Are there historical examples of thought experiments in biology and chemistry?

Question

Thought experiments, imaginary situations designed to ponder conclusions of a theory, have been used throughout history. There is even a Stanford encyclopedia article about them. But the famous ones that come to mind are either from physics (Archimedes's overturning of the Earth, Newton's bucket, Maxwell's demon, Einstein's elevator, etc.) or philosophy/psychology (Plato's cave, Descartes' evil demon, Leibniz's mill, etc.). The article mentions that more recently "noteworthy contributions have been made exploring the importance of thought experiments in disciplines other than mathematics, philosophy, or physics. They include history, the social sciences, and Christian theology".

Conspicuously absent are natural sciences other than physics. Biology is not even mentioned, and chemistry "has none of note at all. Why is this the case? Perhaps it is merely an historical accident that chemists never developed a culture of doing thought experiments".

What kinds of thought experiments appear in biology? Is it true that they were never entertained in chemistry? If so, are there explanations better than "historical accident"?

EDIT: This paper discusses possible "fundamental difference" between physics and chemistry as an explanation for scarcity of thought experiments in the latter. Darwin's thought experiments are discussed here, see also HDE's answer and general discussion on Biology SE.

Answer 1

In biology, so far I've found Levinthal's Paradox. The transcript from a lecture given by Prof. Cyrus Levinthal can be found at the previous link. The gist of the paradox is this (not a quote; the indent is used for emphasis):

There exists a multitude of shapes proteins can take, yet they manage to fold into the correct shape extremely quickly.

The thought experiment proper is as follows:

1. Take an unfolded protein that will fold into a certain state in which it can perform its function
2. Observe the various shapes it folds into
3. Note that (this part is the kicker, and supported by experiment) the protein will fold into the correct shape within a fraction of a second.

The idea is explained slightly clearer here - at least, clearer to a biology layman like myself.

---

There's a long and interesting discourse here. (If it asks you if you want to join, simply click on the 'x' on the left to go straight to the document.) In it the authors (Schlaepfer and Weber) argue that Darwin put forth thought experiments in, among other publications, On the Origin of Species.

After noting that there were quite a few thought experiments in the field of evolutionary biology, the authors then move on to molecular biology, mentioning Levinthal's paradox and a problem regarding protein synthesis - how the body can make so many different types of proteins. I think these are more paradoxes than thought experiments, but that's purely my opinion.

The authors go on in a new angle, talking about how some have argued that computational forays in biology count as thought experiments. They then conclude the text.

Answer 2

"Daisyworld" comes to mind as a thought experiment in ecology/earth-system science (it was also simulated on computer but it is really just a thought experiment).
For those not familiar with it, it is an experiment designed by James Lovelock (of Gaia Theory fame) and Andrew Watson in 1983.
The settings, from the paper itself:

Daisyworld is a cloudless planet with a negligible atmospheric greenhouse on which the only plants are two species of daisy of different colours. One species is dark – ground covered by it reflects less light than bare ground – while the other is light and reflects more than the bare ground.

The thought experiment continue in imagining the growth rate of each species (influenced by the planet temperature) and the temperature change on the planet (influenced by the planet albedo, itself influenced by the daisies).

Watson, A. J. & Lovelock, J. E. 1983. Biological homeostasis of the global environment: the parable of Daisyworld. Tellus, 35B, 284-289.