Why do we know that birds are living dinosaurs?

Abstract

The finding that birds are descendants of certain dinosaurs has been a scientific consensus for over 20 years. Only a very few experts, like the ornithologist Alan Feduccia, whose criticism we discuss in detail, still question it. In the publications of evolution deniers (that is, creationists of various stripes), such criticism is clearly overrepresented. However, unlike the scientists they cite, creationists do not primarily cast doubt on the membership of birds in particular archosaur taxa. Rather, they want to see evolutionary development as such questioned. They achieve this only by mixing the criticism of individual scientists with antiquated and factually incorrect ideas on evolution. In this review, we explain why birds' ancestry from Mesozoic dinosaurs is a scientifically well-established fact. Afterwards, we discuss popular objections against this thesis presented by creationists and by scientists like Alan Feduccia as well. We give reasons why their objections are not tenable from a scientific point of view.

Full text

1
Why do we know that birds are living dinosaurs?
Evaluation of reasoning in anti-evolutionist treatise
M
ARTIN
N
EUKAMM
&
A
NDREAS
B
EYER
Contents
 A. Introduction
 B. Why the descent of birds from dinosaurs is a well-established fact
 C. Discussion of popular objections by creationists
o C.1: Widespread convergences and conflicting phylogenetic trees
o C.2: Discontinuous, “chaotic” evolution in a zigzag course
o C.3: “Mismatched” mosaic forms instead of transitional forms
o C.4: Abrupt appearance of characters and the “waiting time problem”
o C.5: Evo-Devo solutions for bird evolution
o C.6: The irreducibly complex avian body plan
o C.7: Gliding versus flapping flight: another false dichotomy
o C.8: Open questions about the mechanisms of evolution
o C.9: Ghost lineages in the fossil record
o C.10: The “discrepancy” between stratigraphy and phylogeny
o C.11: Does D
OLLO
’s “law” argue against theropod ancestry?
o C.12: F
EDUCCIA
's typological classification of the species Scansoriopteryx
o C.13: On the convergence of feathery integuments in pterosaurs
o C.14: Were pterosaurs feathered?
o C.15: Did feathers evolve for flight?
 D. Summary
 E. Acknowledgement
 F. Literature
© AG EvoBio – Evolution in Biologie, Kultur und Gesellschaft 09/2023

2
A. Introduction
What is the evolutionary origin of birds? The 130-year-old controversy over which
archosaur group birds descended from has been over for about 25 years. Today, the
scientific consensus is that birds evolved from certain dinosaurs. Strictly speaking,
this formulation is not quite correct, because birds are actually highly evolved dino-
saurs. Taxonomists assign them to one of the many nested subgroups descending
from the last common ancestor of dinosaurs (Fig. 4).
Thus, birds are members of the dinosaur subgroup Theropoda (carnivorous bipeds),
of the theropod subgroup Coelurosauria (hollow-tailed lizards), and of the coeluro-
saur subgroup Maniraptora (“hand snatchers”). Today, only a very few dinosaur spe-
cialists and paleornithologists dispute this finding, and the few who do so seem to
have ideological rather than scientific reasons (cf. P
RUM
2003; S
MITH
et al. 2015;
R
AUHUT
&
F
OTH
2020).
It is also undisputed that the most exclusive feature of this highly evolved group of
dinosaurs, the pennaceous feather, did not appear suddenly. From an evolutionary
perspective, biologists predicted that proto-feathers, like keratinous skin appendages
derived from scales, originated among coelurosaurs or other proto-avian archosaurs
before the advent of flight (cf. M
ADERSON
1972; M
ARTIN
1983).
The knowledge that modern birds (crown group birds) differ from early theropods
only by graded similarities has always been a thorn in the side of religious evolution
deniers (creationists). It simply does not fit well into the mould of genealogically sepa-
rated lineages or “basic kinds” of life originated by supernatural acts of divine crea-
tion. Instead, graded similarities between seemingly fundamentally different groups of
animals fulfill a central expectation of the theory of evolution. Hence, it is no surprise
that since the discovery of the famous proto-bird Archaeopteryx, creationists have
been running up against the theropod affiliation of birds.
A biologically skilled creationist who has tackled bird evolution for decades is
Reinhard J
UNKER
, former managing director of the German evangelical organization
W
ORT
-
UND
-W
ISSEN
. In his writings, he presents numerous empirical findings, declar-
ing them “anomalies for evolution and indications for creation” (J
UNKER
2019, p. 66).
Most of his arguments are typical of anti-evolutionist reasoning and are prevalent
among US creationists as well.
In this paper, we elucidate some main lines of this kind of anti-evolutionist reasoning.
1
We
show that it draws its credibility from outdated or even clearly false ideas about evolution.
1
Many sources are originally in German; the authors translated all quotes from them without further mention.

3
B. Why the descent of birds from dinosaurs is a well-established fact
Recent studies suggest that pterosaurs, which are only distantly related to birds,
had feather-like structures on their skin. There is empirical evidence that these
could have been proto-feathers, which means pennaceous feathers evolved from
such structures in the ancestral lineage of birds. J
UNKER
(2022) remarks on this:
Beyond the evolutionary view that birds originated from dinosaurs, one would...
hardly come to the idea that those structures were 'feathers'... One can certainly
speak of a confusion of terms here. It arises from the fact that 'feathers' are ulti-
mately defined not primarily on the basis of morphological characteristics but on the
basis of presumed evolutionary relationships.
Among experts, however, these “evolutionary relationships” are not a conjecture but
rather a corroborated and empirically well-established theory. Why is that? Already
around 1870, a few years after the discovery of Archaeopteryx, Thomas H. H
UXLEY
hypothesized that birds and theropods were closely related (P
ADIAN
&
C
HIAPPE
1998).
In fact, the skeleton of Archaeopteryx is so strikingly similar to that of the predatory di-
nosaur Compsognathus that two apparently featherless specimens of the proto-bird
were mistaken for this non-avian theropod for decades (S
HIPMAN
1999, pp. 43 ff.).
H
UXLEY
’s hypothesis was temporarily sidelined, mainly due to an influential book by
Dutch paleontologist Gerhard H
EILMANN
. He argued that theropods seem to lack
clavicles, which in birds are fused to form a furcula (“wishbone”), and could therefore
not possibly be the ancestors of birds (H
EILMANN
1926). Today, however, we know
that most theropods indeed possessed clavicles that had already been fused into
wishbones (R
AUHUT
et al. 2020). In the 1970s, H
UXLEY
’s hypothesis experienced a
renaissance when the paleontologist John O
STROM
showed that birds share more
features with theropods than with any other archosaurian group (O
STROM
1976).
O
STROM
’s conclusion that birds must have descended from small theropod dinosaurs
met with more and more acceptance as phylogenetic systematics (cladistics) became
the gold standard of comparative biology.
2
The goal of cladistics is to classify organisms
into hierarchically nested groups (called taxa, singular: taxon) defined exclusively by
evolutionary novelties (derived traits or apomorphies). With maximum objectivity, hierar-
chical systems of natural classes are established and displayed as branched diagrams
(cladograms). Cladograms, which we can transform into phylogenetic trees (phylogenies
or evolutionary trees), reveal the common ancestry of species.
2
F
EDUCCIA
(2013) is one of the few in his guild to dispute the evidential value of morphological cladistics. He
suggests that the respective homology assumptions are not justified due to questionable trait weightings, that
the taxon samples are too small, etc. However, S
MITH
et al. (2015) show that cladistics is well founded and uses
additional knowledge from almost all biological disciplines to assess plausibility. Many independent findings from
disciplines such as paleontology, physiology, histology, developmental biology, and behavioral biology fit into the
picture of theropod ancestry. The authors also show that F
EDUCCIA
himself is not consistent. He is biased by
accepting a few data sets and controversial studies that allegedly support his alternative ancestry thesis.

4
G
AUTHIER
(1986) described 84 synapomorphies (shared derived characters) of Sau-
rischian dinosaurs (which also include theropods and birds) and fully confirmed O
S-
TROM
’s inference. Employing cladistics methods, he showed that birds belong to
Maniraptora, these to Coelurosauria, and the latter to Theropoda. The data support-
ing this analysis increased considerably until today, as did the knowledge of the suc-
cessive acquisition of avian traits (cf. B
RUSATTE
et al. 2015; S
MITH
et al. 2015; C
AU
2018; R
AUHUT
&
F
OTH
2020). This includes morphological as well as molecular se-
quence-based data, studies of nesting behavior, histological data, etc.
As remarked above, in the 1970s and 1980s, biologists predicted the existence of (proto)
feathers in non-avian dinosaurs because birds are related to theropods. However, they
found not even one. Hence, the discovery of feathery filaments in Sinosauropteryx in
1996 and pennaceous feathers in Caudipteryx in 1998 created a sensation. Since then,
scientists have found numerous other feathered non-avian dinosaurs in China.
The morphological gap between filaments and pennaceous feathers was still quite
large at the time.
Thus, Richard P
RUM
(1999) predicted a series of evolutionary inter-
mediate feather forms on the basis of embryological differentiation processes in
birds. If the theropod hypothesis is correct, then certain feather stages, which birds
transiently pass through in their ontogeny, should have existed as mature feather
types in adult dinosaurs (Fig. 1).
Fig. 1. Steps in the evolution of pennaceous feathers according to P
RUM
(1999). Stage 1 proposes an un-
branched, hollow filament that develops from a cylindrical invagination of the epidermis around a papilla. The
feather emerges at the base of the follicle through the continuous division of keratin-forming cells. The growth
zone forms a follicle collar, from which the cells push out. Stage 2 involves the differentiation of the follicle collar
into barb ridges; a tuft of unbranched filaments emerges. Stage 3a represents the formation of a central rachis
(shaft) via fusion of barbs and the development of a planar feather with unbranched barbs. Stage 3b displays
the development of barbules that branch from the tufts of barbs; this corresponds morphologically to a downy
feather. In stage 3a+b, the features of stages 3a and 3b combine to produce a planar feather with a central
rachis, secondary branched barbs (barbules stem from the barbs), and an open vane. In stage 4, the barbules
differentiate into hooklets and bow barbules, generating a closed pennaceous vane. Finally, in stage 5, lateral
displacement of the new barb locus by differential new barb ridge addition to each side of the follicle leads to the
growth of a closed pennaceous feather with an asymmetrical vane resembling modern remiges. Drawing by
James Paul B
AELLO
, compiled from S
UES
(2001), P
RUM
&
B
RUSH
(2003), and P
ERRICHOT
et al. (2008).

5
The rest, as they say, is history. Gradually, all of the feather subtypes predicted from
P
RUM
's ontogenetic model have so far been discovered in theropod skeletons or in
amber (Figs. 2 and 3). Another intermediate form, not explicitly predicted, even me-
diates between stages 2 and 3a (Fig. 3).
Fig. 2. Fossil feathers in amber. The morphology of the specimen on the left is consistent with stage 3b of P
RUM
’s
widely accepted model (from R
OY
et al. 2020). The center photo shows a stage 3a feather (from C
ARROLL
et al. 2019).
Right: stage 3a+b feather (from M
C
K
ELLAR
2011; www.tinyurl.com/8h5edctm). Images licensed under CC BY-NC 4.0.
Fig. 3. Left: another intermediate form of the feather preserved in amber. Here, several branches are loosely
connected to the shaft, which consists of secondary branches that are still incompletely fused. The flattened,
bilaterally symmetrical form of modern feathers is already indicated. This stage lies between steps 2 and 3a in
P
RUM
’s model. By P
ERRICHOT
et al. (2008, p. 1200). Right: feather types associated with theropod skeletons. Own
sketch, redrawn and modified from X
U
et al. (2010, p. 1340). Drawing on the left by James Paul B
AELLO
.
Thus, among experts, for the last 20 years, there has been no real controversy over the
insight that birds have dinosaur ancestors. There is no way around this fact, at least if one
accepts today's scientific rationality standards (cf. P
RUM
2003; H
AVSTAD
&
S
MITH
2019).
In short: The predicted feather shapes deduced from the differentiation processes
of embryonic feather development are more than mere constructs. They existed!
Obviously, feather follicles such as those existing in the Middle Jurassic carried the
evolutionary capabilities for the development of modern feathers (R
OY
et al. 2020).

6
As P
ADIAN
&
H
ORNER
(2002, p. 120) put it:
Opponents to the cladistic view rely on other kinds of knowledge. The theropod dino-
saurs in question were too large, too late in time, could not climb trees, lacked postu-
lated ‘key features,’ could not pass through an allegedly necessary gliding phase, or
were physiologically incapable of performing birdlike functions… These are all propo-
sitions that have been answered on their own terms, whether functional, strati-
graphic, or metabolic… but the important point is that none was based on any evi-
dence of relationship, so they do not really test the question of bird origins. No alter-
native hypothesis has withstood cladistic testing; and, in fact, there have not been
any specific alternative hypotheses for >20 years. No other method of phylogenetic
analysis has been proposed and argued to supplant cladistics, which is why the field,
as a whole, remains unconvinced by these objections.
Fig. 4. Phylogenetic tree of Pan-Aves (Avemetatarsalia). This taxon (or clade) includes modern birds (Aves, top
left), birds in a broader sense (basal Avialae), non-avian dinosaurs, pterosaurs, and other basal archosaurs more
closely related to birds than to crocodilians. Modern birds differ from the stem species of Pan-Aves located at the
base of this tree (lower right) by about 1500 morphological changes (derived traits). These acquisitions emerged
successively within the ancestral lineage leading to modern birds over the last 250 million years. As expected, the
groups are hierarchically nested. Thus, Dinosauria include Theropoda, Theropoda include Tetanurae, and Teta-
nurae include Coelurosauria. Maniraptora, in turn, is a subgroup of Coelurosauria. Pennaraptora is a subgroup of
Maniraptora, and so on. Thereby, every node in this phylogenetic tree is a lineage-splitting event. The hierarchical
system and the graded similarity of species contained in it are the strongest evidence for the evolution and de-
scent of birds from early dinosaurs. Illustration by James Paul B
AELLO
, according to C
AU
(2018, p. 9). For the high-
resolution image, see: https://www.ag-evolutionsbiologie.net/bilder/kladogramm-pan-aves.jpg.

7
C. Discussion of popular objections by creationists
C.1: Widespread convergences and conflicting phylogenetic trees
It is hard to argue against the overwhelming phylogenetic evidence discussed above.
Hence, creationists often focus on alleged “anomalies” that do not fit into their flawed
version of evolutionary theory. To this end, J
UNKER
(2019) primarily focuses on the so-
called “convergence problem.” 93 times he points out that, from an evolutionary point
of view, a huge number of bird characters that also occur in non-avian theropods must
have arisen convergently (independently, many times) in different lineages:
Evolutionary convergences must be assumed more or less often for almost all of the
characters examined because of their mosaic-like distributions. (p. 4)
Depending on the characters considered for tree construction, this would lead to differ-
ent and mismatched phylogenetic trees. Cladists call such conflicting trees “incongru-
ent.” In short, incongruent trees are due to “contradictory combinations of characters” in
different species. According to J
UNKER
(2019), this means “that their graphical represen-
tation is more easily possible in a net-like form than in a tree-like form” (p. 53). In his
view, such findings “fit better into a creation model” than into an evolutionary model.
Indeed, evolutionary convergences and conflicting trees are quite common. However,
creationists ignore several elementary facts of evolutionary and developmental biol-
ogy, invalidating J
UNKER
's conclusion cited above:
 They ignore “… the fact that most analyses of morphology and molecules pro-
duce congruent results” (S
MITH
et al. 2015, p. 473). Despite widespread con-
vergences and uncertainty about the position of some taxa in the phylogenetic
tree, “…there is a remarkable consensus on the backbone structure of the
family tree of the ancestors of birds and the relative hierarchical placement of
almost all major clades that constitute this tree” (R
AUHUT
& F
OTH
2020, p. 37).
In short, birds are and remain deeply nested inside Theropoda on the basis of
their specific (shared derived) characters.
 There are observable population-genetic mechanisms explaining incongruences
(cf. P
FENNINGER
2016, p. 29). One such mechanism is hybrid speciation.
3
Re-
stricted gene flow is often still possible for a longer period between species that
split up. Depending on the genes considered, different phylogenetic trees will re-
sult. Another mechanism is “incomplete lineage sorting,” described in Fig. 5.
3
One example: a lineage of cottids (Cottus) observed in the Rhine for a few decades originates from the blending
of two different parent species. Meanwhile, the parent species no longer reproduces with either daughter species
(N
OLTE
et al. 2005). There is also evidence that hybrid speciation plays an important role in bird evolution (B
RELS-
FORD
2011; O
TTENBURGHS
2018).

8
 Some characters preferentially evolve convergently for developmental-genetic
reasons (L
UO
et al. 2007; S
HUBIN
et al. 2009; M
C
G
HEE
2011; H
ALL
2012; N
A-
RAMOTO
et al. 2019). For example, modified expression of genes encoding
growth factors has enabled the convergent evolution of lobed feet in waterfowl
(cf. Fig. 6; T
OKITA
et al. 2020). Convergences occur more frequently the more
species are genetically similar. This phenomenon is based on development
constraints. For instance, ancient homologous regulatory genes can independ-
ently be switched on and off many times in evolution to produce convergent
traits: “The same forms have been produced by the repeated channeling of evo-
lution along the same developmental trajectory” (M
C
G
HEE
2011, p. 7).
Thus, while some cases of convergence are due to the similar response of similar ge-
nomes to similar selection (= parallelism), others can be attributed to the loss or rever-
sal of traits in related species. Especially the reduction of characters, such as the de-
generation of the furcula to separate clavicles in flightless birds, is easily accom-
plished, e.g., by loss-of-function mutations. Reversions, i.e., the renewed emergence
of phylogenetically older character states, are not difficult to explain if the developmen-
tal potential for the given trait is still present (atavisms are an example of reversions).
Sometimes this requires only the reactivation of an old pathway (M
C
G
HEE
2011, p. 7),
usually by a mutation. L
UO
et al. (2007, p. 292) explain this principle using the example
of multiple independent origins of lumbar ribs in some Mesozoic mammals. Of course,
old pathways can be reactivated only if the genes involved have been preserved by
selection, presumably by being involved in other pathways that were not suppressed.
Fig. 5. Example of incomplete lineage sorting. Two speciation events
are shown: first, an ancestral species splits into two species, and later,
once again, into sister species B and C. Consider the phylogenetic
trajectories of the gene G, which originally occurred in a single genomic
copy. Therefore, the common ancestor of A, B, and C initially pos-
sessed only allele G
0
. At some point, a duplication event occurred
(symbolized by the green dot), and in the ancestral population, the copy
G
1
became fixed, and afterwards, both versions evolved independently
from each other, accumulating numerous mutations. Imagine that G
0
was lost in the lineage of A, whereas the ancestors of B and C retained
both copies. After B and C diverged, only G
1
prevailed in B, and only G
0
prevailed in C. Because of the co-occurrence of G
1
in species A and B,
one might now think that they are sister species, although they are not.
This disturbing effect is even stronger when paralogues (generated by
gene duplication) arise and, much later, each linage loses a different
representative. We are dealing with an incongruence that does not
reflect the actual relationships. Own drawing.
Two things follow from all this. First, for the plausibility of the descent of birds from non-
avian dinosaurs, it is irrelevant that several characters arose convergently. For this
reason, individual traits are never particularly meaningful; the multitude of graded simi-
larities corroborating birds' deep hierarchical nesting within Theropoda is crucial.

9
In order to create the impression of “strongly interconnected or even chaotic character
distributions” (J
UNKER
2019, p. 65), a crucial statistical aspect is ignored: even for a small
number of considered organisms, the total number of possible trees is extremely large.
For instance, if we consider 11 taxa, there are already 34 million possible unrouted trees
(P
ENNY
et al. 1982). Thus, the probability of ending up with two similar trees by chance
via two independent methods, or different sets of characters, is extremely small. More-
over, even “incongruent trees” mostly show a very similar hierarchical placement of their
major clades and mismatch only by some branches. To quote T
HEOBALD
(2013):
In general, phylogenetic trees may be very incongruent and still match with an ex-
tremely high degree of statistical significance… The stunning degree of match be-
tween even the most incongruent phylogenetic trees found in the biological literature
is widely unappreciated, mainly because most people (including many biologists) are
unaware of the mathematics involved.
In other words, if the characters of different species were chaotically distributed or
even “freely combined (by creation)” as creationists often claim, it would be extremely
unlikely to calculate even similar trees. We would have to deal with up to 34 million
different trees for 10 taxa, depending on the characters we use as input. In fact,
though, at worst, we end up with a few dozen alternate trees that are broadly consis-
tent and share a very similar backbone structure. As P
ENNY
&
H
ENDY
(1986, p. 414)
calculate, this corresponds to a measurement accuracy of 99.9999%! This is a very
strong phylogenetic signal indeed.
Fig. 6. Comparison of different stages of embryonic
foot development in waterfowl. Altered expression of
genes encoding certain growth factors explains con-
vergent evolution of lobed feet in water birds such as
the common coot (F) and little grebe (C). Single muta-
tions are often sufficient for this. Such a mutation in a
BMP receptor can also initiate the convergent devel-
opment of duck-like webbed feet, for instance, in the
great cormorant (D). Source: T
OKITA
et al. (2020).
Image licensed under CC BY 4.0.
Second, considering developmental biology background knowledge, common conver-
gences are not anomalies but rather an explicit expectation of evolutionary theory.
Cladists must judge, on a case-by-case basis, how plausible convergence is. This re-
mains uncertain without appropriate knowledge of developmental biology. However,
the blanket assertion that widespread convergences speak against evolution is wrong.
On the contrary, the scientific community has known for decades that
...if you are studying a closely knit group such as Hominidae you can never ignore it
[convergence], because the more similar a pair of species is genetically, the more likely
the same detailed morphology is to arise in parallel. (T
ATTERSALL
1995, pp. 167–168)

10
C.2: Non-continuous, “chaotic” evolution in a zigzag course
Linked to the “convergence objection” is the anachronistic idea that evolution must
proceed both linearly and continuously. Accordingly, regarding the flight ability of
birds, J
UNKER
(2019) emphasizes that such a “linear, stepwise mode of develop-
ment”—to be expected from an evolutionary point of view—is not observed (p. 9).
4
Rather, development has been “chaotic.” Regarding some traits, “problematic re-
versions” (p. 48) must be postulated, or
...in terms of evolutionary theory, a degeneration [reduction] or some kind of evolu-
tionary zigzag course, as in the case of the shoulder girdle, must be assumed, which
is generally considered implausible. (J
UNKER
2019, p. 62)
Apparently, only rectilinear, unidirectional changes in single, non-branching lineages
(anagenetic trends) are considered for evolutionary development. However, lineage-
splitting events (cladogenesis) give rise to different lines of development. Subse-
quently, quite separate evolutionary dynamics that unfold convey the image of a
nonlinear and chaotic zigzag course among lineages (see, e.g., M
AC
F
ADDEN
2005).
The very insistence on “continuous changes” (J
UNKER
2019, p. 40) reflects obsolete
ideas concerning evolution and speciation. First, developmental constraints often
cause discontinuous variations (M
AYNARD
S
MITH
1983). For instance, continuous
variation of ontogenetic parameters (e.g., morphogen gradients or biomechanical
forces effecting tissue interactions) can produce discontinuous changes in pheno-
typic traits or, in some cases, even large-scale effects, especially when threshold
values are exceeded (P
ETERSON
&
M
ÜLLER
2016).
Second, continuous changes are not to be expected, because of the “spatial and
temporal heterogeneity of the environment with its limited resources, which requires
ecological segregation to avoid competition” (M
AHNER
1986, p. 68). As populations
establish themselves in different adaptive zones, their traits evolve at different
rates—and often in different directions (F
UTUYMA
2015).
4
J
UNKER
quotes B
RUSATTE
(2017) to show that “the development of flight was chaotic” (p. 792). However, no-
where in B
RUSATTE
's paper is there any mention of the need for “linear, stepwise” evolution. On the contrary, B
RU-
SATTE
refutes the view that theropods developed—or even needed—feathers and wing profiles specifically de-
signed for flight. Instead, numerous lineages existed that possessed various potential makeshift solutions, such
as skin flaps, stiffened coverts, and membranous wings to provide semi-stable wings. For example, the wings and
feathers of Anchiornis were anything but tailor-made for flight (P
ITTMAN
et al. 2022a). Nevertheless, those skin
membranes' “bridge construction” at least allowed for a gliding or weak flapping flight.
On the other hand,
the genus Yi, superficially resembling a bat and solely equipped with a skin membrane be-
tween the fingers, only barely managed even gliding flight. The center of gravity was far behind the gliding
membranes, so its flight was probably very unstable (D
ECECCHI
et al. 2020).
J
UNKER
's assumption that such a chaotic developmental path, in which “dinosaurs experimented with different
ways of flying” (B
RUSATTE
2017, p. 792) speaks against evolution, is a poor straw man argument, born from the
obsolete view that evolution must proceed linearly. The fact that J
UNKER
adds B
RUSATTE
's metaphor of an “ex-
perimental field” as an argument for “creation,” although a chaos of different forms with many dead ends (such
as Yi) fits perfectly into a non-intended natural process, is just the icing on the cake.

11
A well-studied example concerns the evolution of the horse and the splitting of its an-
cestral lineages in the Cenozoic (Fig. 7). As early as the 1950s, evolutionary biologist
George Gaylord S
IMPSON
demonstrated that the phylogenetic tree of the horse does
not reveal a simple, unilinear course of evolution (S
IMPSON
1951). Instead, it has many
side branches that have become extinct.
5
Several complex lineage-splitting events oc-
curred in horse evolution as some of the leaf-browsing genera evolved into grazers.
Multiple lineages established themselves in each adaptive zone. While some grazers
already had well-developed hooves, others retained their toes. Teeth, toes, and body
size evolved at different tempos and modes, with high-rate variability among lineages
depending on climate, vegetation, selection, and random genomic variations (M
AC
F
AD-
DEN
2005; M
IHLBACHLER
et al. 2011). For more than 70 years, this “chaotic” evolution has
been fully consistent with our knowledge of speciation processes. Behind this evolution-
ary zigzag course, a clear trend is recognizable only over many millions of years.
Fig. 7. Left: a simplified (linear) diagram emphasizing an anagenetic trend in horse evolution. Right diagram: how
evolution proceeded considering lineage-splitting events. In the late Oligocene and Miocene, the branchings were so
numerous that we cannot depict all of them. A trend toward increasing body size and reducing toes is visible only over
very long periods and numerous lineages. Silhouettes of the horses: Scott H
ARTMAN
(Hyracotherium), T. Michael
K
EESEY
(Mesohippus), Andrew F
ARKE
(Merychippus), Julián B
AYONA
(Pliohippus), and Mercedes Y
RAYZOZ
(Equus).
Source: www.phylopic.org | License: CC BY 4.0. Based on a template from
www.sofatutor.com/biologie/videos/stammbaum-der-pferde. Courtesy of S. K
IEFER
. Phylogeny of horses according to
M
IHLBACHLER
et al. (2011), own sketch.
To sum up, morphological evolution is most commonly gradual but non-continuous,
episodic, and fluctuating in direction. Most notably, evolution proceeds on multiple
tracks due to numerous lineage-splitting events causing multiple lines of develop-
ment in parallel. To put it another way, contrary to creationists’ premise, examples of
unilinear phylogenetic paths are very rare. We can trace back phylogeny
…to a last common ancestor by a labyrinthine route, but no paths are straight, and all
lead back by sidestepping from one event of branching speciation to another, and not
by descent down a ladder of continuous change. (G
OULD
2011, p. 67)
5
Note that “side branches” are apparent only in retrospect. The side branches in horses' evolution are the ones
that did not lead to the extant horse (Equus).

12
C.3: “Mismatched” mosaic forms instead of transitional forms
Creationist arguments frequently contain antiquated ideas about the nature of evolu-
tionary transitional forms. For instance, J
UNKER
(2019) quotes many examples in or-
der to show that “the mosaic of features” of the fossil in question is such that it does
not fit as an evolutionary transitional form but must represent an evolutionary lineage
of its own (p. 63). For instance, the bird-like theropod Rahonavis (Fig. 8) was
...more 'primitive' than Archaeopteryx with respect to some features but distinctly more
birdlike with respect to others, thus not suitable as a transitional form. (p. 55)
Fig. 8. Depiction of Rahonavis (left) and Archaeopteryx (right). On the one hand, Rahonavis still has features of
dromaeosaurids (Fig. 4) that proto-birds lack, such as the sickle claw on the second toe. On the other hand, in
some features, it already corresponds more to the anatomy of today's birds than the proto-bird Archaeopteryx. For
example, the shoulder girdle was already quite flexible, in contrast to the fused, rigid shoulder girdle of Archaeop-
teryx. This feature, adapted to active flight, may have evolved in birds convergently. Thus, both mosaic forms
possessed different “transitional characters” “on the way” to the birds. This shows that evolution did not proceed
harmoniously along one single track for birds. Lineage-splitting events cause characters to evolve at different rates
in each organism and in each lineage (heterobathmy). Left graph: artwork by James Paul B
AELLO
, all rights re-
served. Right graphic: Author: DBCLS | Source: www.doi.org/10.7875/togopic.2020.192 | License: CC BY 4.0.
Lineage-splitting events, followed by disparate further development, contribute to the
evolution of such different mosaics of “primitive” and “advanced” characters. This
finding is by no means new. For instance, even M
AYR
(1967, p. 465 f.) says:
When migrating into another adaptive zone, a structure or a structural complex is under
particularly strict selection pressure... As a result, this structure or complex evolves par-
ticularly fast, while others are left behind. The result is not a steady and harmonious
change of all parts of the 'type', as idealistic biology imagines, but far more of a mosaic
evolution. Each evolutionary type is a mosaic of primitive and advanced features, of
general and specialized traits. (Emphasis added)
The fact that in Archaeopteryx some traits remained more “primitive” than in Raho-
navis, while others were more advanced, is not surprising against this background:
the occupation of different ecological zones is accompanied by different ways of life.
As a result, different selection pressures can act on the same traits in two related
species. For instance, Rahonavis was an agile predator of the air with adaptations to

13
sustained flapping flight (P
ITTMAN
et al. 2022b). Archaeopteryx was rather a glider
with lower flapping flight potential (L
ONGRICH
et al. 2012; K
SEPKA
2022), whose life
took place more on the ground (E
LŻANOWSKI
2002). In turn, the more primitive feature
of the sickle claw accommodated the lifestyle of dromaeosaurids (F
RASER
2014).
Consequently, Rahonavis preserved the sickle claw.
Moreover, mosaic evolution is often the result of developmental constraints or func-
tional and genetic burdens that have their roots in the hierarchical, modular organiza-
tion of traits in organisms (cf. R
IEDL
2003, p. 209; F
ELICE
&
G
OSWAMI
2018).
6
Claiming
that “mosaic evolution” is a “foreign body in an evolutionary scenario” (e.g., J
UNKER
2019, p. 65) clearly shows a lack of knowledge of elementary principles of evolution-
ary biology in creationist criticism.
Given that the mode of phylogenetic development is usually mosaic evolution, what
do transitional forms look like? Early anthropologists anticipated discovering fossils of
human progenitors, whose features were transforming steadily into those of current
humans (P
ROTHERO
2017, p. 135). However, due to the mosaic mode of evolution,
linages retain “primitive” features while developing “advanced” traits in parallel. The
branching (speciation) process of founding independent taxa further complicates the
picture. Hence, this classical expectation of the nature of transitional forms is not
tenable any more (P
ROTHERO
2017, ibid.).
For that reason,
P
ADIAN
&
A
NGIELCZYK
(1999) recommend shifting the focus from
transitional forms to transitional features. However, the concept of transitional forms
is still fruitful within the realm of cladistics if the term “transitional form” experiences a
semantic shift: from a cladistic point of view, transitional forms toward birds represent
extinct mosaic forms exhibiting some derived characters of crown group birds (avian
synapomorphies), but not yet all of them. Additionally, those fossils still possess
some ancient characters that crown group birds lack. This is the modern meaning of
the term transitional form (Fig. 9).
6
In general, the phylogenetically older a biological trait or system is, the more other features rest upon its functionality
and the slower it evolves. We can say that it is highly burdened. Therefore, it hardly evolves any more.
In short: Different biological characters (or the same character at different peri-
ods of time) evolve at various rates both within and between species, a phe-
nomenon called mosaic evolution (C
ARROLL
1997). Here, evolution varies from
stasis to “rapid” change, depending on the selection pressures the traits are ex-
posed to in different ecological niches, under different environmental conditions,
and under different behaviors.

14
Fig. 9. Simplified cladogram of Pennaraptora, that is, the theropod clade including living birds (crown group birds). All
species depicted here (and many more not shown here, which may have been direct or indirect ancestors) embody
the ancestral lineage of birds. This implies they already possessed some (but not all) of the derived traits of crown
group birds while still possessing quite a few non-avian theropod characteristics that living birds lack. This is exactly
what is to be expected from a transitional form from a cladistic perspective. Their position in the cladogram tells us the
sequence of origination of derived features in living birds. Own sketch, modified from P
ITTMAN
&
X
U
(2020).
Quite pointless is the attempt to dismantle the status of transitional forms by pointing
out that they represent a side branch:
All in all, this mosaic form with very primitive and highly derived characters can only
find a place in the phylogenetic tree of birds if it is placed on a blind-ending side
branch and significant convergences are assumed. (J
UNKER
2019, p. 55)
Creationists often argue that many fossils exhibit progressive specialization of traits
or unique distinctive characters (autapomorphies), ruling them out as direct ancestors
of extant species. However, it is naive to demand that transitional forms can be
strung like pearls on a necklace in procession from ancestor to descendant in a recti-
linear ladder of change. Such thinking is “simplistic and inaccurate, reminiscent of the
pre-evolutionary concepts of the ‘Great Chain of Being’ or scala naturae” (P
ADIAN
&
A
NGIELCZYK
1999, p. 56).
On the one hand, evolution is a branching process with a great number of dead-end
branches. At least 99% of all species that have ever lived eventually became extinct
(T
AYLOR
2004, p. 1). Thus, fossils usually represent “dead-end” side branches, ex-
cept for those few that directly lead to a crown group. However, even if we found a
direct ancestor, there is no way to determine precisely how close it is to the branch-
ing point due to the incompleteness of the fossil record (P
ADIAN
&
A
NGIELCZYK
1999).
Thus, we must redefine the archaic meaning of the “transitional form”—a point that
creationist arguments usually miss:

15
Tree-thinking shifts the focus from looking for fossils of lineal (direct) ancestors to looking
for synapomorphies that link collateral (side-branch) ancestors. (M
EAD
2009, p. 311)
Character Anchiornis Archaeopteryx Jeholornis Confuciusornis Ichthyornis
Crown group
birds
(Neornithes)
Gastralia
+ + + + + -
Paired temporal
windows
(diapsid skull)
+ - + + - -
Sternal keel
(Carina)
- - - - + + +
Wing claws
+ + + + - - -
Pygostyle
- - - + + +
Horn beak
- - - + + +
Toothed jaw
+ + + - - + -
Elongate, strut-
like coracoid
- - + + + +
Fused
metacarpals
- - + + + +
Ossified breast-
bone (sternum)
- - + + + +
Reversed pubis
- + + + + +
Asymmetric wing
feathers
- + + + + +
Feathers mostly
composed of
β
-keratins
- + + + + +
Plumage
+ + + + + +
Clavicles fused
to a furcula
(wishbone)
+ + + + + +
Hollow bones
+ + + + + +
Fig. 10. Table of characters of some theropods. (+) means the feature is present, (-) the feature is absent, and (±)
the feature is rudimentarily present. Orange boxes indicate the possession of primitive non-avian theropod char-
acters, and green boxes indicate the presence of advanced avian characters. We observe that the number of
avian features (shared derived traits or synapomorphies of crown group birds) gradually increases from Anchior-
nis via Archaeopteryx, Jeholornis, and Confuciusornis through to modern birds, as expected by evolutionary the-
ory. The character distribution also suggests that some avian characters evolved convergently in different line-
ages. For example, in Archaeopteryx, independently of crown group birds, the diapsid skull changed in such a
way that none of the temporal windows is clearly visible. In addition, the loss of teeth in Confuciusornis and to-
day's birds seems to have occurred independently.
In short: The exact position of mosaic forms, such as Archaeopteryx or Raho-
navis, in the phylogenetic tree is irrelevant with respect to the integrity of the the-
ory of evolution. Their probative force derives from the fact that mosaic forms fit
into a system of graded similarities, so that we can put them in a sequence in
which their morphology gradually takes on the shape of modern birds (Fig. 10).

16
C.4: Abrupt appearance of characters and the “waiting time problem”
A gradual appearance of different individual characteristics… does not automatically
imply that their emergence is plausible from an evolutionary perspective. Some fea-
tures appear relatively abruptly. (J
UNKER
2019, p. 49)
This objection is meaningless because the known fossils are not at all a representative
sample of extinct forms. Each instance of a fossil theropod specimen, such as the 12
known Archaeopteryx individuals, is an enormous stroke of luck. In each case, only a
single specimen represents half of all dinosaur genera, and 80% of all dinosaur skele-
tons are only fragmentarily recorded (D
ODSON
1990). According to estimates, fewer than
one to a few percent of species have left a fossil record (R
AUP
1994). Due to the incom-
pleteness of the fossil record, the demand for finely staggered transitions is absurd.
From an evolutionary perspective, many avian traits are regarded as early estab-
lished [in a bird's phylogeny]. They show abrupt fossil appearances. This situation is
a challenge for evolutionary mechanisms; rapid emergence [of traits] is not expected
from an evolutionary perspective. (J
UNKER
2019, p. 50)
Here, J
UNKER
ignores the explanation of punctuated equilibria (cf. E
LDREDGE
&
G
OULD
1972; J
UNKER
&
H
OSSFELD
2001) as well as the ambiguity of the term “abrupt.” When a
paleontologist speaks of the “abrupt” appearance of a feature, he thinks of periods of
time of several tens of thousands to millions of years; creationists think of a lightning-
fast emergence in the sense of a creatio ex nihilo.
Grossly misleading is the claim that evolutionary mechanisms are “clearly over-
strained... with bringing forth a great diversity of forms relatively abruptly in geologically
short periods of time” because of the “waiting time problem” (pp. 67, 93). Why is that?
Before we explain why J
UNKER
's claim is deceptive, we must elucidate the waiting time
problem. In short, advocates of the “waiting time problem” assume that a feature with
specific characteristics would take too long to evolve because evolution must wait until
the complete set of responsible mutations has cumulated (H
ÖSSJER
et al. 2021).
In essence, the “waiting time problem” is based on two premises: First, evolution must
reach a “fixed and pre-specified target” (H
ÖSSJER
et al. 2021, p. 51). Second, finding that
target would require multiple “coordinated mutations” (ibid., p. 5). Given the required ge-
netic “fine-tuning” and the fact that back mutations eliminate potentially beneficial single
mutations again, the argument goes, novelties could not evolve in realistic time periods.
However, creationists such as H
ÖSSJER
et al. are working under a misunderstanding or
misrepresentation of evolutionary theory in order to make their waiting time argument.
7
7
Daniel S
TERN
-C
ARDINALE
, Assistant Teaching Professor at Rutgers University, produced a highly instructive
video on the waiting time problem on his YouTube channel (https://www.youtube.com/watch?v=F748itCI_es).

17
Specifically, they are wrong in assuming that there are pre-specified targets or functions
that evolution must have worked towards. Even if a particular function is given, there is
no need for evolution to wait for pre-specified DNA or protein structures. Each functional
state can be accomplished in countless and totally different ways.
Take antibiotic resistance as an example: Among others, antibiotics can be rendered
ineffective by novel enzymes, modified receptors, efflux pumps, or “up-regulating” an
antagonistic signaling pathway. Each of these pathways, in turn, has multiple routes
open to evolution. In terms of the enzymatic route, for instance, cleavage or acetylation
can inactivate a drug. For each route, evolution can in turn use numerous different op-
tions. For example, the enzyme class of beta-lactamases is highly diverse. It includes
protein families that have little structural similarity to each other (H
UNT
2007a). Finally,
each individual protein can exhibit enormous variability while maintaining its function.
The assumption that multiple coordinated mutations are necessarily required to
achieve a target also proves to be false. The emergence of enzymes with completely
novel properties can often be accomplished by single mutations (D
E
K
RAKER
&
G
ER-
SHENZON
2011). Analogous to this finding, Y
ONA
et al. (2018) showed that ~ 60% of
purely random DNA sequences containing no functional information (!) are only one
mutation away from turning into active promoter sequences. A similar study demon-
strated that a high percentage of randomized peptides (when attached to the end of a
cytosolic protein) can serve as functional targeting signal for specific import into a
certain cell organelle (T
ONKIN
et al. 2008).
Even irreducibly complex systems with multiple well-matched components, like spe-
cific protein-protein binding sites or functionally rearranged genes with suitable pro-
moters, have been shown to arise rapidly (e.g., V
IGAN
&
N
EIL
2010; N
EUKAMM
2012;
S
AUTER
et al. 2012; B
EYER
et al. 2022; N
EUKAMM
2022).
Monte Carlo experiments show that the mechanisms of evolution would not neces-
sarily be overstrained, even if that would require three, four, or even more “matching"
mutations (T
ROTTER
et al. 2014). This is because thousands of (cryptic) genes, sig-
naling pathways, and co-factors imply an enormous number of candidate combina-
tions for complex gene interactions.
Moreover, as long as no one can demonstrate that the proportion of promising muta-
tions and gene interactions is extremely small compared to the universe of possibili-
ties, the waiting time problem will remain a pipe dream.

18
C.5: Evo-Devo solutions for bird evolution
A major step in the evolution of birds was the conversion of limbs into functional
wings. The prolongation of the extremities, reduction of the fingers, and fusion of the
carpus and metacarpals accompanied this conversion, for instance. Evolution den-
iers like to argue that each of these changes required a complicated sequence of
mutations or even the acquisition of entirely new genes. If this argument were true,
such adaptations would be lengthy, and convergences would be unlikely. However,
the argument is not true:
The limb-to-wing transition does not require a complete new set of genes but rather
changes in the control of a few genes that promote or stop growth. These genes pro-
duce chemicals called growth and signaling factors that give directions to the cells in a
growing embryo. When they are turned on and off at different times, that can drastically
change the shape of an animal. (H
ORNER
&
G
ORMAN
2009, p. 11)
Recent research has led to entirely new insights into the emergence of new traits
and body plans. There are a limited number of control genes; their products serve
as signaling molecules and interact with promoters and enhancers of other genes.
In combination with environmental conditions, they orchestrate the morphogenesis
in embryonic development. Slight changes in those interactions may cause funda-
mental shape changes. Evolutionary developmental biology (or “Evo-Devo”) focuses
on these mechanisms.
Many amazing adaptations rest
primarily on changes in the tempo-
ral coordination of developmental
processes (heterochrony). For in-
stance, some mutations affect the
activity of developmental genes in
such a way that juvenile traits are
preserved into adulthood. Such a
case is called paedomorphosis.
These include numerous adapta-
tions in birds such as reduction in
body size; an inflated braincase; a
shortened beak; reduction of teeth;
loss of the metatarsal wing; thin,
flexible, loosely connected skull
bones (cranial kinesis); and many
others (cf. C
HATTERJEE
2015, p.
275).
Fig. 11. Skeletal structure of birds. Skull structure, reduced
digits, fused metacarpal bones, sternal keel, fused metatarsals,
tarsal bones, and fused vertebrae—most adaptations in birds
required changes in the regulation of genes. More explanation
is in the text. Graphics: courtesy of SchuBu Systems GmbH
(Stefan P
ROCHASKA
), drawing only. Source:
www.schubu.at/p172/das-vogelskelett. English description: MN.

19
Other mutations affecting regulatory genes accelerate or prolong the growth of struc-
tures. The prolonged growth can result in structures merging, nesting, or increasing in
size compared to their ancestral status. For instance, recent studies suggest prolonged
growth phases as a cause of the formation of the prominent sternal keel (carina or keel
bone) in birds (Fig. 11) and the convergent structure in bats (L
ÓPEZ
-A
GUIRRE
et al. 2019).
Another distinctive bird feature is the pygostyle, which is a product of fused distal
caudal vertebrae (cf. Fig. 12). It serves birds as a stable base for their tail feathers,
which are erected by folding up the pygostyle. Comparable morphologies can be in-
duced even experimentally (!) by ectopic overexpression of Hoxb13 or changes in the
retinoic acid gradient (R
ASHID
et al. 2014, p. 9). Retinoic acids affect gene expression
and exert an influence on cell differentiation.
P
LATEAU
&
F
OTH
(2020) showed that the
final step towards highly modular, inte-
grated skulls in modern birds is
grounded in an abrupt fusion of cranial
bones. Phylogenetic comparisons sug-
gest that cranial bone fusion represents
a developmental exaggeration of the
ancestral adult trait. In fact, in number
and distribution of modules, juvenile bird
skulls resemble the adult skulls of non-
avian theropods (including Archaeop-
teryx) more closely than their own adult
skulls. Adults possess significantly
fewer cranial modules due to ontoge-
netic bone fusion.
A particularly interesting case is the evolution of bird beaks. The beak (bill or ros-
trum) is the toothless jaw part of sauropsids, covered with hardened horny sheaths
(rhamphothecae).
8
The bony base of a beak is largely formed by the premaxillary,
which is greatly enlarged compared to non-avian theropods (Fig. 13). The premaxil-
lary sits on top of a shortened face and a bulbously enlarged cranium, and it is func-
tionally integrated into the kinetic system of the avian skull. The horny sheaths are
composed of several superposed polygonal scales composed predominantly of
8
Among extant sauropsids, beaks are only found in the crown groups of birds and turtles. In extinct saurop-
sids, beaks are found in various groups of theropods, e.g., oviraptorosaurs, ornithischians, and rhynchosaurs.
Corresponding analogs also occur in cephalopods and a few mammalian species. However, in no other ani-
mal group have horned beaks been differentiated into such unique and diverse mouthparts as in birds.
Fig. 12. Skeleton of a giant petrel with an erected
pygostyle at the end of the tail. Author: Daiju AZUMA |
Source: Wikiwand.com | License CC BY-SA 4.0.

20
specialized beta-keratins (β-keratins) and a small amount of alpha-keratin (

-
keratin). Mixture and layer thickness vary from species to species and determine the
mechanical properties of the beaks.
Transitional forms like Archaeopteryx and various Cretaceous birds such as Ichthyor-
nis show that beaks did not develop abruptly. Their components did not evolve simul-
taneously but incrementally and independently from each other. First, cranial modifica-
tions caused by paedomorphosis took place, such as facial shortening, reduction of
the maxilla (the upper jawbone), enlargement of the cerebral skull, and shrinkage of
the bones, resulting in remarkable mobility (kinesis) of the cranial bones in birds.
Skull comparisons between juvenile non-avian theropods such as Coelophysis
(Fig. 13 at lower left) and proto-birds like Archaeopteryx (Fig. 13 at upper middle)
show that these modifications are results of paedomorphosis. The transition from
thin, loosely connected, significantly movable skull bones to thick, overlapping, and
firmly connected cranial bones happened in the ontogeny of non-avian dinosaurs
and still takes place in extant crocodilians (B
HULLAR
et al. 2016, p. 397).
Fig. 13. Lateral skull view of the non-avian theropod Coelophysis (left column), the proto-bird Archaeopteryx
(middle column), and the extant Andean Tinamou (right column). The skulls of adults are shown at the top, those
of juveniles at the bottom. The different skull bones are color-coded. We can see that the evolution of the beak
was preceded by a marked reduction of the maxilla (MX, dark green). This was the prerequisite for the subse-
quent enlargement of the premaxillary (PM, red), which forms the upper beak in modern birds. Drawing by James
Paul B
AELLO
, modified from B
HULLAR
et al. (2016, p. 392).
In the next evolutionary step, with the appearance of crown group birds, the premaxil-
lary was enlarged and integrated into the kinetic system of the cranial bones in a
relatively short time. Recent studies suggest that functional integration of the
enlarged premaxillary into the skull from a biomechanical point of view could occur

21
only after the paedomorphic shortening of the face and a significant reduction of the
maxilla (B
HULLAR
et al. 2016).
Evolutionary transformations in cranial modules like the premaxillary are not compli-
cated. Findings concerning the molecular control of beak development show that its
parameters are subject to precise control mechanisms that are independent of the
remainder of the snout (S
CHNEIDER
&
H
ELMS
2003). Many adjusting screws can influ-
ence the development, such as changes in concentration of the transcription factor
BMP4, which controls bone growth, among other things, or the BMP antagonist Nog-
gin. Afterwards, mutations that influence the BMP signaling pathway in the maxillary
bone enable “fine-tuning” of the shape and size of the beaks.
Various transitional forms provide information about another evolutionary step,
namely the formation of horny sheaths on the beak. In some Cretaceous birds, only
parts of the snout were covered with horny sheaths, starting from the tip of the beak.
In present-day birds, formation also begins initially in the distal region of the beak
primordia. Ichthyornis, for example, still possessed a small transitional beak with a
toothless, horn-covered pincer tip that may have served as a type of grasping tool for
picking up food.
9
However, Ichthyornis' beak caudally
10
still possessed teeth and a
hornless snout (F
IELD
et al. 2018).
Fig. 14. Origin, duplication,
and subsequent diversifica-
tion of corneous beta-
proteins (CBPs) in different
sauropsids. From H
OLTHAUS
et al. (2019).
Where do the genes involved in the formation of horny sheaths come from? Analyses
show that at least 149 different β-keratins are involved in the formation of horn-like
9
The formation of a surrogate “hand” seems to be a key selective advantage, as the actual hands were integrated
into increasingly specialized bird wings towards the end of the Cretaceous (B
HULLAR
et al. 2016, p. 398).
10 Towards the back of the head.

22
structures, such as claws, beaks, and feathers in birds; they are called corneous
beta-proteins (CBPs) (Fig. 14). Their genes are organized in the epidermal differen-
tiation complex (EDC), and they are expressed in a specific temporal sequence. All
EDC genes are involved in the complex differentiation process of the epidermis. The
EDC contains both structural proteins and regulatory proteins of the epidermis.
However, neither the EDC nor the CBPs arose de novo in the avian lineage. Rather,
the development potential for horny epidermal structures like claws, scales, fibrous
skin appendages, and horny sheaths was already present in the genetic makeup of
early dinosaurs such as Psittacosaurus. In birds, however, a strong expansion and
differentiation of the gene cluster occurred.
A closer investigation of β-keratin gene evolution suggests that multiple waves of
gene duplication within a single genomic locus with subsequent diversification
accompanied the evolution of claws, scales, feathers, and horny scales in birds
(L
I
et al. 2013; H
OLTHAUS
et al. 2019). A similar but independent process accom-
panied the evolution of the scales of the carapace in turtles. In other words, epi-
dermal structures in Sauropsida share a common evolutionary origin that began
with the emergence of the first CBPs more than 300 million years ago (Fig. 14).
In this scenario, a growing number of new variants of CBP genes allowed for the
progressive specialization of integument structures.
11
As an aside, there is additional evidence that, from the viewpoint of developmental
biology, scales and feathers can be considered homologous (M
USSER
et al. 2015).
Thus, remarkable similarities exist in Wnt/β-catenin signaling during the early devel-
opment of feathers and reptile scales, for instance, with respect to the localization of
the transcription cofactor β-catenin. Expression of β-catenin is a reliable marker of
the ability of epithelia to form feathers and scales. Essentially, feather morphogene-
sis differs from scale morphogenesis in that additional differentiation steps such as
follicle formation and the development of an epidermal collar have been added in-
crementally (cf. P
RUM
1999).
A word about the decades-old controversy over whether birds have thumbs
(Fig. 15). What at first glance seems like a trivial question was a highly explosive
matter in the past and occasionally led to questioning of the theropod ancestry of
birds. Why? Well, in principle, terrestrial vertebrates have five fingers per hand,
whereas the bird's wing has three fingers. There is evidence of a fourth digit early in
11
Work on the properties of β-keratins in the epidermis of various reptile species indicated a correlation between
the type and amount of β-keratin expressed and the hardness of the epidermis. Duplicated β-keratin genes were
possibly conserved because a greater amount of β-keratin increases the hardness of the epidermis and allows
the emergence of different morphologies (A
LIBARDI
et al. 2007). Mutations, in turn, caused “fine-tuning” of traits.

23
ontogenesis, but it disappears again. Which digits do survive: the thumb (digit I),
index finger, and middle finger (I-II-III) or the index, middle, and ring finger (II-III-IV)?
On the one hand, successive fossils show the reduction of two fingers on the posterior
side (pinky side) of the hand among the ancestors of Deinonychus (Fig. 15). The re-
maining fingers resemble the three fingers of Archaeopteryx. This and the phalangeal
formula, which is 2-3-4 in Deinonychus, Archaeopteryx, and birds, support the indexing
of the fingers as thumb, index finger, and middle finger (I-II-III). Indeed, the gene expres-
sion patterns of the most anterior avian finger match those of the thumb in other animals.
On the other hand, in terrestrial vertebrates, the ring finger is the first to be formed in
ontogenesis. In birds, it is the finger on the posterior side of the hand, which also
speaks for the ring finger. Since on the anterior side (thumb side) of the hand an em-
bryonic finger begins to develop but quickly disappears, this would have to be digit I.
There are also dinosaurs, such as Limusaurus, that partially reduced their thumbs
and missed a pinky. These data argue for an identification of the fully formed bird
fingers as the index, middle, and ring fingers (II-III-IV).
The conflicting finger counts in theropods were not resolved for a long time. Recent
explanations of evolutionary developmental biology (Evo-Devo) have resolved this
contradiction. What is the solution?
Only a handful of general signaling factors called morphogens orchestrate the embry-
onic development of organisms. These include proteins of the HOX, Wnt, Hedgehog,
and TGFβ families as well as their ligands, such as the growth hormone BMP4. They
influence the expression of hundreds of genes in a context-dependent manner. For
instance, the signaling factor Sonic Hedgehog (Shh) plays a key role in hand develop-
ment. Its gene is activated only on one side of the hand; Shh concentration is highest
Fig. 15. Schematic representation of finger reduction in various archosaurs. The numbering of the digits is given
below each sketch, starting with the thumb (digit I), and moving to the posterior side (pinky side, digit V) of the
hand. Drawing by James Paul B
AELLO
, compiled from W
ELTEN
et al. (2005) and Č
APEK
et al.
(2014).

24
on the posterior (pinky) side of the hand and decreases toward the anterior digits. Now
Shh concentration controls gene expression patterns in the different finger primordia
and thus determines their development. They gain positional information from Shh, so
to speak, about where they are and how they are to develop.
On the basis of this morphogenetic mechanism, Č
APEK
et al. (2014) proposed that
gene regulatory changes initially led to the reduction of the pinky and the partial re-
duction of the ring finger. However, the thumb and pinky form last, and developmen-
tal constraints require the digit primordia that form last to be reduced first. Accord-
ingly, the index, middle, and ring fingers are retained and utilize the available space
by growing further inward.
This causes the biomechanically anteriorly displaced fingers (II-III-IV) to leave the
original Shh activity zone and adopt the gene expression pattern of the anterior digits
(I-II-III) under the influence of altered morphogen gradients. In other words, they ob-
tain anterior digit phenotypes. This concerted mechanism explains why the fingers of
theropods like Deinonychus have the shape of the inner digits (I-II-III). Moreover, it
explains why the transcriptome of the foremost bird finger corresponds to that of the
thumb of other animals.
In other words, there is strong evidence that a partial homeotic frameshift of digit
identity occurred. Scientists call this scenario the axis shift hypothesis.
C.6: The irreducibly complex avian body plan
In order to suggest that the evolution of bird flight is extremely improbable, J
UNKER
&
W
IDENMEYER
(2021) claim that evolution would have had to pass through innumer-
able feature changes and subtleties in the construction of plumage, skeletal struc-
ture, behavior, etc. at the same time in order to achieve flight ability:
In addition to suitable feather material and functionally fine-tuned structure, suitable
anchoring of the feathers in the skin is also indispensable, as is a complex network of
feather musculature, nerve cords, and sensory organs for the motility of the feathers. In
addition, a functional plumage must be formed overall, with diverse control mecha-
nisms and coordination of flight movements, details of the bird's body structure, and
sophisticated behavior with corresponding data processing in the brain. The tasks that
flight feathers must perform place special demands on the construction... First, suitable
construction material is required. This consists of long fibers of a special protein, beta-
keratin... The keratin must be 'built' into the feather shaft, barbs, and barbules in a very
specific way so that the feathers exhibit their special properties... (p. 84)
For these reasons, many researchers point to the aspect of synorganization. The indi-
vidual modules and levels (from building material to behavior) cannot be understood in
isolation from each other, nor can they have evolved separately. In sum, together with
the plumage, we are facing an overall organization that seems to be irreducibly com-
plex with respect to flight ability and represents a clear indication for design. (p. 86)

25
It is one thing to list the features of a highly specialized locomotor system that extant
birds use for perfect flapping flight. However, it is another thing to conclude that all of
these features are indispensable for rudimentary flight and could not have evolved
separately. The weak spot in such reasoning is that this conclusion is invalid.
Consider, for example, Anchiornis (compare the cover picture on the title page); this
airworthy theropod already possessed some (but not all) of the features listed above.
However, it still lacked numerous other components. For instance, the feathers largely
consisted of

-keratin (P
AN
et al. 2019). Hence, they did not have the “special proper-
ties” of modern feathers (like flexibility and buckling resistance). Their structure also
differed significantly from the “functionally fine-tuned structure” of modern feathers. For
instance, there is evidence for open-vaned feathers (S
AITTA
et al. 2017, p. 276).
In addition, compared to modern birds, Anchiornis possessed much shorter wing
feathers in relation to the length of the humerus. The feathers were symmetrical
and poorly differentiated; both the primary feathers and the secondaries were nar-
row and weak (L
ONGRICH
et al. 2012), and the covert feathers of Anchiornis were
not arranged in tracts or rows (W
ANG
et al. 2017). The longest wing feathers were
those nearest the wrist, making the wing broadest in the middle and tapering near
the tip for a more rounded, less flight-adapted profile (H
U
et al. 2009).
In general, creationists overrate the role of feather material, fine-tuned feather struc-
tures, and plumage for flight capability. Experiments and computer modeling re-
vealed that the propatagium (Fig. 16) produces the majority of the lift; the removal of
secondary feathers, leaving six distal primaries and an intact propatagium, did not
noticeably affect flapping flight in house sparrows (B
ROWN
&
C
OGLEY
1996). Even
with the removal of all flight feathers except for the distal six primaries, the loss of
approximately 50% of the propatagium's projected area and its cambered profile did
not render flight impossible! Additionally, for a gliding flight, “motility of the feathers”
is dispensable; it is an optimization step, too (A
LEXANDER
2015).
On the one hand, we can see that early flying theropods lacked or could have lacked
quite a few of the properties listed above. All those “yet missing features” were subse-
quent, successive optimization steps of crown group birds. On the other hand, we can
trace the evolutionary roots of countless features enabling birds to fly back to non-
avian dinosaurs. Experts refer to favorable exaptations,
12
which, in retrospect, paved
the way for the evolution of flight in the first place.
12
Contrary to adaptation, the word exaptation describes a trait whose function is accidentally adaptive
at a given time without having been produced by selection “for” it.

26
To list a few examples (cf. B
RUSATTE
et al. 2015):
 The development of air-filled, hollow bones and a bird-like lung-air sac system
began in the first Saurischia.
 The long legs and the three thin main toes typical of birds developed more than
230 million years before birds emerged. These were accompanied by the trans-
formation of the quadruped “reptilian” body into upright-walking theropods.
 100 million years before birds emerged, a rapid increase in metabolism and
growth rates took place, as well as the development of the avian-typical air
sacs and power lungs. These favorable exaptations had nothing to do with
flight capability either. By means of those adaptations, birds manage their en-
ergy needs today.
 About 50 million years before the appearance of birds, the paired clavicles
fused into a furcula (“wishbone”). Presumably, the wolf-sized raptors used
them to stabilize the shoulder girdle when tearing apart their prey. In their fly-
ing descendants, the innovation helps to save energy when flapping.
 Flightless maniraptorans
such as Deinonychus likely possessed the propa-
tagium even before the origin of flight (U
NO
&
H
IRASAWA
2023). This structure
contains a muscle connecting the shoulder with the wrist and supports flap-
ping. This was another favorable condition for the origin of flight (Fig. 16).
13
In short, the assertion that features or parts of the avian body plan could not have
originated separately from each other is nonsensical. Theropod fossils can be put
into a sequence in which the “irreducibly complex” “overall organization” of birds re-
solves in a series of stepwise trait additions. One does not find any bird that would
differ fundamentally from dinosaurs but only graded similarities within Dinosauria.
13
Admittedly, there are a few publications advocating the unusual idea that Deinonychus and Caudipteryx were
secondarily flightless birds and thus possessed volant ancestors (cf. F
EDUCCIA
2020, p. 281). Currently, the fossil
record does not support this assumption, and this idea requires too many unsupported prior assumptions to be
scientifically respectable (Q
IU
et al. 2019, p. 7; F
OTH
, pers. comm.). See also below in section C12.
Fig. 16. A: Propatagium (red) in Dei-
nonychus, a predator. It is likely that
this structure allowed for a more agile
hunt. B: Sapeornis' wing membrane,
showing the interlocking wing folding
system of birds. Soft tissues are not
preserved, but the elbow joint angles
are good indicators for the presence
or absence of the propatagium.
Drawn by James Paul B
AELLO
accord-
ing to U
NO
&
H
IRASAWA
(2023).

27
These graded similarities indicate that the evolution of avian characteristics such as
feathers and wings was initially not shaped by selection for aerodynamic properties.
Rather, those structures evolved for other reasons like courtship display or brooding
behavior (B
RUSATTE
2017, p. 793). Thus, evolution did not care about the “irreducible
complexity” of the (not yet even existing!) flying apparatus. Instead, one trait after
another evolved in dinosaur lineages because they fit in the given, differing selective
regimes. In this process, the prerequisites for a rudimentary flight emerged gradually,
quite casually, without being intended or even foreseeable.
We can ask how the evolution of flight, coming as it did from non-avian theropods
that had not yet crossed the threshold to flight, proceeded from this point. Doing so,
we must keep in mind the exaptations already present (see above). Then the
emerging picture is that of an “experimental field” combining a simple wing design
with a jumping behavior for a rudimentary gliding flight (F
OTH
2008).
According to F
OTH
(2008), already large, stiffened coverts or skin flaps can consti-
tute a simple but functional wing construction. Sifaka lemurs on Madagascar dem-
onstrate that it can be even simpler: long, thickened hairs on the arms and a small
skin between the upper arm and the body slow down the fall when jumping from tree
to tree and carry the primate up to ten meters wide (Fig. 17).
Fig. 17. Sifaka lemurs from Madagascar show
the simplest adaptations to parachute flight in
combination with jumping behavior. The arms are
covered with long, stiffened hair, and there is a
small flap of skin between the upper arm and the
body, which increases the wing's surface area.
When jumping, the Sifakas stretch out their arms
and legs. Therefore, they can glide more than ten
meters thanks to the enlarged “wing.” Source: ©
Andrey G
UDKOV
| Depositphotos.com.
As shown above, non-avian theropods had exaptations that were more favorable for
gliding. Biomechanical studies also show that flightless representatives with penna-
ceous feathers can also generate dynamic lift from the ground (H
EERS
2016). In this
way, they were able to get over obstacles by gliding or flapping over short distances. In
addition, the buoyancy allows for faster, more agile, and energy-efficient running. Over

28
time, body size, leg-wing coordination, muscle capacity, wing length, and behavior can
thus have been successively adapted to the requirements of ever more enduring flight
(H
EERS
et al. 2018).
So far, it is an open question whether bird flight evolved from the ground up or from
trees down. However, this may be a false dichotomy. At first sight, energetic consid-
erations seemed to speak against the ground-up theory: Archaeopteryx would have
had to run three times as fast as modern birds for liftoff. However, recent biophysical
calculations show that updrafts on mountainsides or cliffs could carry small-feathered
paravians from the ground up into the trees (S
HAHID
et al. 2019).
According to the authors, the meteorological aspect eliminates the existing problems
of both scenarios and makes the virtual contradictions between ground-up (cursorial
theory) and trees-down (arboreal theory) disappear: depending on wind conditions,
paravians glided both upward and downward and required neither climbing aids nor
distinctive running or pronounced flying muscles.
C.7: Gliding versus flapping flight: another false dichotomy
Creationists often attempt to problematize the evolution of active flight (flapping flight)
from gliding by postulating insurmountable hurdles for this transition (e.g., J
UNKER
2018). J
UNKER
says that the “problems of the emergence of bird flight from trees” are
“so numerous and severe that this path seems evolutionarily infeasible.” The reasons
he gives are essentially the following:
“A transition from gliding to flapping flight is complicated and laborious because these
two types of flight are very different (Padian 1982, p. 11). Gliders have comparatively
few changes in their body plan apart from the possession of flight skins, whereas all
active flyers are highly modified in skeletal structure and physiology.”
“There is no evidence that any group of gliding animals... is or ever has been on the
path to active flight (Padian 1982, p. 12; Caple et al. 1983, 475; Paul 2002, p. 117) or
that any glider would use its limbs to actively achieve forward or upward thrust (Dial
et al. 2008, p. 988).”
“Selection conditions for gliders and active flyers are partly contrary to each other. A
glider needs large wings—as large as possible and right from the start. The best way
to get there is to stretch out all the extremities, as today's gliders do. 'In birds, how-
ever, there is nothing to indicate that their legs ever played a major role as part of the
wing' (Peters 2002, p. 425).”
“Already, gliding flight is not 'gratuitous' but requires control mechanisms; this is true
even for poor gliders. The selection pressure for control and stabilization in a gliding
'proto-bird' must have been high (Norberg 1985, pp. 305 ff.).”
At first, it is noticeable that J
UNKER
mainly uses quite old sources to underline his un-
usual opinions. Why? Obviously, because biomechanical studies that are more con-

29
temporary demonstrate that there is a functional continuum with gradual adaptations
between gliding and elaborate flapping flight.
For example, A
LEXANDER
(2015, p. 55) notes under the text section Gliding flight ver-
sus flapping flight: false dichotomy:
Some scientists have argued that weak or poorly developed flapping would be so in-
effective that it would provide no benefit to gliding animals (or might even be less ef-
fective than gliding), so gliding could not have led directly to flapping.
In fact, both theoretical modeling and experiments using flapping robots show that
even low-amplitude, weak flapping can produce enough thrust to be useful, even when
such flapping is too weak to maintain level flight. These results mean that we must
think of gliding versus fully powered flight—flapping flight as used by living birds, bats,
and insects—as two extremes on a continuum. Between these extremes, animals
could use flapping with a range of effectiveness, from weak flapping to slightly extend a
glide to stronger flapping that might increase glide distance by five- or tenfold.
Thus, the assertion that selection conditions for gliders and active flyers are partly con-
trary to each other is simply obsolete. Moreover, the “highly modified” physiology of
active flyers is a gradual optimization of already existing skeletal and feather struc-
tures. Archaeopteryx, for instance, did not yet possess a sternal keel, where the pow-
erful muscles for flapping flight attach in birds. In addition, the rigid shoulder girdle did
not permit a persistent flapping flight. Nevertheless, there is evidence that it was no
longer a pure glider but flew actively at times (V
OETEN
et al. 2018).
Thus, the claim that there is “no evidence that any group of gliding animals... is or
ever has been on the path to active flight” is false. Archaeopteryx simply is to be lo-
cated at a different place in the continuum between primitive gliding and ultimate
flapping flight than modern birds. Anchiornis possessed a lower flapping flight poten-
tial than Archaeopteryx (P
ITTMAN
et al. 2022a, p. 9), and Eosinopteryx, Aurornis, and
Xiaotingia had an even lower one.
That “Mesozoic birds whose flight consisted mainly in gliding and soaring” are
“not known” is at best an argument from ignorance but not an objection: just re-
placing “Mesozoic birds” by “basal Avialae” like Aurornis and Xiaotingia, which
lived between 152 and 166 million years ago, turns this statement invalid.
Even stranger is the often-heard
argument that even gliding flight requires sophisti-
cated control mechanisms (see also J
UNKER
2018). It implies that evolution had to
consider every nuance of motor skills. However, this view underestimates the plastic-
ity and learning curves of neuronal systems. Dromaeosaurids like Velociraptor were
intelligent hunters that followed group strategies to outsmart their prey. Are we to be-
lieve that such animals were too stupid to learn how to balance their extremities for

30
gliding? No control behavior needs to be perfect, and even nowadays, every young
bird must first... yes! learn it! Even humans can easily learn how to operate a hang
glider, and we surely are not made for flying.
Additionally, we must expect primitive flyers, such as Archaeopteryx, to be inherently
stable (“stability configured”), whereas the highly maneuverable, inherently unstable
(“control configured”) systems of crown group birds are more derived (less primitive)
(M
AYNARD
S
MITH
1952; A
LEXANDER
2015). In other words, there is a trade-off between
built-in stability and high maneuverability; the active stabilizing mechanisms required in
modern birds’ nervous systems represent potent specializations, not plesiomorphies.
Interestingly, even many wingless arboreal animals without any aerodynamical adap-
tation, such as certain ants, are gliders or parachuters in its most rudimentary form
(A
LEXANDER
2015). They produce some lift, have orientation about their position, and
can reliably adjust their descent during a fall. In a nutshell:
If many arboreal animals have this ability, as now seems likely, and if some of those
animals experienced selection pressure to extend falls into glides, they would have a
head start in evolving more effective gliding. Ironically, biologists have long consid-
ered the evolution of flight control ability to be one of the major hurdles to be over-
come during the evolution of flight, but this ‘hurdle’ may already be behind many ar-
boreal animals (A
LEXANDER
2015, p. 50).
It is completely unclear what J
UNKER
wants to say with the following: “Land-
ing must work from the beginning.” As
if a botched landing were impossible!
Let us think of the albatrosses, which
fly with perfection but whose takeoff
and landing are associated with con-
siderable problems (Fig. 18). If it were
up to J
UNKER
, these species would
have become extinct long ago.
Fig. 18. No exception: the crash landing of an albatross
(right). So much for the claim that a “landing must work
from the beginning”! Source: R
OYAL
A
LBATROSS
C
AM
.

31
C.8: Open questions about the mechanisms of evolution
[T]he question of evolutionary remodeling... [is] not answered. The presence of putative
intermediates is not evidence of a sufficiently probable mechanism. For these reasons,
it is essentially unresolved how airworthy feathers could have evolved solely by future-
blind variations, selection, and other completely natural processes—and therefore, of
course, whether they could have evolved. (J
UNKER
& W
IDENMEYER
2021, p. 91)
The answer to the question of whether feathered birds are a product of evolutionary his-
tory is logically independent of the knowledge of the evolutionary mechanisms (the an-
swer to the question of how they evolved). In analogous cases, this is indisputable: The
effectiveness of drugs is provable without knowing their mechanisms of action. The gla-
cial theory had gained general acceptance by the end of the 19th century, even though
by that time scientists knew nothing about the causes of glaciation (E
HLERS
2011). Ma-
rine fossils attest to the process of mountain folding even without knowledge of the tec-
tonic forces responsible for it (Fig. 19). The Big Bang is well confirmed, although its
cause is unclear. One could extend this list of examples endlessly.
The very fossil record corroborates that birds are the product of a historical evolu-
tionary process,
14
without requiring knowledge of the molecular genetic details or se-
lection regimes of this transformation. This is even more convincing since descent,
heritable variability, and speciation are facts of experience. Therefore, even
...if we knew nothing at all about the causes, the fact of evolution would remain un-
touched. (R
EMANE
et al. 1973, p. 11)
14
Incidentally, the claim that fossil interpretation is “ambiguous,” i.e., also open to transcendental interpretations like
intelligent design, is not a reasonable objection. Transcendent things can be used for the "explanation” of everything
without being testable (or, more limitedly, falsifiable). Even perfectly natural evolution can be (and is!) easily inter-
preted as a result of design (cf. B
EHE
2008, p. 166). Such omniexplanatory “power,” as philosophers of science call
it, puts Intelligent Design outside any scientific realm (cf. M
AHNER
&
B
UNGE
1997, p. 108).
Left image: Author: R. K
IRCHNER
| Title: ‘Fossile Rippelmarken’ |
Source: Mineralienatlas.de | License: CC BY-NC-SA 3.0. Right
image: Author: Amanda77 | Title: ‘Strömungsrippel im Watten-
meer von Borkum bei Niedrigwasser’ | Source: Wikipedia, Rippel
| License: CC BY-SA 3.0. Image curtailed.
Fig. 19. Left: fossil ripple marks in the Bavar-
ian Hass Mountains. Right: recent ripple
marks on the beach of Borkum, North Sea. If
such structures are found in mountains, often
with embedded fossils of former sea dwellers,
strong evidence is provided that the sea floor
was uplifted thousands of meters. The evi-
dence for mountain folding is logically inde-
pendent of whether we know the forces in the
Earth's mantle, the drift of the individual
continental plates, etc.

32
However,
one point is correct: variation and selection alone do not provide a suffi-
cient explanation for the origin of the flight apparatus of birds. This has a simple prac-
tical reason: variation and selection are general mechanisms. They explain evolution
on a principled level. To explain something as specific as the flight apparatus of
birds, evolutionary biologists must develop a specific model based on the general
theory (M
AHNER
&
B
UNGE
1997, pp. 95 ff.).
Ideally, such a model would show step-by-step how mutations and developmental bio-
logical mechanisms reshaped the plesiomorphic dinosaurian features into derived avian
features under real historical conditions. In this context, it would be particularly interest-
ing to elucidate how, in this remodeling process, the functionality of each individual step
was maintained. In short, we would need to substantiate the general theory of evolution
with additional knowledge about the structural, functional, and developmental details of
the species in question. In addition, the model would need to include data on historical
conditions, such as Jurassic selection regimes.
The problem is that we do not have complete knowledge of all those details and
we never will. We can reconstruct it only fragmentarily and hypothetically. In addi-
tion, we deal with highly diverse, individual, and complex biosystems:
It is precisely the boundary conditions, such as ecological interactions, other histori-
cal circumstances, and coincidences of all kinds, which are not only different in each
individual case but also unique and consequently constitutive of the biological system
under consideration... (M
AHNER
1986, p. 42)
This does not preclude working with highly plausible scenarios that contain well-
known developmental mechanisms (we discussed a few examples in text section
C.5). However, we never know for sure whether these mechanisms played a role in
the past. Moreover, it is easy for evolution deniers to add an endless number of un-
answered questions: Which individual mutations triggered the developmental
change? Through what adaptive intermediate steps did the gene regulatory network
that created the conditions for it emerge? Where did the genes come from? Which
selection pressure caused the phylogenetic change? How and why did selection re-
gimes change? And so on.
Again, we do know in some detail which mechanisms are involved in the assembly
and differentiation of gene regulatory networks.
15
However, analysis of individual
networks is difficult, especially the reconstruction of preceding differentiation steps,
since the genomes of extinct animals are decomposed and lost. Therefore, we see
that doubtlessly confirmed and sufficiently detailed explanations will never be achiev-
15
For those interested in this topic, M
ETTERNICH
(2021) is well worth reading.

33
able. We will never get a complete explanation of any complex natural process, con-
sidering all its interdependencies and boundary conditions. That would be illusory!
Still, creationists believe they have an argument against the plausibility of evolu-
tionary models by arguing this way. Thereby, they overlook the fact that practical
problems in gaining knowledge do not indicate a defect in the theory of evolution.
Moreover, even if the models in question contain only parts of the relevant
mechanisms, they still provide the basis for more complete explanations. Without
this basis, no explanation is possible; with it, at least plausible partial explanations
exist. Plausible means that all premises and mechanisms are empirically well-
founded and harmonize with background knowledge.
Incidentally, it is not only in historical reconstructions that we must deal with simplified,
hypothetical explanations. Models for describing complex developments in the present,
such as climate change, also contain quite a few idealized assumptions (V
OLLMER
2000,
p. 210). Premises very often do not match reality completely. Think of ideal gases and
ideal populations. Although they do not exist, they are the basis for more realistic models.
Natural processes are processes within complex systems. In most cases, one can
resolve and explain only single aspects or interactions and obtain only restricted
knowledge on boundary conditions. This is due to the complexity of nature and,
hence, a problem inherent to the scientific analysis of complex systems. Creationists
misapply this fact as a reason to refuse macro-evolutionary explanations. Conse-
quently, they would have to reject almost all models in all natural sciences for the
same reason—and especially their highly speculative “intelligent design approach.”
C.9: Ghost lineages in the fossil record
Ghost lineages are ancestral lineages of species that have left no fossil evidence for
some time during their existence but can be inferred to have existed because of the
fossil record before and thereafter. J
UNKER
(2019) argues that ghost lineages pose a
severe theoretical problem when they extend over long periods. In his opinion, evo-
lutionary theory can only provide problematic ad hoc explanations:
It must be assumed under evolutionary theoretical premises that many lineages have
left no fossils during 20–30 and possibly even more million years of their assumed
existence, while fossil remains have survived from other lineages from comparable
geological strata. Such a situation is problematic in evolutionary theory and in a long-
term framework. (p. 65)
In short: Martin M
AHNER
, a philosopher of science, notes the following: “What we
are able to achieve in historical contexts as mechanismic explanations, we could
call mechanismic evolutionary scenarios” (pers. comm.). Thus, plausible hypo-
thetical explanations are sufficient because they are just what we can reach.

34
However, many taxa demonstrate that ghost lineages are real at this duration.
Among them is the coelacanth subdivision of marine Latimeriidae (Fig. 20). Fossil
genera are known from the Mesozoic, dating back to the Triassic, but disap-
peared from the fossil record at the end of the Cretaceous (F
OREY
1998).
Throughout the Cenozoic, coelacanths were no longer present in strata and were
thought to be extinct. Since 1938, however, we have known that latimeriid coela-
canths still populate the seas (V
ENTER
et al. 2000). Thus, we are dealing with a
ghost lineage that lasted 70 million years.
Fig. 20. Ghost lineages (shown as red lines) of some selected taxa whose transmission in the fossil record
(grey) starts again tens of millions of years later. This shows that, contrary to J
UNKER
, they are not inventions.
These and further examples are available at https://en.wikipedia.org/wiki/Ghost_lineage.
The ghost lineage of the atoposaurid genus Theriosuchus from the Late Jurassic
turned out to be similarly long. The fossil record of this crocodylomorph broke off
about 135 million years ago and did not resume until the uppermost Cretaceous de-
posits. The duration of this ghost lineage ranges between 55 and 75 million years
(C
SIKI
et al. 2011).
Incidentally, one can also ask for a satisfactory explanation for ghost lineages in a
creationist scenario. Why is there a gap in the fossil record? Did God create those
taxa twice? Alternatively, did God prevent the fossilization of some selected taxa for
a given time span in distinct geological strata?
In short: One must keep in mind that successful fossilization is extremely rare,
and the rediscovery of a fossil is a fortunate coincidence. Hence, it is not a sur-
prise that quite a few taxa remain undiscovered for time spans of various lengths.

35
C.10: The “discrepancy” between stratigraphy and phylogeny
Creationists often argue that the succession of species and taxa in the fossil record is
not in accordance with a phylogenetic scenario. Here, we present some examples:
Most theropod genera that have bird-like features are geologically younger than the
geologically oldest birds. (J
UNKER
2019)
Cruralispennia occupies a derived position among the opposite birds [Enantiornithes]
and is not interpretable as a transitional form. Moreover, this genus is among the
oldest birds after Archaeopteryx, [which means there is] a 'stratigraphic-phylogenetic
discrepancy' (Wang et al. 2017). (J
UNKER
2019, p. 52)
Both Enantiornithes and Ornithurae appear relatively abruptly in the fossil succession in
great diversity, temporally common with forms such as Confuciusornis, Jeholornis, and
Sapeornis, which are classified as more primitive. (J
UNKER
2019, p. 65)
The dromaeosaurids, in turn, are placed in a broader ancestral context with birds (al-
though they have been found in much younger strata than forms with true, flat, flight
feathers). (J
UNKER
2022)
The content of these statements is correct, but they are not suitable as an objection
against evolution. As Fig. 21 shows, from an evolutionary perspective, taxonomists
can insert all these mosaic forms into a phylogenetic scheme without any difficulty.
From a cladistic point of view, the explanation for that “stratigraphic-phylogenetic dis-
crepancy” is simple: when more advanced avian features evolved in some evolutionary
lineages (like Enantiornithes), dinosaurs displaying more primitive features (like Sapeor-
nis but also Dromaeosaurus) did not automatically die out. Why should they? These dif-
ferently evolved theropods coexisted for a very long time.
16
Many basal non-avian dino-
saurs even evolved much later than some proto-birds. For instance, when Utahraptor
appeared, Archaeopteryx was already extinct (Fig. 21). At the same time, the first oppo-
site birds (Enantiornithes) evolved. Why not? Whoever interprets all this as problematic
for the theory of evolution has not understood the basics of evolution.
N
ORELL
(1992) is right in emphasizing that it is the phylogenetic relationships of
groups, not their stratigraphic relations, that matters. Pliocene whales, as an exam-
ple, are not more closely related to Pliocene hippos than they are to modern whales.
16
Finally, “fish” still exist today, some of which belonged to the stem group of tetrapods, the ancestral lineage of
all land vertebrates, 380 million years ago.

36
Fig. 21. Simplified phylogenetic tree of birds (Avialae) with corresponding geological strata of different fossils
(blue, orange, and green horizontal lines). The extinct bird species Jeholornis, Confuciusornis, and Sapeornis are
older and more primitive than the extinct Enantiornithes and the oldest representatives of Ornithurae. Neverthe-
less, they all coexisted over a long period, so it is not surprising that we know corresponding fossils from the
same time horizon (t
1
). The dromaeosaurids, in turn, are more primitive than birds. However, some dro-
maeosaurids, such as Utahraptor, evolved later, so they are found in younger strata (t
2
) than, for instance, Ar-
chaeopteryx (t
3
). Own drawing.
Moreover, there are only a few rich fossil deposits in the world, which allow some
sparse insights into the lives of Jurassic-Cretaceous theropods. Among these are the
150-million-year-old Solnhofen limestones from the Franconian Alb in Bavaria, where
paleontologists found all (!) Archaeopteryx specimens. Since the layers of the former
lagoon system formed within a few millions of years, they provide only spot checks.
Thus, we cannot expect fossils to be representative of the duration of their existence
in geological strata. The apparent patterns of fossil diversity
…are heavily distorted by uneven sampling intensity through time from geological biases
that affect the temporal distribution of fossils and formations, differing preservation poten-
tial across organisms and environments, and heterogeneity in collection practice, report-
ing and even geopolitics. Therefore, the known fossil record is not only an incomplete
sample of the total fossil record…, but that incompleteness is also inconsistent through
time and across space. (F
LANNERY
-S
UTHERLAND
et al. 2022)
Nevertheless, “the succession of fossils in time does not correspond to a random se-
quence with respect to their morphological change” (M
AHNER
1986, p. 61). With the
decreasing age of the layers, we find more and more bird-like theropods.
The following two objections do not come from a creationist. Nevertheless, we must
mention them because they stem from the well-known paleornithologist Professor
Alan F
EDUCCIA
,
whose arguments creationists employ for their argumentation.

37
C.11: Does D
OLLO
's “law” argue against theropod ancestry?
Theropod dinosaurs (still lacking any meaningful morphological definition) are generally
characterized by forelimbs approximately half the length of the hind limbs. If birds and
flight arose from theropods, therefore, it would appear extremely unlikely for the fore-
limbs to elongate into avian wings. This statement relates to the generally accepted
Dollo’s Law (or Rule), which deals with the improbability of reversibility of a once lost or
reduced part of the anatomy. S.J. Gould suggested that irreversibility forecloses certain
evolutionary pathways once broad forms have emerged: '[For example], once you
adopt the ordinary body plan of a reptile, hundreds of options are forever closed, and
future possibilities must unfold within the limits of inherited design.'
In other words, re-elongating once greatly reduced forelimbs of dinosaurs makes it
extremely unlikely that they could re-evolve elongated wings. This is exactly what we
see in flightless birds, where there is no example of any of the flightless lineages re-
elongating forelimbs and developing flight wings.
(A. F
EDUCCIA
, email of 12/30/2021 to MN. Reprinted with permission.)
We asked paleontologist Professor Oliver R
AUHUT
, a specialist in predatory di-
nosaurs (theropods), what he thinks of F
EDUCCIA
's argument. In the following
selected parts of his answer:
F
EDUCCIA
's statement is problematic in so many ways that it is almost difficult to ar-
gue against it…
 'Theropod dinosaurs (still lacking any meaningful morphological definition)…'
Theropoda is a subgroup of dinosaurs recognized since the 1880s. It has been de-
fined umpteen times on the basis of apomorphic features, including more recently by
G
AUTHIER
(1986), O
SMÓLSKA
(1990), S
ERENO
(1999), myself (R
AUHUT
2003), H
OLTZ
&
O
SMÓLSKA
(2004), N
ESBITT
et al. (2009), C
AU
(2018), and many more. For a just-
published discussion of the features that separate the various dinosaur groups at the
base, see N
OVAS
et al. (2021, https://doi.org/10.1016/j.jsames.2021.103341).
However, I fear (from other writings of his) that F
EDUCCIA
means a typological char-
acterization, which has no meaning in an evolutionary context and thus has been in-
creasingly abandoned by most biologists over the last 50 years.
 '…are generally characterized by forelimbs approximately half the length of the
hind limbs.'
This genuine typological statement dates from 80 years ago. Theropods show a very
wide variation in the length of the forelimbs compared to the hind limbs, so this
statement is simply wrong. There are animals with strongly reduced forelimbs, such
as abelisaurids or alvarezsaurids, but also theropods with much longer arms, such as
dromaeosaurids. [Quite a few early coelurosaurs, such as Guanlong, a progenitor of
Tyrannosaurus rex, had relatively long arms as well; the authors].

38
 'If birds and flight arose from theropods, therefore, it would appear extremely
unlikely for the forelimbs to elongate into avian wings.'
I do not know any reason why forelimbs should not be able to elongate evolutionarily.
Studies of contemporary animals have shown that exactly such proportions can be
extremely variable and can often even change over a few generations (no matter in
which direction) when a new habitat is conquered.
 'This statement relates to the generally accepted Dollo’s Law (or Rule), which
deals with the improbability of reversibility of a once lost or reduced part of the
anatomy.'
Several remarks on this. First, D
OLLO
's law targets structures that are either com-
pletely rudimentary (i.e., practically useless) or completely reduced, such as the legs
of snakes. This is not the case with the arms of theropods; most theropods have rela-
tively short but fully functional arms that were presumably used for a variety of func-
tions. Moreover, no one has claimed that birds descended from abelisaurids.
On the other hand, D
OLLO
's 'law' has proved to be an often-observed rule, but it is not
incontrovertible, as numerous atavisms show. Just modern genetics (of which D
OLLO
,
of course, could not know anything) has shown that the genetic 'programs' for many
reduced or lost organs are often still present but are not called up any more. There is,
however, no reason why such a thing might not sometimes be reversed (experimen-
tally, for instance, it is possible to trigger the formation of dentition in present-day
birds by adding certain hormones at a certain embryonic stage, although birds have
been toothless for at least 80 million years).
 'S.J. Gould suggested that irreversibility forecloses certain evolutionary path-
ways once broad forms have emerged: '[For example], once you adopt the or-
dinary body plan of a reptile, hundreds of options are forever closed, and future
possibilities must unfold within the limits of inherited design.'
This is the school of thought of construction morphology, which was very popular in
the 1960s and 1970s. There is certainly something to it: of course, evolution must al-
ways take place within the framework of physical, chemical, and genetic possibilities.
Nevertheless, the statement in this form is problematic. First, what is a “reptile”? The
definition of reptiles still in use until the 1990s was typological, which, as stated
above, has no meaning in an evolutionary context. If I define my groups of organisms
in a very narrow framework and then claim that there is no way out of this framework,
then this makes evolution impossible. This quotation then also raises the question:
does F
EDUCCIA
thus believe that birds are not descended from “reptiles” at all?
Where do they come from, then?
 'In other words, re-elongating once greatly reduced forelimbs of dinosaurs
makes it extremely unlikely that they could re-evolve elongated wings.'
This is, if I may say so, nonsense based on the points made above. The forelimbs
are neither 'greatly reduced' (at least not in a form that is not also the case in numer-
ous other reptile groups), and there is no reason at all why the proportions of a func-
tional arm cannot evolve in whatever direction under changed selection conditions.

39
 'This is exactly what we see in flightless birds, where there is no example of
any of the flightless lineages re-elongating forelimbs and developing flight
wings.'
Perhaps, but that is an argument from ignorance. The fossil record of birds is so in-
complete that I would not rule out the possibility that at some point there were flight-
less birds that extended their arms again (especially our modern ratites, which have
an extremely poor fossil record). However, even that argument is irrelevant in the
context of the origin of birds. Flightless birds descend from airworthy birds. Of
course, they have the same arm and hand configuration that constitutes volant birds,
and almost nowhere is the modification of anatomy in adaptation to flight as severe
as in the arms. That is, modifying these extremely specialized arms again for other
uses is evolutionarily difficult but not impossible, as shown, for instance, by penguins.
Here, it would be interesting to see if there were not extensions of the originally re-
duced arms in certain evolutionary lineages of penguins.
(O. R
AUHUT
, e-mail of 12/30/2021 to MN. Reprinted with permission.)
C.12: F
EDUCCIA
's typological classification of the species Scansoriopteryx
Some years ago, news broke that the feathered glider
Scansoriopteryx had overturned the “doctrine” on the
origin of birds. C
ZERKAS
&
F
EDUCCIA
(2014) hold this view
because of the unusual skeletal anatomy of the pigeon-
sized, 120- to 170-million-year-old “climbing winged
creature,” which is presumably identical to Epidendro-
saurus (Fig. 22). This maniraptoran spent much of its life
in trees, possibly climbing up the trunks.
The authors note that certain traits, such as the anteriorly
directed pubis (hipbone), its short length and proportions,
the large ischium, the widely spaced ilia, and the greater
relative total arm length, are all atypical for theropods. In
addition, scansoriopterygids lacked a fully perforated hip
socket (acetabulum):
A fully perforated acetabulum is a sine qua non for dinosaurian status associated
with major changes in posture and gait, by which a more upright posture and
parasagittal stance is attained. (C
ZERKAS
&
F
EDUCCIA
2014, p. 846)
The authors take the mosaic of primitive skeletal traits and advanced avian charac-
ters as a starting point for a bold interpretation. They claim that Scansoriopteryx
lacks “the salient characters necessary to be regarded as dinosaurs.” Furthermore,
they postulate that birds evolved from basal avemetatarsal non-dinosaur ar-
chosaurs, such as Scleromochlus (Fig. 23).

40
Moreover, they reinterpret the basal, still flightless, maniraptorans as secondarily
flightless birds derived after Scansoriopteryx (cf. C
ZERKAS
&
F
EDUCCIA
2014, p. 850),
ignoring all cladistic work that unanimously identify maniraptorans as non-avian
theropod dinosaurs on the basis of their synapomorphies.
When faced with the strong divergence between this odd ancestry hypothesis and
the generally accepted bird phylogeny, laypeople may get the impression of com-
plete arbitrariness and inconsistency in the reconstruction of evolutionary relation-
ships. However, this impression is deceptive, which brings us to the reasons why an
overwhelming majority of experts does not attach evolutionary significance to the
authors' classification.
As R
AUHUT
has indicated above, the main problem is that C
ZERKAS
&
F
EDUCCIA
(henceforth referred to as C&F) do not refer to the regular Dinosauria clade, which is
consistently defined by derived traits. Instead, they choose the traditional but obso-
lete typological category of “dinosaurs,” which refers to an ideal-typical body plan.
This approach focuses on a few “key features,” while at the same time neglecting the
range of variation within the respective taxon. Real species deviate more or less from
any typological scheme. Many species fall completely out of those categories, which
are defined by some rigid group characteristics.
Fig. 23. Left: a drawing of the non-dinosaur archosaur Scleromochlus, quite closely related to the last common
ancestor of crocodilians and birds. Right: phylogenetic tree of Avemetatarsalia showing the basal genus
Scleromochlus and the highly diverse group of dinosaurs (including theropods) nested deep within Avemeta-
tarsalia. Contrary to the orthodox view, C
ZERKAS
&
F
EDUCCIA
(2014) place birds next to Scleromochlus at the
base of Avemetatarsalia. According to this view, the ancestral lineage of birds would have split off very early
from all other archosaurs (red arrow). Thus, birds would only be distantly related to dinosaurs. A large part of
the bird characters would have developed convergently within the dinosaur lineage. Green arrow: well-
established cladistic placement of birds within Dinosauria, which is also supported by innumerable transitional
forms. Artwork by Wikipedia | Author: Pavel.Ruha.CB | License: CC BY-SA 3.0. Phylogenetic tree: own draw-
ing.
We recognize such a typological view, e.g., in C&F's assertion that only “reptiles” with
a fully perforated acetabulum should be regarded as dinosaurs. The same applies to

41
the assertion that individual traits such as “short, anteriorly directed pubic bones” or
the absence of a “supra-acetabular crest” are “unequivocally non-dinosaurian”
(p. 849). Due to a lack of such alleged key features, they detach Scansoriopteryx as
well as the other maniraptorans from Theropoda. Instead, they assign Scansoriop-
teryx to primitive avemetatarsals like Marasuchus just because it superficially looks
more like them with respect to a few individual features.
Ernst M
AYR
also advocated such a typology with his “evolutionary” classification
system. However, such a classification scheme may have strange consequences,
as M
AHNER
&
B
UNGE
(1997, p. 250) have noted:
…cousins can be more closely related than sisters if the former are more similar to
each other than the two sisters.
The considerable subjectivity of such typological considerations is the reason why, in
fact, all contemporary biologists unanimously reject them. If C&F applied phylogenetic
systematics, the supposed essential differences between Scansoriopteryx and dino-
saurs would appear only in the form of graded similarities, between which quite a few
theropods mediate. As thorough feature analyses have shown, Scansoriopteryx, like
all maniraptorans, belongs to Coelurosauria and, consequently, to Dinosauria:
Pennaraptorans are a clade of vaned feathered coelurosaurian dinosaurs that are
comprised of the Oviraptorosauria, Scansoriopterygidae, Dromaeosauridae, Troo-
dontidae, and Avialae… They include the only dinosaurs to have evolved flight and
the only ones to have persisted to the present day. (P
ITTMAN
&
X
U
2020, p. 38)
The notion that scansoriopterygids are early-branching avialans... has been replaced
by anatomical evidence grouping some or all scansoriopterygids with oviraptoro-
saurians... or as early-branching paravians… (P
ITTMAN
&
X
U
2020, pp. 44–48)
C&F not only tear apart the Theropoda clade but also create an enormous gap be-
tween basal archosaurs and birds (cf. P
ADIAN
&
H
ORNER
2002, p. 121). The artificially
created gap between Triassic archosaurs like Scleromochlus and bird-like forms like
Scansoriopteryx would have to be bridged by corresponding transitional forms now.
However, scientists found not even one such form among the basal Avemetatarsalia
because they appear only in the highly diversified dinosaur lineage. The early
maniraptorans cannot close this gap either, because C&F reinterpret them as secon-
darily flightless birds, regardless of their numerous plesiomorphic features! Phyloge-
netically, C&F’s relationship hypothesis is thus extremely implausible.
In short: C&F tear apart the solidly established descent community of Thero-
poda by focusing only on a few “key features” of a typologically defined dinosaur
body plan rather than neatly using all derived characters for classification.

42
Fatally, the phylogenetic tree favored by C&F would require a maximum of conver-
gently developed traits: all features that evolved within Ornithodira (Fig. 23) and that
are present in both non-avian dinosaurs and birds would have to have evolved in
parallel. Parallelisms are always to be expected in closely (!) related groups, like
Maniraptora (see section C.1). The assumption, however, that dozens, if not hun-
dreds, of anatomical details arose in parallel at the base of the Avemetatarsalia phy-
lum as well as in the phylogenetically distant dinosaur group is completely implausi-
ble. Therefore, an even more primitive archosaur in the lineage of Avesuchia, from
which crocodiles descended, should have had the developmental genetic potential
for such far-reaching parallel developments. Such a scenario is not compatible with
our knowledge of developmental biology.
Keep in mind that we are not talking about the convergent emergence of superficially
similar structures easily explained by functional similarity and adaptation to the same
habitats. Such analogous features would be, for example, the wings of pterosaurs
and the wings of birds. Rather, we are talking about detailed correspondences of hi-
erarchically organized, highly derived feature complexes. Countless features of birds
can be traced in graded similarity back to early maniraptorans, coelurosaurs, thero-
pods, and dinosaurs. These include dozens of details in the fine structure of the
skeleton (C
AU
2018, pp. 5–9), as well as the air sac system, the thin-walled, air-filled
hollow bones connected to the air sacs, the long legs with three thin main toes, the
ultra-structures of the feathers and feathery integuments, and many, many more.
As pointed out, there are graded similarities within Sauropsida and therefore be-
tween birds and other theropods as well. C&F dissolve this pattern of shared apo-
morphic characters (synapomorphies) into arbitrarily constructed convergences.
Hence, it is unclear why they seek the last common ancestral species of birds and
non-avian theropods precisely among archosaurs, of all things. They could just as
easily seek them among basal parareptiles or synapsids and postulate even more
far-reaching convergences.
Since they apparently do not accept consistent patterns of graded similarities as
good evidence for phylogenetic relationships, the question arises why they assume
evolution at all.

43
C.13: On the convergence of feathery integuments in pterosaurs
Let us turn back to the evolution of feathers. J
UNKER
(2022) points out that the in-
teresting feather intermediate form of type 3a (Figs. 1 and 3) has been discovered
in pterosaurs, which are evolutionarily more distantly related to birds. In his opinion,
that questions the interpretation of type 3a as precursors of
“
true feathers
”
:
On the basis of the distribution of type 3b ‘feathers’ [this corresponds to type 3a
above] on the body, one would have to assume—as also noted by Cincotta et al.—a
convergent origin in pterosaurs and dromaeosaurids. Thus, even if one argues evolu-
tionarily, just the interesting stage 3b (resembling the integument structures of Tu-
pandactylus) could not be interpreted as a precursor of true feathers.
First, the presence of feathery appendages in pterosaurs has been known for many
years (Y
ANG
et al. 2018; F
OTH
et al. 2020). Moreover, this finding entails no evolu-
tionary problem at all. Since pterosaurs and dinosaurs are sister groups within Ave-
metatarsalia, it is convincing that the formation of feathery skin appendages had al-
ready been present in the developmental possibilities of their last common ancestor
some 230–250 million years ago (Y
ANG
et al. 2018; Fig. 24).
Fig. 24. Evolutionary relationships in
Avemetatarsalia, which contains ptero-
saurs and dinosaurs as close relatives.
The diagram illustrates the single origin
of feathers (better say: proto-feathers)
in a common ancestor of both groups
some 230–250 million years ago and
multiple losses within different dinosaur
species. The red branches indicate
lineages with proto-feathers; the blue
ones symbolize lineages with scales
only; and the gray lines represent line-
ages without skin fossils. Own sketch,
redrawn from B
UCHHOLZ
(2021).
In other words, the potential for the morphogenesis of proto-feathers has been pre-
served in the ancestral lineage of birds and was lost in some side branches (Fig. 24).
Hence, there is no reason why we cannot interpret the feathery integuments of ptero-
saurs as precursors of avian feathers—as true proto-feathers.

44
C.14: Were pterosaurs feathered?
Remarkably, J
UNKER
(2022) denies that pterosaurs possessed feathers at all by pre-
senting the following argument:
Who does not first think of ‘feathers’ as the flat bird feathers that form part of a complex
flying apparatus? Messages like ‘feathers in pterosaurs’ therefore seem misleading.
However, the notion that pterosaurs possessed feathers seems “misleading” only
against the background of Carl L
INNAEUS
’s traditional systematics, which defined
groups typologically and assumed constancy of traits, neglecting existing variation
(see above in section C.12).
Thus, L
INNAEUS
’s classification still clearly demarcates birds, together with their most
prominent features (the feathers), from “reptiles.”
17
However, we have known for a
long time that birds and “reptiles” are not essentially different groups. Instead, they
form the common taxon of Sauropsida, in which the formerly “great” differences be-
tween “reptiles” and birds exist only in the form of graded similarities (see above in
sections B, C.1, C.7, and C12).
In addition, many bird features appear in the fossil record in a gradual and suc-
cessive way, as we expect from an evolutionary point of view. This holds true
also for the keratinous skin appendages of various dinosaurs, gradually leading
to highly developed pennaceous feathers in maniraptorans.
As far as pterosaurs are concerned,
Y
ANG
et al. (2018) concluded that the different
pycnofiber types on pterosaurs and filamentous structures on non-avian dinosaurs
and birds show profound morphological, ultrastructural, and chemical similarities,
which confirms their homology. In that case, those structures would have had a sin-
gle evolutionary origin some 230–250 million years ago, meaning that pycnofibers
are (proto-) feathers. Then it is purely a matter of taste whether to call these struc-
tures “true feathers,” “feather precursors,” or whatever. Personally, we would prefer
the names “pycnofibers,” “proto-feathers,” or “feathery integuments.”
17
Contrary to birds, the traditional category of reptiles is not a closed descent group. Rather, it is a
paraphyletic assembly of species; that is, not all of their descendant species are included in this group.
To indicate that there are no reptiles in the phylogenetic system (W
IESEMÜLLER
et al. 2003, p.107), we
put the word reptiles in quotation marks.

45
C.15: Did feathers evolve for flight?
A typical problem often encountered in public discussion concerns the “purpose”
of the development of derived structures. Laypeople usually have the idea of a
linear, quasi-intended line of development. Creationists reinforce this opinion by
arguing in a typological way. One example is J
UNKER
2022:
A consequence of the confusion of terms is the confusing statement that pterosaurs
possessed feathers. One will think here spontaneously that this has something to do
with their flight ability. However, what should be the purpose of feathers in a special-
ist that can fly excellently with a sophisticated flying skin (cf. Pittman et al. 2021)?
These formations obviously contribute nothing to flying ability.
If feathers necessarily suggested flight, then Anchiornis would not have had any feath-
ers either. They consisted mainly of thick, inflexible

-keratins (P
AN
et al. 2019), and
there is still dispute over what this feature could have contributed to flight since com-
puter modeling revealed that the propatagium is the major lift-generating component of
the wing (B
ROWN
&
C
OGLEY
1996). Similarly, the feathers of flightless oviraptorosaurs
(“egg thief lizards”) and those of penguins should not be considered feathers either.
As discussed in section C6, a large part of the evolution of avian features occurred in
contexts that had nothing to do with birds or avian flight. This is a principle that, in
general, is typical of evolution. For instance, as discussed before, the highly efficient
lungs of birds, including their associated air sac systems, had already evolved in non-
avian theropods, which thus achieved a significant increase in physical performance
compared to previous performance. That is a crucial success criterion for actively
hunting predators.
It was the same story with the feathers: before birds could use them for active flap-
ping flight, they served for gliding. Before that, they were used in some other func-
tional context, such as thermal insulation, display, camouflage, and brooding (Z
HOU
2014). We know the latter thanks to an oviraptoran covered by a shifting dune; it
died in brooding posture and then fossilized (C
LARK
et al. 1999).

46
D. Summary
The finding that birds are descendants of certain dinosaurs has been a scientific con-
sensus for over 20 years. Only a very few experts still question it. In the publications of
those who deny macroevolution and want to have it replaced by an “intelligent” origin
(that is, creationists of various stripes), however, such criticism is clearly overrepre-
sented. Unlike the scientists they cite, creationists do not primarily cast doubt on the
membership of birds in particular archosaur taxa. Rather, they want to see the evolu-
tionary development as such (and not only that of birds) questioned. They achieve this
only by mixing the criticism of individual scientists with antiquated and factually incor-
rect ideas on evolution.
One of the creationists who is concerned with criticizing avian evolution is Reinhard
J
UNKER
, former managing director of the German evangelical association W
ORT
-
UND
-
W
ISSEN
. His argumentation is typical of creationist criticism. Since such criticism relies
on antiquated views of evolution, numerous findings look like serious anomalies. Open
questions about the causes of certain evolutionary steps are supposed to deepen
doubts about bird evolution.
In this review, we show that creationist criticism is working under a misunderstanding or
misrepresentation of evolutionary theory. This
line of reasoning is influential worldwide.
It is representative of the whole creationist spectrum.
The ten main theses of our analysis are as follows:
 The statement that birds are the product of a long, evolutionary-historical process
is logically completely independent of the question of how this evolution proceeded
in detail. The same is true for other natural processes. For instance, marine fossils
testify to the process of mountain folding even without knowledge of the mecha-
nisms or forces responsible for it in the Earth's mantle.
 The acceptance of avian evolution rests on the fact that we can put theropod fos-
sils into a sequence in which their morphology more and more takes the shape of
modern birds. Given that descent, heritable variability, and speciation are facts of
experience, bird evolution (or evolution in general) would remain untouched even if
we knew nothing about its mechanisms.
 Creationists allege a “waiting time problem” causing a very slow pace of evolution.
Hence, in their eyes, evolutionary mechanisms are overstrained by producing the
great diversity of avian forms “abruptly” in geologically short periods. However,
their reasoning is quite wrong. First, creationists do not seem to have understood

47
how novelties arise in evolution. For instance, evolution never faced the task of
waiting until a “fixed and pre-specified target” was reached. Second, the evolvabil-
ity of novelties, even of irreducibly complex systems, within short time periods is a
well-corroborated and no longer reasonably disputable fact (see, for instance,
H
UNT
2007b; T
ONKIN
et al. 2008; D
E
K
RAKER
&
G
ERSHENZON
2011; S
AUTER
et al.
2012; T
ROTTER
et al. 2014; Y
ONA
et al. 2018; R
AWCLIFFE
2019; B
EYER
et al. 2022;
N
EUKAMM
2022).
 When it comes to the “abrupt” appearance of characters in the fossil record, the
explanation of punctuated equilibria must be considered as well as the ambiguity of
the term “abrupt”. When a paleontologist speaks of the “abrupt” appearance of a fea-
ture, he may still think of periods of millions of years. Here, the biased and fragmen-
tary sedimentary record, both in time and in space, must be taken into account.
Abrupt appearance may hence be a geological artifact.
 Creationists ignore the progress of evolutionary developmental biology (Evo-Devo)
in solving specific problems. This includes, for example, the question of how the
supposedly contradictory counting of fingers in some theropods (apparently, I-II-III)
and birds (II-III-IV) fits together. Evo-Devo can also explain the capability for com-
paratively rapid convergent evolution of quite a few avian features.
 Evolution deniers portray the convergence problem as much more serious than it
is. Despite widespread convergence and uncertainty about the position of some
taxa, there is a remarkable consensus on the backbone structure of the family tree
of the ancestors of birds and the relative hierarchical placement of almost all major
clades that constitute this tree. Birds still lie in a deeply nested position within
Theropoda (R
AUHUT
&
F
OTH
2020, p. 37).
 Contrary to creationists' reasoning, widespread convergences are not anomalies
but rather a clear expectation of evolutionary theory when developmental biological
background knowledge is considered (M
C
G
HEE
2011, p. 7).
 For at least half a century, the idea that evolution must run continuously and line-
arly has not been compatible with contemporary knowledge of the processes of
speciation and differentiation of species (M
AHNER
1986, p. 68). Creationists do not
seem to know that just these processes are accompanied by discontinuities, in-
congruities, and a zigzag course (such as reversions of traits in different lineages).
 Creationists place antiquated expectations on the nature of evolutionary transi-
tional forms and claim to have recognized “contradictory” trait mosaics. Hence,

48
they ignore that mosaic evolution is the result of genetic burdens (R
IEDL
2003, p.
209) and lineage-splitting events (M
AYR
1967, p. 465 f.).
 The claim that the features of the avian body plan could not have evolved isolated
from each other is false. The theropod fossils can be placed in a sequence in
which the “irreducibly complex overall organization” of birds resolves into a series
of consecutive feature addition steps.
 Creationists seem not to understand cladogenesis; otherwise, they would not prob-
lematize the “phylogenetic-stratigraphic discrepancy,” i.e., the chronologically later
appearance of some species with more primitive features in the fossil record. (For
the attempt to compress the geological time scale by six orders of magnitude, see:
https://www.ag-evolutionsbiologie.net/html/2014/kreationismus-und-radiometrische-datierung.html).
E. Acknowledgement
We would particularly like to thank John H
ARSHMAN
, a specialist in dinosaur evolution,
who reviewed this paper and contributed to its accomplishment with his critical com-
ments. Thanks also go to Matt Y
OUNG
for editorial review. Furthermore, we give
thanks to Prof. Oliver R
AUHUT
for his statements, which he allowed us to reproduce in
section C.11. We would also like to thank Dandan W
U
from the Peking Natural Sci-
ence Organization (PNSO) and Stefan P
ROCHASKA
from SchuBu Systems GmbH for
their permission to reproduce their images.

49
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