Science Literature

It is fundamental to the methodology of science that hypotheses are proposed and tested. The human face of science surfaces when researchers enthusiastically endorse false positives, when hypothesis testing is less than rigorous, and when false dichotomies are proposed (i.e. if hypothesis B is falsified, hypothesis A is declared to be verified). The science of origins is well-supplied with examples of hypotheses that were once widely accepted as valid, but which are now discredited. A significant example has recently become apparent and is the theme of this blog. In 2009, Zhang et al. considered integumentary filaments of the theropod dinosaur Sinosauropteryx, knowing that Lingham-Soliar and colleagues had proposed that dino-fuzz filaments are structural collagen fibres released by processes of decay. The work reported that "melanosomes (colour-bearing organelles) are not only preserved in the pennaceous feathers of early birds, but also in an identical manner in integumentary filaments of non-avian dinosaurs". This led Zhang et al. to conclude that the collagen fibre interpretation has been falsified and that the integumentary filaments were proto-feathers. In the summary provided by the editors of Nature:

"But it has been suggested that some of the structures that are not obviously feathers might actually be strands of collagen from under the skin. Zhang et al. refute this notion by demonstrating the presence in these structures of melanosomes - the characteristic bodies that give feathers their colours. Not only do they show that the feather-like structures of dinosaurs such as Sinosauropteryx really are akin to feathers, but also they can speculate in an informed way about their colour - which it seems was reddish brown or ginger."

Type specimen of Sinosauropteryx with filament impressions, Inner Mongolia Museum (source here)

Discovering fossil melanosomes is not in itself controversial. A previous blog on the subject is here. Lingham-Soliar points out that his critique relates to reported work on Sinosauropteryx, because it is "considerably removed phylogenetically" from bird-like animals. Sinosauropteryx is a basal coelurosaurian dinosaur, and if it had protofeathers, then it may be surmised that many different groups of dinosaurs were also clothed with proto-feathers. In Carl Zimmer's write-up for the New York Times, Michael Benton, one of the co-authors, is quoted as saying "Essentially, wherever you look [for evidence of melanosomes], you find it." Consequently, since the publication of the paper by Zang et al., illustrations of dinosaurs with feathery coverings have become widespread. However, Zimmer also reports the words of Lingham-Soliar: "Regrettably, I have to say the study would not pass muster in college science." The paper featured in this blog is the formal documentation of his claim.

Perhaps the most fundamental criticism concerns the criteria for identifying melanosomes. It is not enough to prove that the structures are not bacteria: there is a need for multiple working hypotheses and all of them should be tested. Lingham-Soliar proposes an option not considered by Zang et al. - that the structures are the result of the decomposition of collagen. This hypothesis is tested in the paper and found to satisfy the evidences. The case for melanosomes is examined and found wanting. Lingham-Soliar summarises the "Fallacy of the crucial experiment" in this way:

"Allegations that the structures are melanosomes and a pivotal discovery in a basal theropod are not supported by empirical evidence but rather by metaphysical assertions. While the SEM image is real, the vital questions relating to it are speculative, e.g., (1) allegations of the light and dark stripes; (2) allegations that the melanosomes are "embedded inside the filaments" (implying depth) are made without cross-sections or tangential sections but are based on a single SEM image of the filament's surface or near-surface; and (3) size and shape of the structures, key to their identity, are speculative - they lack vital, basic statistical measurement data." (p.575)

The critique goes further than this. There is a "fallacy of generalisation" in applying knowledge relating to the mechanism of forming stripes or bands in bird plumage to a disparate group represented by Sinosauropteryx. There is tautology, because once the evidence for melanosomes was accepted, this became their warrant for discarding the degraded collagen fibre interpretation ("Proof in one group of animals is used as proof in another disparate group without testing"). There is a false dichotomy, in that the rejection of the bacterial interpretation was deemed sufficient to close discussion of alternatives - and the melanosome hypothesis was regarded as verified. By contrast, Lingham-Soliar's studies of decaying collagen show that there are several other hypotheses to test:

"The structures in Zhang et al.'s (2010) figure 3c, as demonstrated here by experiment and comparative studies are most probably the degraded remains of soft-tissue filaments, probably collagen. However, could they be the degraded remains of melanosomes? This cannot be ruled out, but would be entirely speculative because Zhang et al. (2010) provide no evidence for it by, e.g., comparative studies on the decomposition of melanosomes (native and fossilised), and besides, they claim that the structures are preserved melanosomes not their degraded remains. Although also unlikely, we may not rule out that the filaments could represent structural keratin of a frill either solely or in combination with collagen. For example, external spines, bristles and horns in modern-day lizards are scale derivatives and comprise varieties of [beta]-keratins as do turkey bristles." (p.574)

There are more general implications of this particular controversy. It is not unusual within origins science to find people latching on to one specific finding that clinches the argument and validates a whole package of concepts. Yet Lingham-Soliar gives this warning: "one should be mindful that rarely if ever do we find a "magic bullet" in science as a universal solution." Rather, we should be cultivating multiple working hypotheses and a willingness to follow the evidence wherever it leads. The problem is well displayed in Zhang et al.'s (2010) claim that "Our results demonstrate conclusively that the integumentary filaments of non-avian thropod dinosaurs are epidermal structures" and "Our work confirms that these filaments are probably the evolutionary precursors of true feathers." In the light of Lingham-Soliar's alternative hypotheses, these bold claims are premature.

Thomas Kuhn's conceptual framework is helpful for understanding the way scientists develop their theories and it points the way here. We have two approaches to the evolution of birds: the BAD (Birds Are Dinosaurs) paradigm and the BAND (Birds Are Not Dinosaurs) paradigm. The BAD group are dominant and they are actively developing their paradigm in a way that fits Kuhn's description of 'normal science'. This inhibits them thinking 'outside the box' - so this is why it becomes difficult to work with multiple hypotheses. This is why false dichotomies are not unusual. The problem plagues evolutionary biology. Darwin proposed a false dichotomy when he contrasted his theory of 'evolution by natural selection' with the alternative of 'fixity of species'. This allowed Darwin to claim all evidences of variation as evidence for his theory. Those who perpetuate this false dichotomy are guilty of bad science and erroneous history. Students of origins deserve better. Further reading is here, here and here).

The evolution of the feather: Sinosauropteryx, a colourful tail
Theagarten Lingham-Soliar
Journal of Ornithology, 152(3), (2011), 567-577 | DOI: 10.1007/s10336-010-0620-y (pdf here)

A recent development in the identification of feathers in fossils by means of melanosomes was used to suggest that structures observed in an SEM of a filament in the basal theropod dinosaur, Sinosauropteryx, were phaeomelanosomes and that they represented conclusive evidence that the filaments were early feathers. At the most basic level, the claims of phaeomelanosomes are shown here to be founded on an optical illusion created when the SEM is reproduced at low image size - viewed at larger image size (~2x original) the structures are nondescript in both size and shape and impossible to equate with phaeomelanosomes. At a higher level of investigation, the study is seriously questioned for ignoring standard scientific protocol: despite size and shape being critical to the identification of the phaeomelanosomes, no statistically viable measurements of the structures (particles) were made - the measurements, which are simply conjectured, are shown here to be incorrect in the speculated sizes, and in shapes; inferences made on vital characters from birds and advanced non-avian dinosaurs, e.g. with respect to colour banding, are without confirmation in the test animal but conjectured on circular argumentation; alternative arguments, e.g. that the particles might be bacteria or colour from the overlying skin, are peremptorily dismissed or not considered; suggestions that the particles are embedded within the filament are without support since there is no evidence of cross-sections or tangential sections either made or occurring serendipitously - only a single section is reported, apparently of the filament's surface. False dichotomies such as, if the structures are not bacteria they must be melanosomes, are questioned given that one of the most important factors in the taphonomy of ancient (structures in question, ~130 MYR) fossilised filaments i.e., decomposition - that the structures might reasonably represent the degraded remains of the filaments - is not even considered. Here, from experiments on the decomposition of native collagen in fish and reptilian dermis, SEMs of their ultrastructure show that distinctive spherical, elliptical or oblate particles, even more so than those figured in Sinosauropteryx, typically form during degradation. This is confirmed in SEMs of degraded collagen fibres in a 225-MYR ichthyosaur fossil, virtually point by point. In addition numerous small bead-like structures in the filament of Sinosauropteryx bear a striking resemblance to the unique 67-nm D-bands of collagen, in both shape and size. This paper does not question the value of scientifically meritorious identifications of melanosomes, as indeed of collagen and keratin, in interpreting the integumental structures of fossil animals. However, allegations of phaeomelanosomes in Sinosauropteryx are shown to be without scientific merit.

See also:

Zhang, F, Kearns, SL, Orr, PJ, Benton, MJ, Zhou, Z , Johnson, D, Xu, X & Wang, X., Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds, Nature, 463, 1075-1078, (25 February 2010) | doi:10.1038/nature08740 (pdf here)

A generation ago, children were taught that fishes grew legs and invaded the land. The early tetrapods were finding new environments for food and/or security. However, the evidence-base was thin, and we can look back on this time and realise that children were being fed yet another just-so story. Research showed that the early tetrapods were not terrestrial animals at all, but were aquatic. So the story has changed, and the limbs are thought to have evolved to aid the animals moving through brackish or marine habitats that were crowded with plant life. This changing perspective is alluded to by Jennifer Clack and colleagues in the introduction to their latest paper:

"Early tetrapods, and the fish that gave rise to them, were originally interpreted as being terrestrially capable animals with load-bearing fins or limbs. Since the 1990s, however, new fossil discoveries and anatomical interpretations have demonstrated that the first limbed vertebrates were primarily aquatic in habit and that limbs evolved before the ability to 'walk' on land."

Some of the characters in the evolutionary story (source here)

Researchers have discussed different tetrapod locomotory styles and recognised a gap in knowledge. This has stimulated the recent research, which adopted the following methodology:

"To illuminate the evolution of early tetrapod locomotion, we conducted a computer-aided assessment of limb joint mobility in one of the best known Devonian tetrapods, Ichthyostega. To achieve this goal, we used micro-computed tomography (microCT) to scan suitable Ichthyostega specimens, created a digitally rendered three-dimensional skeletal model, and quantified maximum range of motion in the shoulder, elbow, hip and knee in three orthogonal planes of movement. To interpret joint mobility in a locomotor context, we compared the data of Ichthyostega with those of five morphologically and phylogenetically distinct modern tetrapod analogues with varying joint morphologies and locomotion behaviours. These include a salamander (Ambystoma tigrinum), crocodile (Crocodylus niloticus), platypus (Ornithorhynchus anatinus), seal (Halichoerus grypus) and otter (Lutra vulgaris)."

The findings confirm that the limbs could help the animal in water, but were not suitable for land movement:

"On the basis of our study of limb joint mobility, combined with rib and vertebral morphology, we conclude that Ichthyostega could not use 'normal' quadrupedal gaits. The ability to rotate the humerus and femur longitudinally and use symmetrical gaits (for example lateral sequence walking) must have evolved in other early tetrapod species. Given that a similar type of shoulder and/or hip joint morphology presents itself in some other early tetrapod species, limited limb joint mobility -particularly long-axis rotation - may have been more widespread."

These findings do call for some reassessment of the science and the evolutionary interpretations. BBC News reported on the find and cited comments from two of the researchers:

"Dr Pierce told BBC News: "We're almost bringing the animal back to life by doing this. What we've discovered is that some early tetrapods definitely did not have the ability to walk on land. We at this stage are not actually sure which animals - or group of animals - were the first to do this."
Co-author Prof Jenny Clack from the University of Cambridge added: "Our reconstruction demonstrates that the old idea, often seen in popular books and museum displays, of Ichthyostega looking and walking like a large salamander, with four sturdy legs, is incorrect.""

We are left with the enigmatic trackways from Poland (discussed here) that are thought to date earlier than the known aquatic tetrapods. It seems that there are no candidate fossil animals that could have made the tracks.

"Given our results, could an Ichthyostega-like early tetrapod have produced similar trackways to some of those recently described from the Middle Devonian? All available evidence from limb joint mobility and axial anatomy indicates that such animals could not have made symmetrical gait 'foot' prints. In particular, these early tetrapods probably lacked the necessary rotary motions in their limbs (and perhaps lateral flexion of the vertebral column) to push the body off the substrate and progress using alternating limb movements. Maybe as yet unknown tetrapod species (or known taxa that currently lack postcranial material) with different joint mobility and axial anatomy made these traces; available data cannot yet answer this conundrum."

So we can predict that a new tetrapod animal from the Middle Devonian awaits discovery. It is time the hype about Tiktaalik, and any of the other aquatic tetrapods, was dropped. They are not the evolutionary gems they are claimed to be. The fossils that are beginning to populate Romer's Gap are not filling in a gradualist story, as is discussed here. The fossil record typically provides evidence for discontinuity, not gradualism. Evolutionary theorists must be more serious about addressing these evidences (instead of calling them 'gaps in knowledge').

Three-dimensional limb joint mobility in the early tetrapod Ichthyostega
Stephanie E. Pierce, Jennifer A. Clack & John R. Hutchinson
Nature, 486, 523-526 (28 June 2012) | doi:10.1038/nature11124

The origin of tetrapods and the transition from swimming to walking was a pivotal step in the evolution and diversification of terrestrial vertebrates. During this time, modifications of the limbs - particularly the specialization of joints and the structures that guide their motions - fundamentally changed the ways in which early tetrapods could move. Nonetheless, little is known about the functional consequences of limb anatomy in early tetrapods and how that anatomy influenced locomotion capabilities at this very critical stage in vertebrate evolution. Here we present a three-dimensional reconstruction of the iconic Devonian tetrapod Ichthyostega and a quantitative and comparative analysis of limb mobility in this early tetrapod. We show that Ichthyostega could not have employed typical tetrapod locomotory behaviours, such as lateral sequence walking. In particular, it lacked the necessary rotary motions in its limbs to push the body off the ground and move the limbs in an alternating sequence. Given that long-axis rotation was present in the fins of tetrapodomorph fishes, it seems that either early tetrapods evolved through an initial stage of restricted shoulder and hip joint mobility or that Ichthyostega was unique in this respect. We conclude that early tetrapods with the skeletal morphology and limb mobility of Ichthyostega were unlikely to have made some of the recently described Middle Devonian trackways.

See also:

Ichthyostega Animation

John R. Hutchinson: Assessing the Limb Mobility of the Early Four-Legged Vertebrate Animal Ichthyostega