© Joseph Giansante ’76 / Wikimedia CommonsLehigh University campus
Of Course Proteins Are Machines
A basic difference between the views of Greg Lang and Amber Rice and my own concerns the nature of the molecular foundation of life. They object that I consider many biochemical systems to be actual machines. They quote a line from Darwin Devolves stating that protein systems are "literal machines - molecular trucks, pumps, scanners, and more." They write disapprovingly that the book claims "rod cells are fiber optic cables ... The planthopper's hind legs are a 'large, in your face, interacting gear system.'" They do concede that I didn't make up those claims about the machine-like nature of the systems out of whole cloth: "Most of the analogies in Darwin Devolves are not Behe's creation - he has done well to scour press coverage and the scientific literature for relatable metaphors; and he is generous with their use." Nonetheless, they say, "reality remains: proteins are not machines, a flagellum is not an outboard motor."
On this point they are simply wrong. "Molecular machine" is no metaphor; it is an accurate description. Unless Lang and Rice are arguing obliquely for some sort of vitalism - where the matter of life is somehow different from nonliving matter - then of course proteins and systems such as the bacterial flagellum are machinery. What else could they be? Although they aren't made of metal or plastic like our everyday tools, protein systems consist of atoms of carbon, oxygen, nitrogen, and so on - the same kinds of atoms as are found in inorganic matter, nothing special.
A dictionary definition of "machine" is "an assembly of interconnected components arranged to transmit or modify force in order to perform useful work." Take a look for yourself here at the gears of the planthopper, here at the fiber-optic cells of the retina, and here at the bacterial flagellum. Do you think they fit that dictionary definition? Just like arms, legs, and jaws at the macro-level of life, all of which are organized to perform tasks and work by mechanical forces, so too the molecular foundation of life. Biologists routinely use the phrase "molecular machine" (just do a search of PubMed or Google Scholar), and have done so for a long time. For example, consider from 1997, "The ATP Synthase - a Splendid Molecular Machine" and from 1999, "The 26S Proteasome: A Molecular Machine Designed for Controlled Proteolysis." Organic chemists have also long used the term, albeit for much more modest assemblages than are found in life, even if they did win the 2016 Nobel prize in Chemistry. As the Royal Swedish Academy of Sciences announced then:
The Nobel Prize in Chemistry 2016 is awarded to Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa for their design and production of molecular machines. They have developed molecules with controllable movements, which can perform a task when energy is added.Lang and Rice do not argue that proteins are not machines. Rather, they simply declare "proteins are proteins, and not machines," list a few things some proteins do, and assume that makes it obvious they can't be machines: "Proteins are promiscuous. They moonlight, by chance interacting with other cellular components to effect phenotype outside their traditionally ascribed roles." Well, now. So can a nut or bolt be "promiscuous" by, say, holding together various kinds of machines? Can a mousetrap "moonlight" as a tie clip? What exactly is it about those features they list that contradicts the dictionary definition of a machine? Or contradicts the evidence of your own eyes when viewing the images of protein machinery linked above? - Nothing at all.
Hand-Waving at Irreducible Complexity
Lang and Rice use their misunderstanding of molecular machinery as a basis for attacking irreducible complexity: "By acknowledging the reality that proteins are proteins, and not machines, we immediately recognize the shortcomings of irreducible complexity." How so? They quote my definition of IC as "a single system composed of several well matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." They then object that:
The concept of irreducible complexity is flawed for two reasons. First, it considers a system only in its current state and assumes that complex interdependency has always existed. Second, irreducible complexity does not consider that proteins perform multiple functions and, therefore, evolutionary paths that seem unlikely when considering only one function may be realized through a series of stepwise improvements on another function.They are wrong on both counts. There is nothing in the definition of IC that requires their conclusions. Irreducible complexity does focus on the current state of a system, but it does not assume that "complex interdependency has always existed." Rather, it strongly implies (although does not absolutely rule) that the complex interdependency did not arise by Darwinian processes - that it required intelligent input to produce. IC also does not require that proteins do not perform multiple functions. In fact, in 1996 in Darwin's Black Box, I pointed out several that do, and showed why that does not help at all in explaining IC.
On top of those mix-ups, the reviewers then forget the definition of irreducible complexity as "a single system" that they stated just in the previous paragraph and begin to write of it in terms of "essential genes."
Simply because a system in its current form is irreducibly complex is not evidence that it did not evolve by random mutation and natural selection. Essentiality of a gene or protein is relative to its current state. For two closely related strains of yeast, between 1% and 5% of genes that are essential in one strain are dispensable in the other. Conditional essentiality is not simply due to the presence of second copy (or a close paralog) of the gene in one strain but not the other; rather, conditional essentiality is a complex trait involving two or more modifying loci.All of that may be true and interesting, but it is beside the point. A gene that is essential for the growth of an organism is not at all the same thing as a component of a single system that is required for the system's function. For example, the motor is a necessary component of the irreducibly complex bacterial flagellum - in its absence, the molecular machine cannot work. But it is not necessary for the growth of E. coli in Richard Lenski's laboratory evolution project. On the other hand, hemoglobin may be essential for human life, but it is not part of a single irreducibly complex system. Cells and organisms are composed of many molecular machines and biochemical pathways; they do not constitute a "single system" in the sense of the definition of irreducible complexity. I have written explaining such confusions long ago. It's little wonder that the reviewers don't appreciate the problem IC presents to undirected evolution since they misunderstand the concept itself.
Lang and Rice are welcome to think up all the evolutionary pathways they want, and join the long line of critics who have tried and (as I briefly show in Darwin Devolves and at much greater length elsewhere; see here, here, here, here, here, here, and here) failed over the years to figure out how irreducibly complex functional systems could be produced by random, undirected processes. Yet they don't even try. The penultimate section of the long review is entitled "Two Examples to Illustrate the Evolution of Complexity." (Hmm. Do you, dear reader, notice that an important word is missing from that title?) The reviewers dredge up a couple of old experiments that, at the time they were first published, were furiously spun as grave problems for irreducible complexity. (One sure way to get an otherwise-unremarkable paper noticed over the past several decades has been to claim it refutes those bothersome ID folks.) However, the results were actually quite modest and the relevance to ID claims nonexistent, as I wrote at the time. For those who want the details, click on the following links. Suffice it to say here that the first example cited by the reviewers (an investigation of a complex molecular machine called a vacuolar ATPase) at the very best concerned sideways evolution - no new functions, let alone new complex machinery, were involved. With the second example, a virus in a lab evolution experiment swapped out a binding site for a certain protein in the membrane of E. coli for a binding site for a second, homologous protein. In the process several E. coli genes were broken to help the bacterium survive.
Color me unimpressed. Yet it's reasonable to think that, in preparation for writing the review, Lang and Rice would search for the very best studies that have so far been produced that they think challenge irreducible complexity and intelligent design. Perhaps they found them.
Toward Mutual Understanding
In the Conclusion of their review Lang and Rice raise a plaintive cry, first celebrating in general the skepticism of scientists and then bemoaning the skepticism of the public toward grand Darwinian claims.
Scientists - by nature or by training - are skeptics. Even the most time honored theories are reevaluated as new data come to light. ...Perhaps I can help. After all, I used to believe that a Darwinian process did indeed build the wonders of life; I had no particular animus against it. Yet I believed it on the say-so of my instructors and the authority of science, not on hard evidence. When I read a book criticizing Darwin's theory from an agnostic viewpoint it startled me, and I then began a literature search for real evidence that random mutation and natural selection could really do what was claimed for them. I came up completely empty. In the over thirty years since then, I've only become more convinced of the inadequacy of Darwinism, and more persuaded of the need for intelligent design at ever-deeper levels of biology, as detailed in my books.
[O]ver 150 years after On the Origin of Species - less than 20% of Americans accept that humans evolved by natural and unguided processes. It is hard to think of any other discipline where mainstream acceptance of its core paradigm is more at odds with the scientific consensus. ...
Why evolution by natural selection is difficult for so many to accept is beyond the scope of this review; however, it is not for a lack of evidence: the data (only some of which we present here) are more than sufficient to convince any open minded skeptic that unguided evolution is capable of generating complex systems.
Clearly Greg and Amber honestly disagree. How to explain that? To help answer, let's first consider a different scientific discipline - physics. The history of physics offers powerful lessons that widespread agreement on even the most basic ideas in a field is no guarantee that there is sufficient evidence to support the theory, or indeed that there is any evidence for it at all. Just ask James Clerk Maxwell, who wrote the article "Æther" in 1878 for the ninth edition of the Encyclopedia Britannica:
Whatever difficulties we may have in forming a consistent idea of the constitution of the æther, there can be no doubt that the interplanetary and interstellar spaces are not empty, but are occupied by a material substance or body, which is certainly the largest, and probably the most uniform body of which we have any knowledge. [Emphasis added.]Maxwell, one of the greatest physicists of all time, calculated the density - to three significant figures - of the æther, a substance that doesn't exist. If that doesn't make the case for the peril of over-reliance on theory - and the need for profound scientific humility - nothing will.
But surely no branch of contemporary science could go so far astray, could it? - Maybe. In the past few years a theoretical particle physicist named Sabine Hossenfelder has made a splash by criticizing the reliance of other theoreticians on a gauzy concept of "beauty" to guide their calculations. She thinks that pretty much the whole field has been barking up the wrong tree for thirty years. Last summer she released a book on the topic, Lost in Math, which was favorably reviewed in Nature. She also maintains a blog, BackReaction, and holds forth regularly and entertainingly. Recently she put up a typically insightful, acerbic post, "Particle physicists excited over discovery of nothing in particular." The first reader to comment at the site wrote sympathetically: "I believe it's hard for anyone on the inside of a tribe to see the limitations of their own thinking. One has to step outside of the protection ring of orthodoxy."
Respect the Views of the Public
Precisely. It's hardly news that a group can share strong views on topics of mutual interest to its members, which many on the outside find less than compelling. Theoretical particle physicists, lawyers, members of the military, union members, business people, clergy, and on and on. It would be hard to find a group that didn't have such shared views. Of course, that includes evolutionary biologists and scientists in general. I would like to delicately suggest that a large chunk of the disconnect (although certainly not the only factor) between the public and biologists over evolution is that, as a rule, biologists share a commitment to Darwin's theory that the general public does not. That shared commitment leads biologists (and scientists in general) to require substantially less evidence to persuade them of the theory's verity and scope than someone outside the tribe.
Contra Lang and Rice, it's preposterous to say that the data "are more than sufficient to convince any open minded skeptic that unguided evolution is capable of generating complex systems." Unless one defines a skeptic of Darwin's theory (the most prominent proposed "unguided" explanation) as closed-minded, a quick visit to the library will disabuse one of that notion. (See here, here, here, here, here, here, and here.) Even in their own review, at best the authors argue that they see no obstacle to Darwinian processes producing functional complex systems; they surely don't demonstrate that it can. And of all the relevant literature in books and journals, the two papers they pointed to as examples of the power of Darwin's mechanism are quite modest indeed. When my first book, Darwin's Black Box, was published in 1996 it elicited comments by bona fide evolutionary biologists such as: "there are presently no detailed Darwinian accounts of the evolution of any biochemical system, only a variety of wishful speculations," and "There is no doubt that the pathways described by Behe are dauntingly complex, and their evolution will be hard to unravel.... We may forever be unable to envisage the first proto-pathways." It's hard to reconcile such statements with an assertion that the data are "more than sufficient."
As quoted earlier, Lang and Rice write: "Scientists - by nature or by training - are skeptics. Even the most time honored theories are reevaluated as new data come to light." That claim wouldn't survive even a short trip through the history of science, which is of course replete with people (that's another name for scientists) fighting tooth and nail to defend their ideas. Few scientists are as emotionless as Mr. Spock, and to maintain otherwise is little more than group-flattery. More to the point, scientists do not have a corner on the market for skepticism. In all walks of life that trait has its uses. A banker evaluating a loan, a voter listening to a politician's speech, a teacher wondering whether the dog really did eat this student's homework, a judge considering whether a defendant is indeed remorseful, an historian evaluating the direction of her academic field - pretty much everyone is skeptical when they smell a rat. And "pretty much everyone" is another way to say "the public."
For what it's worth, my advice on this matter for Lang, Rice, and others with similar views is to respect the opinions of the public, even if one disagrees with them and thinks them ill-founded, because, when it comes to the grand claims for Darwin's theory, many folks think they smell a rat and are prudently exercising their skepticism. Indeed, instead of blaming the public, they should consider the possibility that perhaps the evidence for the vast scope of Darwin's theory really isn't as strong as biologists over the years have been telling each other.
That's a very strong argument there.
It's pretty bizarre that Darwinists, the people who basically view the whole universe as mechanistic and devoid of purpose, would have a problem with proteins as machines. What's the suggested alternative? (Other than the childish "proteins are proteins", which doesn't explain anything.) That they are living beings, with feelings and all?
And then there's of course the obligatory attack on Irreducible Complexity, which, as always, involves failure to understand what it is. The scientific consensus is: If we say "Darwinism", we get money and make lots of friends. If we say "Intelligent Design", money isn't coming and nobody likes us. So Darwinism is the clear winner.