Intelligent design proponents claim to base their views entirely on scientific data, and argue that the design perspective is more productive than an evolutionary approach. One area where this is particularly evident is in discussions of “junk DNA”. Indeed, with every new discovery (by evolutionary biologists) that some part of the genome shows signs of function, ID proponents suggest that it is they, and not evolutionary biologists, who predicted from the outset that non-coding DNA would prove to be functional. I won’t repeat the discussion of why it is incorrect to suggest that most biologists have stubbornly refused to consider functions for non-coding DNA (see here and here). Instead, what I want to do is to give ID proponents an opportunity to show that their perspective really is scientific and that it can lead to a better description and explanation for biological phenomena than evolutionary science can.
Here is what ID proponents need to do:
1) Specify the basis for assuming that all non-coding DNA must be functional. This makes implicit assumptions about the designer and the design process (namely, that he/she/it would not produce non-functional features of organisms). This assumption must be justified. It also opens the discussion to more philosophical questions, such as why the designer would choose to design such a massive number of pathogens and parasites. Either one can know the designer’s plan or one cannot; if the former, then the way that one would come to know this must be explicated.
2) Specify how one would go about demonstrating evidence of functions for non-coding DNA in the absence of a framework based on common descent. To date, most evidence for function comes from demonstrations of conservation of non-coding sequences, which indicates that constraints imposed by natural selection have maintained these sequences over long spans of evolutionary time. ID would need to propose a testable means of identifying functional sequences that does not rely on the assumption of common descent. Also, it should be recalled that, at present, there is suggestive evidence that about 5% of the human genome is functional. It will be necessary to specify how function will be demonstrated in the other 95% of the genome.
3) Make specific predictions about what function(s) all non-coding DNA is likely to be fulfilling, and propose ways to test those predictions. A vague prediction that all non-coding DNA will prove to be functional is not useful. Moreover, strict Darwinian theory in which natural selection is assumed to remove any non-functional features makes exactly the same prediction, so this does not distinguish ID from Darwinian theory.
4) Propose functions for transposable elements that take into account their parasitic characteristics (e.g., as disease-causing mutagens) but do not invoke the notion of co-option. There are clear examples of transposable elements (TEs) that are functional, for example as regulatory sequences, in the vertebrate immune system, and in cellular stress response. However, this represents a very small percentage of TEs, most of which are neutral or deleterious in the genome. The evolutionary explanation is that, in some relatively rare cases, these former parasites have become integrated into the functional system of the genome. This process of co-option of function is the same process that evolutionary biologists use in explanations of the evolution of complex structures such as eyes or flagella. If co-option is ruled out a priori, then it cannot be used to explain the acquisition of function of formerly parasitic elements and a different explanation must be provided.
5) Provide a specific explanation for how the great majority of transposable elements in the human genome can be functional while showing clear signs of being inactive. Most TEs in the human genome have experienced mutations in regions that render them incapable of undergoing transposition. Many are so degraded by mutation as to be hardly recognizable. How these highly mutated elements carry out a specific function needs to be explained.
6) Provide an explanation for why the DNA sequences of non-coding regions in different species appear to correspond to degree of relatedness. If species do not share common ancestors, then an alternate explanation is required for why species that are claimed to be close relatives exhibit similar sequences whereas those that are claimed to be more distant relatives possess DNA sequences that are not as similar.
7) Propose a testable explanation for why similar species may have widely different quantities of non-coding DNA in their genomes. A simple example is provided by onions and members of the same genus.
8) If one does accept common descent, propose a testable explanation for how there can be significant reductions in DNA content in some lineages. There is evidence that many lineages have experienced losses of non-coding DNA. For example, the evolution of saurischian dinosaurs appears to have included a reduction in DNA amount. How this loss of DNA could occur requires explanation under the assumption that all non-coding DNA in the ancestor’s genome was functional.
More could be added to such a list, but I suspect that this will be enough to provide ID proponents with a prime opportunity to demonstrate their scientific credibility.