The Stem-Mammals–a Brief Primer (with remarks)

Preface added the day after posting: M. Mortimer gratefully informed me that some authors consider all taxa closer to mammals than to other living taxa as ‘stem’ mammals. Perhaps that is how ‘stem’ taxa are defined. That came as news to me because I understood the term ‘stem’ to refer to immediate outgroups only based on the terms usage in other works. So you learn as you go. The broad definition quickly loses relevance and adds to confusion. In M. Mortimer’s example, Diplodocus is a ‘stem’ bird. Please read the following with these caveats in mind. 

Preface added 10/26/2016: Just found out there is are two definitions for ‘stem’ taxa, one in the wider sense and one in the narrower sense, the one is was familiar with. Learn more at Wikipedia here

Usually I cover published academic papers
here at Today we’ll cover a Tetrapod Zoology blog post published online by Dr. Darren Naish a month ago. Unfortunately the post was sprinkled with traditional misconceptions.

the Naish text is copied in italic and his captions are copied in their original ALL CAPS. Remarks are in red. You can see the original blogpost here. This is how all good referees mark up submitted manuscripts, with precise comments intended to help the writer improve the next draft. To that end, Naish notes he is currently writing a book that includes this subject.

The Stem-Mammals–a Brief Primer
Mammals are but the only surviving members of a far grander, older lineage
By Darren Naish on September 20, 2016

Figure 1. Strangely Naish labeled this illustration "Non-synapsid-mammal-montage" Most of these taxa, caseids and Tetraceratops exempted, are indeed synapsids. The problem is, all of the red taxa are not stem mammals, nor are they in the mammal lineage at any node. Rather they represent extinct offshoots.

PROVISIONAL AND IN-PREP MONTAGE (FOR MY TEXTBOOK ON VERTEBRATE HISTORY) DEPICTING A SELECTION OF STEM-MAMMALS. I’VE DRAWN FAR MORE THAN THE SELECTION SHOWN HERE. CREDIT: DARREN NAISH Strangely Naish labeled this illustration “Non-synapsid-mammal-montage” Most of these taxa, caseids and Tetraceratops exempted, are indeed synapsids. The problem is, all of the red taxa are not stem mammals, nor are they in the mammal lineage at any node. Rather they represent extinct and distant offshoots. Virtually all science journalists accept what they read in publication without criticizing it. But Naish is also a PhD, so it is his duty to keep a laser focus on his headline topic, not to stray off subject, and most importantly, to clarify for his readers the inconsistencies present. Otherwise, as above, there is confusion and lack of clarity for the reader.

“For some considerable time now I’ve been promising that one day — one day — I’ll devote time and energy to coverage of that enormous, diverse, long-lived tetrapod group that we variously term the non-mammalian synapsids or stem-mammals. The most traditional term for them is ‘mammal-like reptiles’: while still in use, this term should be avoided given that the animals concerned are simply not part of the reptile lineage. Not true. According to the large reptile tree (LRT) all descendants of the first reptile/amniote, Gephyrostegus, are also reptiles, and that includes mammals and their long list of descendants. Unfortunately Naish is repeating an old and invalid tradition. The vernacular terms protomammal and paramammal have both been used for the group as well, though both have problems. Stem-mammals will be used here. If so, it is important that Naish restrict his discussion to just the immediate precursors of mammals, not the long list going back to basal synapsids, but that is not what he does.

Anyway, we’re talking about that group of tetrapods that are not mammals but are ancestral to them, and which occupy all those points on the mammal lineage outside of Mammalia. The presence of a laterotemporal fenestra (a single skull opening behind the eye socket) is a key feature distinguishing them from other amniotes. Not true. Several clades by convergence developed such a skull opening including 1. the millerettid clade and their descendants from Oedaleps to Australothyris, including the caseids. Emeroleter and Lanthanosuchus had that fenestra. So did bolosaurids. And then there are the prodiapsids from Heleosaurus to Archaeovenator and the last common ancestor of synapsids and diapsids, VaughnictisThe early members of this segment of the mammal lineage have often been called pelycosaurs while the members of the more mammal-like segment of the lineage are termed therapsids. Actually finback pelycosaurs are an offshoot clade, not in the lineage of mammals, which proceeds from a sister to Ophiacodon to Cutleria without including finbacks. The importance of these animals concerns the fact that their comparatively excellent fossil record charts transition from an ancestral ‘reptile-like’ form to mammals via a near-perfect series of intermediates. Alas, their relative obscurity and the lack of good popular syntheses means that they are not the poster-children of evolution that they really should be… at least, not outside the palaeontological community.  Those animals were featured on both versions of Cosmos.

TETRACERATOPS FROM THE EARLY PERMIAN OF THE USA, AN EARLY SYNAPSID SOMETIMES IDENTIFIED AS ONE OF THE OLDEST THERAPSIDS BUT LATER RE-INTERPRETED AS OCCUPYING A MORE ROOT-WARD POSITION IN THE TREE. CREDIT: DMITRI BOGDANOV WIKIPEDIA CC BY 3.0. The LRT nests Tetraceratops with Tsejaia and Limnoscelis, whether it had a lateral temporal fenestra or not. Massive crushing adds doubt to that. It doesn't look like any other synapsid and it nests better with other reptiles, so why include it?

TETRACERATOPS FROM THE EARLY PERMIAN OF THE USA, AN EARLY SYNAPSID SOMETIMES IDENTIFIED AS ONE OF THE OLDEST THERAPSIDS BUT LATER RE-INTERPRETED AS OCCUPYING A MORE ROOT-WARD POSITION IN THE TREE. CREDIT: DMITRI BOGDANOV WIKIPEDIA CC BY 3.0. The LRT nests Tetraceratops with Tsejaia and Limnoscelis, whether it had a lateral temporal fenestra or not, far from the synapsids. Massive crushing adds doubt to that. It doesn’t look like any other synapsid and it nests with other reptiles, so why include it?

This article is not the time and place to start a group-by-group review of the many lineages concerned… I know from experience how those projects quickly expand into gargantuan multi-part monsters that can never be finished. Rather, this is just a brief primer, a placeholder. If you want to see the lineage of mammals going back to stem tetrapods, click here then peruse at your leisure the taxa that interest you.


COVER OF KEPT (1982). THE BEST BOOK ON THE GROUP OF ANIMALS SO FAR. NOW OUT OF PRINT (BUT AVAILABLE AT REASONABLE PRICES ONLINE. CREDIT: ACADEMIC PRESS LONDON. This is indeed the go-to book for synapsid data and has been for more than 30 years. See for updates since then. 

Before anyone asks, the one crippling, punishing problem with these animals is that – even today – there is no single, good, up-to-date, go-to volume on their diversity, history, evolution and biology. But you can go online here for the latest data. Yes, there are books on these animals, but they’re technical and mostly out of print. The best is Tom Kemp’s Mammal-Like Reptiles and the Origin of Mammals (Kemp 1982). There’s also Nick Hotton et al.’s The Ecology and Biology of Mammal-like Reptiles (Hotton et al. 1986) (a collection of papers by different authors). I have a substantial, well illustrated chapter on these animals in my giant textbook (on which go here, if you wish), but a good, dedicated, modern volume just does not exist. There are several decent review articles on the group as a whole, among the most recent being Angielczyk (2009).

MUCH-SIMPLIFIED CARTOON CLADOGRAM OF STEM-MAMMALS BASED ON TOPOLOGIES RECOVERED IN SEVERAL RECENT STUDIES. EXPANDED VERSIONS BEING PREPARED FOR MY IN-PREP TEXTBOOK (MORE HERE). CREDIT: DARREN NAISH As above, caseids are not related. Pelycosaurs are offshoots. The basal dichotomy of therapsids separated the Anomodonts from the Kynodonts.

MUCH-SIMPLIFIED CARTOON CLADOGRAM OF STEM-MAMMALS BASED ON TOPOLOGIES RECOVERED IN SEVERAL RECENT STUDIES. EXPANDED VERSIONS BEING PREPARED FOR MY IN-PREP TEXTBOOK (MORE HERE). CREDIT: DARREN NAISH As above, caseids are not related. Pelycosaurs are offshoots. The basal dichotomy of therapsids separated the Anomodonts from the Kynodonts.

The oldest stem-mammals date to the Moscovian part of the Carboniferous (here again, an inappropriate use of the term ‘stem’) and have conventionally been depicted as very reptilian in appearance. That’s because they are or were reptiles, as recovered by the LRT.  This is probably true in broad terms but is open to some question, there being indications that their integument and so on was not ‘reptilian’ as we conventionally imagine it. Likely without scales, based on the scant evidence at hand, but living dinosaurs are also without scales, except for those transformed from feathers. These early forms belong to those lineages conventionally lumped together as ‘pelycosaurs’ – a term that clearly refers to a paraphyletic assemblage given that therapsids evolved from somewhere among them. Not true. The LRT recovers a clade of pelycosaurs, a resurrected clade Pelycosauria. 



Animals from this ‘pelycosaur’ part of the tree include the long-snouted, mostly predatory varanopids and ophiacodontids, the omnivorous and herbivorous caseasaurs, and the edaphosaurids and sphenacodontids, the latter including the famous Dimetrodon. Why waste time on these non stem-mammals? While many of these animals (especially the early members of these groups) were small (less than 50 cm long), large size (3 m or more) evolved several times independently. There are lots of other significant events here as well, including the evolution of high-fibre herbivory and the independent evolution of dorsal sails.  Why waste time on these non stem-mammals? Even in these animals there are indications of social behaviour and parental care (Botha-Brink & Modesto 2007, 2009).

RECONSTRUCTION OF AN ASSEMBLAGE (A FAMILY GROUP?) OF THE VARANOPID HELEOSAURUS, PICTURED IN THE POSE IN WHICH THEIR SKELETONS WERE DISCOVERED. CREDIT: BOTHA-BRINK & MODESTO (2009). This is Heleosaurus, which is a pro-diapsid, an outgroup to the Synapsida, but the concept is probably true of young ones nesting with an adult.

RECONSTRUCTION OF AN ASSEMBLAGE (A FAMILY GROUP?) OF THE VARANOPID HELEOSAURUS, PICTURED IN THE POSE IN WHICH THEIR SKELETONS WERE DISCOVERED. CREDIT: BOTHA-BRINK & MODESTO (2009). This is Heleosaurus, which is a pro-diapsid, an outgroup to the Synapsida, but the concept is probably true of young ones nesting with an adult.

Dimetrodon – one of the most familiar and famous of all stem-mammals (Not true, merely an offshoot)– is a fascinating creature that has recently undergone something of an image change: ideas regarding the evolution, function and anatomy of its sail have all been challenged, its ecology and lifestyle have been the source of some debate, and its life appearance and gait have undergone revision in recent years. I plan to devote an article to these issues.

YOU MIGHT HAVE SEEN THIS ANIMAL BEFORE. IT'S DIMETRODON. CREDIT: D'ARCY NORMAN WIKIMEDIA CC BY 2.0 Not sure why Naish is bothering with these popular but irrelevant taxa.

YOU MIGHT HAVE SEEN THIS ANIMAL BEFORE. IT’S DIMETRODON. CREDIT: D’ARCY NORMAN WIKIMEDIA CC BY 2.0 Not sure why Naish is bothering with these popular but irrelevant taxa when so many taxa much closer to mammals, the REAL stem mammals also make for good stories. Seems like he doesn’t know or doesn’t care. 

Animals close to sphenacodontids gave rise to therapsids. A more erect gait and faster metabolism occurred at the time of this transition, numerous additional changes associated with dentition, palatal structure, limb posture and so on occurring as well. It’s within this vast group (Therapsida) that we find the often herbivorous, beak-jawed dicynodonts and kin, the often predatory biarmosuchians, gorgonopsians and therocephalians, and the often striking, often large dinocephalians. That last group includes both predators and herbivores, hippo-sized animals, and species with thickened skull roofs probably used in head-butting. They dominated many continental animal communities in the Permian, being best known from the fossil records of South Africa and Russia. Still not talking about stem mammals here. When are we going to get to them? The text does not follow the headline. 



Gorgonopsians and therocephalians are exciting groups that include various macropredatory, often ‘sabre-toothed’ species; both have been the subject of various recent revisions. Species within these groups have been likened to weasels, wolves and bears in approximate body form, though any resemblance would have been highly superficial. Sometime during the Late Permian, cynodonts arose from an ancestor closely related to therocephalians (both groups form the therapsid clade Eutheriodontia): Cynodontia is the group that includes mammals as well as a number of additional lineages that have their own histories and evolved their own specializations. Now we’re getting closer to the stem-mammals, members of the clade Tritylodontia within the Cynodontia!

And because this was meant to be a very, very brief primer, that is all I’ll say for now. There is so much more to do… WAIT! Naish never once wrote about or illustrated a stem-mammal here! I read this whole blog post without learning anything new about the stem-mammals, the Tritylodontidae and their immediate predecessors.. As we’ve seen before, Naish sometimes cruises on the invalid past rather than exploring today’s cutting edge data and latest discoveries. Pity, all that talent going for the low-hanging fruit. Darren, as you write your book on synapsid relationships, feel free to reference and the large reptile tree. It will help you understand the issues and enigmas generated in Kemp’s 1982 book.

Stem-mammals have been covered on scant occasions at Tet Zoo. But see…

Sometimes Dr. Naish referees manuscripts offered for academic publication. With his stuck-in-the-past bias, good luck if he referees your submission. I would not want wish that on my worst enemy, especially if you’re promoting new hypotheses.

Many scientists like to play it safe, resisting and waiting for the tide to shift on advancing new hypotheses before jumping on the bandwagon. Don’t be like that. Follow the data. Test as much as you can yourself. Be a skeptical Scientist, not a nodding Journalist. 

What do I expect from these remarks?
Based on his vocal antipathy toward the results recovered by the LRT, Dr. Naish will probably cling to his invalid traditions. After all, based on his writings, he has ‘painted himself into a corner’ from which he cannot escape without an about face apology and acknowledgment. That’s something primates, like us, do very very rarely. PhDs are not wired for it. But if Naish did run the tests he would find what I found. If not, I’d like to hear why not.

Refs – –
Angielczyk, K. D. 2009. Dimetrodon is not a dinosaur: using tree thinking to understand the ancient relatives of mammals and their evolution. Evolution: Education and Outreach 2, 257-271.
Botha-Brink, J. & Modesto, S. 2007. A mixed-age classed ‘pelycosaur’ aggregation from South Africa: earliest evidence of parental care in amniotes? Proceedings of the Royal Society B 274, 2829-2834.
Botha-Brink, J. & Modesto, S. 2009. Anatomy and relationships of the Middle Permian varanopid Heleosaurus scholtzi based on a social aggregation from the Karoo Basin of South Africa. Journal of Vertebrate Paleontology 29, 389-400.
Hotton, N., MacLean, P. D., Roth, J. J. & Roth, E. C. 1986. The Ecology and Biology of Mammal-like Reptiles. Smithsonian Institution Press, Washington and London.
Kemp, T. S. 1982. Mammal-Like Reptiles and the Origin of Mammals. Academic Press, London.

Let’s open up an old can of worms…

Three and half years ago got a sound thrashing from Dr. Darren Naish writing form his Scientific American blog, Tetrapod Zoology. Today with 350 more taxa added and the tree still fully resolved, let’s add some ‘post-its’ to ten images of Darren’s blogpost (Figs. 1-10) to see how things stand today. Both adversaries are still out there on the Internet. Neither has buckled under.

This will be a long post
So the gist of it is:

  1. Naish paints me as an outsider, only part of the paleo background. True – for most workers
  2. Naish uses art and hypotheses that are not in my website. Some perjorative art he uses are from other artists. He had permission to use all my artwork, so bringing in these oddities was not necessary given his headline. 
  3. Naish spends many paragraphs talking about pre-ReptileEvolution errors that I made. One reason for starting a fresh website was to rid myself of old errors, but with this ‘history’ tainting all of my present work Naish provides no possibility for future redemption or honor.
  4. Naish claims that I see certain things in fossil photos that are not there in fossils. None of these are present in If so, let me know so I can remove them.
  5. Naish claims that I see certain things in fossils that are not visible in fossil photos. So, what can one do? (see below)
  6. Naish blackwashes the entire ReptileEvolution website, all of its data, all of its images, then and forever in the future. He leaves no stone unturned.
  7. Naish supports traditional trees, even those that nest pterosaurs close to phytosaurs and erythrosuchids and those that refuse to include fenestrasaurs. These are problems that need to be resolved in academia.
  8. Naish wants me to add hundreds of more characters. As we’ve seen earlier, that doesn’t statistically help much after 200 traits and can be a never ending request.
  9. Several times Naish provides high praise before he buries the knife. I won’t do that.
  10. Both of us are unmoved regarding our stances.

Bottom line:
No one is perfect. No matrix is perfect. No interpretation is perfect. Even so, superior provisional hypotheses can be advanced by increasing the number of taxa in a taxon list. The more data, the less any single error affects the rest of the matrix and the more unbiased opportunities are present for nesting. If, in the end, all sister taxa look like sisters, with gradual accumulations of traits for all derived taxa, and the tree is completely resolved with high Bootstrap scores, isn’t that what we’re all looking for? Doesn’t that more closely model actual evolutionary events?

On the other hand, if Naish is correct
If my cladogram is built on (hundreds of) thousands of errors, even after fixing tens of thousands of errors, how is a fully resolved tree demonstrating gradual accumulations of derived traits for every taxon even possible?

When Naish is writing on his blog
and as I am writing here, we lose our scientist mantles and become journalists. In that role we have the obligation to name sources, be specific, inform the reader, write about what the headline promises, and try to maintain a balanced unprejudiced view. Any variation from this becomes propaganda. To that end, if you have any questions regarding topics that arise here, look up the answers on previous blog posts or on or drop me a note.

All of these pages can be enlarged with a click.
Some Carl Sagan quotes break up the long page images here and give you time to digest.

Figure 1 of 10. Click to enlarge. Monitor shot of Tet Zoo blog with annotations in yellow.

Figure 1 of 10. Click to enlarge. Monitor shot of Tet Zoo blog with annotations in yellow.

Below (Fig. 2) you’ll see some bizarre Pterodactylus art
that Naish says was illustrated as if my hypotheses were correct. To be fair, I show you a Pterodactylus from (Fig. 1a). Why did Naish choose to show the bizarre artwork of another artist instead of using one from the website he was critical of?

Pterodactylus scolopaciceps.

Figure 1a. Pterodactylus scolopaciceps, BSP 1937 I 18, No. 21 in the Wellnhofer 1970 catalog.


Figure 2 of 10 from Tetrapod Zoology.

Figure 2 of 10 from Tetrapod Zoology.

“For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring.”
— Carl Sagan —

Figure 3 of 10 from Tetrapod Zoology.

Figure 3 of 10 from Tetrapod Zoology.


The truth may be puzzling.
It may take some work to grapple with.
It may be counterintuitive.
It may contradict deeply held prejudices.
It may not be consonant with what we desperately want to be true.
But our preferences do not determine what’s true.
— Carl Sagan —

Figure 4 of 10 from Tetrapod Zoology.

Figure 4 of 10 from Tetrapod Zoology.

Here’s one Pteranodon from 
(Fig. 4b) Why didn’t Naish use this one by hand instead of the Pteranodon from Hell? Did he venture into propaganda? Did he want to make my work look unworthy of respect?

Figure 3. The UALVP specimen of Pteranodon. Note the lack of taper in the rostrum along with the small size of the orbit.

Figure 4b. The UALVP specimen of Pteranodon. Note the lack of taper in the rostrum along with the small size of the orbit.

Figure 5 of 10 from Tetrapod Zoology.

Figure 5 of 10 from Tetrapod Zoology.

The poor graduate student at his or her Ph.D. oral exam
is subjected to a withering crossfire of questions
that sometimes seem hostile or contemptuous;
this from the professors who have the candidate’s future in their grasp.
— Carl Sagan —

Figure 6 of 10 from Tetrapod Zoology.

Figure 6 of 10 from Tetrapod Zoology.

Every kid starts out as a natural-born scientist,
and then we beat it out of them.
A few trickle through the system with their wonder and enthusiasm for science intact.

— Carl Sagan —

Figure 7 of 10 from Tetrapod Zoology.

Figure 7 of 10 from Tetrapod Zoology.

I think people in power have a vested interest to oppose critical thinking.
— Carl Sagan —

Figure 8 of 10 from Tetrapod Zoology.

Figure 8 of 10 from Tetrapod Zoology.

It is undesirable to believe a proposition
when there is no ground whatever for supposing it true.
— Carl Sagan —

Figure 9 of 10 from Tetrapod Zoology.

Figure 9 of 10 from Tetrapod Zoology.

At the heart of science
is an essential balance between two seemingly contradictory attitudes –
an openness to new ideas, no matter how bizarre or counterintuitive,
and the most ruthlessly skeptical scrutiny of all ideas, old and new.
This is how deep truths are winnowed from deep nonsense.
— Carl Sagan —

Figure 10 of 10 from Tetrapod Zoology.

Figure 10 of 10 from Tetrapod Zoology.

In the end
is it good to have an an adversary/nemesis? Does conflict help advance Science? I think of it as necessary and invigorating. An adversary can be like a cleaner fish, helping one get rid of errors. I think it is also important to recognize value where present and to discuss specifics and details whenever possible.

On the subject of outsiders and insiders
JL Powell 2014 writes: “Luiz Alvarez was another resented outsider, resented by author and geologist Charles Officer. 

Outsiders do not know the mores for a given field and would be unlikely to uphold them if they did. Outsiders can resurrect a question that insiders have long stopped asking, 

Insiders may find it almost impossible to change their mind publicly, which may be equivealent to renouncing their life’s work. Even if insiders do not cast aspersions on the character and training of an individual outsider, they may still resent the implication that their discipline is incapable of solfing its won problems using its own methods.” 

Powell JL 2014. Four Revolutions in the Earth Sciences: From Heresy to Truth. Columbia University Press.


Data denial you can listen to on a podcast

Dr. Mark Witton

Dr. Mark Witton

Dr. Mark Witton is a paleontologist,
author and illustrator, but based on a Liz Martin interview podcast denies the existence of pterosaur ancestors. Like his friends, Dr. David Hone (another data denier), and Dr. Darren Naish, Dr. Witton believes pterosaurs “appeared fully formed in the fossil record. We don’t have the pterosaur Archaeopteryx.”

Sadly this purposefully ignores 
the published literature (Peters 2000 is now 15 years old) online phylogenetic analyses (now 4 years old) and YouTube videos (just a few weeks old) that all provide a long list of pterosaur ancestors that demonstrate a gradual accumulation of pterosaur traits. Why does Dr. Witton prefers to hide his head in the sand rather than examine, test and/or accept published studies? Could this be academic bigotry? (definition: intolerance toward those who hold different opinions from oneself)

Witton believes pterosaurs “are close relatives of dinosaurs.”
If so, then were are the common ancestors that show a gradual accumulation of character traits? Answer: You can’t find them because they are not there. Other taxa share more traits with pteros and dinos than either does with each other. This is the outmoded “Ornithodira” concept.
Witton says he did not expect
that the Jurassic pterosaur, Dimorphodon would be adept at walking on the ground (despite having digitigrade pedes and fully interned femoral heads). Again, published literature demonstrates just the opposite (Padian 1983). Glad to see that Dr. Witton is getting on board with a more terrestrial Dimorphodon.
Dr. Witton waxed on about Solnhofen juvenile and subadult pterosaurs,
agreeing with Bennett (1995) who lumped Rhamphorhynchus into one species by plotting long bone lengths on a graph. Witton thought different species should have a dramatic difference in wing shape. Not so. He didn’t mention foot shape and overall morphology, which varies quite widely and logically when phylogenetic analysis is employed (Fig. 2).
Figure 3. Bennett 1975 determined that all these Rhamphorhynchus specimens were conspecific and that all differences could be attributed to ontogeny, otherwise known as growth to maturity and old age. Thus only the two largest specimens were adults. O'Sullivan and Martill took the brave step of erecting a new species. The n52 specimen is at the lower right. Click to enlarge.

Figure 2 Bennett 1975 determined that all these Rhamphorhynchus specimens were conspecific and that all differences could be attributed to ontogeny, otherwise known as growth to maturity and old age. Thus only the two largest specimens here were adults. Witton agrees that all these are conspecific. Do you agree with Witton? Decide for yourself. Click to enlarge.

Witton follows the Lü et al. (2009) analysis
that nested Darwinopterus as a transitional fossil combination of pterodactyloid skull and basal pterosaur post crania. Other analyses ( Wang et al 2009, Andres 2013, Peters online) do not support that hypothesis. Only Peters online (based on Peters 2007) includes a large selection of sparrow-sized Solnhofen pterosaurs, keys to the origin of all later clades. Along the same lines, Witton believes in Modular Evolution, which is falsified in phylogenetic analysis and apparently occurs only in their vision of Darwinopterus.
Witton reports that some azhdarchids had short necks.
Not sure which azhdarchids he is talking about. Evidently that is sneak preview on unpublished papers. The large pterosaur tree indicates that going back to the Late Jurassic, all azhdarchids and their ancestors had very long necks, even as hand-sized taxa (Fig. 3).
The Azhdarchidae.

Figure 3. The Azhdarchidae. Click to enlarge. No short necks here, except way down toward the left. Not saying they could not evolve. Just saying I haven’t seen them yet. 

Witton reports there are small birds but no small pterosaurs
from the Upper Cretaceous — but no small dinosaurs either — so suggests there may be a preservational bias in the lack of small pterosaurs… but no such bias for small birds. Actually there are small bird fossils from the Late Cretaceous, and they ARE dinosaurs, and no small pterosaurs. Lacking tiny pteros in the Late Cretaceous spelled their doom. Only small and tiny pterosaurs survived the Latest Jurassic extinction event and only these were basal to later giants. So no darwinopterids had descendants in the Cretaceous. Because there were no tiny Late Cretaceous pterosaurs, none survived the Late Cretaceous extinction event.
Can we blame this on a bad mentor?
Dr. Witton has accumulated a great deal of pterosaur knowledge and expresses it wonderfully in his many paintings. Unfortunately, like Hone and Naish, he was ‘raised’ by wrong-minded mentors and continues his false beliefs (= he has not tested his or competing hypotheses in phylogenetic analyses) to this day. Earlier we looked at the many problems in Dr. Witton’s book on pterosaurs.
Dr. Don Prothero

Dr. Don Prothero

Some insight into that sort of thinking…
it’s not that uncommon.
Dr. Don Prothero in a YouTube Video provides great insights into the Creationist mindset that finds strong parallels in the current thinking of Dr. Mark Witton, Dr. David Hone and Dr. Darren Naish.

Notes from the Prothero video
  1. Humans are not rational machines
  2. We all employ motivated (emotional, wants and needs) reasoning, not logical reasoning
  3. We are all belief engines and we all create a world view or core belief
  4. Because of that we don’t like to hear anything that does not fit our world view
  5. AND we use reason to do what we want data to do, not what its telling us. We use ANY tricks to make the evidence of the world fit our beliefs, or twist it to fit, or deny it or ignore it. Michael Shermer, founder of the Skeptics Society and author of “The Believing Brain” writes, “We all support the world we already have.”

Bottom line:
Witton, Hone and Naish don’t like because it doesn’t support the paleo world they already have. Like Creationists they display the following traits raised by Prothero:

  1. Reduction of cognitive dissonance (= the state of having inconsistent thoughts, beliefs, or attitudes, especially as relating to behavioral decisions and attitude change) when presented with evidence that works against that belief, the new evidence cannot be accepted.
  2. Tribalism = we learn our world from whoever we were raised by. And all three professors are friends of one another.
  3. Deep innate psychological tendencies are genetic = there are some people who readily accept new ideas and there are some people who do not. Unfortunately, all three appear to have the same gene.
  4. Confirmation bias (= the tendency to interpret new evidence as confirmation of one’s existing beliefs or theories.) Thus when Hone and Benton (2007, 2009) come out with the worst paper I have reviewed, Naish and Witton support it anyway.
  5. Cherry picking (= remembering the hits, forgetting the misses). Hone, Witton and Naish like to pick on poor Longisquama, which was difficult, but not impossible to interpret and all three like to ignore the whole point of, the cladograms, both the large reptile tree and the large pterosaur tree. Note that no other pterosaur worker has produced competing interpretations of Longisquama of equal detail nor competing cladograms that include tiny pterosaurs. In this regard these pterosaur workers are exactly like Dr. Feduccia and the late Dr. Martin (who deny the theropod-bird link and never employ phylogenetic analysis) and also like extant Creationists, who likewise never employ phylogenetic analysis. Remember when Hone and Benton first deleted the taxa that Peters 2000 proposed, then deleted Peters 2000 from the competition? This was cherry picking at its best.
  6. Qiuote mining (= in this case finding images and hypotheses that have been long ago trashed in order to undermine the site. These are essentially ad hominem (directed against a person rather than the position they are maintaining) attacks as they blackwash my methods (which they practice too) and the entire website while they could have gotten specific about one problem or another.
  7. Missing the forest for the trees (= The big picture) is the large reptile tree cladogram. This is created by a huge mass of data and becomes strengthened with every additional taxon – all of which affect every other taxon. In such an analysis you can remove data, remove taxa, remove characters and nothing falls apart. The subsets are just as strong as the dataset itself. But Hone, Naish and Witton refuse to acknowledge that, preferring to continue their thinking that pterosaurs appeared suddenly in the fossil record, like on the fourth day of Creation. Phylogenetic analysis would solve their quandary, if only they would give it a chance.

Dr. Prothero asks: Why is science different?
Prothero answers his own question in this fashion:

  1. Science (like is always testing with falsification, prove things wrong, correcting mistakes. Presently I’ve made over 50,000 corrections in drawings and scores and look forward to many more. Getting it right is important.
  2. Science (like is always tentative, no claim to final truth. I am always looking for a competing hypothesis. Witton, Hone, Naish, Bennett and other referees are making sure my papers are not getting published. They don’t like it when their claims are disputed here at PterosaurHeresies.
  3. Science (like works! It provides answers that make sense, can be replicated, and can provide predictions.
  4. In Science peer review cancels individual biases. Sadly the current pterosaur referees, Hone, Witton, Naish and others, are all from the same school of thought. Every day I hope to change that, to open them up to accept more valid hypotheses that work!
  5. In Science, if you’re not pssing people off, you’re not doing it right. Well, I must be doing something right, because Witton and Naish are never praising my work. It would be great if we could argue about it. I guess we’re doing that here.

Prothero finished with a cartoon
of a professor who was showing his cognitive dissonance: “If P is false, I will be sad. I do not wish to to be sad. Therefore, P is true.”

This is human nature.
We all have it. We all get jealous, ambitious. disappointed. As scientists we have to get over our human nature and let testing and experimentation rise above human nature. We have to be like Galileo, not Aristotle.

Bennett SC 1995. A statistical study of Rhamphorhynchus from the Solnhofen limestone of Germany: year classes of a single large species. Journal of Paleontology 69, 569–580.
Lü J, Unwin DM, Jin X, Liu Y and Ji Q 2009. Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull. Proceedings of the Royal Society London B  (DOI 10.1098/rspb.2009.1603.)
Padian K 1983. Osteology and functional morphology of Dimorphodon macronyx (Buckland) (Pterosauria: Rhamphorhynchoidea) based on new material in the Yale Peabody Museum, Postilla, 189: 1-44.
Peters D 2000. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.
Peters D 2007. The origin and radiation of the Pterosauria. Flugsaurier. The Wellnhofer Pterosaur Meeting, Munich 27
Wang X, Kellner AWA, Jiang S, Meng X. 2009. An unusual long-tailed pterosaur with elongated neck from western Liaoning of China. Anais da Academia Brasileira de Ciências 81 (4): 793–812.

Much appreciated support ‘out there’ for

I found
a blog that repeated and supported Darren Naish’s diatribe, “Why the world has to ignore” That was answered in a multipart reply here, here and in links therein back in 2012.

The name of that blogpost is:“the-best-scientific-smackdown-about-evolution-youll-read-this-week. from If I read things correctly, the blog is hosted by Annalee Newitz under the topic Science Scandel, Newitz reports, “Since that time, he [David Peters] has become a bane of the paleontology community by insisting that he’s invented a new kind of technological analysis for fossils. And using this analysis — which he calls Digital Graphic Segregation — he believes he’s proven that pterosaurs are far more distant from dinosaurs in the reptile family tree than previously believed.”

The bane? Is that true?
As loyal readers know, DGS is a technique I applied a name to, but did not invent. Paleontologists, like Michel Laurin (1996), had been tracing photographs of fossils long before I came on the scene. And, as loyal readers (and all pterosaurologists) know pterosaurs don’t really fit will with dinosaurs. Just look at the fingers.

The Newitz blogpost goes on repeating Naish’s logic and images. What I found interesting were some of the blog’s comments. Most ganged on, disliked my web code or worried about SEO and Google robots. A few others took the opposite tack and urged caution before continuing the attack and those are re-printed below:

  1. KipHansen wrote: Nothing wrong about proposing an alternate hypothesis, certainly in a field as based on opinion as Reptile Evolution. I was expecting Naish to blow Peter’s out of the water with carefully researched DNA evidence or something equally scientifically strong – instead we get “I don’t see what you see.” — which, in all honesty, adds up to zero – zip – nada – and nothing. Certainly Naish can come up with *something* more concrete? In science, “I don’t agree with you and I am, after all, an Expert” doesn’t cut much ice. Peter’s may be full of it but Naish has done nothing to convince me of the superiority of his position.
  2. KipHansen wrote: “Is not Peters just proposing shifting some of these things around about? I can’t quite see what is so exasperating about some single person suggesting a different arrangement of something that we are unlikely to be sure about for some time yet. Just because paleontologists have finally agreed, at least for the time being, about reptile evolution doesn’t mean that we have finally ‘found the truth’. The current consensus is just your collective best guess based on available data and techniques and seems to be supported, for the most part, by what we know so far. This consensus will be shattered when someone makes a new remarkable find, or develops a new technique or method of investigation and is brave enough to publish an alternate view. Meanwhile, is there nothing whatever to the DGS techniques in the viewing of fossils, irrespective his interpretations? Is this a interesting new digital technique that could add something to our ability to understand rock encased fossils? Has anyone asked Peters to clearly mark his interpretation as an “alternative hypothesis” to a linked exposition of the consensus view?”

  3. KipHansen wrote: Annalee Newitz: You fail to mention that Mr. Peters, who you characterize as an ‘amateur paleontologist”, is the lead author on a half a dozen or so peer-reviewed papers in respectable paleontology journals. And not just in the 1980’s and 90’s. What’s up with that? Are you sure this isn’t just one of those silly academic wars where some outlier publishes papers in the journals but the entrenched consensus refuses to deal with them, instead resorts to ad hominem attacks via gullible journalists?”

  4. David Marjanovic wrote: “On a few things, he [David Peters] may turn out to be right. One of his first papers (yes, published and peer-reviewed) was on the origin of pterosaurs: he thinks they’re not close relatives of the dinosaurs (the consensus view), but close relatives of (to say it in a neutral way) lizard-shaped animals like Cosesaurus and Langobardisaurus. Peters is the first to have tested this idea by including enough species in a phylogenetic analysis; “the establishment” has never done this, because it’s too much work (it would be at least one complete PhD thesis). Unfortunately, Peters hasn’t put enough work in to this either: his analysis lacks several characters that support the consensus.”

  5. Alanborky wrote: “As an artist/visual type he [David Peters] sees and extracts vastly more visual data from whatever he’s looking at than a none artist (eg most people see a blue sky but artists see literally millions of shades and tones of blue as well as myriads of other colours derived from objects peripheral to their eyes bleeding into those blues subtly influencing how those blues differ in appearance as the eyes shift their focus around the sky) which’s probably why Goethe spotted the intermaxillary bone before none artists did.”

  6. jazzraptor wrote: “How has Peters “muffled” his opposition? Promoting ones own ideas is very different than censoring other people’s ideas. Disagreements about details of evolution are typical and ever-present in the field — not one bit unusual. Isn’t Peters entitled to his opinion? Obviously the guy has put a ton more hours than you have into his studies. And it’s not fallacious to ask for a better explanation for evidence than the one put forward. (Of course his request for competing hypothesis doesn’t mean that he’s right. But there’s nothing wrong with the argument. Ever hear of Occam’s Razor?) Your article looks way too much like a hatchet job. Science is tentative and provisional after all; how will you feel if Peters eventually gains consensus? I’ll answer for you: like an idiot.”

I also wrote a reply to the Newitz blog post. It follows:

Hi Annalee,  David Peters here. Sorry to be late to the party. In 2012 I replied to Darren Naish’s blogpost in a seven-part series that ended here:  You’ll find links to the first six posts within. A few quick notes here will clear up some issues.

1. The latest cladogram at includes 504 taxa and they nest in near complete resolution. All sister taxa resemble one another (you can see the reconstructions throughout the website), a great clue that that cladogram reflects actual evolutionary lines of descent. Add to that 59 therapsids and their kin plus 219 pterosaurs and their kin and you have the largest phylogenetic analysis ever attempted for reptiles. (That, I think, is the extraordinary evidence requested by Carl Sagan and one of your readers.)

1a. More characters would be great, as D. Marjanovic requests, but they are not necessary. Fewer characters will recover the same tree. 228 characters is enough to provide complete resolution as proven at Almost all characters can be correlated, like vertebral counts and limb lengths. Correlated characters are hard to avoid.

2. With so many taxa, you can trace the lineage of pterosaurs, or any included genus, back to Ichthyostega or to any node in-between. You can delete large branches or individual taxa from this tree and it will recover the same topology. The fact that this tree nests mammals (synapsids) in a different place than some DNA studies do is a problem that has not been resolved yet. You probably know that many DNA studies do not agree with one another. You may not know that embryological studies support a closer relationship between mammals and archosaurs than with turtles and lizards, which matches my cladogram.

3. Current and traditional cladograms (i.e. Nesbitt 2011) nest pterosaurs with parasuchia and proterochampsia, two croc-like clades that everyone realizes are bad matches for pterosaurs. Pterosaurs nest where they do in Nesbitt 2011 because he excluded the taxa that nest around pterosaurs at Some workers ignore Nesbitt 2011 and nest pterosaurs with dinosaurs, all the while realizing that there is no way the vestigial lateral fingers of even the most basal dinosaurs and their ancestors could ever evolve to become the long wing-fingers of pterosaurs. The same goes for the lateral digits of the foot.

4. The sternal complex of pterosaurs, as the name implies, is a fusion of the interclavicle, the clavicles and the sternum. My work with DGS shows how that happens in Cosesaurus and Longisquama, non-volant pterosaur sisters. Dinosaurs are not a more parsimonious match.

5. The fact that Darren Naish does not see both prepubes of Cosesaurus (in your illustration above) does not mean that everyone agrees with Naish. I encourage you and your readers to see for yourself at and let me know the consensus. Those prepubes are 2mm long in life, so they are tiny, but well formed. Naish reported he saw the stems in the photo. No sister taxa have such stems on their pelves. Those stems are the prepubes, even if Naish wants to deny it.

6. In Science we don’t ‘trust’ –anything– because in Science we can prove everything for ourselves. Many of the taxa I present are the reconstructions of others. Yet other taxa have never been reconstructed, so I’ve done the work with as much detail as can be gleaned from the best available data. You don’t have to trust those reconstructions –or– my color tracings. You are invited and encouraged to repeat the experiment, make your own observations and either refute or support any part or all of what I have presented. It’s simply a presentation. Rarely it’s an alternative. My best contribution to paleontology is simply adding more taxa to the cladogram so that more nesting opportunities are provided, minimizing the effects of bias, tradition and paradigm.

7. Digital Graphic Segregation (DGS) is a name I proposed for a technique that has been used by paleontologists for several years prior to my first attempt at it. Laurin (1996) used it in tracing Utegenia and I dare say anyone tracing fish bones and scales is going to trace a photo rather than get lost in the chaos of those repeating structures without some sort of mechanical aid. I use DGS to color every other reptile rib another color, again, to avoid confusion in a smashed roadkill. Then, I can lift those colors and move them around (usually slightly) to reconstruct the ribcage with the precision of the original.

8. I realize that D. Naish carries a lot of weight with the paleo-blog community. Unfortunately Naish published some of my work that has been in my trash bin for several years. In Science you can admit you made a mistake and you can propose a new reconstruction or cladogram to reflect the latest data. I have made tens of thousands of scoring errors in my cladogram, as I’ve reported at www. That also means I’ve made tens of thousands of corrections to past errors. With all of those corrections the tree topology has changed a little here and there, but overall, not so much. With 228 traits and 504 taxa the matrix can handle nearly 115,000 scores.

9. Finally, unless you have other unanswered questions, it’s true I have not seen for myself the vast majority of the fossils shown at However I’ve taken three trips to Europe, one to China and several others to USA museums to visit specimens and see them in person. Longisquama and Sharovipteryx both came to St. Louis several years ago, so I was able to study them both. I spent several days with Cosesaurus in Barcelona. Some of the rumors to the contrary have gotten out of hand.

Let me know if YOU have any issues that need clarification. I am here for you.

And I’ll give you the same challenge I gave Darren Naish. If what I’ve done is so off the mark, then the results cannot possibly make sense. The challenge is, please send me two taxa that should not nest together, but they do at If you do find two mismatches, please let me know so I can make yet another correction. If you cannot find two mismatches, I hope you’ll let me and others know that maybe what I’ve done has some value.

PS. I am not a professional web designer. I was an agency art director who wrote and illustrated some books in the 1980s and 1990s, then published, with peer review, a half dozen papers, some with co-authors. D. Marjanovic is correct that I have submitted several other manuscripts for peer review. They were rejected, not sent back to correct errors. Often referees note that what I’m proposing in those manuscripts cuts across traditional paradigms.

Thank you one and all.
The Internet is full of ideas and images. Decide for yourself which have value and which make the most sense. Feel free to follow the links above to see the original Annalee Newitz post and the replies that followed.

Laurin M 1996. A reappraisal of Utegenia, a Permo-Carboniferous seymouriamorph (Tetrapoda: Batrachosauria) from Kazakhstan. Journal of Vertebrate Paleontology 16(3):374-383.

The DGS label, comments by Darren Naish at TetZoo

A recent TetZoo blog post by Darren Naish reported the colorizing of skull bones does not represent an application of DGS (digital graphic segregation), which I earlier posted. I think its the label that bothers him. Naish thought it was so important to remind others what a bad influence I am on our profession that he interrupted a discussion on ichthyosaurs with an illustration of Longisquama.

D. Naish wrote: “Claims [by Peters] that colour-coded images like those you seen (sic) in this article (and Fischer et al. 2014a, and Valentin’s other papers) represent application of DGS are an outright lie. DGS (or DGS-like) techniques are not used by working palaeontologists because it’s acknowledged in the real world that you can’t reliably identify structures by tracing their outlines on a computer screen. But do working palaeontologists colour-code bones to aid visual representation? Sure, all the time.”

The caption
to his example photo (ichthyosaur skull above, colorized skull below) reads, “No, David, no: this sort of thing is NOT the same as DGS. Skull of the ophthalmosaurine Leninia stellans from the Lower Albian of Russia (from Fischer et al. 2013b), labelled interpreted below. Again – this is NOT DGS.”

According to Naish
the difference between what I do and what the pros do is this (and I quote from the above): I “identify structures by tracing outlines on a computer screen” while the pros “color-code bones to aid visual representation.”

I’ll remind Naish 
that the pros are also color-coding bones on screen, not with an airbrush and masking tape. And I also color-code bones, not just trace outlines. (See how Naish adds separation that really isn’t there?)

So, what’s the difference?

I can think of one other difference. Typically the working pro has the specimen in front of them. But that doesn’t stop them from taking a photograph and colorizing it, a technique that I fully support because the accuracy cannot be beat. A telephoto lens and some distance effectively gets rid of all perspective and key-stoning issues.

Another difference:
I sometimes put more effort into difficult fossils than others are do. See examples here and here. Other times I take what is given and simply expand the inclusion set to find a new nesting.

DGS is colorizing (or outlining) digital photographs on screen to aid visual representation. That the bones are identified in the process is an added bonus. This is a much better technique than simply using arrows to identify bones. Also better than using a prism and a pencil. Furthermore, these colors can then be digitally transferred to reconstructions to assure fit without fudging.

Bottom line:
Evidently Naish supports others who colorize bones to share their findings, but he doesn’t like it when I do the same.

Is it because I sometimes make mistakes? 
Reliability seems to be the cornerstone of his arguments. Sure I make mistakes, but some of what I trace is difficult material. If it’s easy their’s no reason to revisit it and I ignore or accept it. Only when I think I can make a contribution do I put out the effort. That’s why much of my work is with the long forgotten specimens.

I’m sure Naish can find a few other workers who have made mistakes that have made it to the literature, just look for any paper with the word “reinterpretation” in the title. If so where are the diatribes against those workers?

On the other hand I love finding mistakes.
And I don’t mind when others find mistakes in my work — if valid. Making corrections is what I do, both in my work and the work of others. This is the essence of science.

Let’s recall
that two years ago Naish dredged through my wastebasket of discarded ideas and employed the work of other artists to satirize and discount my work rather than bringing up specific examples of web work that included errors (and, if valid, these would have been repaired post haste).

Or is it because I’ve made discoveries that might be correct?
Every discovery I make is one less for him, or anyone else to make. And we’re all in this to make discoveries. It’s what powers our drive.

There are just so few mysteries out there, after all. When they’re all cataloged, we’ll all have to retire.  ;  /

If you’re having trouble figuring all this out,
you’ll know the bad guys from the good guys by the refusal of the former to grant any sort of credit. A few days ago a contribution from Naish got a big thumbs up here. 

And his post on ichthyosaurs was first-rate, except for that little detour he took in the middle. An editor might have suggested cutting that out as irrelevant to the discussion at hand.

No, this goes deeper.
And, apparently two years of making corrections to has not placated Naish. Something about what I do and have done just raises his ire.

Sorry to see that.
We’re all working toward the same goal, trying to figure out and describe the Tree of Life.

If I really – lied – by calling the colorizing of bones by others for visual representation “another example of DGS,” please let me know so I can stop doing that.
 and Tetrapod Zoology – part 7

Earlier we discussed in parts 12345 and 6 the criticisms leveled at by Darren Naish, author of the Tetrapod Zoology blog titled “Why the world has to ignore Here is part 7.

Darren grants credit for my attempt to use species-level taxa and for my criticisms of previous analyses for not including enough of these. He disagrees with my novel nestings because “(1) he finds the ‘conventional’ positions to be far more convincingly supported by character data, and (2) because Dave’s alternative positions are based on erroneous or incomplete analysis of the data available.” Unfortunately, once again, no details are given.

Darren suggests my character list needs to be longer than 228. By comparison, he is working on a project in which 800 characters are employed. I don’t have the references, but I remember the thesis on a paper on cladistic analysis. The more characters the better, of course, but after 150, the logarithmic curve starts to flatten and you don’t get greatly different results thereafter. You’re already in the high 90th percentile of reliability between 175 and 200.

Darren was deeply perplexed by my statement that I didn’t intend to add more characters to my matrix. Of course that would involved reexamining every one of my over 300 taxa for each new trait and I’m going to leave that for the next guy. I have a job, a life, a blog… I can only give paleontology so much and no more. I hope you all understand. Adding taxa is relatively easy by comparison and with a single tree result, so far so good.

Darren asked, “What the hell happened to Test. Test. and Test again?” Well, Darren, I have tested again and again over the past two decades. I am adding taxa and none have shaken the tree. I do make corrections. When I say, “Test,” that’s for those guys and gals who refuse to test lizards and archosaurs and pterosaurs and thalattosaurs together. Get it?

Darren considers my character list to be cherry-picked. Well the list was put in place long ago when their were just 150 to 200 taxa. Since the list has grown to twice that size, I don’t think I a priori picked any cherries. I don’t include the number of characters for ANY particular clade needed for a more focused study. My aim was to include characters that could be applied to as many reptiles as possible. That’s why there is no “plastron” associated with my turtles and no “wing” associated with my pterosaurs.

Darren notes that I really don’t know how to read a cladogram. He says it’s not such a good thing to recover only a few trees in a cladogram (complete resolution). First time I’ve heard that. There are no “findings” without resolution. I also misunderstand the concept of sister taxa, according to Darren. Lucky for me, PAUP understands. Darren then explained that pterosaurs and phytosaurs nested together because they diverged from a common ancestor. That common ancestor was derived from a sister to Erythrosuchus, according to the tree. I don’t know about you, but I’d like to see much less of a mental leap between related taxa, as I found closer sisters among the little fenestrasaurs. And it scares me when professionals stand by such hypotheses.

Concluding, Darren, provides personal praise, but notes that my work will never be accepted (so be it), that (quoting Bennett 2005), I have made no attempt to convince academic palaeontologists of my findings (btw, Chris is the one who said he refuses to read my emails that attempt to convince him of my findings), and I have taken my ideas directly to the general public  and presented them as true and correct, (doesn’t everybody??).

All I can say is what I’ve said before: 1) Don’t be afraid to test lizards and fenestrasaurs with pterosaur and archosaurs. 2) Don’t be afraid to trace fossils, even if they seem daunting and difficult. 3) Don’t be afraid to let your results give you your hypothesis, even if it differs from the status quo. 4) Don’t be afraid to make changes when necessary and 5) When others shun you, hang in there if you’ve done good work.

Tomorrow, we’ll ‘cleanse the palate’ with a “nude” Archaeopteryx.

See you then. and Tetrapod Zoology – part 6

Earlier we discussed in parts 1234 and 5 the criticisms leveled at by Darren Naish, author of the Tetrapod Zoology blog titled “Why the world has to ignore Here is part 6.

How Not to Change the World
Darren reported, “If you think you’ve discovered something radically new and absolutely contradictory to previously accrued evidence, you don’t go round saying “Hey everyone – I’ve solved all your problems…You ask other people what they think before your announcement, you try and test it using alternative methods (for fossils, the application of CT-scanning and UV light to specimens is showing us stuff we can’t clearly see with our own eyes) and, essentially, you state your incredible discovery in appropriately conservative fashion.”

Well, as Darren mentions earlier in his criticism, he (and others) did receive my manuscripts and abstracts several years ago. All but a few were rejected, often with emotion-filled comments. Those manuscripts that did make it through to publication made it through somehow, but even those suffered negative referee comments, which is not at all uncommon in the world of academic submissions as I understand it. So, the comment about “appropriately conservative fashion” was followed to the letter.

In the wake of those submissions, some paleontologists have cautioned me to never submit comments to their blog. Others have said they trash my emails without reading them. Others have been seriously venomous in their remarks. Hone and Benton (2008) gave credit to Chris Bennett for my ‘pterosaurs are fenestrasaurus’ hypothesis and took all references to my work out. This is especially odd since the preceding work (Hone and Benton (2007) stated this was going to be a test of the Bennett tree vs. the Peters tree. David Unwin’s book failed to mention a single reference for my several publications, but was otherwise extremely comprehensive. The book also mentioned the “prolacertiform” hypothesis without giving credit. Darren notes this when he reports, “and indeed Dave’s work is ignored by publishing scientists.” 

Such a climate out there causes concern and is the prime motive for creating both websites. I have asked Helmut Tischlinger for certain UV images of key areas. So far I have only received copies of what he has done for others and they have been gratefully accepted and used. (Good to know that working from SOME photographs is okay).

Darren continues, “Some people actually take years or even decades to announce their major, groundbreaking discoveries because they want to be as sure as they can be that they’ve considered all the weaknesses, alternative explanations and possible flaws in what they’re proposing. Dave is a bit of a contradiction on this front. He’s thrown a million radically strange new discoveries out there at a phenomenally rapid pace, and indeed the rate at which his ‘discoveries’ occur is unprecedented.”

A ‘million’ may be a little over the top. Actually many of the so-called “discoveries” emanates from one point, the cladogram. Having a large reptile tree that I can pop new taxa into is a great advantage over the trees of others that only include one focused branch or so. The observational “discoveries” emanate from one point also, an interest in specimens that others have given up on.

The skull of Jeholopterus is a case in point. Originally it was figured as a mere outline with indistinct lines indicated within the outline. With DGS (digital graphic segregation) I was able to colorize one bone after another, taking over a month to do so (as if time was an important factor, which it is not) until all of the bones were identified with no “nuts and bolts” left over. I was the first to discover right manual digit 1 was on top of the skull and that the palatal elements had slid left beyond the limits of the maxilla. I sent my results to several other paleontologists on CD back in 2003. Manuscripts went out a little later. Rejections followed. So I followed the rules.

Paleontologists, as you can tell by now, absolutely hate it when amateurs with computers pull out data that they were unable to recover while staring at the original specimen with binocular microscopes. Most of the problem comes from the nature of crushed material. It’s hard to segregate one bone from the other visually and keep that bone in mind with your eyeballs alone. It’s like looking at a house after a tornado has hit. Instead a computer permits you to graphically segregate the elements one at a time then use those elements to reconstruct the skull. Hopefully all the elements will fit together precisely, as they do in my reconstructions. If they don’t, it’s back to the drawing board. Then phylogenetic analysis is undertaken. Any elements that stand out as autapomorphies are re-examined to see if an observational identification was mistaken. Sometimes that happens. In the end a tracing of the in situ fossil is offered along with a reconstruction of same. Then comments are requested from other workers.

Darren goes on, “But, when others don’t see what he sees, when they criticise his interpretations and his methods, he remains steadfast in his opinion that they’re wrong because they’re biased, because they’re refusing to use the same method that he does (read on), or because they can’t provide a superior hypothesis.” Unfortunately the criticism is usually not very constructive. When Darren reports, “I’m unconvinced” that doesn’t help. Darren’s figure of my interpretation of the pelvic region of Cosesaurus is a case in point. His captions reads, “The pelvic region of Cosesaurus (at left), with the Dave Peters/ reconstruction in the middle and at right. You can see that Dave identifies markings on the slab as prepubes. But we can’t be sure what they are and cannot regard them as prepubes.” Certainly this area is difficult to understand, but when two identical paired elements are found (and evidently Darren sees them, too) and they follow patterns seen in sister taxa (based on other traits) then Occam’s Razor suggests we go with the simplest explanation. I didn’t do that in my 2000 report in which I followed Ellenberger’s interpretation of seeing the unusual projection anterior of the ilium as an anterior process. When I realized there could be a prepubis there (considering the affinities of Cosesaurus), I looked with a different attitude and found two matches. Of course, if Darren does admit that there are prepubes in Cosesaurus, his whole house of cards comes tumbling down with a paradigm shift that I earlier experienced. Perhaps this is why he can’t admit what has been fairly obvious to others who have seen the photo and interpretation. Refusals to accept certain facts that run counter to one’s world view are what keep paradigms going. It’s not uncommon, especially when reputations are at stake.

Darren reports, “Dave proclaims frequently that he changes his ideas when he’s wrong, and indeed he invites others to test his claims. So far so good. But, when others don’t see what he sees, when they criticise his interpretations and his methods, he remains steadfast in his opinion that they’re wrong because they’re biased, because they’re refusing to use the same method that he does (read on), or because they can’t provide a superior hypothesis.” What Darren doesn’t seem to understand is not all critical comments are correct. Saying one is unconvinced is fine but it doesn’t move one toward solving problems. I haven’t moved in Darren’s direction because he hasn’t offered any solutions that work.

Steadfast? I don’t think so (maybe with Darren, but that’s his anecdote). Just today I was in contact with Dr. David Dilkes correcting the illustration of Mesosuchus. We went through several rounds and I don’t mind going through a few more either. It’s better now.

Darren doesn’t like pterosaurs close to lizards, but he refuses to test even one, so the onus is on him. I’ve tested dozens of archosaurs. And like the other detractors, Darren can’t provide the much needed series of taxa within the archosaurs that demonstrate a gradual accumulation of pterosaurian traits. I can with lizards.

Darren reports, “I’ve now corresponded with Dave on several occasions about the structures he reports to find. He seems very confident that he’s always right, yet I don’t think that he ever is.” Darren, “EVER” is such an inclusive word. This is not a judicious use of speech. Certainly not scientific. Today’s communication with Dr. Dilkes (see above) falsifies Darren’s contention.

The Core Problem: Digital Graphic Segregation
Darren tackled my tracing techniques by saying they are “rotten to the core,” perhaps not remembering that nearly all fossils are traced in order to more clearly identify the elements. He illustrates his contention with my tracing of the skull of Sharovipteryx, a reptile that preserves bones and soft tissue on a bed of matrix filled with various insects. In fact the allure of well-preserved insects first attracted entomologist A. Sharov to the area where he found this reptile. Darrens caption reads, “Just one example of Dave’s application of DGS. At top, the disarticulated skull as preserved. At bottom, the information that Dave think he has discovered via DGS (note the insect inside the mouth!!).” The skull of Sharovipteryx has never before been studied in such detail and no one has ventured to create a reconstruction despite a rather complete gathering of elements.  I have studied the specimen in person and retain an 8×10″ transparency that provides plenty of detail for further study. I gather from Darren’s rather neutral comments that he has no constructive or alternative criticisms to offer with regard to bone identification. He was most shocked by the presence of an insect inside the orbit, likely above the palate and therefore not in the mouth proper. A close look at the matrix reveals dozens of beetles and other insects all over the place, so to find one burrowed into the eye — or died their randomly — is not so unusual. I encourage Darren to be more critical of the interpretation if he thinks errors were made. If not, why is he complaining about someone trying to figure out a previously indecipherable problem? Or one that everyone else previously ignored?

Darren thinks many fossils worthy of DGS are “not the ‘high-resolution, high-fidelity’ objects that Dave assumes.” That’s unfortunate, but I also see his point. Some fossils are nothing to look at. Others are chaotic aftermaths and it does take serious effort over several days or weeks to pick apart the elements. Earlier I used every photo I could to tease out every object I could. I was educating myself. Certainly when higher resolution is available, more precision is the result, as in the case of the IVPP embryo. Even the raw tracings of this specimen are indecipherable until one applies color or tone to the individual elements. We know that that  embryo is a complete fossil because it’s still in its original package!! Once again, no one else attempted to get closer to this fossil to figure out what was really inside that egg, so I stepped forward. There’s no sin in that.

Darren reports, “I have no doubt whatsoever that, with literally one or two exceptions, every single element Dave is identifying via DGS can be explained in one of three ways. (1) It’s not a genuine anatomical structure or feature.  (2) Some of the big, ragged structures that Dave interprets as frills, dewlaps, wattles, pouches or crests might actually be sloughed patches of tissue that have broken away from the animal’s corpse during decomposition. Dave’s default assumption for such structures is that they can be interpreted as being preserved in the ‘in life’ position, but other options need to be considered first. Decomposition and fossilisation are messy. (3) In a few cases, Dave is seeing real bones, but interpreting them as something else. Broken, indeterminate rod-like elements that might be bits of ribs or gastralia, for example, become reconstructed as if we can be sure what their identity is.” Darn it Darren, this is where I need you to be specific! Your shots are not hitting specific taxa! Your comments would be more helpful if they were better directed. Darren illustrated his point by providing his illustration of a Campylognathoides that is not in So why is he again complaining about an image that is not in the website? In court this would be considered improper.

Darren reports, “Dave relies almost wholly on images from the published literature – he doesn’t look at actual fossils).” Unfortunately, Darren, this is lie. I’ve been to numerous museums here and abroad (Europe, China). I’ve peered down the microscope. I’ve done everything other paleontologists do. So why are you trying to damn me with such statements?

Langobardisaurus, etc. 
Darren remarks on one valid genuine discovery, the head and neck of Langobardisaurus, thanks to my method.  He considers this a “red herring” because you don’t need a special technique for seeing the head and neck. And he’s right. This was a case of the original worker overlooking what was pretty plain to see. Darren reports, “Compare this with the other fossils where Dave claims to make ‘discoveries’. They are not the same.” No, they never are. Some are easier and don’t require DGS, only a big family tree. Others are really easy. When Dr. Dino Frey found Muzquizopteryx he originally considered it a cycnorhamphid. I told him it was a nyctosaurid. Dr. David Hone had a model Rhamphorhynchus featured in his blog, but he identified it as a Dorygnathus. I steered him right without seeing the actual model. The model maker later confirmed my assessment. See I can be helpful!

It’s a Tidal Wave!
Darren reports, “Every single researcher who has expressed an opinion on this issue has said exactly the same thing, and you can see from discussions in chatrooms, message boards and blogs that interested amateurs, fanboys/girls and idly curious commenters tend to note that Dave’s views and DGS ‘discoveries’ are suspicious or obviously erroneous too. Chris Bennett published an excellent article on Dave’s methods and observations in which he pointed to specific case studies (Bennett 2005). That article is required reading for anyone interested in the Dave Peters issue.” Fortunately none of those pre-2004 images are in, so once again, Darren is mining rejects. This isn’t fair Darren. Please stick to your thesis. Please stick to elements one is likely to find in By the way, Chris Bennett is not immune to “seeing things” and making misinterpretations, all documented here with evidence.

Darren simply “rejects” my interpretation of prepubes in Cosesaurus. Well, that doesn’t make him right or me right. This is a presentation of evidence. It’s difficult to even see the pelvis in this specimen and when I first looked at Cosesaurus I overlooked the prepubes, so I understand Darren’s conviction. The only difference between then and now is time  –and attitude in my case. Perhaps time will change Darren’s outlook too. Prepubes are not the only evidence for this relationship. They are only two of dozens of traits restricted to this clade. And this is where the conversation needs to continue, because there really is a suite of traits here, just what paleontologists are looking for. You’ll note the prepubes in Cosesaurus are only about 2 mm in length. Not much, but it’s a start.

Darren reports, “I look at the images (or at a replica, or at the actual specimen) of Cosesaurus, for example, and I make my own decision about the structures that Dave is purporting to identify. I therefore have tested his hypothesis, and I’ve rejected it.” 

This is the first time I’ve heard that Darren has seen Cosesaurus. Or did he? Rejecting a hypothesis doesn’t make you right, by the way. I do it all the time and Darren doesn’t consider me right. Darren rejects virtually all of my results gleaned form DGS. He says, “Remember that this affects all of his work, since his character codings, and hence his phylogenetic hypotheses, are heavily dependent on information gleaned from DGS.” Actually not as true as Darren would have you believe. Many, if not most of the illustrations were made my others and scored as is. And I wish Darren would offer alternative interpretations for the things that really needed DGS to understand. That would put things on an even footing.

Next time: Data Sets and Tetrapod Zoology – part 5

Earlier we discussed in parts 1, 2, 3 and 4 the criticisms leveled at by Darren Naish, author of the Tetrapod Zoology blog titled “Why the world has to ignore Here is part 5.

Next Darren featured “An example of how good Dave’s diagrams are. This one – from The Pterosaur Heresies blog – shows how Kadimakara (known from a partial skull, shown at top left) compares to various other reptiles that Dave considers to be diadectomorphs and protorosaurs respectively.” Then he tosses in the hand grenade: “Remember that Dave’s grouping of the animals shown here as ‘diadectomorphs’ and ‘protorosaurs’ are likely not correct.” That’s it. No evidence. No reason. Just tossing out a statement. In like fashion, I should caution readers, remember, Darren has NOT spent years creating a reptile family tree, and no one else EVER has created a tree that includes this scope of taxa, but I have.

Darren’s remark reminds me of something I heard in an evangelical church one day: “Folks, there is no evidence for evolution.” Yeah, that’s pretty much where the pastor left it, just like Darren did. It’s so easy to toss out those hand grenades. That’s why and throws so much data, reason and illustration behind as many statements as possible, knowing that naysayers like Darren Naish are out there. If anyone needs further evidence or illustration, please let me know. I will provide it. If anyone has changes to suggest to the data, please let me know that also.

A Whole Lot of Heresy
Darren reported, “David Peters would have us believe that just about the whole ‘mainstream’, accepted structure of the tetrapod tree is wrong, and that he – uniquely – has discovered a wholly new, paradigm-busting one. According to Dave, (1) reptiles and all other amniotes can be placed along either a lizard branch, or a mammal-croc-bird branch; (2) pterosaurs are not archosaurs or even close, but deeply nested within lizards; (3) synapsids (the amniote clade that includes mammals) are on the croc-bird branch, close to (or part of) Archosauromorpha; and (4) Dinosauria does not consist of Ornithischia and Saurischia, but Theropoda and Phytodinosauria (and the latter clade includes several traditional non-dinosaurs, like Lotosaurus and silesaurids).”

Basically true. But #3 was earlier covered by #1. And I’m not asking anyone to believe this. This topology is what I recovered after entering tens of thousands of scores to a very large matrix of data that resulted in a completely, or virtually completely resolved tree. I’m asking for someone, anyone, to duplicate the taxon list, use whatever characters you need to (but they should number 150+ and describe traits from head to tail) and tell us all the results you recover. Priests and pastors ask you to believe. As a scientist, I ask you to test to see if we can replicate this. If not, let’s discuss the differences, like scientists. There’s little reason to brand something as “wrong” if the person doing the branding has never attempted to test the results on their own. Yet Darren feels he needs to do so to protect “the naive reader.”

With regard to the large reptile tree, Darren reports, “This tree cannot be considered reasonable based on other lines of evidence, nor has Dave compiled or analysed enough data to show that it is viable (see text).” How much is enough? This is the largest study scope ever attempted with regard to reptiles. How much MORE effort needs to be added? The current character list is sufficient to fully resolve the tree. All sisters share a large list of character traits in common. Will more data change the tree or cement relationships? So far adding over 100 taxa has only cemented relationships. It could be, given the evidence of the large reptile tree that Darren is wrong, at least in part and likely in whole with regard to his criticisms.

Darren reiterates the results of the large reptile tree, then reports, “If you’re not familiar with the generally accepted structure of the tetrapod family tree, it would take me a while to explain why these proposals are so heretical and contrary to other studies. Suffice it to say that they are odd indeed, totally discordant with the careful, detailed work that other workers have documented in the peer-reviewed literature.”

Yes, these results run counter to generally accepted trees! Traditional studies link Rhynchosaurs and Tanystropheids (falsely labeled protorosaurs) with Proterosuchus and these taxa could not be more different. Who can defend these misfits as sisters? Who can defend pterosaurs as archosaurs? Not Bennett (1996). Not anyone else either UNLESS they delete more parsimonious sisters reported by Peters (2000, 2007) and those featured in As you realize by now, that’s just cheating with a priori exclusion, kinda like baseball in the 1930s.

Now Here’s Something to Consider
Darren reports, The specific details of phylogenetic hypotheses – that is, the specific positions of species relative to one another – will, in many cases, always fluctuate between studies. But the general pattern of the tetrapod cladogram as a whole is universally agreed on: mammals are the sister-group to the turtle-lizard-croc-bird clade; lizards (and other lepidosaurs) are the sister-group to the croc-bird clade. This pattern has been consistently recovered in morphology-based analyses (e.g., Laurin & Reisz 1995, Müller 2003, Lee et al. 2004, Hill 2005) and is also overwhelmingly supported by molecular data (e.g., Hedges & Poling 1999, Janke et al. 2001, Rest et al. 2003, Shedlock et al. 2007, Lyson et al. 2011). Embryological, biochemical and behavioural data also shows, pretty much unanimously, that lizards form a clade with archosaurs while mammals are outside this lizard + archosaur group.”

Darren fails to report that no prior study includes the scope of the present large reptile tree based on the genus. Virtually all prior studies used suprageneric taxa. How do you score those ephemeral conglomerations of several morphologies?

Embryological data? Pterosaur eggshells are closer to lizard eggshells than to bird or croc eggshells. Biochemical and behavioral data, well no lizards, turtles, crocs or birds have hair and breasts. Is that what is meant here?

Extent of the Wing Membrane
After illustrating an example of my narrow chord wing membrane, which is supported by all known pterosaur specimens, Darren reports, “Based on my examination of fossil specimens, I am confident that the wing membranes DO contact the tibia (and extend as far as the ankles) in some and perhaps most or all pterosaurs.” The only examples Darren and other have produced with such a possibility have been dismissed here. Notably the UV specimen provided by Darren also shows the wing membrane trailing edge curling aft of the elbows with lateral tibia connection.  If other examples are known, please provide them. I want to see them. Confidence doesn’t cut it. Show examples.

Insect within the mouth?
Darren claims I discovered “prey items (like insects) preserved within the mouths of some animals.” Well yes and no. I did find an insect in the orbit of Sharovipteryx, but I never said it was ‘prey.’ There are dozens of insects in the matrix surrounding Sharovipteryx. One happens to be closer than the others and could have crawled in there while the carcass was rotting, or perhaps it was random.

Pterosaur Babies
Darren reports, “But Dave’s claim that numerous unossified baby pterosaurs are preserved alongside – or on or even in – the bodies of adult specimens is discordant with this, since their ‘presence’ led Dave to argue that pterosaurs were viviparous.” This old hypothesis was suggested before pterosaur eggs were discovered. It is not found in ReptileEvolution and therefore its presence in Darren’s diatribe against my website is misguided and inappropriate. I did suggest that the IVPP embryo was a miniature sort of pterosaur because it was an anurognathid (not an ornithocheirid as originally identified) AND it was the size of all other anurognathids. So the leap in logic is not so far-fetched. Further study revealed the fact that embryo pterosaurs were virtual copies of adults, so the embryo would have grown to be an anurognathid eight times larger than virtually all other known anurognathids. Again, the mistake is not found in ReptileEvolution, only in Darren’s files.

Tiny Pterosaurs
Darren reports, “Dave thinks that a number of small pterosaur specimens – interpreted by everyone else as juveniles of Pterodactylus and other taxa – are actually miniature adults. His interpretations are dependent on his digital tracing technique, and on the incorporation of the characters he finds via digital tracing into his phylogenetic analyses. Given that he interprets these tiny animals as adults, and given that he contends that growth in pterosaurs was isometric, he proposes that the babies of these miniature pterosaurs were less than 10 mm long. Yes, less than 10 mm long.”

Darren may not be aware that some birds (the Bee Hummingbird) and certain tiny Caribbean geckos can be incredibly tiny. Their hatchlings are similarly extremely incredibly tiny. As I’ve noted earlier, if the tiny pterosaurs are juveniles, which pterosaurs are they juveniles of? Indeed, when placed into phylogenetic analysis a series of pterosaur specimens  become smaller, then reverse this trend and become gradually larger. This tells us they are adults. Furthermore, we know from embryo pterosaurs that they are virtual copies of adults, only 8x smaller. So they do not experience the morphological changes that would be necessary to morph into some sort of different looking adult. This was found by studying the specimens. I’m looking forward to someone else to replicate my results with a similar study. I don’t create these results out of thin air. They come from phylogenetic analysis. No one else has employed tiny pterosaurs in their analyses, so this discovery went to the first person to do so.

Next part 6. and Tetrapod Zoology – part 4

In parts 1, 2 and 3 of this series of rebuttals we examined the first portions of the new Tetrapod Zoology blog headlined, “Why the World has to Ignore Here, in part 4, we’ll look at Darren Naish’s arguments against my interpretations of Longisquama and pterosaurs.

Perhaps the most elaborate reptile to ever walk this planet, Longisquama has perplexed paleontologists for decades, yet relatively few, other than Sharov (1970) and Peters (2000, 2002) have published skeletal tracings and reconstructions of this Triassic oddball. Darren republished my tracings of the Longisquama holotype, one for soft tissue and one for bones. These were originally traced at 600 dpi and quite large. Their reduction to web scale and screen is unfortunate, but unavoidable. Even so, the point was to map out where the elements could be found. They are difficult to see at any scale. Nothing is easy. All of the paired left and right elements were found twice, which should add to their credibility. The stomach area and hips are the most disarticulated. One hind limb is straightened out and has been traditionally mistaken for a displaced plume by all prior workers. So, its visible. The other limb is bent at about 170 degrees at the knee but oriented dorsally, so it was also camouflaged with the plumes. The feet were at the base of the plumes where Jones et al. (2000) reported subdivided feather shafts. These are actually unrecognized pedal phalanges. That’s why they appear subdivided. The tail parallels a plume and is likewise camouflaged by it.

There are no baby specimens in the slab. That was hopeful thinking in 2004 that did not make it into So Darren mentions yet another item plucked from my garbage bin that is NOT in the website he is telling everyone to ignore.

Darren often mentions the term “weird” in connection with Longisquama, not noting that the weirdest aspect of the reptile has been widely observed, studied and written about, the plumes. I only added hind limbs, a pelvis, tail and some elongated fingers that anticipate the long wings of pterosaurs. The long legs are found in sister taxa, Sharovipteryx and the basal pterosaur MPUM6009. The pectoral complex and stem-like coracoids go back to Cosesaurus.

Darren claims that I said Longisquama-like plumes were present in ALL pterosaurs. Well, I didn’t say that in, so once again, Darren has mined my wastebasket for crap. Darren, for some reason you keep warning people away from stuff that doesn’t appear in…except in one place… the most basal pterosaur, the one most like Longisquama, the one and only MPUM6009. And, of course, this is what sister taxa do: share character traits. Cosesaurus had a frill. Huehuecuetzpalli had a dorsal frill (homologous to that found in Sphenodon). Not sure why I can’t find one on Sharovipteryx. Shows, I suppose, how quickly such frills can appear and disappear.

Darren presents another artist’s vision of Pteranodon with frills like Longisquama. He reports, “The Dave Peters vision of Pteranodon, as reconstructed by Nemo Ramjet (Mehmet Kosemen) in 2008. I’m no longer entirely sure whether Dave still supports the idea that pterosaurs looked like this, but he argues for all of the features you see here in his published articles (e.g., Peters 2004). Dave doesn’t like illustrations such as this as he thinks people are lampooning or making a fool of him. Maybe that’s so, but the fact remains that the reconstruction shown here (and those elsewhere in this article) is accurately based – without embellishment – on a reconstruction that Dave has produced himself.” If so, once again, no such illustration or reconstruction appears in, so Darren is showing you spooks that aren’t even present in the website. And he thinks this is justified. (I’m just glad he hasn’t talked to my mother about all the bad things I did growing up.)

Stage 4, Phylogenetic Nesting
Darren next tackles the large reptile tree. He reports, “As noted above, the general thinking on this issue is that pterosaurs are archosaurs, closely related to dinosaurs and their kin, and forming with them the clade Ornithodira. A list of anatomical characters appears to support this position.” Darren does NOT report that this list is extremely short and that a much longer list of anatomical characters can be found elsewhere, in the Fenestrasauria.  Bennett (1996) commented that his list of pterosaur/archosaur traits included chiefly hind limb characters and that removal of those characters moved pterosaurs away from Scleromochlus and dinosaurs. This is a problem. In the real world, as demonstrated by any taxon, you can take away the skull or the limbs or anything in between and, for instance, pterosaurs (but it could be elephants), will not shift in the tree, but continue to nest with basal fenestrasaurs (or other elephants). That tells you pterosaurs are fenestrasaurs from head to toe. This also holds for all well-known reptiles. If they do shift they are most likely not nested correctly.

The Origin of Pterosaurs
Darren published a figure of mine showing a series of taxa from Cosesaurus to Austriadactylus and commented, “It looks good, but many of the details key to this hypothesis have been ‘discovered’ via Dave’s digital tracing technique and hence are not trustworthy or repeatable.” Then Darren, I suggest you discard those details, add some of your own and see what you get! That’s okay! Test to your own specs. Of course, I disagree with you on the possibility of repeatability of the details. That’s why I published all this data on so people could test and repeat my results. Once again, don’t dismiss the taxon list just because you dismiss the observer and his methods. Those fossils are still out there. Study them to your heart’s content. Do your own test. Tell us all what you find. Senter (2003) gave this a shot and, to my eye, bungled many character scores. See what you think.

The Return of the Thesis
Darren reports, “ is a huge problem, and those of us involved in research on tetrapod evolution need to somehow counteract its influence.”

The Helveticosaurus Problem
Darren posted two of my Helveticosaurus figures, one with a new skull. Helveticosaurus is known from a complete skeleton, but no one, other than myself, has attempted to do a reconstruction using all the elements. The earlier illustration was based on a long shot photo (not very distinct). The new skull was added when a closeup of the skull appeared on the web. Darren remarks, “Dave frequently revises his reconstructions. That’s ok, but I’m often left confused why the differences between revisions are so great – is this because his digital tracing technique is utterly unreliable?”  I would have to say, based on experience, that with higher resolution data, the technique becomes more reliable. Hence the improvements. However, in an effort to be all inclusive (as I can be) I grab data from every source I can. Sometimes that data is not so good. Other times: excellent.  Trying is traditionally good in Science. Even failing is usually not frowned upon.

Competing Analyses
Darren writes, “The high visibility of is exacerbated by the fact that Dave’s ‘competitors’ – those who publish the sort of big-scale, taxon-heavy analyses that contradict his own trees – either have no internet presence at all, or are not interested in putting images, diagrams and other representations of specimens online.” There are large analyses in the literature, but nothing comparable to the scope of the large reptile tree with its 300 reptiles from all over and every age. Trees that apparently contradict mine, like the recent Gauthier et al. (2012) tree, (which IS online here) are typically missing many key taxa or are much smaller and more focused in scope. My tree is focused on basal taxa from every large clade. Darren also overlooks the presence of Wikipedia, which generally toes the traditional line. Thus the competitors are indeed online, but none have the scope of the large reptile tree. Not yet.

More in part 5.

Jones TD et al 2000. Nonavian Feathers in a Late Triassic Archosaur. Science 288 (5474): 2202–2205. doi:10.1126/science.288.5474.2202. PMID 10864867.
Peters D 2000a. Description and Interpretation of Interphalangeal Lines in Tetrapods. Ichnos 7:11-41.
Peters D 2000b. A reexamination of four prolacertiforms with implications for pterosaur phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106: 293–336.
Peters D 2002. A New Model for the Evolution of the Pterosaur Wing – with a twist. Historical Biology 15: 277–301.
Peters D 2007. The origin and radiation of the Pterosauria. In D. Hone ed. Flugsaurier. The Wellnhofer pterosaur meeting, 2007, Munich, Germany. p. 27.
Peters D 2009. A reinterpretation of pteroid articulation in pterosaurs. Journal of Vertebrate Paleontology 29: 1327-1330
Senter P 2003. Taxon Sampling Artifacts and the Phylogenetic Position of Aves. PhD dissertation. Northern Illinois University, 1-279
Sharov AG 1970. A peculiar reptile from the lower Triassic of Fergana. Paleontologiceskij Zurnal (1): 127–130.
Sharov AG 1971. New flying reptiles from the Mesozoic of Kazakhstan and Kirghizia. – Transactions of the Paleontological Institute, Akademia Nauk, USSR, Moscow, 130: 104–113.
Unwin DM and Bakhurina NN 1994. Sordes pilosus and the nature of the pterosaur flight apparatus. Nature 371: 62-64. and Tetrapod Zoology – part 3

Earlier (here and here) I responded to the first parts of the Tetrapod Zoology criticism of Here is part 3, all about my run-ins with Sordes and Cosesaurus.

Figure 1. Sordes interpreted by me in Nature 1995. At that time. remember, no one had ever heard of a uropatagium, separate uroptagia, yes.  And the purported “fact” that this flap of skin spanned the hind limbs without connecting to the tail seemed pretty hard to swallow for a majority of paleontologists. The only images available were small and indistinct. Even so, an attempt was made here to understand the taphonomy of the specimen and how it came to sport such a strange autapomorphy that has not been seen since on any pterosaur fossil. Despite the sincerity of this effort, it includes several mistakes rectified now in  traced from a recent publication of the specimen in a larger format with higher resolution.

Darren Naish picks up with a 1995 criticism of my first published work, which happened to be in Nature, as I reconstructed Sordes pilosus prior to the apparent drifting of the elements (Fig. 1). Admittedly sophomoric. The work was crude and based on crappy photographs, but at its core was more or less correct. The left forelimb had drifted, as shown here in photographic detail. The wing membranes had a narrower chord than others had imagined. The myth of the purported “uropatagium” in Sordes is detailed here in and here.

Uropatagium of Sordes according to Sharov 1971 and Unwin/Bakhurina 1994.

Figure 2. Uropatagium of Sordes according to Sharov 1971 (above) and Unwin/Bakhurina 1994 (below). Color and captions added by me.

At left are the only two images of Sordes published before my Nature paper. Note the Unwin/Bakhurina (1994) image omits many of the details found in the earlier Sharov (1971) paper. So really, what was gained? Darren wrote of my Nature drawings (Fig. 1), “This is a speculation based entirely on examination of published photos. It cannot be considered anywhere near as reliable as Unwin & Bakhurina’s examination of the actual fossil.” Of course this is speculation. It’s an idea, an explanation for a weird phenomenon. Science permits such speculation because Science likes ideas. (How did the rings of Saturn form? Do continents really drift?) I still haven’t seen the Sordes specimen, but I have found in the specimen (here in overlooked bones that explain why the mass of wing membrane is where it shouldn’t be.

With regard to the uropatagium
All other pterosaurs (and fenestrasaurs) have twin uropatagia that span the area behind each knee, arcing to the pelvis and heel. So how does one explain the anomaly of a single uropagagium in Sordes? Now I think the material between the feet of Sordes includes unattached wing membranes carried there by disarticulated and drifted forearm elements as shown here. The paired uropatagia are smaller and less distinct, but still visibile here. If there is a better explanation out there, I’d like to see it. Remember, this is only an idea and Science likes ideas. As you can tell by the Unwin and Bakhurina (1994) drawing, attention to detail was not their strong point.

If you want reliability, don’t take my word for it. Don’t take their word for it. Take a look at the specimen yourself using all the published materials as your guides. Science is all about repeatability, not taking someone’s word for it, but testing it youself. Unwin and Bakhurina (1994) provided their interpretation. I provided another. Nothing to raise hackles about.

Cosesaurus and the Rivisita Italiana Paper
Darren reports he was initially impressed by my paper on pterosaur origins (Peters 2000b) noting that I had reconstructed elements of Longisquama and Sharovipteryx with more detail than prior workers (which means only Sharov’s (1970, 1971 short papers and small illustrations). With regard to Cosesaurus a great deal of detailed work was earlier provided Ellenberger (1978, 1991). All three of these specimens were examined personally and under the microscope — and even so, I made mistakes due to my lack of experience. Darren reports that despite his initial enthusiasm for the results, “[others] were far from enthusiastic; the overwhelming opinion being (1) that you just couldn’t see the things reported in that paper in real life (that is, the interpretations were in error), and (2) that the phylogenetic analyses included in the paper were completely erroneous, since they wholly relied on those problematic observations (in the paper.,”

In order to get that paper (and all my many others) published it had to pass peer review. And it passed. More to the point, you’ll note that once again critics are painting my work with the broadest of brushes, dismissing my direct observations (using established paleontological techniques) without providing alternative observations that could then be considered side-by-side for comparison. Here’s a fact that you can look up: Dr. Paul Ellenberger (1978, 1993) saw all of the items that I saw in Cosesaurus, only our interpretations differed, which I covered earlier here and here. He correctly identified the strap-like, bird-like scapula which I dismissed because I had the prolacertiform bias (since corrected here.) He correctly traced two wrist bones outside of the wrist, which I earlier ignored then later realized they were the pteroid and preaxial carpal. The list goes on (see more here). Oddly, no one has made a serious attempt at reconstructing the skeletons of the basal fenestrasaurs since my work in 2000, despite the importance and despite their dismissals (“step aside and let a REAL paleontologist look at that specimen!). Wonder why that is? Wouldn’t it be awful is someone actually confirmed our (Ellenberger and myself) observations? It would literally bring down the house.

Pterosaurs and Dinosaurs
Darren continues by reiterating traditional thinking, “other workers have continued to find support for a close affinity between pterosaurs and dinosaurs (e.g., Brusatte et al. 2010, Nesbitt 2011, Butler et al. 2011), and they’ve ignored the results and proposals of Peters (2000).” You’ll note in none of these papers do these workers test the fenestrasaurs in their matrices to see what would happen. They don’t even look at them. For some reason they are content to simply stay the course. Darren reports, “It’s because his [meaning my] observations, and hence his character codings and the trees that result from them, are regarded as wholly unreliable.” Fine! Then create your OWN observations and character codings! What’s wrong with that? There should no “trust” in Science as there is in Religion.  There should only be testing! No reliability! Only skepticism! In 2000 I simply suggested an alternative. It really is up to others to repeat the experiment, but so far others have refrained from doing so.

Darren continues, “Remember that the workers who produce the trees that support the ‘conventional’ view of pterosaur affinities have spent a lot of time looking at actual fossils.” As if I haven’t (see above). He continues, “Furthermore, these researchers have done an excellent job of explaining and documenting the characters they use in their phylogenies, and they have proven track records of showing that they understand how to reconstruct phylogeny and analyse phylogenetic data.” And that’s why they can’t explain how pterosaurs suddenly appeared in the fossil record without apparent antecedents. And that’s why they can’t explain why Vancleavea has no antorbital fenestra or mandibular fenestra despite claims that it is an archosauriform. Etc. etc.

Let’s also remember that in that landmark pair of papers by Hone and Benton (2007, 2009) they didn’t even look at the specimens in question and discarded two of them outright (Longisquama and Sharovipteryx) while only retaining a quarter of the characters for Cosesaurus. This is how the battle has been waged: ignore the specimens, attack the methods, dismiss the wise guy in St. Louis, don’t upset the status quo. It’s a sad state of affairs in paleontology if this is really what it has come to.

Hopefully someday Darren will reexamine Hone and Benton (2007, 2009) with the same vigor and find out why these two PhDs didn’t notice that their supertree could not nest Choristodera with the choristorderes Champsosaurus, Cteniogenys and Lazarusuchus. And it failed to nest Lepidosauromorpha with the lepidosaurs, Gephyrosaurus, Sphenodontia and Squamata and more errors detailed here. They found that Cosesaurus nested next to Proterosuchus, for instance. Crazy results slipping past everyone’s radar…

Next up: the Longisquama Controversy

Ellenberger P and de Villalta JF 1974. Sur la presence d’un ancêtre probable des oiseaux dans le Muschelkalk supérieure de Catalogne (Espagne). Note preliminaire. Acta Geologica Hispanica 9, 162-168.
Ellenberger P 1978. L’Origine des Oiseaux. Historique et méthodes nouvelles. Les problémes des Archaeornithes. La venue au jour de Cosesaurus aviceps (Muschelkalk supérieur) in Aspects Modernes des Recherches sur l’Evolution. In Bons, J. (ed.) Compt Ren. Coll. Montpellier12-16 Sept. 1977. Vol. 1. Montpellier, Mém. Trav. Ecole Prat. Hautes Etudes, De l’Institut de Montpellier 4: 89-117.
Ellenberger P 1993. Cosesaurus aviceps . Vertébré aviforme du Trias Moyen de Catalogne. Étude descriptive et comparative. Mémoire Avec le concours de l’École Pratique des Hautes Etudes. Laboratorie de Paléontologie des Vertébrés. Univ. Sci. Tech. Languedoc, Montpellier (France). Pp. 1-664.
Hone DWE and Benton MJ 2007. An evaluation of the phylogenetic relationships of the pterosaurs to the archosauromorph reptiles. Journal of Systematic Palaeontology 5:465-469. PDF online
Hone DWE and Benton MJ 2009. Contrasting supertree and total-evidence methods: the origin of the pterosaurs. In: Hone DWE, Buffetaut E, editors. Flugsaurier: pterosaur papers in honour of Peter Wellnhofer. Vol. 28. Munich: Zittel B. p. 35-60.
Peters D 2000a. Description and Interpretation of Interphalangeal Lines in Tetrapods. Ichnos 7:11-41.
Peters D 2000b. A reexamination of four prolacertiforms with implications for pterosaur phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106: 293–336.
Peters D 2002. A New Model for the Evolution of the Pterosaur Wing – with a twist. Historical Biology 15: 277–301.
Peters D 2007. The origin and radiation of the Pterosauria. In D. Hone ed. Flugsaurier. The Wellnhofer pterosaur meeting, 2007, Munich, Germany. p. 27.
Peters D 2009. A reinterpretation of pteroid articulation in pterosaurs. Journal of Vertebrate Paleontology 29: 1327-1330
Sharov AG 1970. A peculiar reptile from the lower Triassic of Fergana. Paleontologiceskij Zurnal (1): 127–130.
Sharov AG 1971. New flying reptiles from the Mesozoic of Kazakhstan and Kirghizia. – Transactions of the Paleontological Institute, Akademia Nauk, USSR, Moscow, 130: 104–113.
Unwin DM and Bakhurina NN 1994. Sordes pilosus and the nature of the pterosaur flight apparatus. Nature 371: 62-64.

Tetrapod Zoology