|An example of a basic analogy (Ѻ) or comparison between two things in similarity, namely the front of a car and human face, according to which head lights are likened to eyes, the grill is likened to the mouth, the hood to the nose, etc.|
Analogies, in science, come in a number of varieties.
In 1802, William Paley proposed his famous "watch analogy", wherein he compared a watch to a human, arguing that they each have a "purpose" designated by their maker, the gist of which is as follows:
In 1996, Michael Behe introduced his so-called mouse trap analogy, wherein he argued, via analogy, that bacteria flagella are complex machine like entities that couldn't have been created by blind random chance accident, therefore they, like humans, were designed by a creator, i.e. god:
See main: Thermodynamic analogyIn 1952, English physicist C.G. Darwin defined 'human thermodynamics' as the "thermodynamic study of systems of human molecules", in his book in his The Next Million Years, wherein he used the word 'analogy' 19 times, comparing humans, by analogy, to the molecules of a body of gas governed by Boyle's law, to the behavior of a wild animal, and to the behavior of ants. The following are few representative quotes:
“The analogy I have cited of the gas laws is the simplest example that is furnished by statistical mechanics, and it is only fair to mention that, when the subject is pursued further, it does get a good deal more complicated. Thus much greater difficulties arise in considering how the gas can condense into a liquid or solid, but it would not be profitable to follow the analogy into these intricacies.
We may, so to speak, reasonably hope to find the Boyle's Law which controls the behavior of those very complicated molecules, the members of the human race, and from this we should be able to predict something of man's future.
The possibility depends on finding out whether there are for humanity any similar internal conditions, which would be analogous to the condition of being a conservative dynamical system, and external conditions analogous to the containing vessel.
In the gas, the external conditions were given by the containing vessel, and the analogy here is obviously the earth itself. The internal principle, which is to be analogous to the property of being conservative dynamical systems, of course lies deeper. It must depend on the laws governing the nature and behaviour of the human molecules. When I compare human beings to molecules, the reader may feel that this is a bad analogy, because unlike a molecule, a man has free will, which makes his actions unpredictable.
Though the individual collisions of the human molecules may be a little less predictable than those of gas molecules—which, as I have said, do not have to be considered in detail either—the census returns show that for a large population the results average out with great accuracy. The internal principle then of the human molecules is human nature itself. On the analogy between human history and the molecules of a gas, the different civilizations are to be ranked as fluctuations from the average.”
In objection to this definition, many argue, on what seem to be emotional, religious, or philosophical grounds, that this statement is pure analogy.
In 2006, Polish science-philosopher theologian Jozef Zycinski stated that in his 2000 article “God, Freedom, and Evil: Perspectives from Religion and Science” he “offers an interpretation of human behavior with consideration of analogies from thermodynamics”. 
In 2008, American physical chemist Thomas Wallace argued that the rise and fall of civilizations can be explained thermodynamically on the analogy of the five-year operational life of a car battery. 
See main: Chemical analogy; Chemical aphorismIn 1800, German poet Friedrich Schlegel, supposedly, used a vast range of chemistry metaphors and allegory in his literary work; a subject on which he was said to have more than a passing knowledge of, but not a systematic understanding of. 
In his 1948 book We Human Chemicals, American writer Thomas Dreier gives the following view: 
“I am aware that when I talk about human beings as combinations of chemicals it is like using an extremely crude, but nonetheless practical, graduated laboratory beaker as a measuring device. We can, I believe, employ the analogies and examples of chemical reaction and other reactions which each of us will develop out of experience with the confidence we feel when we take measurements with a yardstick.”
The classic example of a scientific analogy is Greek philosopher Empedocles’ fifth century BC explanation of the mixing of social groups to the chemical solubility of liquids in stating that:
“People who love each other mix like water and wine; people who hate each other segregate like water and oil.”
Empedocles, the first to formulate a standard model of physics, insisted that the two ruling passions of human life, love and hate, are the two ruling principles which pervade and rule the whole universe. In one sense, the debate continues to this day, with people split as to whether or not the above statement is pure analogy, or whether some people do separate like un-emulsified chemicals, owing to chemical properties.
Often, in analogy comparisons, wherein terms are borrowed from either the physical-sciences-to-explain-humanity, e.g. Johann Goethe’s 1809 culling from chemistry to compare people to chemical species to explain love as affinity reactions, or from the humanities-to-explain-the-physical-sciences, e.g. James Maxwell’s 1861 borrowing from Henry Buckle’s census statistics on history of civilizations to formulate the kinetic theory of gases, the line become what is factually true and what is pure metaphor becomes blurry.
When, for example, one argues that the moon is blue like cheese, therefore the moon must be made of cheese, the analogy becomes obviously nonsensical in a modern view. When, conversely, American chemical engineer Scott Fogler states, in his 1992 Chemical Reaction Engineering textbook, that: 
“A catalyst is a substance that affects the rate of a reaction but emerges from the process unchanged. A man inciting a mob to riot and then ducking out before the tanks roll in can be regarded as a catalyst.”
One may wonder is Fogler using analogy, or can in actuality a person be a catalyst, no analogy? Fogler would likely state that he used analogy, given the context of the book, but from a modern post-2000 point of view, wherein people have begun to calculate actual molecular formulas for human beings, on can clearly say that the people can in actuality be defined as ‘human catalysts’. The issue here comes down to a scalability factor: with some arguing that the laws, principles, and terminologies of small scale atomic and molecular reactions, such as oxygen and hydrogen reacting to form water, do not and cannot be scaled up, whereas others argue that humans are molecules no different than any other molecule, and that such matters can be scaled up.
To give an example of this, where an author ambiguously leaves the subject in a gray area, is American physiologist Lawrence Henderson’s 1935 explanation of Vilfredo Pareto's 1916 sociology treatise using what he called Gibbsian thermodynamics "analogies", wherein where a social system is said to contains individuals roughly analogous to "Gibbs’ components".  In a modern sense, however, we know that a human being has a molecular formula, as determined independently by American scientists Robert Sterner, James Elser, and Libb Thims, whereby the supposition of people being analog components, becomes incorrect. 
The updated 2002-view, according to Sterner and Elser, wherein the analogy perspective dissolves, is:
“Animals are abstracted as local thermodynamic perturbations—repositories of chemical energy—whose feeding, metabolism, growth, and reproduction and analyzed by application of energy concepts of thermodynamics: calories, free energy, work, entropy, heat, efficiency, and productivity [modeled on] the basic assumption that flows of energy organize thermodynamic systems, including biological ones. Animals [are viewed] as repositories of multiple chemical elements; in the stoichiometric view, they are mixtures of multiple substances, as for example in the ‘human molecule’.”
Even in this quote, from two people who actually calculated the human empirical molecular, defining it as the formula for a 'human molecule', it may still be the case that they believe that they are still using abstracted analogy. Others, such as American chemical engineers Libb Thims or Andrew Morrow, conversely, have no reservations or ambiguity with the reality that they are made of atoms and that a bound state structure of atoms is a molecule, no analogy. When polled, similarly, about 57% of people believe that they are a 'giant molecule', no analogy. 
It is said that German physicst Max Planck discovered his new radiation formula, approaching the problem through thermodynamics, in which he drew an “analogy” between radiation trapped inside a cavity and the properties of a gas confined within the walls of a container. 
The following are related quotes:
“And I cherish more than anything else the ‘analogies’, my most trustworthy masters. They know all the secrets of nature, and they ought to be least neglected in geometry.”— Johannes Kepler (c.1620), Publication (Ѻ)
● Black cat analogy
● Chemical analogy
● Exact analogy
● Mathematical analogy
● Physical analogy
1. (a) Fogler, H. Scott. (1992). Elements of Chemical Reaction Engineering (catalyst, pg. 242). Prentice Hall.
(b) Thims, Libb. (2007). Human Chemistry (Volume One) (Fogler, human catalyst, pg. 94). (preview), (Google books). Morrisville, NC: LuLu.
2. (a) Henderson, Lawrence J. (1935). Pareto’s General Sociology: a Physiologists Interpretation (keyword: thermodynamics, pgs. 10, 47, 82, 90, 92; note 5: “The Sources of Pareto’s Social System”, pgs. 91-93). Harvard University Press.
(b) Cannon, Walter B. (1943). “Biographical Memoir of Lawrence Joseph Henderson 1878-1942”, US National Academy of Science, Vol XXIII, Second Memoir.
3. Thims, Libb. (2008). The Human Molecule, (preview) (pg. 20). Morrisville, NC: LuLu.
4. Sterner, Robert W. and Elser, James J. (2002). Ecological Stoichiometry: the Biology of Elements from Molecules to the Biosphere, (chapter one) (term: "human molecule", pgs. 3, 47, 135). Princeton University Press.
5. Running Poll: "Are You A Giant Molecule?" (by English physicist Jim Eadon) - 2001-2008.
6. Baggott, J. E. (2004). Beyond Measure: Modern Physics, Philosophy, and the Meaning of Quantum Theory (pg. 13). Oxford University Press.
7. Dreier, Thomas. (1948). We Human Chemicals: the Knack of Getting Along with Everybody (pg. 4). Updegraff Press.
8. Wallace, Thomas P. (2009). Wealth, Energy, and Human Values: the Dynamics of Decaying Civilizations from Ancient Greece to America (pg.xi). AuthorHouse.
9. (a) Zycinski, Jozef. (2000). “God, Freedom, and Evil: Perspectives from Religion and Science” (abstract), Zygon, 35(3): 653-64.
(b) Zycinski, Jozef. (2006). God and Evolution: Fundamental Questions of Christian Evolutionism (pg. 132). CUA Press.
10. Chaouli, Michel. (2002). The Laboratory of Poetry: Chemistry and Poetics in the Work of Friedrich Schlegel. Johns Hopkins University Press.
● Daniel, Vera. (1955). “The Uses and Abuses of Analogy”, OR, Vol. 6, pgs. 32-46.
● Zencey, Eric. (1986). “Some Brief Speculations on the Popularlity of Entropy as Metaphor” (abstract). The North American Review, 271: 7-10.
● Philip, Mirowiki. (1989). “How not to do things with Metaphors: Paul Samuelson and the Science of Neoclassical Economic.” (abstract). Studies in the History of Philosophy of Science Part A, Vol 20, Issue 2, June, pgs. 175-91.
● Best, Steven. (1991). “Chaos and Entropy: Metaphors in Postmodern Science and Social Theory” (abstract), Science as Culture, 2: 188-226.
● Hannon, Bruce M. (1997). “The Use of Analogy in Biology and Economics: From biology to economics, and back, Structural Change and Economic Dynamics”, Structural Change and Economic Dynamics, 8:471-488.
● Analogy – Wikipedia.