There are numerous specific criticisms that have been leveled against examples that Lovelock, Margulis, and other proponents have put forth as evidence for Gaia. Only one is given here for brevity. For example, Lovelock invoked Gaia to explain life's survival during the rise of oxygen in the early Earth atmosphere. Photosynthetically produced high levels of oxygen (the so-called 'oxygen crisis') were lethal for the largely anaerobic lifeforms of the day. Ultimately, the oxygen atmosphere probably enabled a net increase in biodiversity and total biomass over time, but it spelled doom for many of the organisms then alive. If Gaia favors life, how can changes that favor some life but destroy large numbers of other organisms be reconciled? How can a mechanism be proposed that would amount to altruistic suicide on the part of many organisms on behalf of unrelated organisms? Kirchner summed up the dilemma in his 1989 paper, ''If the most destabilizing biotic event in Earth's history can be construed as evidence for Gaia, and the relative stability since then can also be cited as evidence for Gaia, one wonders what conceivable events could not be interpreted as supporting the Gaia hypothesis. If there are none, Gaia cannot be tested against the geologic record If Gaia stabilizes and Gaia destabilizes... is there any possible behavior which is not Gaian?''
If Gaia cannot be disproved in any case, then it does not meet the criterion for falsifiability developed by philosopher of science, Karl Popper, in the 1930s. An idea must, in principle, be able to be proved false for it to be considered testable. Popperian falsifiability has itself been attacked, notably by Alan Sokal and Jean Bricmont in their 1998 book, Fashionable Nonsense. Some argue that Popperian falsifiability is already biased toward only the methodology of reductionism, and that it may be inherently unable to fully define the essence of extremely complex and closely coupled systems, especially those that change over time in some sort of ontological process. Nevertheless, it is a useful indicator of whether a concept can be considered scientifically testable at least in the narrow sense. The major result of Kirchner's criticism has resulted in attempts at crisper formulations of the ideas and has pushed Gaia to the weaker versions.
The highly reductionist geneticist Richard Dawkins believes that individual genes are in control of evolution and has entirely dismissed Gaia on that basis. Genes are grouped together into replicator packets. These are the functional units that Dawkins contends were both the first form of life and still remain the functional unit of selection. He dubs cells and organisms survival machines, and claims that they serve only to help the replicators propagate. Certainly any superorganismic concept violates Dawkins' notion of a single exclusive level of selection. Such an intensely reductionistic view does not take into account higher-order properties that may emerge from complex system interactions, and some scholars working on the mathematics of complex systems have in turn dismissed Dawkins' views as overly simplified.
Countering the reductionist view, J. Z. Young pointed out in the book Doubt and Certainty in Science that ''Biology, like physics, has ceased to be materialist. Its basic unit is a non-material entity, namely an organization." Here the emphasis is on pattern, because matter is frequently replaced and thus, transient, in biological processes. An organism is not a particular chunk of matter, but a persistent pattern through which material flows. With such a definition, the notion of the Earth system as a superorganism becomes less strained and does not require a slavish point-by-point comparison to the properties of individual organisms.
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