Science Literature

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