Science Literature

The polar bear (Ursus maritimus) exhibits numerous adaptations to cold environments, fur, foot pads, head shape, exclusively carnivorous diet, heightened sense of smell, etc. Their close relationship to the brown bear (Ursus arctos) has long been recognised. Fertile hybrids are well-documented in captivity and there are rare examples of hybrids in the wild - the most recent being in 2006. Interbreeding, however, has not outweighed other taxonomic criteria, although it has been a factor in moving the polar bear from the genus Thalarctos back to the genus Ursus. "With their distinctly different morphology, metabolism, and social and feeding behaviors, the polar and brown bears are classified as separate species." Interestingly, a cluster of brown bears (known as ABC bears) have been found with close genetic links to polar bears.

"Recent genetic studies have shown that polar bears evolved from within brown bears, and that a genetically unique clade of brown bear populations that live exclusively on the Admiralty, Baranof, and Chichagof (ABC) islands of southeastern Alaska's Alexander Archipelago are more closely related to polar bears than to other brown bears."

The cold and dry conditions where this ancient polar bear jaw and canine were fossilized kept DNA within well preserved. (Credit: O. Wiig/University of Oslo's Natural History Museum, source here)

Speciation, then, has occurred, but when? how? and over what timescale? The opportunity to constrain the answers to these questions has come with the discovery of a jawbone with diagnostic polar bear traits from a site in Norway estimated to be 130-110 ky old. This makes it the most ancient sub-fossil yet to be recovered. Approximately 0.1 g of bone powder was used to generate a "complete, high-quality mt genome" using next-generation sequencing technology.

"The organization and length of the genome is comparable to that of extant bears, showing clear sequence similarity to both ABC bears and modern polar bears."

Using these data, phylogenetic analyses have been performed to probe relationships between the fossil bear (the Poolepynten specimen), modern-day polar bears, ABC bears and the modern brown bear variants.

"The phylogenetic results clearly demonstrate, with high support, the close relationship of the subfossil specimen to modern polar bear. Intriguingly, however, this ancient polar bear, which exhibits a very short branch length, lies almost directly at the branching point between polar bear and the genetically unique clade of ABC brown bears. Thus, both cladistically and anagenetically, this ancient specimen existed very close to the most recent common ancestor of polar bears and brown bears."

It is known that the diet of modern polar bears is dominated by ringed seals and bearded seals. Using the stable isotopes of carbon and nitrogen, it is possible to assess whether animal teeth (modern or sub-fossil) have a marine or a terrestrial signature.

"The stable isotope values for the ancient tooth [. . .] were within the range found from extant polar bear teeth and other tissues and were reflective of marine feeding. Importantly, these isotope values are distinct from those found in Late Pleistocene brown bears, including from the ABC brown bear lineage, as well as present-day coastal Alaskan brown bears. Thus, our results clearly demonstrate that the jaw is from an individual that had a feeding ecology similar to present-day polar bears, at the top of the Arctic marine food chain."

Using a molecular clock approach, the divergence time for the split between ABC bears and polar bears was estimated to be 152 ky. A further estimate was made of the emergence of the crown group of polar bears:

"Even more surprising, the age of the modern polar bear crown group (the clade containing the last common ancestor of all extant members) is estimated to be less than 45 ky, slightly older than the age of the ABC bears, a date that is also found with the expanded dataset of control-region sequence fragments. These estimates suggest a very recent and rapid expansion of modern polar bear populations throughout the Arctic since the Late Pleistocene, perhaps following a climate-related population bottleneck, although data from more modern and Holocene polar bear specimens will be required to establish this."

The authors conclude that speciation was rapid, consistent with the punctuated equilibrium (PE) model proposed to explain persistent patterns in the fossil record.

"The stable isotope data, phylogenetic analysis, and the geological and molecular age estimates of the Poolepynten specimen indicate that ancient polar bears adapted extremely rapidly both morphologically and physiologically to their current and unique ecology within only 10-30 ky following their split from a brown bear precursor and, subsequently, within the course of ~100 ky, spread to the full perimeter of the polar basin. As such, the polar bear is an excellent example of evolutionary opportunism within a widespread mammalian lineage. Moreover, the extreme proximity of the Poolepynten specimen to the polar bear ancestor provides a unique case of a morphologically and molecularly validated fossil link between living mammal species."

This research raises important questions for advocates of Darwinism. The PE model has been interpreted by them as a broad brush perspective. Consequently, the fossil record is considered too coarse to pick out the gradual transformation they insist must have occurred (because gradualism is the 'only way' to build complexity and achieve adaptation). However, this polar bear study shows that the timescales for change are too short to permit a viable gradualist explanation. This research shows the PE framework (of abrupt appearance followed by stasis) is realistic. Evolutionary theory must address issues like this and Darwinists should cease their confident rhetoric about the sufficiency of the mechanisms of mutations and natural selection.

Furthermore, Darwinists should realise that mere evidences of speciation are not the same as evidences for their theory. Polar bears display sophisticated adaptations, and if they are not gradualist phenomena, how can they be explained? If biological information is not acquired gradually, where does it come from? The ID perspective on this draws on numerous indicators of pre-existing information (for example, it is now widely recognised that much genetic information and associated regulative systems preceded the Cambrian Explosion). From this perspective, rapid speciation is possible because pre-existing information can be restructured and re-expressed in novel ways. The scientific challenge is to determine the mechanisms responsible for this type of information-rich speciation.

By contrast, Darwinism explains only information-neutral (finch beaks and peppered moths) or information-degradation (antibiotic resistance) scenarios. For confusing these various types of biological transformations, Darwinism's influence on biology has been unhealthy and scientific progress has been inhibited.

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear
Charlotte Lindqvist, Stephan C. Schuster, Yazhou Sun, Sandra L. Talbot, Ji Qi, Aakrosh Ratan, Lynn P. Tomsho, Lindsay Kasson, Eve Zeyl, Jon Aars, Webb Miller, Olafur Ingolfsson, Lutz Bachmann and Oystein Wiig.
Proceedings of the National Academies of Science, USA, March 16, 2010 vol. 107 no. 11 5053-5057 | doi: 10.1073/pnas.0914266107

Abstract: The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

See also:

Kaplan, M., Ancient polar-bear fossil yields genome, Nature News, online 1 March 2010 | doi:10.1038/news.2010.99

Tyler, D.J. Unexpected genome complexity in the starlet sea anemone, ARN Literature blog (11 July 2007)

On molecular clocks, go here and here.

It was 15 months ago that Science carried a story about the completion of a rough draft of the Neandertal genome. Palaeogeneticist Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig was reported as saying "he can't wait to finish crunching the sequence through their computers". It has been quite a long time coming, as it is more than a decade since Paabo first demonstrated it was possible to analyse Neandertal DNA sequences. Earlier reports suggested that Neandertals were sufficiently distinct from humans for them to be classified as a separate species of Homo. The draft genome has more than 3 billion nucleotides collected from three female Neandertals.

"By comparing this composite Neandertal genome with the complete genomes of five living humans from different parts of the world, the researchers found that both Europeans and Asians share 1% to 4% of their nuclear DNA with Neandertals. But Africans do not. This suggests that early modern humans interbred with Neandertals after moderns left Africa, but before they spread into Asia and Europe. The evidence showing interbreeding is "incontrovertible," says paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not involved in the work. "There's no other way you can explain this"."

Neanderthals once bred with Homo sapiens. (credit PHOTOLIBRARY, source here)

Genetically, then, Neandertals are not altogether extinct. Paabo is quoted as saying: "They live on in some of us". Therefore, the 'Out-of-Africa' model needs revision, as the migrants interbred to some extent with Neandertals and their genetic signatures spread through the migrant populations. According to Rex Dalton in Nature:

"That revelation is likely to revive the debate about whether or not the two groups are separate species, says anthropologist Fred Smith of Illinois State University in Normal, who has studied Neanderthals in Europe. Smith thinks that they are a subspecies of H. sapiens. Now that the genomes can be compared, it will be possible to investigate the genetic roots of some shared features."

This theme is picked up in the pages of New Scientist, and especially noteworthy is the editorial: "Welcome to the human family, Neanderthals". It calls for Neanderthals to be given a warm reception as truly human relatives.

"Svante Paabo, the pioneer of palaeogenetics, equivocated when a reporter asked whether his genome study suggested Neanderthals are the same species as us: "I would more see them as a form of humans that were a bit more different than people are from each other today, but not that much."
Why so shy? Putting aside the vexing question of what defines a species - which flummoxed even Linnaeus and Darwin - it is hard to see why Neanderthals should now be considered as anything other than Homo sapiens. We know that Neanderthals bred with our ancestors and produced fertile offspring, which is one hallmark of a species. And there is plenty more evidence to support giving them the status of Homo sapiens neanderthalis. Neanderthals shared a common ancestor with modern humans around 500,000 years ago. Its descendants went their separate ways as the Neanderthals adapted to colder climes, but then, at least 50,000 years ago, they resumed relations in the eastern Mediterranean, where the two populations met again. This pattern wouldn't necessarily merit separate species status for most animals, so why for us and Neanderthals?"

There is undoubtedly some journalistic enthusiasm here, because the claimed "hallmark of a species" is not valid: hybridisation is not that unusual between species and sometimes it occurs between genera (within the same family). This in itself is not a decisive argument. However, when we combine genetics, morphology and behaviour, the picture looks much clearer.

"There is, of course, more to the concept of being human than ecology and genetics: we are human because we think, talk, love and believe. It is impossible to know the mental life of a Neanderthal, but there is reason to think that it was not so different from our own. The Neanderthal genome differed little from ours, encoding fewer than 100 changes that would affect the shape of proteins. True, some of these differences occur in genes linked to brain function, but similar variation is found among humans today. Moreover, Neanderthals share with us a version of a gene linked to the evolution of speech, and recent archaeological evidence suggests that their minds were capable of the symbolic representations that underlie language and art. If that's not human, then what is?"

This brings us to why Neandertals have been so misinterpreted over the years. Why has it taken us so long to reject the picture of a brutish, grunting caveman devoid of aesthetics and reason? The Editorial starts with these words: "WE HUMANS like to see ourselves as special, at the very pinnacle of all life. That makes us keen to keep a safe distance between ourselves and related species that threaten our sense of uniqueness. Unfortunately, the evidence can sometimes make that difficult." Is this interpretation valid? Do we like to keep a safe distance between ourselves and anything that threatens our uniqueness? Perhaps we should reflect on on the history of scientific racialism, that portrayed races as occupying different rungs of the evolutionary ladder - was this also to keep a safe distance from races that threatened our uniqueness? Furthermore, is it true that we, the population at large, like to keep this safe distance? Why is it that any reports of animals showing apparent cognitive and creative skills are deemed newsworthy, whereas other studies showing a big divide between humans and animals languish in obscurity? I leave these questions for further thought and reflection.

One thing I have noticed over the years is that people with a design perspective have been far more receptive to the idea that Neandertals were part of the human family. They have been impressed by morphological considerations, but the cultural artifacts of Neandertals have made a big impression. In the early days, these were relatively meager, but more recent years have seen a flowering of reports of Neandertal culture. In this blog, these issues have been explored on several occasions: Burying the view that Neanderthals were half-wits, Darwinist thinking on the origin of religion, The cognitive skills of Stone Age Man, Images of evolution as secular icons, Walks like a man, talks like a man - is it a man?, and Rethinking Neanderthals. There is a pattern here, and it is evident even in the original reception given to Neandertal finds. The Darwinian scientists were looking for intermediates and they found one in Neandertal Man. He was portrayed as an ape-man and used to prop up an evolutionary story of ape-to-man evolution. After it was realised that the original finds were bones from someone deformed by disease, the story did not change much. The icon was too important to lose. Darwinism had created a blind spot for palaeoanthropologists and impaired the progress of science. Those able to make design inferences within science have been ahead of the game, but now the genetic data is published, all have to follow. However, would you believe, the same issue of New Scientist that carried the editorial noted above also had an article with the title: "Neanderthals not the only apes humans bred with". Apes? Really! Outdated traditions do not die when it comes to Darwinism - they just get repackaged!

A Draft Sequence of the Neandertal Genome
Richard E. Green [et al] and Svante Paabo
Science, 328, 7 May 2010: 710-722 | DOI: 10.1126/science.1188021

Abstract: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

See also:

Dalton, R., Ancient DNA set to rewrite human history, Nature, 465, 148-149, (12 May 2010) | doi:10.1038/465148a

Editorial, Welcome to the human family, Neanderthals, (New Scientist, 12 May 2010)

Gibbons, A., Close Encounters of the Prehistoric Kind, Science 328, 7 May 2010: 680-684.

A previous blog drew attention to Glial (or Muller) cells that conduct light from the surface of the eye's retina to the photoreceptor cells. These cells provide a low-scattering passage for light from the retinal surface to the photoreceptor cells, thus acting as optical fibres. Their function was reported to "mediate the image transfer through the vertebrate retina with minimal distortion and low loss". New research in this area has increased knowledge of their functionality after constructing a light-guiding model of the retina outside the fovea. As a result, the "retina is revealed as an optimal structure designed for improving the sharpness of images".

Schematic of Muller cells funnelling light (source here)

These specialised cells do this in two ways: filtering out stray light and reducing colour dispersion. Stray light is a form of noise, so that the objects of interest are seen less clearly. It is found that the glial cells improve the signal-to-noise ration as light passes through them.

"The simulations showed that the Muller cells transmit a greater proportion of the former to the rods and cones below, while the latter tends to leak out. This suggests the cells act as light filters, keeping images clear. The researchers also found that light that had leaked out of one Muller cell was unlikely to be taken up by a neighbour, because the surrounding nerve cells help disperse it. What's more, the intrinsic optical properties of Muller cells seemed to be tuned to visible light, leaking wavelengths outside and on the edges of the visible spectrum to a greater extent."

The second mechanism relates to colour vision. "Just as light separates in a prism, the lenses in our eyes separate different colours, causing some frequencies to be out of focus at the retina". However, the glial cells have a diameter that is wider at the surface of the retina than at the cone photoreceptor at its base. The optical fibre structure of these cells brings significant improvements.

"Another notable result is that parafoveal color vision is less affected by chromatic aberrations. The longitudinal chromatic aberration spans the focal spot along the retina, where blue focuses before red. Thus both colors cannot be focused simultaneously on the cones. But with glial light guiding the configuration changes: Regardless of the volume of the focal spot, set by chromatic and monochromatic aberrations, the incidence angles are still within our analysis range of a few degrees. That means that they will still be guided by the same glial cell and lead to the same cone."

According to the report in New Scientist, these findings open up potentially fruitful areas for biomimetic research. "The new understanding of the role of Muller cells might find applications in more successful eye transplants and better camera designs, says Ribak." The human eye, which is already a remarkable example of functional engineering, continues to yield more evidences of exquisite design. All the more surprising, then, that Darwinians are persisting in their view that the eye should be listed among evolution's biggest "mistakes". An Editorial in New Scientist reaffirms the validity of this claim:

"Sure, sending light through Muller cells enhances vision, but that is not an argument for choosing to put the wiring in front of the sensors. It still creates a blind spot, where the nerves dive through the light-sensitive cells on their way to the brain. It would make much more sense to put Muller-like cells in front of the sensors, with the wiring behind. Rather than provide evidence in support of intelligent design, the new work is actually yet another example of evolution's extraordinary ability to create workaround solutions to problems arising from earlier iterations. Kenneth Miller, a biologist at Brown University in Providence, Rhode Island, and an untiring veteran of the creation-evolution wars, calls the Muller cells "a retrofit: a successful and highly functional adaptation made necessary by the original architecture of the retina, but a retrofit". The eye's structure, and the blind spot in particular, bears the unmistakable fingerprints of Darwinian evolution."

What we are seeing here fits what Thomas Kuhn called "normal science" in action. Darwinists never predicted the function performed by Muller cells, but once they were recognised, they are dubbed a "retrofit", with credit given to the amazing powers of mutation and natural selection (without any valid supporting evidence). This strategy is to Darwinism what epicycles were to the Ptolemaic cosmology. Actually, Kenneth Miller is retrofitting glial cells into the Darwinian model of the eye's evolution. He has to do this in order to save the theory in which so much intellectual capital is invested. But like the financial markets of today, crises will ensue. Just as commercial markets could not sustain high levels of debt indefinitely, so also Darwinism: they have borrowed excessively in order to sustain mutation and natural selection as viable mechanisms. When people look for substance, they find peppered moths and bird beaks. When they look carefuly, they find exquisite design - not tinkering evolution. All the Darwinists have left to defend their case is the blind spot - that is all that keeps them from the conclusion of optimal design.

Retinal Glial Cells Enhance Human Vision Acuity
A. M. Labin and E. N. Ribak
Physical Review Letters, 104, 158102 (April 2010) [4 pages] | DOI: 10.1103/PhysRevLett.104.158102

Abstract: We construct a light-guiding model of the retina outside the fovea, in which an array of glial (Muller) cells permeates the depth of the retina down to the photoreceptors. Based on measured refractive indices, we propagate light to obtain a significant increase of the intensity at the photoreceptors. For pupils up to 6 mm width, the coupling between neighboring cells is only a few percent. Low cross talk over the whole visible spectrum also explains the insensitivity to chromatic aberrations of the eye. The retina is revealed as an optimal structure designed for improving the sharpness of images.

See also:

Editorial, The eye was evolution's great invention, New Scientist (6 May 2010)

McAlpine, K. Evolution gave flawed eye better vision, New Scientist (6 May 2010)

John Avise commences his paper with a quotation from Michael Behe affirming that research into the molecular workings of the cell leads unambiguously to the conclusion: "design!". To counter this, Avise presents the human genome as clear evidence for non-sentient design. He thinks that conventional evolutionary mechanisms are perfectly capable of explaining complexity, declaring: "it is not my intent here to repeat the voluminous evidence for how natural selection in conjunction with other nonsentient evolutionary forces can yield complex adaptations". Instead, he suggests that the decision as to whether the design is intelligent or non-sentient can be made by looking at the imperfections and flaws evident in the cell's molecular systems.

"Both a Creator God and natural selection are powerful shaping forces that might be expected to have engineered beautiful functionality and efficiency into complex biological features, such as the human genome. The much greater challenge - for proponents of ID and for scientists alike - is to explain complex biological traits that operate inefficiently or even malfunction overtly. On closer inspection, the human genome itself becomes a prime example of a highly complex trait with serious molecular shortcomings."

"The Hopeless Dawn" by Frank Bramley. Don't look to science for a way to face suffering, pain and loss. (source here)

Avise draws our attention to the large number of genetic mutations that have been discovered (most of which are associated with disease or impairment). The figure of 75,000 different disease-causing mutations is mentioned. It should not be necessary to point out that this is not news to ID scholars (some of whom have a professional interest in providing medical treatments for these conditions). The existence of large numbers of deleterious mutations has been used to argue against the efficacy of Darwinian mechanisms of evolutionary transformation (especially as the comparable list of advantageous mutations is not noted for its length). Nevertheless, the reason why Avise presses this information on us is that he thinks ID scientists have been blind to them as witnesses to 'tinkering' evolutionary mechanisms.

"An apologist for the intelligent designer might be tempted to claim that such deleterious mutations are merely unavoidable glitches or secondary departures from a prototypical human genome that otherwise was designed and engineered to near perfection. As I will briefly describe in the next two sections, however, this excuse would be untenable, because all human genomes are also littered with inherent (endogenous) design flaws."

The first of these sections is concerned with "gratuitous genome complexity". Avise presents an argument based on the phenomenon of "split genes". Protein-coding loci are split into coding regions (exons) and non-coding regions (introns). A vast infrastructure of molecular machinery exists to extract the coding information and splice it all together. This is suggested to add time and metabolic cost to the process of making proteins. But the real punch-line is that there are many mutations associated with both intron/exon borders and the splicing machinery. The disadvantages are said to completely outweigh any advantages emerging from the split gene design. After considering other examples of complexity, Avise concludes:

"Why an intelligent and loving designer would have infused the human genome with so many potential (and often realized) regulatory flaws is open to theological debate. [. . .] From an evolutionary perspective, such genomic flaws are easier to explain. Occasional errors in gene regulation and surveillance are to be expected in any complex contrivance that has been engineered over the eons by the endless tinkering of mindless evolutionary forces: mutation, recombination, genetic drift, and natural selection. Again, the complexity of genomic architecture would seem to be a surer signature of tinkered evolution by natural processes than of direct invention by an omnipotent intelligent agent."

This style of argument is in the tradition adopted by Charles Darwin: theological arguments are used to reject intelligent causation, allowing "mindless evolutionary forces" to win by default. ID advocates have responded to these arguments on numerous occasions: design flaws cannot provide a valid argument against intelligent agency because design can co-exist with flaws. For example, flaws in human designs do not imply that the work is the product of a mindless process (design office manager's comments notwithstanding!). Furthermore, in this case, Avise is confusing his theological objections to an intelligent (and loving) designer with his assertion that the complexity of genomic architecture is a "surer signature of tinkered evolution by natural processes". The latter claim is of relevance to the ID perspective, but Avise has only offered his opinion and he has not demonstrated that tinkering can produce anything like spliceosomes, the associated processing machinery or the operational code.

The second category of evidence is "wasteful design". He refers to duplicons, pseudogenes and the "abundance of mobile elements" (collectively known as junk DNA). The argument is essentially the same as was developed for the first category: since a large number of genetic disorders in humans can be traced to mutations affecting these components of the genome, ID is incoherent. The general conclusion drawn is as follows:

"From scientific evidence gathered during the past century, and especially within recent decades, we now understand that the human genome and the metabolic processes it underwrites are riddled with structural and operational deficiencies ranging from the subtle to the egregious. These genetic defects register not only as deleterious mutational departures from some hypothetical genomic ideal but as universal architectural flaws in the standard genomes themselves. The findings of molecular biology thus offer a gargantuan challenge to notions of ID. They extend the age-old theodicy challenge, traditionally motivated by obvious imperfections at the levels of human morphology and behavior, into the innermost molecular sanctum of our physical being."

This paper certainly reinforces the view that the primary argument against intelligent design is theological. Once the concept of intelligent agency is removed, we can relax in the arms of the pitiless, uncaring, blind forces of nature.

"No longer must we anguish about the interventionist motives of a supreme intelligence that permits gross evil and suffering in the world. No longer need we be tempted to blaspheme an omnipotent Deity by charging Him directly responsible for human frailties and physical shortcomings [. . .]. No longer need we blame a Creator God's direct hand for any of these disturbing empirical facts. Instead, we can put the blame squarely on the agency of insentient natural evolutionary causation."

We need to return to the claim that the human genome exhibits the tinkering characteristics of a blind watchmaker. Avise is saying, in effect, that the genome is chaotically complex and highly vulnerable to degradation. What needs to be said in response to this is that we are just beginning to analyse this complexity. The first casualty resulting from new knowledge is the concept of Junk DNA, which is now linked to all sorts of regulatory functions in the cell. Why were so many molecular biologists confident that 98% of our DNA was functionless? Ultimately, their quest for simplicity at the genomic level made them blind to complexity, and the designation "junk" fitted into their preconceived notions of a wasteful evolutionary process. The pendulum has now swung to where complexity is acknowledged - but they still think of it as an unplanned (nonsentient) complexity. The ID prediction is that the pendulum will swing further and reveal an intelligently organised complexity with numerous regulatory feedback mechanisms in place. In his Nature column, Philip Ball correctly cautions against some of the assumptions made by Avise:

"However [. . .] it is worth pointing out that some of the genomic inefficiencies Avise lists are still imperfectly understood. We should be cautious about writing them off as 'flaws', lest we make the same mistake evident in the labelling as 'junk DNA' genomic material that seems increasingly to play a biological role. There seems little prospect that the genome will ever emerge as a paragon of good engineering, but we shouldn't too quickly derogate that which we do not yet understand."

So, are the findings of molecular biology "a gargantuan challenge to notions of ID"? The answer is a resounding no. ID does not set out to address the theodicy argument but to establish whether intelligent design and purposeful information characterises the natural world. It stands in the empiricist tradition. We are not justified in rejecting the findings just because we find them unpalatable. Further, Avise has not provided a robust defence of tinkering evolutionary processes. If anything, his argument is based on ignorance. As we learn more of the complexity of biological systems (probably using the tools of systems biology), we will become better informed about tinkering vs exquisite design. Every week, new research brings relevant information to our attention: this week it is the deciphering of the splicing code (undermining Avise's view that the cell would be better off without introns and that the protein-coding regions of DNA are chaotic). There are good books that base they arguments on what we do know (books like Darwin's Black Box and Signature in the Cell), and these provide us with strong reasons for reaching the conclusion that the design we see is exquisite.

Footprints of nonsentient design inside the human genome
John C. Avise
Proceedings of the National Academy of Sciences, Published online before print May 5, 2010 | doi: 10.1073/pnas.0914609107

Abstract: Intelligent design (ID) - the latest incarnation of religious creationism - posits that complex biological features did not accrue gradually via natural evolutionary forces but, instead, were crafted ex nihilo by a cognitive agent. Yet, many complex biological traits are gratuitously complicated, function poorly, and debilitate their bearers. Furthermore, such dysfunctional traits abound not only in the phenotypes but inside the genomes of eukaryotic species. Here, I highlight several outlandish features of the human genome that defy notions of ID by a caring cognitive agent. These range from de novo mutational glitches that collectively kill or maim countless individuals (including embryos and fetuses) to pervasive architectural flaws (including pseudogenes, parasitic mobile elements, and needlessly baroque regulatory pathways) that are endogenous in every human genome. Gross imperfection at the molecular level presents a conundrum for the traditional paradigms of natural theology as well as for recent assertions of ID, but it is consistent with the notion of nonsentient contrivance by evolutionary forces. In this important philosophical sense, the science of evolutionary genetics should rightly be viewed as an ally (not an adversary) of mainstream religions because it helps the latter to escape the profound theological enigmas posed by notions of ID.

See also:

Ball, P. What a shoddy piece of work is man, Nature News, 3 May 2010 | doi:10.1038/news.2010.215