You don’t understand what analogies mean.
To use an obviously absurd example on purpose: let’s suppose I say that, since the earth is a planet and has a lot of liquid water, it is therefore likely that Mercury has a lot of liquid water as well because it is a planet too. This is an example of analogous reasoning. But wait! Analogous you say? Those two are “literal” examples of a ‘planet’, aren’t they? Yes, however, because such definitions only entail a few commonalities, it only makes them analogous. Likewise, even if you define ‘motor’ such that some biological complexes can be considered ‘motors’, you are only citing the few commonalities that makes them analogous to man-made motors.
Still, regardless of what definition you use, I would argue (like Daniel Nicholson has, see here and here to name a few examples) that such analogies, along with many others; e.g. Genomic blueprint, genetic program, molecular machines, etc; are very “poor and rather misleading representations of biological reality”, because “the distinctive features of organisms are fundamentally different from those of (man-made) machines”. You may see in static images in textbook, or those neat animations showing the so-called ‘molecular machines’ in action, but if you actually could shrink down to the molecular scale and view these things in action (assuming you could see individual molecules and slow everything down such that you are actually able to comprehend anything that is happening), you would observe endless objects forming a chaotic storm as they move about by Brownian motion, and everything is in a constant state of turn-over via synthesis and breakdown. Even the so-called ‘motors’ are no exceptions. They are not rigid objects. Such protein complexes behave more like dense liquids or molten solids, which rapidly change conformation between different low-energy states, and some proteins don’t have stable conformation at all. The “motors” would rotate in a herky-jerky manner, and wiggle and wobble according to thermal fluctuations resulting from the endless bombardment of water molecules, which are moving faster than the speed of sound. If you were to experience that in real life, then it wouldn’t be so obvious to call any of these “motors”. It would be unlike anything you have ever seen before.
My favorite example to illustrate this is the ribosome. If there is anything in the cell that can be called a “machine”, it’s the ribosome. Yet, Peter Moore describes the reality very differently in his review paper on “How should we think about the ribosome?”.
My apologies for the long quote, but I think this is all needed to explain it in full detail.
Emphasis mine - quote:
Movies Make the Ribosome Appear to Be Something It Is Not
In principle, it is easy to make structure-based movies of the activities of macromolecules. Their key frames are drawn directly from the structures available. In order to keep such movies from being unpleasantly jerky, and to ensure that they last more than a second or two, additional frames are added that join one structure smoothly to the next. Computer programs already exist for doing this kind of structural interpolation in a stereochemically acceptable way, which is called morphing. (Both of the movies referenced above were generated by morphing.)
One obvious drawback of such movies is that there is no way of knowing whether the conformational trajectories devised by morphing programs are realistic, let alone are the trajectories always followed by the macromolecules depicted, as the typical movie of this sort is likely to imply. Thus, even though the naive viewer is unlikely to realize it, the movie of elongation that emerges from whatever set of structures is used to create it will be no more than a visually attractive summary of those structures, organized to provide a “just so” story that purports to describe in atomic detail the way the ribosome elongates polypeptide chains.
One might be willing to overlook the polite fictions embedded in that movie if it did not have another, more serious shortcoming for its naive viewers, e.g., students. Like the structures on which it is based, the movie will actively invite viewers to think that the ribosome works the same way as a clock, or a machine for making candy bars. It is no help that macromolecules capable of coupling the hydrolysis of nucleoside triphosphates to directional movements, e.g., the translocating ribosome, are commonly called molecular machines. The use of the word “machine” in this context is pernicious because of its implication that the functional properties of macromolecules can be explained mechanically, which is simply not true.
WHAT KIND OF DEVICE IS THE RIBOSOME ANYWAY?
If the ribosome is not a mechanical device, why does it progress through its elongation cycle in the apparently machine-like, orderly, reproducible manner that generations of biochemists have worked so hard to elucidate? The answer, of course, is that this is the only outcome possible, given its structure and the laws of physical chemistry. (The reader may not find this explanation deeply satisfying.)
Macromolecular Devices Are Not Machines
The physical laws obeyed by macromolecular devices such as the ribosome are not the same as those applicable to macroscopic machines. For example, the motions of the components of a macroscopic machine are perfectly coupled. When the gear rotates, the shaft to which it is connected rotates in synchrony, a spring is compressed, a latch released, etc. Everything unfolds in a temporal sequence the device can accurately repeat ad infinitum, and the motions of its parts all conform to Newton’s laws of mechanics, i.e., F = ma. The effects of friction on its operation are modest, and in principle, it should work perfectly well at 0 K.
Macromolecular devices immersed in liquids are completely different (54). Friction is king; at all but the shortest time intervals (see Table 2), F = γv, where γ is a frictional coefficient, and v is the velocity of the entity experiencing that force. Furthermore, the thermal forces experienced by macromolecular devices are much greater than the forces they are capable generating. [At 310 K, the average thermal force experienced by a ribosome is about 270 pN (see Table 2), whereas the forces produced by force-generating macromolecular devices are one-tenth of that or less.] Thus, all the functionally significant movements of the ribosome, both internal and external, are biased random walks, and it is most unlikely that any given ribosome will ever do exactly the same thing twice as it elongates some polypeptide. Furthermore, even if the medium in which the ribosome operates remained a liquid at low temperatures, at 0 K it would do nothing useful at all because it would be unable to cross energy barriers (25). There is no chemistry at 0 K!
It follows that if a movie of elongation is not to be totally misleading, it must depict the endless series of meaningless, thermally driven, conformational fluctuations that separate one functionally significant event from the next. However, even if it did so with perfect accuracy, it would still provide its viewers with far less useful information than a movie of a macroscopic machine would provide. A movie of a macroscopic machine can explain why the machine works because the motions of its components, which the movie displays, are all directly related to its function. By contrast, 99.99% of the motions portrayed in a realistic movie of elongation will be random fluctuations that have nothing to do with function. In fact, the progress of the ribosome through its duty cycle is driven by changes in relative free energies of its conformational states, and free energy is something that cannot be seen in movies based on 3 ̊A resolution structures. Thus, structure-based movies of macromolecular processes have no explanatory power. The only reason for making them is that they are fun to look at.
Lastly, here is also an excellent lecture by Johannes Jaeger summarizing the points made by Daniel Nicholson.
