Inelligent Design - part III

Does Intelligent Design explain biological concepts more effectively than mainstream science?
To really ascertain whether or not ID proves Darwin wrong it is useful to examine how each theory explains basic biological concepts. Given that the three most prolific promoters of ID consist of a lawyer, a mathematician and a biochemist, biological evidence is often misunderstood, misrepresented or just ignored. Fundamental concepts, such as biogeography, palaeontology and comparative anatomy have not even been addressed in any substantial way by the major players of ID (or have been seriously distorted). Behe (1996) totally dismisses such crucial fields of knowledge, asserting that '[a]natomy is quite simply, irrelevant to the question of whether evolution could take place on the molecular level. So is the fossil record.' The following three examples examine how well ID explains particular biological concepts and how it compares to the current understanding of them within modern evolutionary synthesis.

The Cambrian Explosion. Within rocks of the middle-Cambrian period approximately 530 million years ago there is a relatively sudden appearance of a large number of fossils of what we now recognise as discrete phyla within a geologically short time span. ID advocates (and Creationists in general) leap on this as evidence of a brief and spontaneous 'creation' of all modern animal phyla rather than the slow, gradual appearance of more complex animals from earlier precursors predicted by Darwinian evolution. For example, a chapter on the subject written by Meyer et al. (2003) in the book Darwinism, Design and Public Education suggests that “the pattern of fossil appearance in the Cambrian period contradicts the predictions or empirical expectations of neo-Darwinism and other materialistic theories of evolution”. Phillip Johnson stated in Darwin On Trial that the Cambrian explosion represents the 'single greatest problem' that the fossil record poses evolution. This is a typical charge made by ID advocates who, naturally, believe that these fossils are best explained by Intelligent Design.
As is typical of ID arguments, the whole story is not being told. ID advocates claim that modern phyla appear suddenly in the fossil record of the Cambrian without evident precursors. This is simply untrue. Diverse Pre-Cambrian faunal assemblages are known from a number of different fossil sites. New discoveries of the last few decades have fueled exciting research on the nature of these animals and their relationships to modern taxa (e.g. Dzik, 2003). Some of the earliest of these discoveries were made in South Australia in 1946 by geologist Reg Sprigg – what is now known as the Ediacaran biota. These fossils often possess strange body-plans that are hard to interpret, but there are some which suggest relationships to later metazoans such as Kimberella which is a potential precursor of molluscs (Fedonkin et al., 2007) or Spriggina which has been identified as an arthropod with trilobite affinities (McMenamin, 2003). Ediacaran fossils have now been found all over the world and suggest a diverse, though morphologically simple, fauna of metazoans that existed around 60 million years before the Cambrian explosion.
In addition to this, Pre-Cambrian metazoans were soft-bodied animals with no shells or skeletons and therefore rarely fossilised. The Cambrian explosion is more accurately described as the sudden appearance in the fossil record of animals with hard parts which are more easily fossilised. Therefore the Cambrian explosion is partially an artifact of the fossil record more so than an exact gauge of metazoan evolutionary processes.

Transitional forms. This claim of abrupt appearances of organisms without precursors is also made about the fossil record in general. It is often asserted by the ID movement that there are no transitional forms or ‘missing links’ between species found in the fossil record, as would be predicted by Darwinian evolution. Casey Luskin (2008) of the CSC states that ‘new fossil forms come into existence without clear evolutionary precursors’ and that this phenomenon is best explained by Intelligent Design theory. In Darwin On Trial Phillip Johnson dedicates a lot of time to discussing the supposed absence of transitional forms in the fossil record (in a chapter titled 'The Fossil Problem') and asserts that little progress has been made in their discovery since Darwin published On The Origin of Species in 1859. Similar to the claim regarding the Cambrian explosion, the ID movement simply ignores supporting evidence found in the fossil record. For example, within the last few decades there has been an abundance of fossil finds of primitive whales illustrating the transition from a terrestrial to a marine environment resulting in a significant amount of research on whale evolution (Bajpai & Gingrich, 1998, Gingrich et al, 1983, Thewissen et al, 1996). An example from the early Eocene of Pakistan is Ambulocetus natans, an amphibious carnivore with paddle-like hind legs that probably swam with vertical undulatory movements of the body similar to extant swimming mammals. Fossil finds from the late Eocene have shown that whales such as Basilosaurus and Dorudon had adapted completely to a marine lifestyle, but still retain vestigial hind limbs and had not developed the melon organ used by cetaceans for echolocation. From various fossil sites around the world, a clear continuum of terrestrial to aquatic adaptations is able to be discerned within the whale family.
Johnson states, specifically in relation to whales, that although transitional forms are expected, “none of these appear in the fossil record”. Either the ID movement is ignorant of pertinent peer reviewed articles in mainstream scientific journals or they are intentionally avoiding such information because it contradicts their claims. Neither of these options seems appropriate for a movement that claims to be on the cutting edge of science.

The Flagellum. The flagellum is a tail-like organelle used for motility in both prokaryotes and eukaryotes. It is an extremely complex and efficient biological machine – the only example of a rotary motor found in the natural world. Due to its intricacy, the flagellum has become the ID proponent's favourite example of what is known as irreducible complexity. The term 'irreducible complexity' (IC) was coined by Michael Behe and has become one of the intellectual flagships of the ID movement. Behe (1996) defines IC as “a single system composed of several well-matched, interacting parts that contribute to the basic function wherein the removal of any one of the parts causes the system to cease functioning.” According to Behe, an irreducibly complex system could not have evolved in a series of gradual steps from a precursor because anything less than the current system would be missing parts necessary for its requisite function. Due to the elaborate interaction of parts within the flagellum, Behe concludes that it is an irreducibly complex system. Dembski agrees with this claim and uses the flagellum as a major example in his book No Free Lunch (2002). On Dembski's personal blog (2003) he has gone so far as to characterise the supposed inability of the biological sciences to provide a Darwinian explanation for the evolution of the flagellum as a 'global disciplinary failure'.
These claims are nothing but hyperbole and pleas to ignorance; 'irreducible complexity' is a fundamentally flawed concept. A system may appear irreducibly complex simply because we don't yet understand the mechanisms of its evolutionary progression. Two hundred years ago, one could make a reasonable claim that almost every natural system was irreducibly complex. That doesn't preclude obtaining that answer in the future through study and research. In Charles Darwin's time, the vertebrate eye was lauded in similar tones as being unexplainable by natural causes but now the evolutionary pathways of its development are well known. Probably due to the huge advances of evolutionary biology over the last half a century the ID movement cites very few examples of what they consider truly IC systems. Tellingly, the majority of these are from biochemistry, a field with which laypeople have little familiarity.
So how did the flagellum evolve? Almost certainly from a modification of existing secretion organelles already present in bacteria. Across the range of bacterial motility systems there are links to secretion. For example, some bacteria employ a gliding motility – they glide along a trail of secreted material in the manner of slugs and snails (Musgrave in Young et al, 2005). In particular there are many homologies between flagellar proteins and parts of the type-III protein-secretion system (Macnab, 1999). These homologies suggest a transition from simple secretory systems to gliding motility to rotary motility.
Even within bacteria there are different kinds of flagella and varying degrees of rotary motility. A functional precursor to complex flagella may be imagined by examining the archaeobacterial flagellum. The example that is used by the ID movement is the eubacterial flagellum, which can be thought of consisting of a motor, a shaft and a propeller. Archaeobacterial flagella however consist of only a motor and a combined shaft-propeller. The two flagella are not homologous, but clearly show that there is a plausible simpler precursor to the eubacterial flagellum and that the organelle itself is able to be structurally reduced while still retaining its motility (Thomas et al, 001).
Rather than being the irreducibly complex swimming machine depicted by ID advocates the flagellum is a versatile, plastic organelle used for motility, secretion and also adhesion. It represents one end of a continuum of motility-secretory systems. If you remove any of the flagellum's structural components it will cease to function in motility. But it will retain its secretory functions. It is not irreducibly complex.