Analogies to Motors

I don’t think they’re analogies. I would go so far as to call them literal examples.

I would actually say that some biological systems meet the textbook definition of a machine or a motor as well as any man-made machine or motor. It’s just in biology they’re machines and motors that evolved.

When I look at what the definition of a machine or a motor is it’s just obvious to me that things like flagella and ATP synthetases meet those definitions.

They have unusual properties not found in man-made machines or motors (for example that some parts of them can litterally self-assemble). But nowhere in the definition of a motor or a machine is it stated that those properties disqualify them from being machines. I mean I wouldn’t stop calling the engine in a car a machine if someone invented one that could self-assemble.

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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.

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I understand perfectly well what analogies are, thank you.

Any discussion of what constitutes a machine must begin by assessing the various definitions of a machine you’re going to encounter in dictionaries. It is obviously pointless to discuss whether some thing X belongs to some category or deserves some label if you don’t first discuss what are the defining characteristics of the category. Since this doesn’t occur anywhere in your posts or any of your links, it’s wasted effort.

Nowhere in any of the many different definitions of a machine you can find online (some of which aren’t exactly or always entirely compatible) is the relative magnitudes of effects such as friction or the degree of perfection of coupling between components stated as somehow being critical to the definition of a machine. It just isn’t.

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IMO, you don’t seem to be, given the flawed reason you gave for why you think this is not an analogy. Just because you can define ‘Category A’ to include X, Y and Z, that doesn’t mean X, Y and Z are no longer analogous to each other.

Rather ironic, considering that you also haven’t assessed any of the “various definitions of a machine” nor did you discuss any of “the defining characteristics”. By your own criteria, your previous posts forwarded against me were wasted efforts as well.

Missing the point again.

The point is not “these biological complexes don’t meet ANY definition of the word ‘machine’”

Rather, the point is that he mechanisms that underpin biological processes are fundamentally different from those of man-made machines. This is what makes such analogies between the two very poor and often misleading, regardless of what definition you want to use for words to describe both man-made machinery and biological processes. As Nicholson puts it:

The problem with the machine conception of the organism (MCO) stems from the failure to recognize that in any comparison between two entities the most immediately perceptible similarities are not necessarily the most important ones. Valid analogical arguments are precisely those that effectively distinguish accidental and non-accidental relations and use only the latter as the basis for comparisons (Juthe, 2005; Weitzenfeld, 1984). It is the successful identification and mapping of the distinctive features of the compared entities that guarantees the explanatory power of an analogy. If the mapping relations do not capture these distinctive features, then the metaphorical redescription of one entity on the basis of the other results in a distorted characterization of the redescribed entity. In this section, I will argue that the inadequacy of the MCO derives from the fact that the distinctive features of organisms are, in the last analysis, fundamentally different from those of (man-made) machines.

And I do want to add that I think your links and the quoted material provides very good explanations for why the sorts of intuitions we build up around man-made machines, and macroscopic objects in general, don’t apply well at the molecular level, and why the behavior of atoms and molecules at these scales have many counter-intuitive properties that completely undermine the sort of appeals to intuition many pro-ID arguments rely on.
A typical argument goes something like “what are the odds that if you just randomly throw parts together they’re going to assemble into a fully functioning car engine?” and of course the odds of that are basically zero. Tossing a handful of cog-wheel at an engine block isn’t going to somehow make it snap into place. They’re just going to bounce off and lie on the floor.

But such an argument doesn’t apply at the molecular level because here short-scale electrostatic forces of attraction and repulsion dominate, and everything is jiggling around under brownian motion, so things can literally move around randomly until it finds itself in a position where the local forces of attraction and the structural match between parts make them able to self-assemble.

But even despite these many crucial differences between man-made macroscopic machines and objects, and biological molecular machines, I think the category of machine, and motor, are broad enough that biological molecular machines and systems meet enough of the basic requirements to be called, entirely literally, machines or motors.

They’re molecular machines that evolved, and we can know they evolved and even how, and that this is possible in part due to the very fact that they have these counter-intuitive properties that only manifest at scales measured in angstroms and nanometers.

If by that definition a flagellum is a ‘motor’, then a hurricane is also a ‘motor’.

Regardless, this is missing my point (see the last paragraph to my last reply to @Rumraket)

My motive for this argument is not to oppose ID. ID proponents just seem to make use of the flawed machine concept of organisms that is being perpetuated even by many scientists.

What a strange way to use the word analogy. To say that something is “no longer analogous” is to say it has become so different in it’s attributes or their degree, they can’t even be analogized. As in the very idea of a commonality or similarity has become so stretched or vague as to defy sensible comparison. In other words that the analogy fails because the entities being compared basically share no or too few similar properties. Like comparing numbers and emotions, or something like that.

But I am the one saying they are so much alike that they’re not only analogous, I would go even further and say they are so much alike in these crucial respects that I think they meet the definitions in a way that qualify them to be members of the set. They are not only analogous, they are examples.

You are the one saying they are not enough alike to be considered members of the set, just merely analogous to members of the set. That they are similar enough to be considered analogous, but not sufficiently similar to be considered examples of members of the set.

But I do consider them so similar to members of the set that I would call them examples, not only or ** analogous. So it doesn’t really make sense to accuse me of considering them “no longer analogous” to each other.

I understand the point of your argument and what it is based on, I just don’t think it is necessary to argue for a denial that these entities are machines in order to understand how they differ from man-made machines and macroscopic objects in general.

I would go so far as to say that I agree that merely calling them machines, or characterizing them with metaphors about man-made factories and combustion engines can definitely be misleading if that is all you’re doing.
But it is obvious to me that one can both understand that they differ from man-made machines and macroscopic objects more generally in crucial ways(and that these characteristics are necessary to understand how they behave and how they evolved), yet also still have sufficiently many characteristics to still be considered machines. I know this is possible because I am a person doing that right now.

I genuinely don’t believe anything is gained by refusing to call them machines. I think however a lot can be gained by working to alleviate misunderstandings by putting more emphasis on explaining to people how things work in biology at the atomic and molecular level, rather than just calling them machines and then sort of pretending you’re done explaining things.

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You misunderstood (though not your fault). Let me clarify. You said that since biological complexes (e.g. flagella) are - by definition - ‘motors’, this means it is not an analogy - rather it is ‘literal’ to say they are motors. However, I object to this by pointing out that putting things under the same category does not mean they are ‘literal’, nor does it negate the fact that they are analogies. This is what I meant to say when I said “no longer analogous”.

Let me reword my previous statement:

As I have already pointed out, providing clear explanations with references, at the crucial respects, these are fundamentally NOT alike whatsoever. You inadvertently admit this when you say the following:

In one sentence you say they are “so much alike” - yet - what does it mean when you must have a “broad enough” definition in order for the category to encompass biological complexes such that they meet *enough of the basic requirements"? To me, this just furthers my point that the machine analogy only gives attention to few similarities, which we happen to find significant as it makes the object much more familiar to us than they really are. This is a quirk of our heuristics. Whenever we find something we don’t understand, we frequently will compare it with things we do understand (or - at least - with things that seems more familiar to us).

I would say that this makes the machine analogy (at the very least) extremely poor and (very often) misleading, since such statements are counter to what they fundamentally are and how they work. Viewing the cell as a machine presents a cognitive hurdle to understanding the true nature of life. Even you yourself admit that it can be misleading. Indeed, it often is.

Anecdote.

Also, I would say that your understanding may be affected by the misleading machine analogies, at least to some degree, without realizing it. A clear sign of this is when you said that they are “so much alike”, even though they are not.

Literal examples, is the term I used. They are examples of machines, or motors, not just analogous to them.

That is a very confused statement I’m sorry to have to tell you.

Category A is supposed to be machines, right? The set of things we call machines. Things included in the set of machines is X, Y, and Z.

X, Y, and Z are supposed to be members of the set, they are not “comparisons” or “analogies”. X, Y, and Z can be analogous to, or they can be compared to some other things C, D, E, or whatever, but the members of category A(machines) is not a “literal comparison” or “only analogies”.

That doesn’t parse meaningfully into English.

None of which contain a survey of the definitions of a machine.

But that is just outright and demonstrably incorrect. You can find many simple and straightfoward definitions of a machine in which it is just obvious that these entities meet the requirements of the definition, and nowhere are the properties you characterize as “crucial” part of the definition.

You’re just flat out wrong mate.

It means because there are numerous definitions of the word, and according to several of these definitions that just have a few characteristics that define it which are so broadly encompassing that two entities can differ in many other respects than these, that they can still obviously belong to that same set because they share the actual defining characteristics.

So no, no inadvertent admission is going on there.

The term organism encompasses a huge number of phenomena(all known forms of life are organisms) that are unlike each other in an incredible number of ways, and yet they can all be classified as being organisms by a comparatively small set of defining characteristics even despite the fact the things that are different among any two arbitrarily picked organisms are way more numerous in both number and degree than the things we define them as being organisms by.

You’re the one making a machine analogy. I’m the one saying they’re actual examples of machines. I have to assume you didn’t mean the analogy is the misleading one, unless you actually want to abandon even that and not even analogize biological and man-made machines at all.

But they aren’t counter to what they fundamentally are and how they work as machines, given many perfectly normal definitions of a machine. You don’t get anywhere with these counterfactual assertions.

Yes if you don’t explain the nature of molecular behavior. But then the real problem is such a person haven’t been educated on the nature of behavior at the atomic and molecular level. We don’t somehow magically come to understand the nature of living cells by not using the word machine, you still have to actually do the work of describing how things work at the molecular level.

So it’s entirely possible to both understand that there is a perfectly workable sense in which cells contain entities that are examples of machines, and yet they also have properties that are very unusual and counterintuitive because they’re extremely small.

I think it can be misleading if you don’t explain how things work at the molecular level.

Meaningless dismissal.

It takes a single example to prove that something is possible. There are even more than one of us here who seem to have to trouble doing this.

I would say it is obvious that you are just completely mistaken here when, given various definitions of a machine or motor or what have you, many biological molecular machines meet the definition.

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Rum, I would agree with you if the people using the machine analogy were those who knew better, but just decided to play along. The machine analogy (just as the DNA-blueprint analogy, you and Mercer worked hard to correct me of) deceived me for a long time. I also know how many times its gotten thrown in my face by naive individuals arguing for intelligently designed cellular machines.

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Just wanted to thank @Dan_Eastwood for making a seperate topic on this.

I did this argument before regarding planets, but now let’s get more abstract.
Look at the following argument:

X, Y and Z are similar in respect to sharing properties α, β, and γ (which define category A).
X has been observed to have further property δ.
Therefore, Y and Z probably has property δ also.

Note that this is analogous reasoning. The reason for why the argument appeals to an analogy (not “literal” examples) is because the definition of “category A” cites analogies, i.e. they are similar in respect to sharing properties α, β, and γ. To give an example that an ID-creationist would use:

Flagella and man-made propellers are motors
The man-made propellers are known to be designed
Therefore, flagella are probably also designed

Analogous reasoning, since calling both “motors” IS the analogy; i.e. calling them “motors” is pointing out that they are similar in certain aspects.

I am not sure what you mean when you say “they are ‘literal examples’ of machines/motors, not just analogous to them”. What exactly are you referring to with “machines/motors” in this particular sentence? It’s almost like you are referencing the platonic abstract object of “motor” and that you think flagella are - quote - “literal examples” of this abstraction. I don’t, and I also think you wouldn’t say that either. I take the phrase “they are motors” to mean “they are similar in regards to sharing certain properties”. In other words, “motors” are analogous to each other.

As I said before: “The point is not “these biological complexes don’t meet ANY definition of the word ‘machine’”. Rather, the point is that he mechanisms that underpin biological processes are fundamentally different from those of man-made machines. This is what makes such analogies between the two very poor and often misleading, regardless of what definition you want to use for words to describe both man-made machinery and biological processes.

Rephrasing - The point is NOT these things don’t share any similarities whatsoever. Rather, the point is: what they are and how they work is fundamentally different, such that the machine analogy is more often very misleading rather than helpful in understanding the true nature of biological processes.

Every time you want to cite the definitions of “machine/motor”, you are missing the point.

I have highlighted the part where you are inadvertently admitting my point again. Calling both ‘machines’ is only in reference to “just a few characteristics” that “are so broadly encompassing”, such that biological ‘machines’ still “differ in many other respects”. In other words, you inadvertently admit here that they are NOT “so much alike”.

I would agree that all organisms are analogous (i.e. similar to each other) to varying degrees (some more than others). Although, I would point out that the similarities that the analogy is referencing are the universal processes of biology, and which are thus fundamental in contrast to the similarities you want to draw between biological complexes and man-made machines.

Straw man. I have not said we “somehow magically come to understand the nature of living cells by not using the word machine”. I am saying that such analogies are often misleading. Obviously, avoiding misleading concepts is not the ONLY part of education, and I never said otherwise. Don’t misrepresent my position.

And sure, it is possible to be convinced by misleading concepts and also develop proper understanding, but that is utterly trivial. It’s possible for a smoker to live to 90 years of age, despite their habits, but very often it doesn’t end up that way. It’s possible possible someone can come to a proper understanding IN SPITE of being exposed to misleading concepts, but it very often doesn’t end up that way. It is always better to leave things out that are misleading… or …even better …we bring up these misleading concepts that are common and explain why they are misleading.

We aren’t talking about what is “possible”, but rather, we must think statistically and ask what should we do to avoid misunderstanding as much as we can. I would argue as other have done also that perpetuating machine analogies of organisms very often (NOTE: not always, but still frequently) misleads people into misunderstanding the nature of life, as it has historically been the case.

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I did my best to disentangle the topic, but there was a lot to sort thru. Let me know where I screwed up.

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If design is an attribute of motors, then flagella are definitely not motors, so the comparison would be not literal and only partially analogous. There is nothing, however, in any dictionary, or technical or common usage that defines design as such an essential attribute of motors or engines, so the premise is flawed. You mentioned hurricanes, and phenomena such as accretion disk driven jets are clearly not designed, although referenced as engines in commonly accepted diction. If design is not an attribute of motors, the conclusion does not follow. Now an ID proponent could explicitly state that she considers design part of the definition - fair enough - but that would exclude natural phenomena and render the syllogism circular, among its other problems.

I see your point, but I would rather be a stickler for definition than be effective, I suppose. I think we are all pretty aligned on the substance of the whole motor - flagella comparison.

I think I will bow out with the observation by Lewis Carroll:

“When I use a word,’ Humpty Dumpty said in rather a scornful tone, ‘it means just what I choose it to mean — neither more nor less.’
’The question is,’ said Alice, ‘whether you can make words mean so many different things.’
’The question is,’ said Humpty Dumpty, ‘which is to be master — that’s all.”

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Motors are a purposeful arrangement of parts. Therefor we can infer they are designed. The flagellar whether clarified as a motor or not is still a purposeful arrangement of parts. It has over 30 well matched parts and its purpose is mobility through liquid. Again based on this criteria we can infer the flagellar is designed.

The argument I gave as an example doesn’t define “motor” as designed in any of the premises. It says that these things are ‘motors’, and since one is known to be designed, it is therefore probable that the other is designed as well by virtue of the previous similarity.

Regardless, the point of me bringing up this argument was not about the definition. It was to illustrate the point that calling a ‘flagellum’ a ‘motor’ is indeed an analogy. The argument was an example of an argument from analogy, and the analogy that is used in this argument is “Flagella and man-made propellers are motors”.

I am not, for the reasons I have explained. Such analogies to machines, blueprints, programs, etc, often misleads people regarding the the nature of biological processes, even very smart people. It’s like the old description of the atom, comparing it to a solar system, since the electrons orbit the nucleus just like planets orbit the star.

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That’s just a textbook question begging fallacy.

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Wrong, they are not purposefully arranged objects according to a predetermined ‘design’ or ‘blueprint’ for a specific purpose, like machines are. Biological structures are self-organized, transient, and their functions are highly context dependent. The material is in a constant state of flux and turn-over, via synthesis, assembly, dis-assembly, and breakdown. Your description is like saying that a storm is purposefully arranged to provide rainfall.

@Rumraket This type of teleological thinking that is promoted by the machine analogies is one of the reasons for the objections I provided here.

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Exactly. We even made that mistake. Displacing myosin Vb from its cargo by overexpressing its tail led to the conclusion that it was moving cargo. It must be, right, because as a motor it must move things:

But when we locked it down onto actin, it made no sense at all unless one concludes that it’s a tether instead of moving things from one place to another:

https://www.pnas.org/doi/10.1073/pnas.0305895101

It would be better to say that one can define “motor” so broadly that these are included, but doing so without mentioning that those similarities vanish when one looks in more detail is irresponsible.

Myosins hydrolyze ATP to produce movement, but the ATP isn’t really analogous to fuel–it’s just producing a conformational change that directionally biases the force exerted by Brownian motion.

Adaptation to a given environment will be in that sense “purposeful”, so biological purpose would not distinguish special creation from natural selection.

There is a huge gap between your premise and your conclusion. You need to explain why a purposeful arrangement of parts is necessarily designed.

A river channel is a purposeful arrangement of parts. It serves the purpose of moving water from the parts of a watershed to the sea. Was it therefore designed?

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