May 4, 2018 | David F. Coppedge

Molecular Machines Show Same Design Principles as Big Machines

Life needs molecular machines before natural selection can even be considered as a possible Darwinian explanation for them.

The discovery that living cells operate real machines and motors has to rank as one of the greatest discoveries of the late 20th century. It continues to fascinate engineers who want to imitate what cells do. Here are recent news articles that discuss the subject, and one that tries to “evolutionize” them.

Molecular rotary motors: Unidirectional motion around double bonds (PNAS). Nano-engineers are taking baby steps toward imitating what cells do. Notice how Roke, Wezenberg and Feringa speak of the “design principles” of artificial rotary motors at the nanoscopic scale:

The field of synthetic molecular machines has quickly evolved in recent years, growing from a fundamental curiosity to a highly active field of chemistry. Many different applications are being explored in areas such as catalysis, self-assembled and nanostructured materials, and molecular electronics. Rotary molecular motors hold great promise for achieving dynamic control of molecular functions as well as for powering nanoscale devices. However, for these motors to reach their full potential, many challenges still need to be addressed. In this paper we focus on the design principles of rotary motors featuring a double-bond axle and discuss the major challenges that are ahead of us.

Having mentioned “design principles” for scientific work, they now look to the rotary engines in living cells.

Bacterial flagellum (Illustra Media)

Control of motion at the molecular scale has intrigued chemists for a very long time. The quest for overcoming random thermal (Brownian) motion has culminated in the emergence of synthetic molecular machines, including motors, muscles, shuttles, elevators, walkers, pumps, and assemblers. By taking inspiration from the fascinating dynamic and motor functions observed in biological systems (e.g., ATPase and bacterial flagella), the field of synthetic molecular machines has evolved rapidly in recent years.

There’s a use of the word “evolved” in a clear intelligent-design context. Nano-engineers are gradually improving their little machines by design, not by natural selection. Having mentioned the two famous rotary motors (see animations of ATP Synthase and the bacterial flagellum), they focus for the rest of the paper on human-engineered motors. But the comparison is clear: if humans cannot approach the efficiency and functionality of the living motors using their own “design principles,” how could anyone claim that there are no design principles in the living motors?

Researchers propose a model for how the parts of a bacterial flagellum are assembled (Science Daily). In Illustra’s classic film Unlocking the Mystery of Life, Dr Scott Minnich explains why the assembly of the bacterial flagellum is even more irreducibly complex than the flagellum itself. Now in 2018, scientists are bringing the assembly process into sharper focus. Just like Minnich says in the film, researchers in Japan describe the assembly as a complex, orchestrated process with feedback:

Many bacteria are equipped with a flagellum, a helical propeller that allows bacteria to travel. The flagellum is assembled in a highly organized manner involving the stepwise addition of each of its internal parts. However, there are many open questions as to how this orderly construction is achieved. In a study published in Science Advances, a Japanese research team centered at Osaka University has uncovered new molecular details and provided a model explaining how stepwise flagellar assembly occurs….

Flagellar assembly is a complex process involving more than 70 genes,” lead author Naoya Terahara explains. “First, the basal motor is assembled, followed by the hook, and finally the helical filament. Each structure is built by sending a unique set of proteins to the site of assembly. The cell can somehow sense when each structure is complete, triggering a switch to export the next series of proteins. We wanted to develop a more detailed picture of how this switching occurs.”

The open-access paper in Science Advances gives the details of their work. They’re only trying to figure out how one of the rings in the membrane shuttles proteins out to the growing tip, but statements about “assembly” dominate the paper, with no mention of evolution.

New details of molecular machinery that builds plant cell wall components ( For an example of an unfamiliar molecular machine, read this article about two researchers at Brookhaven National Laboratory who are figuring out “the enzyme ‘machinery’ that makes building blocks for lignin, a plant cell wall component.” Then listen to a podcast on ID the Future by Douglas Axe about how lignin challenges Darwinian evolution (link at Evolution News).

Molecular machines and the place of physics in the biology curriculum (Mike Klymkowsky, Public Library of Science, via In this PLoS blog post, Mike Klymkowsky tells how he read a paper that reminded him of an earlier conviction that learning about the physics behind molecular machines is important for biologists:

On reading the paper, I found myself returning to my original belief, yes, understanding physics is critical to developing a molecular-level understanding of how biological systems work, BUT it was just not the physics normally inflicted upon (required of) students. Certainly this was no new idea. Bruce Alberts [former editor of Science] had written on this topic a number of times, most dramatically in his 1989 paper “The cell as a collection of molecular machines“.

And yet at the end of his article, Klymkowsky espouses mindless materialism. Not only does he attribute molecular machines to blind evolution, he attributes everything to it. First, he sets up a false dichotomy between physicalism and mysticism, assuming that this will dispense with all design arguments or non-materialistic views of biology. Then he shows a very simplistic view of Darwinian evolution, assuming that genetic reorganization conjures up creative powers. Then he resorts to mysticism again. Let’s give him enough time to saw through the branch he’s sitting on:

NASA has been promoting materialism for many years as the only “scientific” view.

The value of introducing students to the idea of molecular machines is that it can be used to demystify how biological systems work, how such machines carry out specific functions, whether moving the cell or recognizing and repairing damaged DNA. If physics matters in biological curriculum, it matters for this reason – it establishes the core premise of biology that organisms are not driven by “vital” forces, but by prosaic physiochemical ones. At the same time, the molecular mechanisms behind evolution, such as mutation, gene duplication, and genomic reorganization, provide the means by which new structures emerge from pre-existing ones, yet many is the molecular biology degree program that does not include an introduction to evolutionary mechanisms in its required course sequence – imagine that, requiring physics but not evolution?

One final point regarding requiring students to take a biologically relevant physics course early in their degree program is that it can be used to reinforce what I think is a critical and often misunderstood point. While biological systems rely on molecular machines, we (and by we I mean all organisms) are NOT machines, no matter what physicists might postulate – see We Are All Machines That Think. We are something different and distinct. Our behaviors and our feelings, whether ultimately understandable or not, emerge from the interaction of genetically encoded, stochastically driven non-equilibrium systems, modified through evolutionary, environmental, social, and a range of unpredictable events occurring in an uninterrupted, and basically undirected fashion for ~3.5 billion years. While we are constrained, we are more, in some weird and probably ultimately incomprehensible way.

For reasons why materialism is unscientific, see this Illustra film.

Nowhere is the blindness of fallen man more evident than when they can stare at the most elegant designs in the universe, including their own brains, and then attribute them to “undirected” forces, which amount to chance—the Stuff Happens Law. What can we say, other than to keep pointing everyone to Romans 1:20-22.

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  • tjguy says:

    Last sentence in the OP:

    “While we are constrained, we are more, in some weird and probably ultimately incomprehensible way.”

    Translation: We might never be able to figure out, but we KNOW it has nothing to do with God!

    In the end, we all have faith and personal beliefs, including scientists.

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