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Seeing Past Darwin I:
The Machine Metaphor

The gradual crumbling of the Darwinian consensus, and the rise of a new theoretical outlook in biology is one of the most significant but under-reported news stories of our time.*

It's a scandal that science journalists have been so slow to pick up on this story. For, make no mistake about it, the story is huge. In science, they don't come any bigger.

The story is this:

The official explanation of the nature of living things---and therefore of human beings---that we've all been led to believe in for the past 60 or 70 years turns out to be dead wrong in some essential respects.

What have we been so wrong about? It's complicated, but in a phrase, it's this:

The machine metaphor was a mistake---organisms are not machines, they are intelligent agents.

What does that mean? That's what's hard to explain in a brief compass, but here's one way of putting it:

We are finally beginning to realize, on the basis of irrefutable empirical evidence, as well as more careful analysis of Darwinian theory itself, that purposeful action in living things is an objectively real phenomenon that is presupposed, not explained, by the theory of natural selection.

What do I mean by purpose?

Purpose is the idea that something happens, not because it must tout court, according to physical law, but rather because it must conditionally, in order for something else to happen. This ubiquitous property lies at the heart of living systems, and it's what makes them so puzzling, from a physical point of view.

Traditionally, the machine metaphor and the theory of natural selection have served jointly to allay this sense of puzzlement. However, it is now clear that both the metaphor and theory have been fundamentally misleading in crucial ways.

Admittedly, comparing living things to machines---like the steam engine (above)---seemed like a good idea at the time. After all, the parts of machines clearly have a purpose, just like the parts of organisms do. There is nothing in the laws of nature that dictates how machines must be put together tout court, and yet they must be put together in a certain way in the conditional sense---if they are to function properly. Just like organisms.


The analogy seemed to be very strong indeed.

And the beauty of it was that we don't find machines mysterious. So, the traditional logic in biological theory went like this:

  • Machines are not mysterious
  • Organisms are machines
  • Therefore, organisms are not mysterious

Except that machines like steam engines or automobiles would be very mysterious indeed, if we just found them lying about in nature!

What makes steam engines and automobiles seem unmysterious is that we know how and why the parts were assembled as they were. Namely, the parts were put together that way by human beings to serve human purposes.

But this means that machines don't make sense all by themselves. They don't just pop into existence. The parts of an automobile neither know nor care what they are for, nor do they have the slightest inherent tendency to assemble themselves into a whole automobile.

This means the concept of purpose that we associate with machines is wholly external to the machines themselves. In other words, machines only make sense when thought of together with an external intelligence that assembles them for its own purposes.


That is why the machine metaphor for living systems leads naturally to the idea that God assembled them, by the following reasoning:

  • Machines have to be assembled by an external intelligence
  • Living systems are literally machines
  • Therefore, living systems have to be assembled by an external intelligence

But if that is correct, then who could the external intelligence be in the case of living machines, if not God?

There is nothing new about any of this, by the way. For example, it was all pointed out very clearly by Robert Boyle---the great pioneering chemist and the discoverer of Boyle's Law---more than 300 years ago.

Now, supposedly Darwin managed to square this circle.

The idea was supposed to be that living things arose by chance and that random changes in them which happened to increase their chances of surviving and reproducing would increase in frequency in a population over time. That is natural selection, in a nutshell.

This way of thinking proposed to solve the problem of purpose by denying it was real.

Living systems were just accidental conglomerations of parts that happened by pure chance to work together as a functioning whole. And all the changes that organisms have undergone during the process of evolution---ditto.

In other words, nothing in organisms happens so that the whole organism may live. Rather, stuff happens, and organisms just happen to live as a result.

A pretty nifty theory, that---if it made sense.

The trouble is, it never made any sense. For one thing, it meant that all  purpose is an illusion, even in ourselves, which is absurd. We know that is not true from the direct evidence of our own experience.

So, one important difficulty with the theory of natural selection is that it contradicts everything we understand about how we ourselves work.

But that is only the beginning of the trouble with Darwinism. An even bigger shortcoming of the theory is that it simply took all the hardest parts of the problem of purpose as given.

How did those incredibly complicated systems imbued with purpose through and through, which we call "cells," come to be in the first place? Nobody has a clue.


That's one big difficulty with the theory---it has nothing to say about the origin of life. Here's another:

How can living systems be so robust (dynamically stable), when they consist of thousands of chemical interactions that must all be coordinated precisely in time and space? From the point of view of physics, cells (not to speak of more complex organisms) should not exist, and yet they do. How is that possible?

The only suggestion Darwinism has to offer is chance: those systems that just happened to be stable are the ones that we see today. But no one imagines this sort of explanation would ever do for a moment when it comes to something much simpler, like the stability of the atom or the stability of stars. And yet in evolutionary biology, which deals with objects many orders of magnitude more complicated than atoms or stars, invoking chance is accepted as an adequate explanation.

That's another very severe drawback to Darwinism---it is wholly inadequate and indeed unscientific by the standards prevailing in real sciences, like physics and chemistry.

Finally, we now know that living systems are autonomous agents, capable of highly flexible intelligent behavior. For example, even the simplest, single-celled organisms, such as bacteria, are able to adjust themselves to altered circumstances in a purposeful way. And they can do this even if the circumstances are unlike any ever encountered by their ancestors during their evolutionary history.

How are systems physically capable of this sort of intelligent, adaptive behavior? Again, all the Darwinist has to say is: Intelligent agency would be a great thing to have from the point of view of natural selection, therefore natural selection will see to it that it comes into existence.

In summary, for the Darwinian explanatory framework to make sense, we have to suppress all the toughest questions about living things and simply take their adaptive capacity, their robustness, and their very existence for granted.  Then---and only then---does natural selection make sense.

But in that case, we are just assuming  that organisms are intelligent agents. We are not explaining  how there can be such a thing as intelligent agents.


On the other hand, if we assume that organisms are just stupid, inert machines, then Darwinism makes no sense at all.

These deep, inherent conceptual problems with Darwinian theory can no longer be swept under the rug. The reason is that a new generation of scientists has come along, who are no longer content with the status quo and who have the courage to say so. Thanks to their joint efforts, a new science of intelligent agency is now in the offing.

One of the scientists contributing to this quiet revolution in biological thought is University of Chicago's James A. Shapiro. I will examine his work in the next installment of this series.

* This post inaugurates a series exploring contemporary attempts by scientists to better understand living systems by moving beyond the Darwinian theoretical framework. Today, I focus on the most basic problem with Darwinism: The analogy between organisms and machines, which lies at its heart, is question-begging and fundamentally misleading. [This series originally appeared on TheBestSchools.org blog, running from April through July of 2012.]