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Why We’re Right to Call Them Molecular “Machines”

Casey Luskin

Over at Discovery Institute’s YouTube animation “ATP Synthase: New Video Shows Intelligent Design of Molecular Machines in the Cell,” a critic claimed recently that the video contains an error. He wrote:

There’s actually a direct lie in this video — ATP synthase is not required for all life. Organisms that function on fermentation alone are quite common, especially in low-to-no-oxygen environments.

While the commenter is correct in saying that ATP synthase is not required for all life, he is wrong in suggesting that the video states otherwise. As I wrote in response:

You’re misinterpreting the video. It states: “ATP synthase is one of thousands of elegantly designed molecular machines inside your cells that make your life — and all known life — possible.” The point is molecular machines are needed for “all known life” — a true statement. The video correctly notes ATP synthase is “one of thousands” of such molecular machines. It isn’t saying “all known life” needs ATP synthase to make ATP (it doesn’t). Rather, it’s saying molecular machines are required for life.

The commenter is also wrong to imply that relying upon fermentation means you therefore don’t use ATP synthase. While there are some organisms that don’t use ATP synthase at all, even some anaerobic organisms that use fermentation still use ATP synthase for creating proton gradients.1 None of this contradicts or challenges what the video says.

So that’s settled, right? Nope. This led to a reply from another commenter — one who had previously offered various profanity-laced tirades against “creatards,” but who now sought to offer a reasonable argument:

You are misinterpreting the use of the word “machines.” Biologists use the word machine as an analogy. It does not imply that the molecule is designed by a creator, only that the molecule works “like” a machine.

By studying the genetics of such molecules we can see that they evolved in various ways, not that they were created out of whole cloth, definitely not “intelligently”.

In claiming that we understand how these molecular machines evolved, the commenter is of course bluffing. Very few attempts to explain the origin of molecular machines have been made (and those that have been made have been highly inadequate), and he offered no citation to back up his claim. Indeed, Franklin Harold stated in an Oxford University Press book, The Way of the Cell: “We must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”2

But what about the claim that the comparison between these biological systems and machines is a mere “analogy”?

According to, an “analogy” is “a similarity between like features of two things, on which a comparison may be based.” In fact in the first entry for “analogy,” even gives an example that draws a comparison between biological systems and machines: “the analogy between the heart and a pump.”

I fully recognize that the comparison between biological systems and machines is an analogy (and I never stated otherwise). But the fact that something is “just” an analogy doesn’t mean that the comparison is meaningless. An analogy is a “comparison” based upon “a similarity.” Analogies can be weak, or they can be strong. They can be based upon few similarities, or many similarities. Saying a comparison is “just an analogy” can be like saying an idea is “just a theory” — that could mean it’s a very strong claim as much as a weak one. So how strong is the “analogy” between biological systems and machines? Very strong.

To show why, I’ll repost here some comments I made in response to the YouTube commenter (with citations added at the end):

Michael Polanyi: “Biological systems, like machines, have, therefore, functions and forms inexplicable by chemical and physical laws. … By virtue of the principle of boundary control, mechanistic structures of living beings appear to be likewise irreducible.”3

James Shapiro: “No human contrivance operates with either the degree of complexity, the precision, or the efficiency of living cells.”4

Former National Academy of Sciences president Bruce Alberts: “The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines…Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.”5

Nature Reviews Molecular Cell Biology: “Today biology is revealing the importance of ‘molecular machines’ and of other highly organized molecular structures that carry out the complex physico-chemical processes on which life is based.”6

Nature Methods: “Most cellular functions are executed by protein complexes, acting like molecular machines.”7

Many other similar quotes could be provided. For example, I might have also quoted Michael Polanyi writing in Science, stating:

From machines we pass to living beings, by remembering that animals move about mechanically and that they have internal organs which perform functions as parts of a machine do – functions which sustain the life of the organism, much as the proper functioning of parts of a machine keeps the machine going. For centuries past, the workings of life have been likened to the working of machines and physiology has been seeking to interpret the organism as a complex network of mechanisms.Organs are, accordingly, defined by their life-preserving functions.

Any coherent part of the organism is indeed puzzling to physiology – and also meaningless to pathology – until the way it benefits the organism is discovered. And I may add that any description of such a system in terms of its physical-chemical topography is meaningless, except for the fact that the description covertly may recall the system’s physiological interpretation – much as the topography of a machine is meaningless until we guess how the device works, and for what purpose.

In this light the organism is shown to be, like a machine, a system which works according to two different principles: its structure serves as a boundary condition harnessing the physical-chemical processes by which its organs perform their functions.8

In any case, in my comment I then wrote, “If these authorities can compare biological systems to ‘machines,’ I see no problem doing the same,” and concluded by asking: “And where, in our observation-based experience, do things ‘like’ machines always come from?”

The commenter’s reply to me was predictable. He again noted that these authorities compared biological systems to machines through analogy, and then strangely argued as if this somehow this nullified my argument.

My comment never denied that the comparison between biological systems and machines is an analogy — in fact I used the word “like” intentionally, to show I was using the language of analogy. Again, the fact that a comparison is an “analogy” doesn’t mean it’s a weak argument. In this case, the analogy is quite strong.

As you’ll see in the citations above (and I could provide many more), biological systems share many properties with human-designed machines. In fact, if the analogy fails in any way, it’s because, as James Shapiro notes, biological systems are more complex than human-designed systems. As Shapiro puts it, “No human contrivance operates with either the degree of complexity, the precision, or the efficiency of living cells.”

The commenter also predictably argued that because the authorities I quoted aren’t pro-ID, therefore I can’t quote them as part of an argument for design. But I never said that these authorities are pro-ID, or that their views about ID somehow made my argument valid. I quoted them simply to point out that the comparison between biological systems and machines is strong. I then asked:

And where, in our observation-based experience, do things ‘like’ machines always come from?

Abductive Reasoning
My final question prompted a claim from another commenter that my argument commits the fallacy of “Affirming the consequent.” That charge would have been valid only if I’d claimed to be making a deductive argument, where the conclusion of design is guaranteed to be correct.

But I didn’t make that kind of argument. In fact, to my knowledge no leading ID proponent has said that the argument for design is deductive. ID is a historical science, and historical scientists don’t claim that their conclusions are arrived at through deductive reasoning. Apparently the commenter is unfamiliar with abductive reasoning, which ID uses, and which is a commonly accepted form of reasoning in historical sciences.

In abductive reasoning, one infers a prior cause based upon findings its known effects in the world around us, and determining that that cause explains more of the relevant evidence than does any other known cause. Here’s a classic example of abductive reasoning, paraphrased from the textbook Explore Evolution (pp. 3-5):

Imagine that you go outside one afternoon and see that the driveway of your house is wet. What can you conclude? Maybe it rained. Maybe the automatic sprinklers came on. Based upon the observed evidence, we might infer either explanation. We know that either cause (rain or sprinklers) is capable of generating the observed evidence (that the driveway is wet). To determine which explanation is the best one, we need more data.

We then observe that the lawn and the street are perfectly dry, and there are no clouds in the sky. This is curious. If the sprinklers had soaked the driveway, the lawn should also be wet. And if it had rained, then the street would and lawn would be wet. These explanations are much less likely in the light of the additional evidence. So we make more observations.

We then observe that there is a bucket with soapy water and a sponge sitting behind the car on your driveway. Now there’s only one explanation that can explain all the available data:

  • Driveway is wet.
  • Lawn is not wet.
  • Street is not wet.
  • Bucket of soapy water next to car on driveway.

The “rain” or “automatic sprinkler” hypotheses cannot easily explain all these observations. Only the “just washed the car” hypothesis can explain all of this evidence. It’s not a hard-and-fast deductive conclusion, but it pieces together present clues to infer to the past cause that explains the most clues. It’s an inference to the best explanation. This is abductive reasoning.

Stephen Jay Gould observed that historical sciences use this kind of reasoning to “infer history from its results.”9 Historical sciences (like Darwinian evolution and intelligent design) thus rely on the principle of uniformitarianism, which holds that “the present is the key to the past.” Under this methodology, scientists study causes at work in the present-day world in order, as the famous early geologist Charles Lyell put it, to “explain the former changes of the Earth’s surface by reference to causes now in operation.”

Darwinian evolution applies this method by studying causes like mutation and selection in order to recognize their causal abilities and effects in the world at present. Darwinian scientists then try to explain the historical record in terms of those causes, seeking to recognize the known effects of mutation and selection in the historical record.

Intelligent design applies this same method by studying causes like intelligence in order to recognize its causal abilities and effects in the present-day world. ID theorists are interested in understanding the information-generative powers of intelligent agents. ID theorists then try to explain the historical record by including appeals to that cause, seeking to recognize the known effects of intelligent design in the historical record.

What does all this tell us about molecular machines? Do we have any experience with unguided mechanisms producing machines? No, we don’t. There is only one cause we know that, in our experience, produces machines. In fact, in every case where we know the origin of a machine, it may be traced back to a mind, or an intelligent agent.

It’s not a hard-and-fast deductive conclusion, but the best explanation for the origin of molecular machines, like the ATP synthase rotary motor, is intelligent design.

[1.] “ATPase is reversible. The hydrolysis of ATP supplies torque for ?? to rotate in the opposite direction from that in ATP synthesis, and this catalyzes the pumping of H+ from the inside to the outside of the cell through Fo. The net result is generation instead of dissipation of the proton motive force. Reversibility of the ATPase explains why strictly fermentative organisms that lack electron transport chains and are unable to carry out oxidative phosphorylation still contain ATPases. As we have said, many important reactions in the cell, such as motility and transport, require energy from the pmf rather than from ATP. Thus, ATPase in organisms incapable of respiration, such as the strictly fermentative lactic acid bacteria, for example, functions unidirectionally to generate the pmf necessary to drive these important cell functions.” (Brock Biology of Microorganisms, p. 105 (Benjamin Pearson, 2012).)
[2.] Franklin M. Harold, The Way of the Cell: Molecules, Organisms and the Order of Life, p. 205 (Oxford University Press, 2001).
[3.] Michael Polanyi, “Life transcending physics and chemistry,” Chemical and Engineering News, 45(35): 54-66 (August 21, 1967).
[4.] James A. Shapiro, “21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering,” Gene, Vol. 345: 91-100 (2005).
[5.] Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, Vol. 92: 291 (February 6, 1998).
[6.] Marco Piccolino, “Biological machines: from mills to molecules,” Nature Reviews Molecular Cell Biology, Vol. 1:149-153 (November, 2000).
[7.] Thomas K�cher & Giulio Superti-Furga, “Mass spectrometry-based functional proteomics: from molecular machines to protein networks,” Nature Methods, Vol. 4(10):807-815 (October, 2007).
[8.] Michael Polanyi, “Life’s Irreducible Structure,” Science, New Series, Vol. 160 (3834): 1308-1312 (June 21, 1968).
[9.] Stephen Jay Gould, “Evolution and the triumph of homology: Or, why history matters,” American Scientist, 74: 61 (1986).

Casey Luskin

Associate Director, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.



Films and Videomolecular machines