Bio-Mechanics

Don't the Intricacy & Ubiquity of Molecular Machines Provide Evidence for Design?

In Salvo 19, we saw that engineers often turn to nature for inspiration when designing human technology. But long before the advent of modern technology, students of biology saw similarities between living organisms and machines. In 1697, the Italian life-scientist Marcello Malpighi observed: "Nature, in order to carry out the marvelous operations in animals and plants, has been pleased to construct their organized bodies with a very large number of machines."¹

Many of these comparisons were obvious: skeletons and muscles interact to form movable structures reminiscent of man-made contraptions. Other biological functions, however, lacked clear analogues in machine world. For example, how do machines help our bodies digest food? While machines may help our bodies pump blood, what produces blood in the first place? Malpighi boldly predicted that to explain such enigmatic functions, "machines will be eventually found not only unknown to us but also unimaginable by our mind."²He had no idea how right he was.

In the past few decades, modern biology has discovered not only that microscopic molecular machines are running much of the show in biology, but also that their complexity would have blown Malpighi's mind. A modern Italian biologist, Marco Piccolino, puts it in more gentile prose: biomolecular machines "surpass the expectations of the early life scientists."³

Molecular Machines: "Countless"

Molecular machines are ubiquitous in all living organisms. A 2004 article defined them as "devices that can produce useful work through the interaction of individual molecules at the molecular scale," and noted that "countless such machines exist in nature."⁴ Likewise, a paper in Nature Methods observed that "most cellular functions are executed by protein complexes, acting like molecular machines."⁵ One individual research project reported the discovery of over 250 new molecular machines in yeast alone.⁶

As anticipated by early scientists, molecular machines use components we commonly recognize in human machinery. They may have joints, gears, propellers, turnstiles, brakes, and clutches, which form motors, tweezers, vehicles, assembly lines, transportation networks, intelligent error-checking systems, and much more.

But biomolecular machines have a major difference that distinguishes them from human technology: their energetic efficiency dwarfs our best accomplishments. One paper observes that molecular machines "are generally more efficient than their macroscale counterparts,"⁷ and another suggests that the efficiency of the bacterial flagellum "could be ~100%."⁸ Human engineers can only dream of creating such devices. (For a discussion of the flagellum, see "Motor Works" in Salvo 15.)

Darwin's Theory Breaks Down

Molecular machines also pose a stark challenge to Darwinian evolution. In Origin of Species, Darwin famously stated that, "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." While Darwin claimed he could find no biological examples that failed his test, biochemist Michael Behe argues that modern discoveries of molecular machines provide case-closed evidence that disproves Darwin's theory.

Because molecular machines cannot perform their functions until many parts are present and coordinated, they cannot be built by the "numerous, successive, slight modifications" required by Darwinian evolution. As Behe notes, "The complexity of life's foundation has paralyzed science's attempt to account for it; molecular machines raise an as-yet impenetrable barrier to Darwinism's universal reach."⁹

Even those who disagree with Behe marvel at the complexity of molecular machines. In 1998, the former president of the U.S. National Academy of Sciences, Bruce Alberts, praised the "speed," "elegance," "sophistication," and "highly organized activity" of these "remarkable" and "marvelous" structures. He explained what inspired those words: "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."¹⁰

Three Marvelous Machines

While there are numerous types of molecular machines in biology, let's take a closer look at a few well-known examples.

The ATP Synthase: This is a molecular machine that works like a rotary engine. It has many parts we recognize from human technology, including a rotor, a stator, and a camshaft. The machine's basic purpose is simple but vital for all life forms: it produces adenosine triphosphate (or ATP)—the energy molecule used by living cells to drive many biochemical reactions.

In the ATP synthase illustration below, the barrel-shaped section at the top-left is called the F0 subunit. Powered by protons, this subunit spins around, transmitting mechanical energy into the grey driveshaft that sticks out of its bottom.

At the bottom of the diagram, the green and red teardrop-shaped components surrounding the driveshaft make up the F1 subunit. Much like a camshaft in a car engine, bumps on the driveshaft push these subunits open and outward as it spins around.

When the green and red subunits are pushed open, spent-energy molecules called adenosine diphosphate (or ADP), enter the machine. The mechanical motion of the ATP synthase machine causes an additional phosphate group to join with the ADP, creating ATP. After another 360-degree turn, the camshaft re-opens the subunits, releasing the newly formed ATP molecule to drift off into the cell and power some biochemical­reaction.

Kinesin: This is a protein machine used for transporting materials inside a cell. As seen in the diagram, kinesin machines literally walk along microtubules, dragging cargo to their proper destination.

The walking motion of kinesin is not entirely unlike a man walking with two legs. Powered by ATP, one leg swings over the other, allowing the kinesin to crawl along the microtubule. According to molecular machine modeler David Goodsell, "at each step, one motor domain holds on tightly while the other one releases its hold, flips up to the next step on the microtubule, and grabs on there."¹¹

Kinesins are more than just a motorized pair of legs. The "tail" end of the machine is highly specified to grab onto the proper cargo and pull it behind the walking machine.

The Ribosome: While most molecular machines are made of proteins, some are also composed of RNA. The ribosome is a large RNA-based molecular machine comprising over 300 proteins and RNAs whose function is to translate the information in messenger RNA (mRNA) so that proteins can be created.¹² In this sense, the ribosome is basically a code-reading machine: it reads the nucleotide sequence of the mRNA molecule and links up the proper amino acids as specified by the sequence. (For a discussion of this process, see "Premature Falsification" in Salvo 14.) The end result is the accurate construction of proteins.

Craig Venter, a leader in genomics, has called the ribosome "an incredibly beautiful complex entity" that requires a minimum of "53 proteins and 3 polynucleotides," leading some evolutionary biologists to fear that it may be irreducibly complex.¹³

Machine-Induced Cognitive Dissonance

In 2005, German biologist Walter Neupert published a letter in Biological Chemistry that unwittingly illustrates the cognitive dissonance faced by evolutionary scientists when they try to explain molecular machines. "Upon wondering and pondering about how similar dynamic protein structures are to products of machines engineered by humans," he wrote, evolutionary biologists face "a fundamental scientific challenge to understanding the laws of nature that unite evolved and designed systems." He concluded: "Nothing in biology makes sense except in the light of evolution": we know that Dobzhansky must be right. But our mind, despite being a product of tinkering itself strangely wants us to think like engineers."¹⁴

In other words, biologists must deny their scientific intuition that molecular machines appear to be the engineered products of intelligent design, and instead must remind themselves that "nothing in biology makes sense except in the light of evolution."

And what happens when evolutionary biologists stop repeating mantras and put pen to paper, trying to describe the evolution of molecular machines? In 2009, a team of scientists published a paper in the Proceedings of the National Academy of Sciences purporting to do just that. The media were so encouraged by the prospect of an evolutionary explanation for a molecular machine that Wired magazine published a piece triumphantly titled "More 'Evidence' of Intelligent Design Shot Down by Science."¹⁵ Instead, Darwin lobbyists shot themselves in the foot.

The technical paper—and the media frenzy that surrounded it—offered explanations like "'pre-adaptation' . . . ahead of a need for protein import," "parts accumulate until they're ready to snap together," or "machineries emerge before there's a need for them."16 So molecular machines evolve by just spontaneously appearing before they're needed, for no apparent reason?

The authors thought they had explained the evolutionary origin of a molecular machine. But their goal-directed language shows that blind and unguided mechanisms cannot produce irreducibly complex molecular machines. Their explanatory struggles reflect a simple truth: only one known cause has the ability to look forward and produce the integrated complexity we see in molecular machines. That cause is intelligence. •

Drawings by Joseph Condeelis, Light Productions. © Discovery Institute, 2012.

Endnotes
1. Quoted in Marco Piccolino, "Biological machines: from mills to molecules," Nature Reviews Molecular Cell Biology, Vol. 1:149–153 (Nov. 2000).
2. Ibid.
3. Marco Piccolino, op. cit.
4. C. Mavroidis, et al., "Molecular Machines," Annual Review of Biomedical Engineering, Vol. 6:363–395 (2004).
5. Thomas Köcher & Giulio Superti-Furga, "Mass spectrometry-based functional proteomics: from molecular machines to protein networks," Nature Methods, Vol. 4(10):807–815 (Oct. 2007).
6. See "The Closest Look Ever at the Cell's Machines," ScienceDaily.com (Jan. 24, 2006).
7. Op. cit., note 4.
8. David J. DeRosier, "The Turn of the Screw: The Bacterial Flagellar Motor," Cell, Vol. 93: 17–20 (April 3, 1998).
9. Michael Behe, Darwin's Black Box: The Biochemical Challenge to Evolution (Free Press, 1996), p. 5.
10. Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, Vol. 92:291 (Feb. 6, 1998).
11. See David Goodsell, Kinesin (Apr. 2005), at www.rcsb.org/pdb/101/motm.do?momID=64.
12. Jonathan P. Staley and John L. Woolford, Jr., "Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines," Current Opinion in Cell Biology, Vol. 21(1):109–118 (Feb. 2009).
13. See "Life: What A Concept!" (The Edge Foundation, 2008), at www.edge.org/documents/life/Life.pdf.
14. Walter Neupert, "Highlight: Molecular Machines," Biological Chemistry, Vol. 386(8):711 (Aug. 2005).
15. www.wired.com/wiredscience/2009/08/reduciblecomplexity.
16. Ibid.; see also Abigail Clementsa, et al., "The reducible complexity of a mitochondrial molecular machine," Proceedings of the National Academy of Sciences (Aug. 26, 2009).

From Salvo 20 (Spring 2012)
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