…or, an article that can be summed up by the following rhetoric:
“On this 200th anniversary of the birth of Charles Darwin, perhaps the greatest evolutionary biologist of all time, I ask, has the care and caution that characterized Darwin’s work taken a downward spiral in many of the evolutionary interpretations associated with the fossils from China today? Good fossils or bad science?” — Theagarten Lingham-Soliar, 2009 (J. Ornith) 
It is not enough, perhaps, to perform the work, or even make the comparisons, but to also have the framework established on which your theory is based.
Lingham-Soliar begins his latest paper with a quote:
“‘Assuming an answer before the investigation has begun is an all-too-common human failing…an abandonment of the intellectual process.’ – Ralph Ellis 2002 (Solomon)”
In the past decade, TLS (for short) has done some pretty decent (downright good) exploratory work on the structure of the dermal tissues of fossils. This began with many marine reptiles (ichthyosaurs, mosasaurs) and provided data that supported the lattice-like structure of the skin collagen, as seen in dolphins (among other animals). He then turned his attention to our tiny “fluffy” friends from China who, among other things, suffer the fault of being preserved in an anoxic dump at the bottom of a ash-layered lake, unlike the more expedient and perhaps pleasant preservation at the bottom of a simply anoxic, limestone-layered lagoon, such as the Solnhofen Formation. As if their life wasn’t already hard.
Fossils from the Jehol Biota (predominately the non-basal Yixian and the Jiufotang Formations) preserve almost unerringly with “haloes” of degraded integumentary tissues, assumed to be decomposition from the skin, muscles, ligaments, and even extradermal tissues like “hair” and “pycnofibers” and “dinofuzz” and yeah, even “feathers.” (note: the basal Yixian does not preserved “haloes.”) This preservation is uncanny, and resembles that seen in the Messel Formation of Germany, the Quercy of France, portions of the Eocene Green River Formation, and others. Dermal structures are so ubiquitous in Messel that the associations of shape and structure are uncontested with their identification as “hair” or “feathers.” The real question not asked in the opening paragraph of TLS’s latest paper, should have been “What other animals preserved like this?”
A quick check would have produced quite a variety of birds and mammals. It would not preserve lizards, snakes, frogs, or turtles, or even crocodilians, with frayed, ragged margins of their “haloes” seeming like tufts of “hair” or “feathers.” Solnhofen, for example, preserves crocodilians, pterosaurs, and even lizards with clean, smooth margins for their haloes. The Yixian preserves pterosaurs, mammals, birds, etc., all with “haloes” and all, to this date, uncontested as to their integumentary preservation. This is, however, not the case for the (obligatorily, “non-avian”) dinosaurs preserved here.
Most recently, TLS has turned his attention to two “cornerstone” fossils in the “feathered” dinosaur debate: Sinosauropteryx, which practically started this whole thing and led to such euphemisms as BAND (Birds are Not Dinosaurs, who look for any reason to determine this); and Psittacosaurus, which is known to include specimens with particularly fascinating “quills” sticking out over the hips and tail. In the former, debate has focused on one of two things: branching of the fibers present, and continuity and placement of the fibers; in the latter, the idea that these “quills” are collagen has never been raised, and thus, it has never been tested … by anyone. The latest paper is a review of this work, and it is thus necessary to refer to this as we discuss the review.
In the latter, TLS has examined material (MV53 ) that differentiates sections of “skin” apart from the “quills” which show a lattice structure that has been noted in ichthyosaurs. This is distinct from that of the tail structures, and there is an accompanying “halo” around the animal that is regular, smooth-margined, and does not seem at all like it’s “hairy.” This paper is probably one of the more important pieces of this puzzle, and why TLS is (rightly) accreditable for doing primary work on determining the structure of the skin in many fossil organisms. The reason, however, is that he is capable of showing the structure of the skin fibres in an animal that does not, in any case, seem “feathered” or “hairy.” When TLS turned his attention to Sinosauropteryx , reapproaching the work done by Currie and Chen , this investigative finding, which had previously yielded results from sharks and ichthyosaurs, was missing.
One should note here that the “lattice” of collagen is noticeable: There is a system of primary and wholly parallel fibers, and a contrary, almost perpendicular system that appears as a weave of black lines (or colored, depending on the preservational medium, and in the Yixian, it’s colored). When we find this absent, we do not assume therefore that this system is representative of a collagen lattice, as appears in skin. Instead, we assume there are other things present. For example, when TLS et al. looked at Sinosauropteryx, they found two sets of structures, including bundles of tightly parallel fibres between the chevrons, and the remainder as looser, apparently “branched” fibers as part of the “halo.” Of course, some of the fibres in the “halo” are not branched, and at a resolution that is much broader and therefore not as close as seen in Psittacosaurus or in the work done earlier on ichthyosaurs when the scale was in the micron, not the centimeter (although I am being slightly disingenuous as some of this work has the scalebars in the millimeters, but that’s hardly close to the resolution using SEM for Psittacosaurus in the study one year later and several years earlier for other taxa), they do seem similar. The regular spacing of the fibers in TLS et al. (fig. 3a) really does seem very neat and tidy, and as it comes from the tip of the tail, we can assume this is part of the “halo” and not material like the deep skin structures shown in fig. 4.
In an act of shortsightedness, perhaps, TLS describes for one taxon at a higher resolution than another, perhaps more problematic one, and does so one year later. Lacking the SEM study, we are left with personal, manual microscopic analysis, and in this, TLS does not disappoint. Almost amazingly, Currie and Chen described for *Sinosauropteryx* “hollow” fibers, with a distinct reference to a collapsed tubular morphology as shown by single strands having a light, inner core surrounded on each side by a darker, denser rim. This is characteristic in collapsed tubes, as TLS affirms this when referring to the “EBFF”s of Zhang et al in his latest paper . It is significant that when Currie and Chen described this, TLS does not when he describes a “beaded” aspect with sinuousness to the Sinosauropteryx fibers. The omission is telling as in TLS et al., the word “hollow” appears but once, in connection to the Sinosauropteryx fiber descriptive paper  (which is followed by ), and because TLS describes the hollowness of the Psittacosaurus fibers in the latest paper.
Stepping beyond the framework that TLS himself established, however, he begins to argue that others have not performed adequate descriptive work to determine the structure of the “haloes” and other preserved fibers in (again, obligatorily, “nonavian”) dinosaur fossils from China. This results in most of the paper’s body, which is a detailed (and rhetorical) review of various short-form/long-abstract papers from Nature and Science (for the most part). He details herein many perceived faults, primarily that the workers begin using the term “feathers” instead of a more generic phrase.
I stress, now, that my argument of “nonavian” dinosaurs is important: TLS himself has done work to determine the microstructure of fossil marine reptile skin, comparison to sharks, etc., and then transfered this direct attention to the Liaoning fossils. I argue that TLS has faltered in the framework he argues others did not follow; this is apparent also in the review works of Feduccia and others who have written extensively as counterarguments to the “birds are dinosaurs” theory that is so contentious here. The basis for this faltering is thus: TLS has not examined the structure (and comparability) of the fibers to those found in birds and mammals, and done so also outside of Liaoning. It should be important, as some fossils (such as *Confuciusornis*) have been described which seemingly sport non-pennaceous feathers, while at the same time, many, many mammals are know with extensive “haloes” that go uncontentested as to their identity.
I hesitate to offer an hypothesis as to this faltering, but given that TLS has written twice (both methodological) with Feduccia, who is an outstanding critic and opponent of the theory of avian descent from within theropod dinosaurs (or really, dinosaurs and potentially the dinosaur/bird–crocodilian group of reptiles, and even archosaurs in general), it becomes apparent that the framework is not only at fault (not for being faulty itself, but for being insufficient), it is also its perspective that is in error. Were we to argue that we could only use one group of animals to establish a perspective from which to view fiber arrangements, and this group bore no integumentary structures beyond the surface of its skin; stepping out of this box, we can look at animals that have both several types of integumental structures, and those that do not, and form a spectrum of comparison. TLS did not only refrain from doing this, he has done so repeatedly with coauthors whom appear to have a “hidden” agenda. Without a sharp focus on the perspective in which a framework is made, the framework fails, and for TLS, I fear it has done so terribly.
 Lingham-Soliar, T. 2010. Dinosaur protofeathers: Pushing back the origin of feathers into the Middle Triassic? Journal of Ornithology 151(1):193-200.
 Lingham-Soliar, T. 2008. A unique cross-section through the skin of the dinosaur Psittacosaurus from China showing a complex fibre architecture. Proceedings of the Royal Society, London B 275:775–780.
 Lingham-Soliar, T., Feduccia, A. & Wang X.-l. 2007. A new Chinese specimen indicates that “protofeathers” in the early Cretaceous theropod dinosaur Sinosauropteryx are degraded collagen fibers. Proceedings of the Royal Society of London B 274:1823–1829.
 Currie, P. J. and Chen P.-l. 2001. Anatomy of Sinosauropteryx prima from Liaoning, northeastern China. Canadian Journal of Earth Sciences 38(4):1705-1727.
 Zhang F.-c., Zhou Z.-h., Xu X., Wang X.-l. & Sullivan C. 2008. A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers. Nature 455:1105-1108.
 Chen P.-j, Dong Z.-m. & Zheng S.-n. 1998. An exceptionally well preserved theropod dinosaur from the Yixian Formation of China. Nature 391:147–152.
(This post was originally published online as a post to the Dinosaur Mailing List.)
New work has described associated features of the structures of Sinosauropteryx , along with the bird Confuciusornis, an isolated feather that is invariably of the “avian” form, and the dromaeosaurid Sinornithosaurus, with microscopic structures identified as two types of melanosomes. each one apparently tied to a specific group of colors (including black).
After an exchange with Gerald Mayr (one of the original descriptors of the “quilled” Psittacosaurus specimen debated above [8,9], TLS published a new paper approaching MV 53. In this paper, however, little is made of the structures and their association to previous claims made by TLS on the specimen. Instead, work proceeded to describe color and skin structure , although it seems TLS could not resist arguing against the preservation noted in  by commenting:
“Most recently, an SEM image on the theropod dinosaur, Sinosauropteryx (2010) from the Jehol biota purportedly shows the presence of melanosomes [...] in the integumental structures of the tail, which the authors state is evidence that these structures were pigmented protofeathers and not support fibers of collagen [...] Our findings in Psittacosaurus on the other hand indicate a more parsimonious and less profound alternative explanation (accepting for the present that the structures identified were indeed melanosomes)–pigment in the integumental structures of Sinosauropteryx could easily have been absorbed from the overlying decomposing skin, a phenomenon amply demonstrated in the present study in Psittacosaurus SMF R 4970, also from the Jehol biota.”
A not-so-subtle reading of this sentence reveals not only that TLS ignored the recovery of melanosomes in other fossils; a provisional acceptance that the melanosomes are real is permitted only in the authors’ consideration that the melanosomes lie on bone from decayed overlying tissue. In , however (and repeated in  for the troodontid Anchiornis), melanosomes are recovered in isolated patches of integumental structures, including as part of articulated specimens in which the melanosomes are part of the feathers with apparent direct preservation of the underlying material being the origin of the melanosomes themselves. Would only the material overlying bone be transfered? If so, no skin could be preserved in these specimens such that melanosomes on structures can only be transfered; but moreover, it implies that TLS could not allow the direct preservation of nondegraded collagen since any structure could be hand-waived away as transfer material or the product of tissue degeneration and taphonomic processes … such as his own observations. The more parsimonious argument [7,11] indicates that the structures are authentic melanosomes and are preserved in direct association with their originating structures; this then argues that their originating structures are authentically associated and oriented, without need to claim transfer or distortion.
 Zhang F.-c., Kearns, S. L., Orr, P. J., Benton, M. J., Zhou Z.-h., Johnson, D., Xu X. & Wang X.-. 2010. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature 463:1075–1078.
 Mayr, G. 2010. Response to Lingham-Soliar: dinosaur protofeathers: pushing back the origin of feathers into the Middle Triassic? Journal of Ornithology 151:523–524
 Lingham-Soliar, T. 2010. Response to comments by G. Mayr to my paper ‘‘Dinosaur protofeathers: pushing back the origin of feathers into the Middle Triassic?’’ Journal of Ornithology 151:519–521
 Lingham-Soliar, T. & Plodowski, G. in press. The integument of Psittacosaurus from Liaoning Province, China: Taphonomy, epidermal patterns and color of a ceratopsian dinosaur. Naturwissenschaften Online Preprint, DOI 10.1007/s00114-010-0661-3
 Li Q.-g., Gao K.-q., Vinther, J., Shawkey, M. D., Clarke, J. A., D’Alba, L., Meng Q.-j., Briggs, D. E. G. & Prum, R. O. 2010. Plumage color patterns of an extinct dinosaur. Science 327 :1369-1372.