The abstract gives a quick summary of their findings:

In this study, we genetically trapped intermediates in flagellar assembly and determined the 3D structures of the intermediates to 4-nm resolution by cryoelectron tomography. We provide structural evidence that secretion of rod substrates triggers remodeling of the central channel in the flagellar secretion apparatus from a closed to an open conformation. This open channel then serves as both a gateway and a template for flagellar rod assembly. The individual proteins assemble sequentially to form a modular rod. The hook cap initiates hook assembly on completion of the rod, and the filament cap facilitates filament assembly after formation of the mature hook. (Emphasis added.)

So already we see confirmation of the sequential nature of construction, just like Minnich described in the film:

[Minnich] Even if you concede you had all the parts necessary to build one of these machines, that’s only part of the problem. Maybe even more complex — I think more complex — is the assembly instructions. That is never addressed by opponents of the irreducible complexity argument.

[Narrator] Studies of the bacterial motor have, indeed, an even deeper level of complexity. For its construction not only requires specific parts, but also a precise sequence of instructions for assembly.

[Minnich] You’ve got to make things at the right time. You’ve got to make the right number of components. You’ve got to assemble them in a sequential manner. You’ve got to be able to tell if you’ve assembled it properly so that you don’t waste energy building a structure that’s not going to be functional….

You build this structure from the inside out. You’re counting the number of components in a ring structure or the stator, and once that’s assembled, there’s feedback that says, "OK, no more of that"; now, a rod is added; a ring is added; another rod is added; the U-joint [hook] is added. Once the U-joint is add a certain size, and a certain degree of bend, about a quarter turn, that’s shut off, and then you start adding components for the propeller. These are all made in a precise sequence, just like you would build a building.

Paul Nelson then elaborates that the construction of one irreducibly complex machine (like the flagellum) requires the work of other machines; and those machines require other machines for their assembly. The whole assembly apparatus is itself irreducibly complex. In a memorable line, Jonathan Wells says, "what we have here is irreducible complexity all the way down."

What’s New?

In the new paper, the authors do not use the phrase irreducibly complexity, but their description matches Minnich’s. Example:

Assembly is initiated by the insertion of the MS ring (consisting of FliF) into the cytoplasmic membrane. The MS ring then acts as a platform for assembly of the C ring (the switch complex), the stator (the torque generator), and the flagellum-specific type III secretion (T3S) apparatus. Most flagellar proteins are secreted by the T3S system, which is powered by the transmembrane ion-motive force. The secretion and assembly of each substrate is highly ordered; flagellar assembly proceeds in a linear fashion from proximal rod to distal filament.

The authors go on to describe how assembly of one component is required for assembly of subsequent components, all in a sequential, ordered fashion:

On completion of the rod, a cap protein is required for hook assembly. The hook-cap protein, FlgD, has been detected at the distal end of the hook. Hooks are thought to assemble at their distal ends by inserting FlgE subunits underneath the hook cap. After the hook reaches its mature length (?55 nm), two junction proteins, FlgK and FlgL, and a filament cap protein, FliD, are added sequentially to the distal end of the hook.

Their beautiful cryo-electron micrographs and colored models show the exquisite nature of the growing motor, bringing the images shown in the film 11 years ago into sharper focus. The structure of the basal body is wonderfully intricate, quite like a work of art.

The authors freely employ the language of a mechanic’s workshop:

The flagellar rod is a multicomponent complex that functions as an export channel and drive shaft…. we conclude that the proper assembly of the proximal rod requires cooperative interactions between the FlgB, FlgC, and FlhO. FlgGcan then form a distal rod and serve as the substrate for subsequent addition of the P ring and hook.

Hook assembly and filament assembly are mediated by the hook-cap protein (FlgD) and the filament-cap protein (FliD), respectively…. Both the structures can be divided into cap and leg domains … a similar cap-leg architecture was seen in a high-resolution structure of the filament cap. We therefore suggest that the hook cap facilitates assembly of the hook by a rotational mechanism similar to the one used by the filament cap to promote assembly of the filament.

They refer to the work of Japanese scientists whose animations have captured the imagination of many viewers, showing the delicate dance of the cap as filament proteins are rapidly added in a sequential, ordered manner (see "The Flagellar Filament Cap: ‘One of the Most Dynamic Movements in Protein Structures’"). The new work confirms and adds to that understanding.

Their final figure summarizes the sequential assembly. They speak of a "determined length" for the distal rod; how that is measured is not explained, but must surely be an interesting question. The completion of one part "promotes" assembly of the next.

Revisiting Co-option

Is the flagellum like the Type III injectisome? This question was addressed in the film. (Evolutionists have tried to point to the TTSS machine as an intermediate; see "Two of the World’s Leading Experts on Bacterial Flagellar Assembly Take on Michael Behe.") The new diagram shows some similarities between the two machines, but many differences, including the component parts. Here’s their discussion:

The flagellum and the virulence-associated injectisome share an analogous architecture and homologous T3S components. However, the structure and function of the rod are quite different in the two systems. The rod of the injectisome is formed by a protein (PrgJ in S. typhimurium). Rod assembly is required for proper anchoring of the needle structure. The function of the injectisome rod is to provide a conduit for protein transport from the bacterial cytoplasm to the host cell (Fig. 6D). In contrast, the flagellar rod and its complex interactions with the MS ring, P ring, and hook (Fig. 6B) provide dual functions: a hollow channel for protein secretion and a sturdy drive shaft to transmit torque between the motor and filament.

So even if the flagellum "co-opted" parts from the TTSS, many parts are unique. As Minnich stated in the film:

You’re talking about a machine that’s got 40 structural parts. Yes, we find 10 of them are involved in another molecular machine. But the other 30 are unique. So where are you going to borrow them from? Eventually you’re going to have to account for the function of every single part as originally having some other purpose. So you can only follow that argument so far till you run into the problem of, you’re borrowing parts from nothing.

The new paper corroborates Minnich’s remarks. In conclusion, the authors say,

In summary, high-throughput cryo-ET, coupled with mutational analysis, revealed a complete series of high-resolution molecular snapshots of the periplasmic flagella assembly process in the Lyme disease spirochete. The resulting composite picture provides a structural blueprint depicting the assembly process of this intricate molecular machine. This approach should be applicable in determining the sequence of events in intact cells that generate a broad range of molecular machines.

Eleven years is a lot of time to refute the claims about flagellar assembly made in Unlocking the Mystery of Life, if they were vulnerable to falsification. Instead, higher resolution studies confirm them. Not only that, research into the precision assembly of flagella is provoking more investigation of the assembly of other molecular machines. It’s a measure of the robustness of a scientific theory when increasing data strengthen its tenets over time and motivate further research. Irreducible complexity lives!