Summary of problems:The dinosaur ancestors of birds probably did not have diaphragms. The one researcher cited to oppose this view also rejects the evidence that birds evolved from dinosaurs; his views on both topics have been widely refuted.
Paleontologist Matt Wedel explains:
Non-avian dinosaurs did not necessarily have the same pulmonary anatomy as crocodilians or extant birds. As hypotheses of pulmonary anatomy in dinosaurs, "croc lungs" versus "bird lungs" is a false dichotomy. It is more informative to identify the derived features that non-avian dinosaurs share with their extant relatives, and to determine the hierarchical distribution of these characters in archosaurian phylogeny.Wedel, Matt (2007) Postcranial pneumaticity in dinosaurs and the origin of the avian lung, Ph.D. dissertation, University of California, Berkeley, p. 112.
That is exactly the approach that evolutionary biologists and textbooks about evolutionary biology take in addressing the evolution of organisms and particular parts of organisms. An inquiry-based textbook could include exercises allowing students to undertake the same process of investigation. Explore Evolution does not use this comparative approach, and discourages students from further investigation in areas of ongoing biological research, or even areas where the research has already been conducted.
By comparing fossils of dinosaurs to modern birds, it is possible for paleontologists to produce and test hypotheses about the evolution of the dinosaur lung. Wedel describes his approach:
Instead of focusing on particular [traits] that are either not present in all birds (large sternum, uncinate processes of the ribs) or not clearly necessary for air sac ventilation (ossified rather than cartilaginous sternal ribs), it may be more productive to identify the skeletal movements that take place during avian respiration and the effects of these movements on the shape and volume of the thoracic cage, and then to ask whether the skeletons of non-avian dinosaurs were able to produce similar movements.Wedel (2007), p. 119
He concludes that "the respiratory movements in non-avian dinosaurs would have had a similar effect on the volume of the thorax as those of extant birds. there is no basis for inferring that non-avian dinosaurs could not have ventilated an air sac system, based simply on the absence of some avian features" (pp. 120-121).
Wedel's analysis of the fossils shows that a functional intermediate could have existed without the need for the full suite of avian (bird-like) adaptations. Those adaptations may improve the efficiency of bird breathing, but their absence would not be fatal, despite Explore Evolution's claims. Explore Evolution misrepresents evolution as a linear path from reptilian anatomy to avian anatomy, and considers it problematic if a straight line cannot be drawn from ancestral to modern conditions. This is not how evolution works.
As to the particular issue of a diaphragm in the common ancestor of birds and dinosaurs, paleontologists are skeptical. The paleontological evidence used by Ruben to support the claim that the ancestors of dinosaurs had a diaphragm is weak at best. He takes the coloration of rock within a fossil to reflect the location of the liver in the living organism, and then suggests that a liver in that position requires the sort of diaphragmatic breathing found in crocodiles. Even if he were correct that the color in the rock originated in the liver, and if that liver hadn't shifted as the organism decayed, it would still not support his final claim, since living birds have livers in exactly the same position, and do not have diaphragms (see discussion in Wedel, 2007, p. 128).
While crocodilians do breath using a diaphragm, many reptiles do not use a diaphragm, and neither do the amphibians which are ancestral to reptiles, mammals, dinosaurs and birds. By examining the full range of paleontological evidence, scientists can reconstruct probable anatomies not seen in modern species, but which would provide the sort of functional intermediates which evolutionary theory predicts should exist. By contrast, Explore Evolution and the sources it cites take an "approach to inferring soft tissue anatomy, function, behavior and physiology [which] tends to force extinct animals into the reduced spectrum of animals available to us today, without considering substantial evidence of mosaic change in related extinct forms. It lacks an evolutionary component, produces only conundrums, and explains very little" (Kevin Padian and John R. Horner. 2002. "Typology versus transformation in the origin of birds," Trends in Ecology and Evolution, 17(3):120-124).