The mismeasure of machine: why machine metaphors in biology are misleading

Time to indulge in the occasional revisiting of one of my technical papers, in the hope that they may be of more general interest then the original audience they were written for. This time I’m going to focus on one that I co-wrote with my long-time collaborator, Maarten Boudry, and published in 2013 in the journal Studies in History and Philosophy of Biological and Biomedical Sciences. The title of the paper is: “The mismeasure of machine: synthetic biology and the trouble with engineering metaphors.”

We began by noting that the scientific study of living organisms is permeated by machine and design metaphors. Genes are often characterized as providing the “blueprint” for an organism, organisms in turn are “reverse engineered” to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc.

Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., when it comes to deploying optimality assumptions), Maarten and I argue in the paper that they are limited in several important respects. In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics.

Living organisms are far more messy and less transparent than human-made machines, as David Hume famously put it when addressing the classical argument from design. In part II of Dialogues Concerning Natural Religion, he writes:

“If we see a house … we conclude, with the greatest certainty, that it had an architect or builder because this is precisely that species of effect which we have experienced to proceed from that species of cause. But surely you will not affirm that the universe bears such a resemblance to a house that we can with the same certainty infer a similar cause, or that the analogy is here entire and perfect.”

Indeed, Hume continued:

“A continual circulation of matter in [the universe] produces no disorder; a continual waste in every part is incessantly repaired: The closest sympathy is perceived throughout the entire system: And each part or member, in performing its proper offices, operates both to its own preservation and to that of the whole. The world, therefore, I infer, is an animal.”

So, if anything, the universe resembles the messiness and organic development of living beings, not the precision and exact functionality of machines. The analogy with man-made artifacts, he concludes, is flawed and should be rejected. If that’s true at the level of the cosmos, we think it is also true — and for similar reasons — at the level of biological organisms.

A better way to think of evolution is as an opportunistic tinkerer, blindly stumbling on “designs” that no sensible engineer would come up with. This was pointed out by Francois Jacob back in his classical 1977 paper, “Evolution and Tinkering,” where he says:

“The action of natural selection has often been compared to that of an engineer. This, however, does not seem to be a suitable comparison. First, because in contrast to what occurs in evolution, the engineer works according to a preconceived plan … Second, because of the way the engineer works: to make a new product, he has at his disposal both materials specially prepared to that end and machines designed solely for that task. Finally, because the objects produced by the engineer … approach the level of perfection made possible by the technology of the time. In contrast, evolution is far from perfection. … Natural selection has no analogy with any aspect of human behavior. … It works like a tinkerer — a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him whether it be pieces of string, fragments of wood, or old cardboards; in short it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.”

That is, natural selection is a satisficying — not optimizing — process, as well as the ultimate recycler!

If you are thinking that perhaps we are building a strawman, that nobody really thinks of organisms as engineered, here is George Williams, one of the foremost evolutionists of the second part of 20th century:

“Whenever I believe that an effect is produced as the function of an adaptation perfected by natural selection to serve that function, I will use terms appropriate to human artifice and conscious design. The designation of something as the means or mechanism for a certain goal or function or purpose will imply that the machinery involved was fashioned by natural selection for the goal attributed to it.”

And yet, even arch-adaptationist Richard Dawkins — whose popular work was derived in part from William’s — had this to say while watching the dissection of a giraffe’s neck:

“Not only would a designer never have made a mistake like that nervous detour; a decent designer would never have perpetrated anything of the shambles that is the criss-crossing maze of arteries, veins, nerves, intestines, wads of fat and muscle, mesenteries and more.”

Maarten and I also point out that the engineering-inspired idea that natural selection is capable of “solving a near intractable physics-problem,” as Steven Pinker said with regard to the smooth movement of your limbs, though having a kernel of truth, is profoundly misleading. Animals don’t use algebraic fractions to calculate the level of altruism they should extend to their kin (not even unconsciously), any more than birds use latitude and trigonometry to navigate to their brooding places, or dogs compute parabolic trajectories when they’re catching a ball in flight. All these animals use surprisingly simple rules of thumb which, in their specific ecological environments, produce behaviors that more or less track engineering solutions.

Yet in popular science books the language may be ambiguous. Dawkins, for instance, writes in The Selfish Gene:

“When a man throws a ball high in the air and catches it again, he behaves as if he had solved a set of differential equations in predicting the trajectory of the ball. He may neither know nor care what a differential equation is, but this does not affect his skill with the ball. At some subconscious level, something functionally equivalent to the mathematical calculations is going on.”

Well, much hinges on what one means by “functionally equivalent.” Experiments show that humans (and dogs) use a deceptively simple heuristic to catch a ball: keep your gaze fixed at the ball, and adjust your running speed such that the angle of the ball remains constant (for references to this and other claims in this post, see the original paper). When you follow this heuristic, you will be there when the ball hits the ground. As it happens, baseball players are very poor at predicting where a ball is going to hit the ground when they are asked not to run towards it. They just manage to get there when the ball does. This is a little surprising since computing the trajectory of a ball is a very complicated physical problem: one has to take into account initial velocity, angle, direction, spin, as well as the air current and the distance from the player.

We then move on from a preliminary discussion of the use of engineering metaphors in biology to consider more directly the field of synthetic biology. To begin with, there is no such thing as a single research program in this emerging area. The literature distinguishes at least five conceptually distinct, if somewhat overlapping programs associated with synthetic biology:

(1) Bioengineering. Uses standard biotechnology tools to build novel biochemical pathways in host organisms.

(2) In silico synthetic biology. Similar to bioengineering, but carried out using computer simulations of novel metabolic pathways, rather than by experimentation with living organisms.

(3) Synthetic genomics. As the name plainly implies, this is a much broader scale of bioengineering intervention, at the level of whole genomes — rather than individual pathways — being slated into a (de-genomicized) host cell.

(4) Protocell synthetic biology. Here the aim is somewhat complementary to that of synthetic genomics: to bioengineer “living” cells that could then be used as entirely artificial hosts for other bioengineering projects.

(5) Unnatural molecular biology. This approach is arguably the most ambitious, as researchers in this area pursue the goal of producing entirely new molecular biologies, for instance using expanded genetic codes, capable of incorporating more and different amino acids from those used by the natural code.

Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with “programming” the right “software” might have initially suggested. The idea of applying straightforward engineering approaches to living systems and their genomes — isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms — pushes the analogy with human artifacts beyond its limits and onto the breaking point. In the absence of a one-to-one correspondence between genotype and phenotype (which does hold, instead, in the case of blueprints and actual engineering projects), there is no straightforward way to implement novel biological functions and design new life forms.

Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for “engineering” a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic “instructions,” we suggest, is probably intractable for any but the most simple phenotypes, and recent developments in the field of bio-engineering and synthetic biology reflect these limitations.

Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, we suggest that researchers are more likely to make progress by co-opting natural selection itself to “search” for a suitable genotype, or by borrowing and recombining genetic material from extant life forms.

Maarten and I conclude the paper by suggesting that perhaps we should be looking for new metaphors, or even shy away from metaphorical language whenever possible.  One alternative metaphor for thinking about the relationship between genomes and phenomes is the idea of a recipe, where DNA contributes the equivalent of the instructions for cooking, but does not specify all of the details of the process, which are left to a continuous interaction between the recipe itself and the environment and ingredients that are being used.

Although the recipe metaphor does get us away from a straightforward talk of “blueprints,” and particularly from a simplistic, near one-to-one Genotype => Phenotype mapping function, it is of mostly educational use and is unlikely to generate novel insights to guide professional researchers.

The same holds another common metaphor, that of an origami, proposed by Lewis Wolpert. It captures some important elements of embryological development (like the circuitous step-by-step folding), but it obviously will not work as a new master metaphor for thinking about living organisms (nor was it intended as such).

While we acknowledge that metaphorical and analogical thinking are part and parcel of the way human beings make sense of the world, in some highly specialized areas of human endeavor it may simply be the case that the object of study becomes so remote from everyday experience that analogies begin to do more harm than good (Hume docet). In particular, the systematic application of engineering metaphors to a domain that is fundamentally different from the world of human artifacts may send scientists on a wild goose chase. Wittgenstein famously said that “Philosophy is a battle against the bewitchment of our intelligence by means of our language.” Perhaps a contribution of philosophy of biology to the field of synthetic biology is to help free the scientists from the bewitching effects of misleading metaphors, so that they can simply get on with the difficult and unpredictably creative work lying ahead.

_____

P.S.: a few sentences in this essay have been edited to reflect critical points raised by some readers, see below.

249 thoughts on “The mismeasure of machine: why machine metaphors in biology are misleading

  1. Coel

    Hi Robin,

    Look to the top of this page, and see a suggestion that criticism of Dawkins is motivated by dislike of him.

    Well let’s remind ourselves of what I was replying to. First, there is quite a big difference between “dislike” and “hate”. (And that matters, especially in a climate where many countries are passing “hate speech” laws, such that expressing “hate” is now often illegal; we should not use that word lightly.)

    But, in the bit you quoted, I was replying directly to:

    “The point is, a lot of Dawkins’ supporters don’t seem to be able to conceive that one may have very reasonable disagreements with the man’s scientific and ideological positions, without this implying a personal dislike.”

    That is not: “Dawkins supporters too readily suggest that criticism of Dawkins is motivated by dislike of him”. (Which might be a defendable claim.)

    No, it’s way stronger than that. It’s that significant numbers of Dawkins supporters, it seems, cannot even conceive of criticism not being motivated by dislike! That’s a much stronger claim. And, again, the cannot even conceive wording is attributing utter thoughtlessness (literally, so that they are not able to even conceive of something) to Dawkins supporters. As stated the claim is way over the top, and is there simply as a put-down.

    But don’t worry, we New Atheists and scientismists are well used to this sort of stuff, and are well capable of sticking up for ourselves. 🙂

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  2. Robin Herbert

    Coel,

    Right in this thread you seemed to have trouble conceiving that a point I was making that only tangentially involved Dawkins was not motivated by a need to misreprrsent him.

    I have made no criticism at all in this thread of Dawkins but you have somehow made everything I have said here out to be an attack on him.

    I wrote a whole post on the reason why two control systems were functionally differenr and the various consequences of these differences on the behaviour of the system and you interpreted everything I said there as an attempt to misrepresent Dawkins.

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  3. brodix

    Maybe the focus on Dawkins is excessive.

    ““A continual circulation of matter in [the universe] produces no disorder; a continual waste in every part is incessantly repaired: The closest sympathy is perceived throughout the entire system: And each part or member, in performing its proper offices, operates both to its own preservation and to that of the whole. The world, therefore, I infer, is an animal.”

    So, if anything, the universe resembles the messiness and organic development of living beings, not the precision and exact functionality of machines. The analogy with man-made artifacts, he concludes, is flawed and should be rejected. If that’s true at the level of the cosmos, we think it is also true — and for similar reasons — at the level of biological organisms.”

    “That is, natural selection is a satisficying — not optimizing — process, as well as the ultimate recycler!”

    “First, because in contrast to what occurs in evolution, the engineer works according to a preconceived plan … Second, because of the way the engineer works: to make a new product, he has at his disposal both materials specially prepared to that end and machines designed solely for that task. Finally, because the objects produced by the engineer … approach the level of perfection made possible by the technology of the time. In contrast, evolution is far from perfection.”

    The basic difference seems to be that nature is cyclical and man is goal oriented, so we tend to think of objects, but nature is a process. “Life is the journey, not the destination.”

    Coel,

    Not to pile on, since you seem to be getting a bit of pushback, but to repeat, I don’t ignore your arguments, I disagree with them. There is no underlaying dimension, or even Newtonian flow of time, from past to future. Time is the effect and measure of change. That is why two identical clocks, in different physical circumstances, can run at different rates and still remain in the same present. They are separate actions and time is a measure, not basis of action. Duration is the state of the present, as energies coalesce and dissipate to create events. It is the events which come and go, not the present.

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  4. michaelfugate

    Maybe I am missing something, but being able to mathematically model something doesn’t mean one understands that something. Mathematics is a language and an equation is in a sense a metaphor. Because a mathematical model allows one to predict the future is nice and functional, just don’t confuse it with an explanation any more than a “love is a rose” or “love is war” explains love.

    Liked by 1 person

  5. Coel

    brodix, my problem is that, when you say things like:

    Duration is the state of the present, as energies coalesce and dissipate to create events.

    I cannot discern any sensible meaning in that sentence. It just seems to me to be science-y sounding words strung together in a way that makes no sense. So how am I supposed to discuss it with you?

    [If you now take that as an invitation to expound on what sentence means, and if I don’t then respond, please take that as an indication that your exposition also made no sense to me, just as most of your previous ones have not.]

    Trying to interpret this charitably, am I right in thinking (from various clues) that you are relatively elderly? You may have been reading about and thinking about this stuff for decades before the internet era. Before the internet, it would have been relatively hard to ever talk to any physicists about this. You might thus have developed your own ways of thinking about and talking about such things, that essentially have totally gone off on a tangent. Effectively you’ve created for yourself a private language. The problem is that that process has gone so far that the way you speak about such things just doesn’t make any connection to physics any longer, and so doesn’t make any sense to me.

    You seem to very much want to discuss this with people, but you’ll need to find someone who speaks your language. It would be way too much effort to try to become an interpreter between the two languages, since the chances of there being anything worthwhile it doing so are utterly tiny, and further the way you attribute any lack of communication to physicists being narrow-minded defenders of orthodoxy who simply don’t think about things doesn’t make it attractive to try.

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  6. Thomas Jones

    Coel, “In terms of quality of writing and communication, which is what I was asking about, appeal to the crowd is not a fallacy. Indeed the only way of assessing quality of writing and communication is such methods.”

    No, Socratic is right: Argumentum ad populum. I’m not really following the rest of this comment about the method for assessing quality of writing . . . . Mickey Spillane was quite a popular novelist in his day (still sells), but I don’t think his novels are considered exemplary outside the genre, though in fairness to him I don’t think he worried much about that. The point is that his popularity and the critical assessment of his work are two separate matters. Are you suggesting a functional equivalence is in play here?

    Liked by 1 person

  7. brodix

    Coel,

    I’m not sciency and don’t try to be. Maybe that’s the problem. I’ve discussed and debated this with a fair number of people and received a broad range of responses, so I find your lack of perception is not unique, but neither is it universal. It may well be how you see it, given cognition is based on this sequence of events we call time and seeing that in context is disorienting. As a friend who is a cardiologist put it, ‘Stop it, you’re hurting my head.’

    The very first FQXI essay contest, in 2008, was The Nature of Time (http://fqxi.org/community/forum/category/10?sort=author) and this was my entry; http://fqxi.org/community/forum/topic/239
    Some years later, in 2012, it was Questioning the Foundations (http://fqxi.org/community/forum/category/31418) and I entered a slightly more developed paper on the same topic; http://fqxi.org/community/forum/topic/1304
    This contest was community rated and I came in 50th, out of about 300 entries, so some people must have been able to make some sense of it.

    I’m feeling a bit elderly, but at 56, don’t totally qualify. Though a fair number of people I have known have passed on, including my wife.

    As it is, if you are truly unable to make heads or tails of it, I won’t stress you further. Though I am able to make sense of your view, given it is very common, I just don’t agree.

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  8. Coel

    Hi Thomas Jones,

    No, Socratic is right: Argumentum ad populum.

    It is not fallacious to refer to what people think about something when the very topic under discussion is how people react to it. If we were discussing, say, “Is Fawlty Towers funny?” it would not be in any way fallacious to refer to the fact that millions of people find it funny, and that it is regularly repeated on TV or bought on DVD forty years after it was made. Indeed, I really don’t see how one could evaluate the issue “Is Fawlty Towers funny?” except by a reference to what people at large thought of it, because the only meaning of “Fawlty Towers is funny” is that “people find it funny”.

    If someone were to declare “I do not find Fawlty Towers funny”, then ok, no problem, that’s how they feel; but if they were to declare that “Fawlty Towers is not funny”, and if they intended by that more than the former statement, then pointing out the opinion of many others is not in the slightest fallacious.

    Now, if the topic is then the literary quality and clarity of writing in The Selfish Gene, the fact that it is widely regarded as a model of clear science writing (and one of the few such books that can both benefit the academic and be accessible to the layman), and that it is still widely read and bought forty years later, are both relevant, and pointing to how lots of people evaluate the quality and clarity of his writing is not fallacious.

    Indeed, Socratic totally undercuts himself. If it were fallacious to refer to widespread opinion to assess the clarity of Dawkins’s writing, then it must surely be equally fallacious to refer to the opinion of one person such as Socratic on the topic. Yet Socratic pronounces it unclear based purely on his own reaction to it. He can only declare me fallacious if he himself is equally guilty.

    So Socratic doesn’t know how to interpret that passage of Dawkins and finds it unclear. OK fine, but the plenty of people who interpret it just fine and think that the meaning is quite clear are also relevant. I guess one can never write in a way that appeals to everyone (particularly those non-scientists who are unsympathetic to science).

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  9. Coel

    brodix,

    As it is, if you are truly unable to make heads or tails of it …

    I genuinely cannot make head or tails of it. But I’m puzzled, if people over at fxqi understand and like that stuff then why don’t you discuss it with them? Why do you repeatedly post it here where it gets repeatedly ignored and where it is nearly always off topic? (As it is in this thread.)

    Like

  10. couvent2104

    Massimo,

    I accidently – damn keyboard! – liked Coel’s contribution of October 27, 2016 at 11:08.
    Could you unlike it for me?
    I don’t want archeologists who unearth this discussion in 6211 CE to misunderstand my position.
    Many thanks!

    Liked by 3 people

  11. brodix

    Coel,

    Postings on the blog became very irregular and the conversation got a little stale. I stop through there on occasion. I post lots of things here that get ignored, but in case you haven’t noticed, there are very few relatively calm, thoughtful sites, discussing these sorts of issues. So I realize I’m a bit obnoxious and am thankful Massimo hasn’t banned me permanently. As it is, I seem to have heretically different views on lots of subjects, from economics to religion and occasionally find people willing to debate them. Mostly it is quizzical looks, ruffled feathers and clutched pearls when I cross too many boundaries, but there have been a fair number of interesting and enlightening exchanges. I guess the reason I’ve stuck around here is more the flow and pace of the conversation fits my schedule and there is some modicum of feedback.

    Like

  12. Thomas Jones

    Jesu, Coel, 5 paragraphs over this? Whatever. I trust the readership can google this without your going through contortions to defend your denial that such an informal fallacy exists.

    At any rate, you opened the door yourself when you wrote: “. . .The Selfish Gene is widely considered to be a model of clear science writing, that is currently ranking 2445 on amazon.co.uk (and #1 in “evolution”) forty years after it was written. . . .” Why not let the readers decide for themselves whether you are attempting to justify this model of clear science writing on the basis of its popularity by your words? No? Not even a teeny-weeny bit? You must be exhausted.

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  13. brodix

    Ps,

    If it is that you need some authority figure to access these ideas, possibly this might be of help;
    In a conversation over at Aeon some months ago, someone pointed out that Alan Watts described time in a similar way and used the analogy of a boat and its wake; In that the wake, as the past, doesn’t steer the boat, as the present, but that it is an effect of the boat. That events are first in the present, then in the past, as residue. Obviously anything by Watts requires some mind stretching, but it at least shows there are other people as far out as I seem to be.

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  14. SocraticGadfly

    Coel, yes it is. Quoting Amazon book sales numbers as if they’re a determinant of a book’s quality is very much an appeal to the crowd.

    No wonder you don’t “get it,” if you don’t even understand what constitutes one of the classical logical fallacies.

    Maybe Gnu Atheists, like Social Justice Warriors, like the back-of-hand-to-forehead martyrdom pose?

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  15. Coel

    Hi Thomas Jones,

    I trust the readership can google this without your going through contortions to defend your denial that such an informal fallacy exists.

    Sure, of course it exists! It’s just that it applies to statements of objective fact, and does not apply when the very issue under discussion is what people think of something! Which is what my comment said. Was it too long for you to read?

    Why not let the readers decide for themselves whether you are attempting to justify this model of clear science writing on the basis of its popularity by your words?

    Why that is indeed exactly what I was doing! If the issue is whether TSG is written clearly, then pointing out that lots of people consider it to be a model of clear science writing is indeed appropriate and not a fallacy. Afterall, if people in general interpret a piece of writing correctly and consider it to be clearly written, then surely it must be clearly written? What other meaning of “clearly written” can there be other than that people in general interpret it correctly and regard it as clear? And please explain how one can assess the clarity of writing without asking people what they think. What else would one do? Use litmus paper?

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  16. Coel

    Socratic,

    Quoting Amazon book sales numbers as if they’re a determinant of a book’s quality is very much an appeal to the crowd.

    No doubt you hold to some weird “values realism” concept where whether people like something is entirely irrelevant to how good it is. Sorry, but that’s the fallacy here.

    Like

  17. Coel

    If it is that you need some authority figure to access these ideas

    Well no I don’t, but anyhow I would not regard Alan Watts as an authority figure on anything related to science.

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  18. brodix

    So Dawkins wrote The Selfish Gene forty years ago. Thirty years ago, Reagan was elected with the motto that “Greed is good.” Ideas have their day, but occasionally the larger context has to be addressed. (Coel, Don’t try to make any sense of this. You will only short a few more circuits.)

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  19. Thomas Jones

    This really has become an embarrassment. My apologies to Massimo who must be summoning something Stoic; otherwise this nonsense in which I participated would have ended long ago. Last count 230 comments, most of which have little to do with the OP or its merits. I’m done.

    Liked by 1 person

  20. brodix

    For those of us who grew up and came of age between Kennedy and Reagan, the zeitgeist in which The Selfish Gene was written and into which it fed might seem obvious, but to younger generations, for which all this was baked in, I might recommend a recent BBC documentary that covers that era and how it bleeds into his one, Hypernormalization;
    https://thoughtmaybe.com/hypernormalisation/?lang=en
    Given my own time and satellite download issues, I’m only about 1/2 way through it, but it does give some feeling for the era.

    Like

  21. marc levesque

    Massimo,

    I enjoyed the article and totally agree that machine metaphors in biology can be very misleading, for academics and the general public.

    Thomas,

    Can’t speak for Massimo but I’ve really enjoyed most of the comments, yours too.

    Liked by 2 people

  22. marc levesque

    For me a good example of functional equivalency involves software: a teacher asks students “write a program that will produce output b, given input a”. So they do, and there are three functionally equivalent and correct answers. Three ways of doing it that that produce the same output from the same input. Similar example involving math problems rather than a programming language work too. So for me ‘functional equivalency’ implies a function that for the same input produces the same output.

    In that context, I think the idea that there is something functionally equivalent between what happens in the subconscious when humans catch a ball and what happens when it is done by mathematical calculation, inaccurate, because though the output ‘the ball is caught’ is the same in each case the input isn’t, it’s ongoing: “keep your gaze fixed at the ball, and adjust your running speed such that the angle of the ball remains constant”.

    Of course my argument isn’t without caveats, but I think it’s important to note the input has to be the same for the equivalency to hold, and the output is not ‘catching the ball’, but ‘the ball is caught’.

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  23. Robin Herbert

    With the “behaves as if” thing. Suppose I put the two robot arms I described side by side. They might look pretty similar. They have pretty similar ball catch rates. But I don’t know which one is which. Can I tell?

    Yes – each will move the arm to the ball in different ways. The one that solves DEs will pretty much move the arm to place in a predictable pattern, whereas the other will make some generic positioning moves first before refining it. The DE will handle different trajectories consistently, whereas the other will be better at some angles first and not so good at others, then get better.

    So you would be able to tell which was which in terms of the behaviour it exhibits. The one which “behaves as if” it were solving DEs will be that one that is, in fact solving DEs and the one which “behaves as if” it were using some learning, pattern matching behaviour will be the one that uses that method.

    Similarly, scientists know what method we are using to catch the ball by our observable behaviour. We just don’t “behave as if” we were solving a set of differential equations.

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