Meet Rocker, the invention of an international team of scientists, including Gevorg Grigoryan at Dartmouth (pictured above). It’s just a bundle of alpha-coils that sticks through a cell membrane. It can let some ions pass in, and others pass out. That simple function took years of work, and will require years more; it’s just a stepping-stone toward rational design of cellular machines. Science published the achievement of a "de novo design" of a membrane channel that can transport zinc ions:

The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn2+ and Co2+, but not Ca2+, across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity…. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties. (Emphasis added.)

Let’s count instances of the word "design" (and its derivatives) in this paper: 45, not including 16 more in the references. There are only 3 mentions of evolution, and they do not help Darwinists:

A possible reason for the proton-leakiness is the lack of a proton-impermeable hydrophobic gate, which appears to be important for tight coupling in much larger and highly evolved proton-dependent transporters. Future designs will aim to achieve a transporter function similar to that of native proteins. Nevertheless, these findings, along with the very simple structure of Rocker, provide support for the view that transporters may have evolved from very simple pseudo-symmetric precursors.

For that last statement, they passed the ball to an old 2006 paper that speculated about how machines might have evolved. This paper does not point to any "simple pseudo-symmetric precursors" in living cells.

The final paragraph is about design, design, and more design. These engineers are looking up to the living examples for inspiration:

The structural and functional characterization of Rocker indicates that the design community has now passed an important milestone; the first high-resolution structure of a designed membrane protein has been determined through a combination of x-ray crystallography and NMR. Our design strategy combined the strengths of traditional computational design techniques with biophysically motivated conformational ensemble-based reasoning. Although Rocker’s activity falls short of natural transporters, it remains significant that function was achieved without high-throughput screening or directed evolution — and bodes well for future investigations in which computational design is combined with these powerful experimental methods.

Well, "directed evolution" is intelligent design: the process of randomizing inputs until a suitable output is found that the researchers select for their design goals.

So, the "design community" used a "design strategy" to employ "design techniques" and succeeded in getting a simple membrane protein that "falls short of natural transporters." Good work!

In the same issue of Science, Andrei N. Lupas of Max Planck Institute’s Department of Protein Evolution commented on this achievement. For the title of his article, the magazine borrowed Nobel physicist Richard Feynman’s old dictum, "What I cannot create, I do not understand." That’s a nice opening. It focuses the reader on what we often say: intelligent design is not a science stopper, it’s a science starter. If you want to understand how cells work, try to create one.

Does Lupas fill in the Darwin story? No; his only mentions of evolution are (1) "sequence patterns conserved in evolution" and (2) another mention of "directed evolution" (intelligent design). There is this brief excursion:

By the time of the last universal common ancestor of all life on Earth, some 3.5 billion years ago, a tripartite division of labor had emerged among life’s macromolecules, with DNA assuming the role of information repository, proteins providing catalytic activity, and RNA mediating between them. All three require defined three-dimensional structures to fulfill their biological roles. But whereas nucleic acids fold spontaneously and recover their structure robustly after denaturation, protein folding is a complicated process that is easily derailed; after denaturation, proteins typically aggregate and have to be degraded and resynthesized.

But that’s not really helpful to Darwinians either. It points out that cells figured out something that still challenges our brightest designers: how to arrange a sequence of amino acids that can fold into a machine.

Engineering proteins, on the other hand, turned out to be an altogether more difficult proposition due to what has become known as the protein folding problem: How does an amino acid sequence determine a protein’s structure?

His article is shorter but still mentions "design" 19 times. "Although a general solution to the protein folding problem would greatly help design," he says that bioengineers have to get by with short, simple models for now. Solutions for "simplified cases, such as for short, idealized, or repetitive polypeptide chains" have helped biochemists avoid getting "caught up in this [protein folding] problem" and have "allowed the field to move forward." Many proteins spontaneously fold into functional machines though hundreds of amino acid units long.

We noted recently that more scientists are becoming less reticent about using the phrase "design principles." Here it is again:

As in the well-known dictum by Richard Feynman, "What I cannot create, I do not understand," successful design is also a powerful way to show that a design principle has been understood.

Agreed. Design principles, as opposed to reliance on blind, aimless chance, are moving science forward and providing deeper understanding of how cells work.

Image credit: Dartmouth College via Science Daily.