Irreducible Complexity by Natural Selection?

 

Liu, Renyi and Howard Ochman. 2007. Stepwise formation of the bacterial flagellar system. PNAS 104:7116-7121.

 

Summary. The bacterial flagellum is a hair-like structure that is used like a propeller as the bacterial cell moves through a liquid, and in other activities. Evolutionists need an explanation for the origin of the flagellum. The exact structure of the flagellum varies in different types of bacteria, but typically includes six components: a basal body for anchoring the flagellum in the cell membrane; a molecular motor that rotates; a switch capable of reversing the direction of rotation of the motor; a hook that connects the motor with the filament; a filament; and a device to transport protein flagellin molecules to the growing tip of the flagellar whip. The number of different proteins making up a flagellum varies up to more than 50. Genes for flagellar components from 41 different bacterial species were identified and their sequences compared. A set of 24 “core” genes were identified. Many of these core genes are more similar to each other than to other genes. This suggests that the components of the bacterial flagellum may have arisen stepwise by gene duplication and modification from a few, or even one, ancestral flagellar gene. The sequence in which the genes evolved is correlated with the sequence in which the flagellum is assembled -- genes for the basal part of the flagellum appeared first, followed by genes for the hook and, lastly, genes for the filament.

 

Comment. The bacterial flagellum has been proposed by Michael Behe[i] as an example of irreducible complexity, pointing to its origin by intelligent design. Although the authors of the paper take care not to mention the ID claim, it is clear they are attempting to respond to it. The evolutionary argument presented in this paper does not address the ID claim that there is no Darwinian pathway that leads to a flagellum through a series of functional intermediates. Rather, it assumes the flagellum evolved and proposes that genetic evidence is consistent with stepwise addition of genes to complete the structure of the flagellum. It thus begs the question.

Other evolutionary arguments have been presented.[ii] One such argument is that the flagellum originated as a secretory device and evolved greater complexity.[iii] The flagellar filament acts to transport molecules to construct the hook and filament. These are transported up through the hollow filament to the tip where they are used to construct the distal end of the filament. This begs the question of the origin of the secretory device, but it also raises a serious problem for such evolutionary conjectures. The function of the flagellum, as with every molecular machine, depends on precise molecule-to-molecule interactions. These interactions are dependant on molecular shape, which is ultimately dependent on DNA sequence. Ultimately, changes in shape depend on random mutations in the DNA. The problem is that once the first component molecule is determined, the structure cannot grow unless a molecule with the appropriate shape is available to join the starting molecule. Behe[iv] has estimated the odds of producing a shape-specific molecule by random mutation, and they are not good. Unfortunately for the evolutionary theory, the odds get worse at each step in the evolutionary process. If a suitable mutation should occur, addition of another molecule will increase the complexity of the evolving structure. This creates a more complex system that must now be matched by a new random mutation. As the complexity of the structure increases, the required precision of the random mutation also increases, and the odds of finding such a mutation decrease. This means the mutational shape-matching problem tends to get worse at each step. Furthermore, evolutionary theory also requires that the growing structure must be functional and selectively favored at each molecular step. This has never been shown. The only responses are weak arguments that some bacteria have flagella with fewer components than others. The conclusion here is that the claim that the bacterial flagellum is irreducibly complex remains unrefuted.

 

[i] Behe. Darwin’s black box.

[ii] E.g., http://www.health.adelaide.edu.au/Pharm/Musgrave/essays/flagella.htm

http://www.talkorigins.org/indexcc/CB/CB200_1.html

[iii] Molecular phyolgenies are interpreted as showing that the bacterial flagellum originated before the type III secretory device proposed as its ancestor.

[iv]Behe. The edge of evolution.

 

 

 

Paleozoic Sediments Differ from Recent Patterns

 

Peters, S.E. 2007. The problem with the Paleozoic. Paleobiology 33:165-181.

 

Summary. The problem with the Paleozoic is that Paleozoic depositional environments are so different from conditions existing today that it is difficult to analyze patterns in Paleozoic fossils. This problem is approached here by considering marine sediments that lack fossils. Although these are generally ignored by paleontologists, the lack of fossils should provide information about past conditions. A search of the Georef database was conducted, and references to unfossiliferous and fossiliferous sediments counted for each geological period. The results were that unfossiliferous units are more common in Paleozoic sediments than in Cenozoic sediments. The greatest number of unfossiliferous sediments occurs in the Ordovician and a minimum in the Paleogene. In contrast, fossiliferous units were less common in the Paleozoic and Mesozoic and most common in the Cenozoic. The minimum occurred in the Triassic and the maximum in the Neogene.

Differences in Paleozoic and Cenozoic depositional environments were identified from data complied by the Paleobiology Database Marine Invertebrate Working Group. Results showed that most Paleozoic marine fossils are from deeper water, with very few from marginal environments. This contrasts dramatically with the Cenozoic, where fossil collections from marginal environments outnumber those from deeper water. Thus the Paleozoic is characterized by abundance of unfossiliferous sediments and deposition in deep water. Three conditions might contribute to lack of fossils, and each of these conditions might be present in the Paleozoic epicontinental seas. First, lack of oxygen might result from ponding of water in epicontinental seas, and prevent survival of benthic marine fauna. Second, epicontinental seas might have increased salinity, which would be hostile to marine invertebrates. Third, riverine sediments would be deposited in the epicontinental seas, and under storm conditions might produce so much turbidity that marine organisms could not inhabit the area. These effects make it difficult to interpret patterns in Paleozoic fossils.

 

Comment. The Paleozoic presents numerous challenges for understanding earth history. A major change in the types of fossils occurs between the top of the Paleozoic and the bottom of the Mesozoic layers, marking one of the most dramatic features of the fossil record. The Paleozoic fossil record is mostly marine, but Paleozoic fossils are found only on the continents, which apparently were partially covered with relatively shallow seas.

However, the high frequency of unfossiliferous Paleozoic sediments may not be caused by hypoxia or hypersalinity in epicontinental seas.  First, the hypersaline Red Sea contains significant biodiversity, and burial would not likely produce unfossiliferous sediments. Second, unless epicontinental seas were in semi-closed basins such as today's Persian Gulf, currents could be expected to mix the water column and prevent hypoxia or hypersalinity. Modern epicontinental seas such as the South China Sea are generally not hypersaline; rather, rain and run-off often produce reduced salinity. On the other hand, rapid sedimentation might explain some of the nonfossiliferous deposits. With fewer barriers to deflect currents, they might reach velocities significantly greater than currents we observe today. Such currents might produce high turbidity, unstable substrates and habitat destruction. Rapid burial and decay of organic matter could produce anoxia. These condition would discourage establishment of living organisms and reduce the probability of fossilization. In addition, catastrophic deposition might erode sediments from source areas already depleted in living organisms, and produce unfossiliferous sediments.