape. The dynamics to some degree determines the possible attractors (e.g. you cannot have a crystal with a 7-fold symmetry), but which attractor will be eventually reached is totally unpredictable from the point of view of the molecules. It rather depends on uncontrollable outside influences. But once the attractor is reached, it strictly governs the further movement of the molecules.
The same principle applies to less rigid, mechanistic systems such as living organisms. You cannot have organisms whose internal functioning flouts the rules of physics and chemistry. However, the laws of physics are completely insufficient to determine which shapes or organizations will evolve in the living world. Once a particular biological organization has emerged, it will strongly constrain the behavior of its components.
For example, the coding of amino acids by specific triplets of bases in the DNA is not determined by any physical law. A given triplet might as well be translated into a multitude of other amino acids than the one chosen in the organisms we know. But evolution happens to have selected one specific "attractor" regime where the coding relation is unambiguously fixed, and transgressions of that coding will be treated as translation errors and therefore eliminated by the cell's repair mechanisms. 
Downward causation extends from a level above a given system downward to affect that system. When the direction of causal influence extends from beyond the system downward to affect the system we have downward causation. That means the system can’t be explained totally in terms of its individual parts. In terms of consciousness it means consciousness can’t be explained entirely in terms of brain chemistry. Cartesian dualism envisioned only two levels to reality but in modern terms modern emergantism pictures the world in multiple levels. The Cartesian levels were consciousness and extension, but…
…In contemporary emergentism the world is pictured in terms of a multilayered structure, with microphysical entities at the bottom and with higher-level entities (such as molecules, cells, organisms, and social groups) being mereologically composed of these lower-level entities, yet characterized by a set of properties distinctive of the relevant higher level. In a way, so-called nonreductive physicalism, which more or less became the received view in the philosophy of mind of the last quarter of the twentieth century, may be seen as nothing but a modern application of classical emergentism within the philosophy of mind. Although it holds that, ontologically speaking, all there is are physical entities and mereological aggregates thereof, it argues that psychological properties are irreducibly distinct from the underlying physical and biological properties.
There are two other major examples ideological reductionism: (1) Brain/mind; mind is reducible to brain function. (2) Determinism; free will reducible to an illusion by determinism.
Summary and Conclusion:
Reductionism is a valid scientific methodology, but it is more than that. Science itself is infused with ideological and philosophical implication. There is no pure human endeavor that is all knowledge and no politics. Reductionism is basically traceable to the Greeks and implies a metaphysics that would reduce all reality to one thing: in modern time in the scientistic circles that one thing can only be science. This philosophical tendency issues forth in rhetorical strategies that empirical tricks of reducing, such as labeling the loosing the phenomena. The alternative is holism, which offers philosophical alternative as well as methodological and rhetorical options. Holism opens up our thinking to a vast possibility of multidimensional reality. It offers explanations of emergent properties and top down causation that rule out much of the reductionist’s repertoire.
 Healey, Richard, "Holism and Nonseparability in Physics", The Stanford Encyclopedia of Philosophy (Spring 2009 Edition), Edward N. Zalta (ed.), URL =
 Thornton, op cit URL: http://plato.stanford.edu/entries/popper/#SocPolThoCriHisHol
 Massimo Piglicci, “Rationally Speaking: “Lawrence Krauss: Antoher Physcist With an Anti-Philosophy Complex.” Truth from Argument Among Friends. Blog book Review URL: http://rationallyspeaking.blogspot.ca/2012/04/lawrence-krauss-another-physicist-with.html visisted 4/27/2012
 Francis Heylighen, “Downward Causation.” Principia Cybernetica web On line resource. Sept 15, 1995, summarizing work of Donald T. Campbell 1974. Heylighen is research Professor at Free University of Brussels and director of Global Brain Institiute. URL: http://pespmc1.vub.ac.be/DOWNCAUS.html visited 5/9/12
- see also Campbell D.T. (1990): "Levels of Organization, Downward Causation, and the Selection-Theory Approach to Evolutionary Epistemology", in: Scientific Methodology in the Study of Mind: evolutionary epistemology, E. Tobach and G. Greenberg (ed.), (Erlbaum, Hillsdale, NJ), p. 1-17.
- Campbell D.T. (1974): "'Downward causation' in Hierarchically Organized Biological Systems", in: Studies in the Philosophy of Biology, F.J. Ayala & T. Dobzhansky (ed.), (Macmillan Press), p. 179-186
 Mary Ann Meyers “Top Down Causation: An integrating theme within and across the sciences.” A symposium by the John Templeton foundation, Participnats from the Royal Society, Contact Mary Ann Meyers Senior Fellow, 2010, website: URL http://humbleapproach.templeton.org/Top_Down_Causation/index.html visited sept 25,2012.
 George F.R. Ellis, “Top Down Causation and The Human Brain,” Downward Causation and the Neurobiology of Free Will: Understanding Complex Systems. Berlin, Heidelberg: Springer Verlag, Ed.Nancy Murphy, George F.R. Ellis, Timothy O. O’Connor, 2009, 63
 Ibid., Table 4.1
 Meyers, “top Down Causation…” Symposium, Op. Cit.
 Gale Cengage, “Downward causation,” Encyclopedia of Science and Religion. New York: Macmillan, Wentzel Van Huyssteen edit 2003. quoted in Enotes, Downward Causatoin, on line resource for teachers:
URL: http://www.enotes.com/downward-causation-reference/downward-causation visited 5/10/12