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In 1851, in one of the most famous publications in the history of thermodynamics, On the Dynamical Theory of Heat, with numerical remits deduced from Mr JOULE'S equivalent of a Thermal Unit. etc., Thomson (later Lord Kelvin) pronounced his version of the 2nd law as follows: "It is impossible, by means of inanimate material agency, to derive mechanical effect from any portion of matter by cooling it below the temperature of the coldest of the surrounding objects."

Some 45 years later in 1897, Planck in the 1st edition of his book Treatise on Thermodynamics he phrased the 2nd law as: "It is impossible to construct an engine which will work in a complete cycle, and produce no effect except the raising of a weight and the cooling of a heat-reservoir," without even hinting at an inanimate material agency in this formulation.

I assume in 1851 it was still normal to accept some form of vitalism, hence Thomson's restricting his 2nd law to inanimate agencies but not any more 45 years later. What and when the change happened to reject vitalism in physics? When did Thomson himself reject vitalism explicitly, did he ever?

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It was normal to accept some form of vitalism way past 1851, and it was still around at the time of Planck's writing in 1897. In fact, vitalism experienced a resurgence in 1870s in response to the apparent tension between it and the energy conservation law, and somewhat crude applications of mechanics to physiology by du Bois-Reymond and others. Kelvin himself reaffirmed his vitalism in On the Dissipation of Energy: Geology and General Physics (1894). Bergson, who kept current on physics of his time and later debated Einstein, defended vitalism in Creative Evolution (1907), as did Haldane in Mechanism, life and personality (1913). Earlier, in 1870s, some big names in physics, like Maxwell and Boussinesq, argued for compatibility of vitalism with physics.

Although vitalism was not fully abandoned by scientists until 1920s, in 1870s mechanistic determinism a la Laplace started to gain ground. By 1890, the vitalism/determinism debate subsided and 'working physicists', like Planck, preferred to steer clear of the topic.

The history of the debate is discussed in Strien, Vital Instability: Life and Free Will in Physics and Physiology, Bordoni, Unexpected Convergence between Science and Philosophy and Hacking, Nineteenth Century Cracks in the Concept of Determinism. For the 'free will' aspects of it see History of the study of indeterminism in classical mechanics.

Here is from Strien:

"During the period 1860–1880, a number of physicists and mathematicians, including Maxwell, Stewart, Cournot and Boussinesq, used theories formulated in terms of physics to argue that the mind, the soul or a vital principle could have an impact on the body. This paper shows that what was primarily at stake for these authors was a concern about the irreducibility of life and the mind to physics, and that their theories can be regarded primarily as reactions to the law of conservation of energy, which was used among others by Helmholtz and Du Bois-Reymond as an argument against the possibility of vital and mental causes in physiology. In light of this development, Maxwell, Stewart, Cournot and Boussinesq showed that it was still possible to argue for the irreducibility of life and the mind to physics, through an appeal to instability or indeterminism in physics: if the body is an unstable or physically indeterministic system, an immaterial principle can act through triggering or directing motions in the body, without violating the laws of physics."

Here is Maxwell's take from 1879, which sheds some light on the background of his famous thermodynamic demon:

"Science has thus compelled us to admit that that which distinguishes a living body from a dead one is neither a material thing, nor that more refined entity, a ‘form of energy’. There are methods, however, by which the application of energy may be directed without interfering with its amount. Is the soul like the engine-driver, who does not draw the train himself, but, by means of certain valves, directs the course of the steam so as to drive the engine forward or backward, or to stop it?"

Hacking adds more on the rise of determinism:

"Cassirer was wrong to say that our modern universal body-and-mind causal determinism reared its head for the first time in 1872, but he pointed to a remarkable ferment in the concept of determinism that reached a climax at about that time. The very word ''determinism'' became generally current in French and English just before then, and in German it attained Cassirer's sense of the word during the same period. The literature has been full of zany arguments in which bits of mathematics of physics were pulled down from the shelf to make room for freedom of the will. Buckle, whom we have largely forgotten, turned the whole of history into the evolution of statistical determinism. Exactly ten years later, a much more famous work by Marx would speak of ''the natural laws of capitalist production... of these tendencies winning their way through and working themselves out with iron necessity.'' I believe that Cassirer almost inadvertently pointed to a period of tumult and chaos in thought about necessity and determinism."

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    $\begingroup$ Wow, awesome answer! There is only one more thing, did Kelvin ever again speak of this issue explicitly after1851? I know he was a religious man. $\endgroup$
    – hyportnex
    Commented Feb 27 at 1:46
  • $\begingroup$ @hyportnex As late as 1894:"It seemed to me then, and it still seems to me, most probable that the animal body does not act as a thermodynamic engine... The influence of animal or vegetable life on matter is infinitely beyond the range of any scientific inquiry hitherto entered on", quoted from Less Wrong. $\endgroup$
    – Conifold
    Commented Feb 27 at 1:53
  • $\begingroup$ Great, thanks. To be honest, I expected something like that, he really was a man of exceptional honesty and integrity. $\endgroup$
    – hyportnex
    Commented Feb 27 at 2:04

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