Intelligent Design and the Genetics of the Bacterial Flagellum

Excerpts from a research article on Intelligent Design are presented next:

Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria. Second International Conference on Design & Nature; Rhodes, Greece. Scott A. Minnich & Stephen C. Meyer. September 1, 2004.

Excerpt from the Abstract:
"Using a combination of microarray analysis, genetic fusions, and behaviors of specific engineered mutants, we demonstrate how environmental factors influence gene expression of these multigene families, where the influence is exerted within each system, and propose why segregating these systems is critical for the organism."

Excerpts from the Full Text (in PDF):
"Approximately 30 genes are involved in coding for its individual parts with another 10 genes regulating expression and assembly and 10 more for sensory perception or chemotaxis. These 50 genes constitute roughly one percent of the Escherichia coli or Salmonella typhimurium genome, a modest but significant information investment."

"The expression of flagellar genes is tightly controlled and regulated in a sequential genetic hierarchy mirroring organelle assembly from the inner membrane to the outer cell surface."

"This assembly process includes several key check points (feed back loops) that must be satisfied during the expression of each class of genes"

"Additionally, a protein complex of approximately 10 factors is positioned at the base of the flagellum to discriminate the order and number of basal body and flagellin components secreted through the flagellar core. This secretory complex is referred to as a type III secretory apparatus [or type III secretory system, TTSS]"

"Viewed as a whole, the flagellum is a true nanomachine of remarkable complexity in structure and assembly control. This macromolecular machine self-assembles and repairs, displays assembly control and processing, operates with two gears, is fueled by proton motive force, and the apparatus is ‘hardwired’ to a sensory apparatus that functions on short term memory (chemotaxis). Rotor speeds for E. coli are estimated at 17,000 rpm but motors of some marine vibrios have been clocked upwards of 100,000 rpms"

"...along with temperature, calcium limitation is a key environmental cue used by these organisms"

"Temperature also affects several other suits of genes in these organisms."

"... TTSS and flagellum are in fact separate and parallel systems. Further, it was shown by Kubori and co-workers that the TTSS system of Salmonella typhimurium assembles into a ‘needle-like’ structure, remarkably similar to the basal body of the flagellum. This structure acts as a nanoinjector; its hollow core serves as a specific conduit to export virulence proteins"

"Given that the TTSS of the flagellum and virulence systems are separate parallel structures, several factors suggest that the relationship and regulatory parameters of the flagellar and virulence TTSS are still intimately related. Further, as shown below, maintaining the segregational nature of their regulation may be critical for function."

"...the secretory signal of TTS proteins was conserved across genera. Based on this observation, we came full circle back to our original hypothesis of dual function of the flagellar basal body structure. Expression of multiple TTSSs in the same organism by mutually exclusive environmental conditions prevents cross contamination of secreted proteins."

"The potential for cross-recognition between type III exported proteins of different systems in the same cell carries several implications. First, these observations explain why segregation of these systems by specific environmental cues is necessary."

"...flagellin expression is controlled by such high expression promoters, it also suggests that flagellin, if expressed, may competitively interfere with virulence protein secretion. Indeed, this latter suggestion may explain why an important subset of major human pathogens, including Y. pestis, Shigella spp., Bordetella pertussis and recent isolates of E. coli O157:H7, have lost flagellar biosynthetic capacity altogether, even though they have the requisite flagellar genes. Each of these species has mutations in the flagellar master control operon flhDC, shutting down the entire flagellar regulon. For example, Y. pestis has a single T insertion in flhD causing a frameshift mutation. Function of FlhD can be restored by a spontaneous 5 base pair insertion (Smith and Minnich, unpublished observation)."

"To paraphrase the original rendition of the Department of Energy’s Genomes to Life web site, ‘the molecular machines present in the simplest cells... dwarf the engineering feats of the 20th century’."

"The dissection of the complexity and sophistication of simple machines like the bacterial flagellum are indeed a testimony to the power of modern molecular biological techniques.

"Yet, the elegant structural properties, efficiency, and the highly controlled genetic programming to produce these machines was neither anticipated nor predicted. The potential applications of this knowledge are legion and have spawned a new discipline focused on nanotechnology."

"In light of this new information, some scientists have questioned whether the mechanism of mutation, natural selection, and time are sufficient to account for the origin of such machines."

"[Michael Behe's concept of Irreducible Complexity, IC] has been the bread and butter of molecular geneticists allowing them to identify genes in any given system by loss of function [through single artificial mutations]."

"Behe argues that natural selection and random mutation [NS&RM] cannot produce the irreducibly complex bacterial flagellar motor with its ca. forty separate protein parts, since the motor confers no functional advantage on the cell unless all the parts are present."

"Natural selection can preserve the motor once it has been assembled, but it cannot
detect anything to preserve until the motor has been assembled and performs a function."

"If there is no function, there is nothing to select."

"Given that the flagellum requires ca. 50 genes to function, how did these arise? Contrary to popular belief, we have no detailed account for the evolution of any molecular machine."

"The data from Y. pestis presented here seems to indicate that loss of one constituent in the system leads to the gradual loss of others."

"For progression to work, each gene product must maintain some function as it is [functionally interdependent and] adapted to another."

"...possessing multiple TTSSs causes interference. If not segregated one or both systems are lost."

"Additionally, the other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system."

"...the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions."

"Arguably, this system is itself irreducibly complex."

"Molecular machines display a key signature or hallmark of design, namely, irreducible complexity."

"In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system."

"Given that neither standard neo-Darwinism, nor co-option has adequately accounted for the origin of these machines, or the appearance of design that they manifest, one might now consider the design hypothesis as the best explanation for the origin of irreducibly complex systems in living organisms."

"That we have encountered [biological] systems that tax our own capacities as design engineers, justifiably lead us to question whether these systems are the product of undirected, un-purposed, chance and necessity."

"Indeed, in any other context we would immediately recognize such systems as the product of very intelligent engineering."

"Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes."

"We know that intelligent designers [i.e., in Engineering] can and do produce irreducibly complex systems. We find such systems within living organisms. We have good reason to think that these systems defy the creative capacity of the selection/mutation mechanism."