Just curious - Questions I would like to see ID address

The proponents of Intelligent Design claim that it is actually a science. In order to be a science, a model must enable researchers to make substantive and testable hypotheses – and then, of course, those hypotheses must be tested. To this end, I have compiled a list of questions, some from traditional biology and some involving specific aspects of molecular biology, which I for one would particularly like to see ID tackle. I do not expect anyone to come up with definitive answers, but I would like to see, as I said, substantive and testable hypotheses. (By substantive and testable, I mean that "the mind of the Designer is unknowable"-type answers do not qualify.)

Given the basis of design by an intelligence, please explain:

1 Why, out of 61 available amino acids, does life use only 20 of them? Some are obviously disqualified from biological functions by being too reactive or not reactive enough, however there are many which fall well within a range of usability which are nevertheless not used.

2 What are probable reasons for the peculiar and utterly puzzling presence of ribonucleotide fragments in biochemical cofactors?

3 Why is the ribosome a ribozyme? These vital protein synthesis machineries involve only 3 RNA molecules and more than 50 proteins; but it is the RNA molecules which play the most fundamental roles despite the fact that those roles could well have been fulfilled by proteins.

4 With the premise that they have been designed, what are probable reasons for the forms of the Wnt proteins and the subsequent signalling pathways vital for embryogenesis? Bear in mind that “elegance” and “efficiency” are not descriptors which could possibly be applied to the Wnt signalling pathways by anyone sane. (See for a wildly oversimplified diagram of a human Wnt signalling pathway.)

5 Why is the human genome >=96% entirely nonfunctional? (This is a generous estimate of functionality; currently only 1.5-2.0% of the genome is thought to have any function at all. On the basis that there are likely to still be unidentified control elements, even though structural elements have all been mapped, for the purpose of this question I propose to double the estimate of functional region. Despite the fact that control elements are often several factors of ten smaller than protein-coding genes, there are likely to be more of them.)

6 During the embryogenesis of birds the protein BMP4 is produced at a certain stage, which specifically induces apoptosis in the tissues between the toes of the hind limb, leading to separated toes. Ducks, however, retain the webbing between their toes rather than have it die away. Given the premise of deliberate design, what are probable reasons is this webbing retained, not through a lack of BMP4, but through the production of both normal amounts of BMP4 and the additional production of the protein Gremlin, which simply blocks the action of BMP4?

7 Why are cactus spines built out of the same elements as “normal” leaves, despite their very different form and function?

8 Why are reptilian scales and bird feathers built from very nearly the same proteins?

9 What are probable reasons for the similar morphology but very dissimilar use of bones in pterosaur, bird, and bat wings, given that all these have the ultimate function of flight? (For a visual comparison, see .)

10 Why aren’t there any flying marsupials?

11 What are probable reasons that approximately 1 in every 100,000 whales are born with apparently vestigial and functionless leg buds at the position that hind limbs would likely be?

12 Why do baleen whales develop and calcify teeth in utero, which are then resorbed just before birth?

13 Why do so many creatures of phylum Mollusca have better eyes than we do? (I.E. the molluscan eye has a far more efficient optical design and has no “blind spot” such as the mammalian eye has, due to the fact that light does not have to pass through several layers of tissue before striking the light-sensitive surface, and the optic nerve fibres do not have to pass through the retina in order to enter the visual cortex of the brain. Also, molluscan eyes have a spherical lens which can be moved back or forth to focus, rather than a fixed lens which must be forced to change shape, which means that molluscan eyes are far more unlikely to develop hyperopia, myopia, or indeed any form of astigmatism.)

14 With the principle of design in mind, why do box jellyfish, creatures which lack even a central nervous system, have three different types of eyes ranging from a simple pigmented pit with a central photoreceptor, to a complex camera eye with a retina, a lens superior to ours, and an adapting iris? Why, despite the optical properties of the perfectly-corrected lens, is the lensal image focussed well behind the retina, leading to the conclusion that all they would be able to see are large, extremely blurry and diffuse images?

15 What are the probable reasons that despite their skeletal adaptations to a bamboo diet (i.e. dentition and the famous “thumb” used for stripping bamboo leaves), pandas have a carnivore’s lower digestive system, which unfortunately leaves most pandas in the wild in a perpetual state of near-starvation?