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Journal Prints “Intelligent Design”! But…

intelligent design

You’re not likely to see the phrase “intelligent design” in any typical science journal, except to mock it. A recent example by a doctrinaire evolutionist is, not surprisingly, intended to subvert the design inference for a molecular machine. Did his intention backfire? Read on.

J.C. Phillips is a physicist at Rutgers University who has taken an interest in the concept of “self-organized criticality,” something that sounds as credible as “unguided excellence.” Phillips believes that unintelligent Darwinian natural selection moves molecular machines toward optimum performance. It’s kind of like how computers and other technology get more and more sophisticated the longer you leave them left outside to be buffeted by wind, rain, and ice storms. In his recent paper in PNAS, he takes on a marvelous walking machine, dynein, to illustrate “Darwinian evolution of dynein rings, stalks, and stalk heads” as examples of self-organized networks. It’s a tall order, because, as we will see, some of dynein’s features are truly remarkable, all the way down to the quantum-mechanical details.

A Deplorable Phrase

Papers in PNAS usually begin with a “Significance” statement, which serves as a layman-level abstract. Here’s where Phillips sneaks in the deplorable phrase “intelligent design” —

Proteins are the prime example of self-organized networks, as they have benefited from extensive natural (Darwinian) selection. Here, we quantify the dynamical shapes of dynein as they have evolved through interactions with water films. The interactions are long-range and are easily identified, and their improvement by evolution varies with the functions of parts of this molecular motor. It appears that evolution has brought human dynein close to a dynamical critical point, indicative of intelligent design. [Emphasis added.]

Essentially, he’s restating the “blind watchmaker” thesis. Science doesn’t need to consider a designer, the idea goes, because natural selection is fully capable of achieving functionally optimized machines that give the appearance of design. Dynein’s “dynamical critical point” (i.e., functional perfection), he intends to show, may appear “indicative” of intelligent design, but that indication is an illusion. So he thinks.

Interestingly, Phillips never again uses the phrase. The editors of PNAS apparently tolerated this infraction, because they must have been assured he would defeat it, and keep the crown on Darwin’s head. In his ending discussion, he claims success. “Here, we have found that the positive effects of evolution are especially dramatic in dynein,” he says.

What Is Dynein?

Dynein is a motor protein that walks on microtubules, the highways that make up the cellular skeleton. It cooperates with kinesin (see “The Workhorse of the Cell: Kinesin”) but moves in the opposite direction (see “Researchers Find that in Cells, Trains Run on Time”). Like kinesin, it is long and skinny, with “feet” that move along the microtubule, a long stalk composed of two coiled coils (called CC1 and CC2), and a “stalk head” at the other end, made up of a ring of AAA proteins (members of a family of “ATPases Associated with diverse cellular Activities”). AAA proteins bind to ATP, which channel power to various machines by undergoing conformational changes. These twists and bends at the stalk head of dynein can cause changes throughout the machine, such as moving the “feet” along the microtubule forward, one step per ATP.

Dynein’s job, like kinesin’s, is to transport cargo in the cell, and to create bending motions. Dynein motors help sperm cells to swim. In the axonemes of cilia, they move cargo in the intraflagellar transport process, and also provide the bending motion of motile cilia. Cytoplasmic dyneins also perform cargo-carrying work in the Golgi complex, the endoplasmic reticulum, and in the centrosomes, where they help position the spindle assembly during cell division. The wave-like beats of cilia along our air passages are powered by dynein.

Michael Behe included dynein as his first example of irreducibly complex molecular machines in Darwin’s Black Box. Perhaps that is one reason Phillips selected it; he may have been motivated to prove that Darwinism could defeat Behe’s design inference, and answer the claim that no evolutionist had ever shown how it could evolve. Behe did a masterful job explaining to the layman how dynein works and what it looks like, but that was 24 years ago. Much more has been learned in the interim.

The News on Dynein

One question Phillips examines in detail is how the ATP power released in the AAA+ ring in the stalk head gets down to the “feet” that attach to the microtubule, which are a long distance away at that scale. In the Abstract, he describes a remarkable mechanism: the power is assisted by a water wave that travels like a tsunami down the stalk. (Ignore the Darwin dogma for now.)

Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin, and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). Dynein has three distinct titled subunits, but how these units connect to function as a molecular motor is mysterious. 

Now, the mystery solved:

Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP at a ring 1,500 amino acids away. Here, we show how many details of this extremely distant interaction are explained by water waves quantified by thermodynamic scaling. Water waves have shaped all proteins throughout positive Darwinian evolution, and many aspects of long-range water–protein interactions are universal (described by self-organized criticality). Dynein water waves resembling tsunami produce nearly optimal energy transport over 1,500 amino acids along dynein’s one-dimensional peptide backbone.

This is a remarkable thing: living matter cooperating with nonliving matter (water). Cilia are known to cause currents to flow by their beating, and such currents participate in moving cells during development to their destination. In the case of dynein, the use of water waves is much more delicate and precise. Phillips is saying that the conformational changes in the stalk head set up waves of water molecules that surround the stalk, carrying the energy down to the microtubule (MT) binding domains (the “feet” mentioned earlier). He likens it to tsunamis that can transport the energy of an earthquake clear across an ocean with little loss.

Clearly, this has to be a tightly regulated process to work. The energy cannot just spread out at random. How do the water molecules confine their positions to the stalks, CC1 and CC2?

These linear shallow surface waves explain the remarkable distance covered by ATP excitation in AAA1 across a thousand amino acids to reach the stalk head. The more hydrophobic features of CC2 suggest that it can reflect the ATP wave from AAA1 back to the stalk head, increasing the intensity there, much like a nonlinear tsunami wave approaching shore. Note that the role of gravity in shallow water waves is played in protein hydropathic waves by the van der Waals dispersion attraction between water and amino acids. Also note that all our profiles are based on linear average; nonlinear tsunami effects could be even larger but are beyond present methods.

Even More Irreducible Complexity

Behe could have fun with this finding. Consider the genetic coding required to get amino acids into such an order that they attract water molecules that would position themselves so precisely as to focus energy received from the AAA+ ring’s conformational change all the way down to the other end of the stalk – a distance 1,500 times the diameter of a single amino acid! Imagine a beach game with 1,500 players lined up. They try to pass a volleyball overhead down the line to the far end by gently hitting it to keep it going, without grabbing it. Then the player at the far end reverses the direction, and all the players must nudge the ball up the line to the starting position. Just one goof would ruin the game. Dynein plays this game in the dark, rapidly and without mistake, thousands of times a minute. (A paper in NIH Biochemistry says that kinesin, a similar machine to dynein, hydrolyzes 80 ATP per second. If that corresponds to one step on the microtubule, that would represent 4,800 operations per minute, and 4,800 “tsunami” waves down the stalk.)

Moreover, Phillips says that the amino acids in the stalk function like mechanical springs, “tilting the stalk head to drive cytoskeleton cargo.” The two stalk coils, CC1 and CC2, are open enough to permit the association of the needed water molecules, which allows the water waves to become excited with less energy. As a result of this fine tuning of both the linear and cross-sectional structure, “linear water film surface waves can travel along the dynein surface great distances, much as linear seismic water waves travel across oceans.” How is evolution going to explain this?

The Evolutionary Tale

If Phillips ever thought he had a defeater for intelligent design, he has dug a deeper hole to climb out of. One tactic is an appeal to homology, comparing dynein between slime molds, worms, and humans (but see “Long Story Short: Is Homology Evidence for Evolution?”). His main tactic, though, is simple assertion. Natural selection, he claims, is in the business of optimizing molecular machines. Just believe in the power of self-organized criticality!

Here, we have found that the positive effects of evolution are especially dramatic in dynein, where the linear waves in monolayer water films propagate along the protein chain 1,500 aa from their source in AAA1 to the dynein stalk head tubulin binding sites. Within a W = 1 perspective, such “action at a distance” looks impossible in the presence of thermal fluctuations, while it is natural enough in terms of shallow water waves with W ∼10–30 bound to an aqueously and critically self-organized amino acid backbone. Note that close to a critical point large-density fluctuations may involve only small energy differences incorporated over long wavelengths.

One Last Thing

In a final flourish, to make his evolutionary hypothesis appear less absurd, Phillips engages in name-dropping. He appeals to historical examples of physicists and biologists who also used some of the concepts he used. What a convoluted, motley group he comes up with!

An historical note: The underlying mechanism of molecular motors has been discussed for decades, for instance by Huxley (1957) and Feynman (1963), usually in terms of harnessing thermal fluctuations, a task apparently involving Maxwell demons for “thermal rectification”. We have shown here that Darwinian selection has shaped motor proteins so that even linear water waves can transmit chemical energy over very long distances. Our statistical mechanical approach was anticipated by Schrodinger in 1943. Self-organized criticality was used in a schematic model to derive modular (or “punctuated”) evolution in 1995, and fractals emerged explicitly in 2007. The concept of self-organized criticality, with potential applications to living matter, has been widely discussed for decades.

Surely you’re joking, Mr. Feynman! Maxwell? Huxley? Schrodinger? Stephen Jay Gould? Mandelbrot? What does punk eek have to do with molecular machines? Dynein is not a fractal, and Maxwell’s thought experiment about the “demon” presupposes an intelligent agent able to violate the second law of thermodynamics locally and temporarily, using directed energy for a purpose. Readers can ponder whether this name-dropping paragraph helps Phillips’ case at all.

If Phillips intended to show that design is an illusion, he did it by assertion, not by demonstration (e.g., “Proteins are the prime example of self-organized networks, as they have benefited from extensive natural [Darwinian)] selection”). Then he flabbergasted his readers with descriptions of fantastically fine-tuned machinery. One thing everyone can agree with on. He said that dynein is close to a “dynamical critical point, indicative of intelligent design.” To that, Darwin skeptics can all respond: yea, verily, and amen.

Diagram: Cytoplasmic dyneins perform cargo-carrying work in the Golgi complex, among other functions; by TheTrappist / CC BY-SA.