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ID’s Top Six — The Origin of Irreducibly Complex Molecular Machines

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Editor’s note: In the past we’ve offered the top 10 problems with Darwinian evolution (see here for a fuller elaboration), and the top five problems with origin-of-life theories. But somehow we neglected to offer a parallel listing of the top evidence supporting intelligent design. Many different sources pointing to design in nature could be adduced, but we decided to distill it all down to six major lines of evidence. Sure, five or ten would have been more conventional, but when did ID advocates start playing to expectations?

So here they are, their order simply reflecting that in which they must logically have occurred within our universe. Material is adapted from the textbook Discovering Intelligent Design, which is an excellent resource for introducing the evidence for ID, along with Stephen Meyer’s books Signature in the Cell and Darwin’s Doubt.

4. The Origin of Irreducibly Complex Molecular Machines

Molecular machines are another compelling line of evidence for intelligent design, as there is no known cause, other than intelligent design, that can produce machine-like structures with multiple interacting parts. In a well-known 1998 article in the journal Cell, former president of the U.S. National Academy of Sciences Bruce Alberts explained the astounding nature of molecular machines:

[T]he 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.

There are numerous molecular machines known to biology (this article describes 40 of them). Here’s a description of two well-known molecular machines from Discovering Intelligent Design:

Ribosome: The ribosome is a multi-part machine responsible for translating the genetic instructions during the assembly of proteins. According to Craig Venter, a widely respected biologist, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. Bacterial cells may contain up to 100,000 ribosomes, and human cells may contain millions. Biologist Ada Yonath, who won the Nobel Prize for her work on ribosomes, observes that they are “ingeniously designed for their functions.”

ATP Synthase: ATP (adenosine triphosphate) is the primary energy-carrying molecule in all cells. In many organisms, it is generated by a protein-based molecular machine called ATP synthase. This machine is composed of two spinning rotary motors connected by an axle. As it rotates, bumps on the axle push open other protein subunits, providing the mechanical energy needed to generate ATP. In the words of cell biologist David Goodsell, “ATP synthase is one of the wonders of the molecular world.”

But could molecular machines evolve by Darwinian mechanisms? Discovering Intelligent Design explains why this is highly improbable due to the irreducibly complex nature of many molecular machines:

Many cellular features, such as molecular machines, require multiple interactive parts to function. Behe has further studied the ability of Darwinism to explain these multipart structures.

In his book Darwin’s Black Box, Behe coined the term irreducible complexity to describe a system that fails Darwin’s test of evolution:

“What type of biological system could not be formed by ‘numerous successive slight modifications’? Well, for starters, a system that is irreducibly complex. By irreducibly complex I mean a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.”

As suggested earlier, Darwinism requires that structures remain functional along each small step of their evolution. However, irreducibly complex structures cannot evolve in a step-by-step fashion because they do not function until all of their parts are present and working. Multiple parts requiring numerous mutations would be necessary to get any function at all — an event that is extremely unlikely to occur by chance.

One famous example of an irreducibly complex molecular machine is the bacterial flagellum. The flagellum is a micro-molecular propeller assembly driven by a rotary engine that propels bacteria toward food or a hospitable living environment. There are various types of flagella, but all function like a rotary engine made by humans, as found in some car and boat motors.

Flagella contain many parts that are familiar to human engineers, including a rotor, a stator, a drive shaft, a u-joint, and a propeller. As one molecular biologist wrote in the journal Cell, “[m]ore so than other motors, the flagellum resembles a machine designed by a human.”

Genetic knockout experiments by microbiologist Scott Minnich show that the flagellum fails to assemble or function properly if any one of its approximately 35 genes is removed. In this all-or-nothing game, mutations cannot produce the complexity needed to evolve a functional flagellum one step at a time, and the odds are too daunting for it to assemble in one great leap.

What about the objection that molecular machines can evolve through co-option of pre-existing parts and components? Again, Discovering Intelligent Design explains why this proposition fails — and why molecular machines point to design:

Irreducibly complex structures point to design because they contain high levels of specified complexity — i.e., they have unlikely arrangements of parts, all of which are necessary to achieve a specific function.

ID critics counter that such structures can be built by co-opting parts from one job in the cell to another.

Co-option: To take and use for another purpose. In evolutionary biology, it is a highly speculative mechanism where blind and unguided processes cause biological parts to be borrowed and used for another purpose.

Of course we could find many more pieces of evidence supporting ID, but sometimes shorter is more readable, and five makes for a nice concise blog post that we hope you can pass around and share with friends.

But there are multiple problems co-option can’t solve.

First, not all parts are available elsewhere. Many are unique. In fact, most flagellar parts are found only in flagella.

Second, machine parts are not necessarily easy to interchange. Grocery carts and motorcycles both have wheels, but one could not be borrowed from the other without significant modification. At the molecular level, where small changes can prevent two proteins from interacting, this problem is severe.

Third, complex structures almost always require a specific order of assembly. When building a house, a foundation must be laid before walls can be added, windows can’t be installed until there are walls, and a roof can’t be added until the frame complete. As another example, one could shake a box of computer parts for thousands of years, but a functional computer would never form.

Thus, merely having the necessary parts available is not enough to build a complex system because specific assembly instructions must be followed. Cells use complex assembly instructions in DNA to direct how parts will interact and combine to form molecular machines. Proponents of co-option never explain how those instructions arise.

To attempt to explain irreducible complexity, ID critics often promote wildly speculative stories about co-option. But ID theorists William Dembski and Jonathan Witt observe that in our actual experience, there is only one known cause that can modify and co-opt machine parts into new systems:

“What is the one thing in our experience that co-opts irreducibly complex machines and uses their parts to build a new and more intricate machine? Intelligent agents.”

Two videos, produced by Discovery Institute, explain the complexity and design of some well-known molecular machines, with memorable animations. First, on ATP synthase:

Second, on kinesin:

Image at top: Kinesin at work in the cell, from “Kinesin: The Workhorse of the Cell,” via Discovery Institute.