Evolution: bibliography of confusing new discoveries


Richard Moore

Original source URL:

By: Various
Discovery Institute
January 1, 2004

NOTE: On Monday, 11 March 2002, Stephen Meyer and Jonathan Wells of the 
Discovery Institute submitted the following Bibliography of Supplementary 
Resources to the Ohio State Board of Education. These 44 scientific publications
represent important lines of evidence and puzzles that any theory of evolution 
must confront, and that science teachers and students should be allowed to 
discuss when studying evolution. The publications are not presented either as 
support for the theory of intelligent design, or as indicating that the authors 
cited doubt evolution. Discovery Institute has made every effort to ensure that 
the annotated summaries accurately reflect the central arguments of the 

The following scientific articles, papers, and monographs are drawn from leading
journals in the respective disciplines represented: e.g., Cell (for molecular 
biology), Nature and Science (for general science), Trends in Ecology and 
Evolution and Annual Review of Ecology and Systematics (for evolutionary 
biology), or from prominent university presses (e.g., Cambridge University 
Press). The publications represent dissenting viewpoints that challenge one or 
another aspect of neo-Darwinism (the prevailing theory of evolution taught in 
biology textbooks), discuss problems that evolutionary theory faces, or suggest 
important new lines of evidence that biology must consider when explaining 

Over half of the papers listed below were published within the past 2-3 years, 
with the remainder published throughout the 1990s. The resources are organized 
in three broad categories: (a) Questions of Pattern, (b) Questions of Process, 
and (c) Questions about the Central Issue: the Origin and Nature of Biological 
Complexity. ³Pattern² concerns the large-scale geometry of biological history: 
how are organisms related to each other, and how do we know that? ³Process² 
concerns the mechanisms of evolution, and open problems in that area. Lastly, 
³Biological Complexity² concerns the origin of what makes organisms 
distinctively what they are: the source of the specified complexity of 
biological information.

Questions of Pattern

1. Ying Cao, Axel Janke, Peter J. Waddell, Michael Westerman, Osamu Takenaka, 
Shigenori Murata, Norihiro Okada, Svante Pääbo, and Masami Hasegawa, ³Conflict 
Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian 
Orders,² Journal of Molecular Evolution 47 (1998): 307-322.

It is widely believed that molecular data confirm morphological data when the 
history of groups such as the mammals is being reconstructed. Many cases exist, 
however, where molecules (such as proteins) give ³false² or erroneous 
phylogenies. This paper, by a team of researchers from Japan, Germany, and 
Australia, demonstrates that different mitochondrial proteins can give 
different, and contradictory, groupings. In particular, the protein NADH 
dehydrogenase (ND1) places primates and rodents together as closest relatives, 
with ferungulates (artiodactyls + cetaceans + perisodactyls + carnivores) as 
more distantly related to primates -- in contradiction to most other data, which
places primates and ferungulates together as closest relatives. The authors 
conclude that this anomalous phylogenetic grouping ³is not due to a stochastic 
error, but is due to convergent or parallel evolution² (p. 321), suggesting that
molecular evidence is not free from the confounding (historically misleading) 
effects known to plague other types of systematic data, such as anatomical 

2. Simon Conway Morris, ³Evolution: Bringing Molecules into the Fold,² Cell 100 

In this article, Conway Morris (a paleontologist and professor in the Department
of Earth Science, Cambridge University) argues that ³when discussing organic 
evolution the only point of agreement seems to be ŒIt happened.¹ Thereafter, 
there is little consensus, which at first sight must seem rather odd.² Conway 
Morris goes on however to stress that ³our understanding of evolutionary 
processes and mechanisms is incomplete² (p. 1), and ³constructing phylogenies 
[evolutionary histories] is central to the evolutionary enterprise, yet rival 
schemes are often strongly contradictory. Can we yet recover the true history of
life?² (p. 1). He concludes his review of current problems in evolutionary 
biology with a provocative thesis:

...if evolution is in some sense channeled, then this reopens the controversial 
prospect of a teleology; that is, the process is underpinned by a purpose. It is
no coincidence that interest in the Anthropic Principle, which broadly seeks 
evidence for the boundary conditions of the Big Bang and the ensuing physics and
chemistry uniquely favoring the emergence of life...is being extended to the 
fields of biochemistry and molecular biology (for one view, see Denton, 1998)

The book Conway Morris cites here -- by the New Zealand geneticist Michael 
Denton -- is entitled Nature¹s Destiny: How the Laws of Biology Reveal Purpose 
in the Universe.

3. W. Ford Doolittle, ³Tempo, Mode, the Progenote, and the Universal Root,² in 
W. Fitch and F. Ayala, eds., Tempo and Mode in Evolution (Washington, DC: 
National Academy Press, 1995), pp. 3-24.

4. W. Ford Doolittle, ³At the core of the Archaea,² Proceedings of the National 
Academy of Sciences USA 93 (1996): 8797-8799.

5. W. Ford Doolittle, ³Uprooting the Tree of Life,² Scientific American, 
February 2000, pp. 90-95.

6. W. Ford Doolittle, ³Phylogenetic Classification and the Universal Tree,² 
Science 284 (1999):2124-2128.

7. W. Ford Doolittle, ³The nature of the universal ancestor and the evolution of
the proteome,² Current Opinion in Structural Biology 10 (2000):355-358.

A professor in the Department of Biochemistry and Molecular Biology of Dalhousie
University (Canada), W. Ford Doolittle is one of the world¹s leading molecular 
evolutionists. In these three related articles (the Scientific American piece is
aimed at a general audience), Doolittle argues that recent discoveries in 
molecular biology have begun to fracture the root of Darwin¹s single Tree of 
Life. ³Thus, there is no more reason to imagine only a single first kind of cell
as the progenitor of all contemporary life,² he argues (p. 356 of the Current 
Opinion article), ³than there is to imagine only Adam and Eve as progenitors of 
the human species.² Doolittle contends that biology must rethink Darwin¹s single

Some biologists find these notions confusing and discouraging. It is as if we 
have failed at the task that Darwin set for us: delineating the unique structure
of the tree of life. But in fact, our science is working as it should. An 
attractive hypothesis or model (the single tree) suggested experiments, in this 
case the collection of gene sequences and their analysis with the methods of 
molecular phylogeny. The data show the model to be too simple. Now new 
hypotheses, having final forms we cannot yet guess, are called for. (p. 95, 
Scientific American article)

8. Douglas H. Erwin, ³Early introduction of major morphological innovations,² 
Acta Palaeontologica Polonica 38 (1994): 281-294.

Is the puzzle of the Cambrian Explosion -- the geologically sudden appearance of
the major animal body plans -- merely an artifact of taxonomic methods, a 
consequence of retrospectively classifying disparate groups that, at their 
origin, were not distinct? Douglas Erwin, a paleontologist at the Smithsonian 
Institution, says no. He argues that ³the primary problem is the generation of 
the novel morphologies accorded high rank² -- forms as distinctive as 
arthropods, mollusks, and chordates -- ³not higher taxa per se. ... The 
asymmetric pattern of morphological innovation [exhibited in the Cambrian 
Explosion] would be with us even if systematists eliminated ranks entirely² (p. 
282, 284). In other words, the arthropod body plan by any other name would be as
strange if it appeared suddenly in the Cambrian, as do actual arthropods. Given 
that the problem of the Cambrian Explosion is real, asks Erwin, how are we to 
solve it? In this article, he reviews several competing (albeit not necessarily 
exclusive) theories: empty ecospace (the idea that the animals radiated because 
they could, ³ecospace² -- i.e., specific niches -- stood open and waiting to be 
occupied); genetic hypotheses, such as elevated mutation rates and novel genetic
mechanisms; developmental hypotheses, which postulated that rapid morphological 
change was driven by the ³discovery² of novel cell types and ontogenetic 
architectures; and lastly, complexity models, which regard initial bursts of 
innovation, followed by stabilization, ³as an expected consequence of complex 
systems² (p. 289). Erwin does not decide in favor of any of these hypotheses, 
noting that although future work may alleviate the problem of testing, tests 
cannot ³be conducted with much confidence today because of uncertainties in 
metazoan [animal] phylogeny² (p. 291).

9. Trisha Gura, ³Bones, molecules...or both?² Nature 406 (2000):230-233.

This article from Nature, one of the top two science journals in the world (the 
other being Science), explores the conflicts that arise in biological 
systematics -- the science that deals with the large-scale relationships of 
organisms -- between anatomical lines of evidence, such as skeletal data, and 
newer sources of evidence, such as DNA or proteins: the molecular data:

When biologists talk of the Œevolution wars¹, they usually mean the ongoing 
battle for supremacy in American schoolrooms between Darwinists and their 
creationist opponents. But the phrase could also be applied to a debate that is 
raging within systematics. On one side stand traditionalists who have built 
evolutionary trees from decades of work on species¹ morphological 
characteristics. On the other lie molecular systematists, who are convinced that
comparisons of DNA and other biological molecules are the best way to unravel 
the secrets of evolutionary history. (p. 230)

Science writer Gura explains how molecules and morphology in evolutionary 
systematics are frequently in conflict, giving different histories for groups of
organisms, and the attempts that are being made to sort out the contradictions.

10. Michael S. Y. Lee, ³Molecular Clock Calibrations and Metazoan Divergence 
Dates,² Journal of Molecular Evolution 49 (1999): 385-391.

Laypeople (and scientists from other fields) often assume that evolutionary 
biologists have successfully dated the historical divergence points of species 
using molecular data -- and that such dates provide evidentially independent 
confirmation of evolutionary hypotheses. The so-called ³molecular clock² thus 
conveys an aura of analytic precision in phylogenetic estimation. In this paper,
however, Michael Lee (a molecular evolutionist at the University of Queensland, 
Australia) explains that molecular clocks in fact rest on paleontological 
assumptions for calibration, and thus that their reliability can be no better 
than the fossil data (and hypotheses) that they employ. As he explains,

Molecular clocks need to be calibrated, and this can be done only by direct 
recourse to (hopefully reliable) dates in the fossil record. Calibration of 
clocks indirectly through use of dates inferred from other molecular clock 
studies (which in turn are ultimately based on the fossil record) is less 
desirable, as it adds an extra layer of uncertainty, especially if these 
molecular inferences are highly controversial. (p. 386)

Reviewing several molecular clock studies, Lee is troubled that only a single 
fossil calibration point is used, and yet ³it appears that none of these 
molecular studies have critically examined the reliability of this fossil dating
by consulting the primary palaeontological literature, which is surprising in 
light of their conclusions that the fossil record is liable to be very 
misleading² (p. 386). In summary, Lee urges great caution in putting much weight
on molecular clocks, given their reliance on palaeontological calibration:

Even if one makes the bold assumption that molecular clock models have little 
error, there seems little objective reason for accepting as sacrosanct a few 
fossil dates used in calibrations and rejecting as unreliable the much more 
numerous fossil dates that contradict the resultant molecular estimates. ... 
Unfortunately, molecular clock studies have yet to provide a set of rigorous 
criteria for justifying which fossil dates are to be used in calibrations and 
which are to be treated with skepticism. (p. 389)

11. Michael S. Y. Lee, ³Molecular phylogenies become functional,² Trends in 
Ecology and Evolution 14 (1999): 177-178.

It has been widely believed that ³molecular convergence² is impossible: i.e., 
that gene and protein sequences could not evolve to the same sequence via 
natural selection. While morphological patterns may exhibit misleading 
functional similarities -- misleading, that is, because the similarity in 
question would exist not for historical, but adaptive reasons -- molecular data 
were thought to convey a reliable historical signal. If a high enough degree of 
similarity were observed, the molecular data indicated true (evolutionary) 
history, or homology. In this report, however, Michael Lee of Queensland 
University explains that such ³optimistic views of sequence data have now been 
challenged by recent studies that suggest that molecular data, like 
morphological traits, can exhibit concerted adaptive evolution² -- meaning that 
molecular similarities may not always give reliable historical information. As 
Lee reports, of one such study,

...the mitochondrial cytochrome b gene implied...an absurd phylogeny of mammals,
regardless of the method of tree construction. Cats and whales fell within 
primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, 
bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably 
the most commonly sequenced gene in vertebrates, making this surprising result 
even more disconcerting. (p. 177)

Lee concludes that ³morphological and molecular systematics might have more in 
common than previously assumed² (p. 178), meaning that misleading similarities, 
long the bane of classical evolutionary systematics, may also infect molecular 

12. Detlef D. Leipe, L. Aravind, and Eugene V. Koonin, ³Did DNA replication 
evolve twice independently?² Nucleic Acids Research 27 (1999): 3389-3401.

Replicating one¹s store of genetic information (DNA) is a basic process in all 
known organisms. While functional similarities exist among bacterial and 
eukaryotic (and archaeal) DNA replication systems, many of the component 
proteins of their respective replication machines are, surprisingly, 
non-homologous. As Detlef Leipe (of Department of Biology at Texas A & M 
University) and his co-workers explain,

DNA replication is an essential, central feature of cellular life....It is 
therefore surprising that the protein sequences of several central components of
the DNA replication machinery, above all the principal replicative polymerases, 
show very little or no sequence similarity between bacteria and 
archaea/eukaryotes. (p. 3389)

Given these fundamental differences in basic cellular machinery, Leipe et al. 
suggest that the process of DNA replication may have evolved at least twice 
independently -- a hypothesis quite unexpected on neo-Darwinian (common 
ancestry) assumptions. ³The hypothesis of an independent evolution of DNA 
replication,² conclude Leipe et al., ³offers a parsimonious explanation for the 
strange assortment of apparently unrelated, homologous but not orthologous and 
orthologous components in the DNA replication machineries of bacteria and 
archaea/eukaryotes² (p. 3401).

13. Peter J. Lockhart and Sydney A. Cameron, ³Trees for bees,² Trends in Ecology
and Evolution 16 (2001): 84-88.

The relationships of the four major groups of bees (the highly eusocial honey 
bees, the stingless bees, the bumble bees, and the solitary orchid bees) 
presents a classic challenge to evolutionary analysis. Lockhart (Massey 
University, New Zealand) and Cameron (the University of Arkansas) explain that 
³molecular and morphological data have suggested strikingly different 
phylogenetic relationships among corbiculate bee tribes² (pp. 84-85), an 
unresolved problem that they conclude does not stem from the different methods 
used by different investigators trying to reconstruct the history of the bees. 
³Disagreement exists because analyses of [DNA] sequences and morphology suggest 
different hypotheses, and not because researchers have used different criteria 
for building and testing evolutionary trees² (p. 87).

14. David P. Mindell, Michael D. Sorenson, and Derek E. Dimcheff, ³Multiple 
independent origins of mitchondrial gene order in birds,² Proceedings of the 
National Academy of Sciences USA 95 (1998): 10693-10697.

The genetic information possessed by mitochondria, cell organelles with their 
own small complement of DNA (in a circular chromosome coding for 37 proteins, 
usually abbreviated as ³mtDNA²), has been widely viewed as a good marker of 
phylogeny: the historical branching pattern that links organisms. In this study,
however, David Mindell of the University of Michigan and his colleagues found 
that the specific order of mtDNA in birds ³has had multiple independent 
originations...based on sampling of 137 species representing 13 traditionally 
recognized orders.² This suggests that -- contrary to expectations -- patterns 
such as gene order may be under functional constraints. If so, mtDNA may be 
subject to the same kind of historically misleading similarities that affect 
other types of systematic data. ³Our finding of multiple independent origins for
a particular mtDNA gene order among diverse birds,² conclude Mindell et al., 
³and findings by others of convergent evolution for mt sequence duplications in 
snakes and lizards...suggests that some constraints on gene order mutation are 
in effect² (p. 10696). This may considerably complicate the use of mtDNA as a 
historical marker in evolutionary studies.

15. Paul Morris and Emily Cobabe, ³Cuvier meets Watson and Crick: the utility of
molecules as classical homologies,² Biological Journal of the Linnean Society 44
(1991): 307-324.

Molecular data are widely employed in attempts to reconstruct the history of 
life -- in large measure because such evidence is thought to be free from the 
interpretative difficulties that have plagued anatomical and other larger-scale 
data since Darwin¹s time. This article by the evolutionary theorist Paul Morris 
of Harvard University (and his colleague Emily Cobabe, at the time of 
publication working at the University of Bristol) challenges this viewpoint, 
however, suggesting that ³similar or even chemically identical molecules may be 
unrelated² (p. 307). If molecules (like morphology) is under strong functional 
constraints, similarities may indicate not history, but equivalent functional 
demands faced by diverse organisms. ³As with anatomical data,² Morris and Cobabe
conclude, ³structural identity in molecules is not always indicative of 
relatedness. Molecules can be highly structurally and functionally constrained. 
In proteins, this may require a demonstration of homology beyond sequence 
identity² (p. 322).

16. Arcady R. Mushegian, James R. Garey, Jason Martin, and Leo X. Liu, 
³Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of 
Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes,² 
Genome Research 8 (1998):590-598.

The authors of this article work in the growing field of bioinformatics, where 
large amounts of genetic data are analyzed (by computer) for patterns of 
similarity and difference. In this study, Mushegian and his colleagues found 
that ³different proteins generate different phylogenetic tree topologies² (p. 
591), meaning that some proteins may give an ³incorrect² evolutionary history 
for the organisms from which they have been taken. Protein A, for instance, may 
indicate that humans and flies are more closely related, whereas Protein B may 
indicate that humans and nematodes are more closely related. Mushegian et al. 
advise that genetic and protein data should be treated with caution as markers 
of evolutionary history, because ³different proteins can generate different 
apparent tree topologies [evolutionary histories], strongly suggesting that 
historical phylogenies should not be inferred based on a single protein-coding 
gene² (p. 596).

17. Gavin J. P. Naylor and Wesley M. Brown, ³Amphioxus Mitochondrial DNA, 
Chordate Phylogeny, and the Limits of Inference Based on Comparisons of 
Sequences,² Systematic Biology 47 (1998): 61-76.

A popular perception (even among evolutionary biologists) is that molecular 
lines of evidence -- in particular, DNA sequence data -- strongly confirm more 
classical lines of evidence, such as fossils, and anatomical data drawn from 
extant species. In this study, however, by two molecular systematists Gavin 
Naylor (Zoology & Genetics, Iowa State University) and Wesley Brown (Biology, 
University of Michigan), mitochondrial DNA (mtDNA) drawn from 19 animal species 
failed ³to yield the widely accepted phylogeny for chordates, and, within 
chordates, for vertebrates² (p. 61). This incorrect result was generated no 
matter what analytical method was used:

Given the breadth and the compelling nature of the data supporting [the 
expected] phylogeny, relatioships supported by the mitochondrial sequence 
comparisons are almost certainly incorrect, despite their being supported by 
equally weighted parsimony, distance, and maximum-likelihood analyses. The 
incorrect groupings probably result in part from convergent base-compositional 
similarities among some of the taxa, similarities that are strong enough to 
overwhelm the historical signal. (p. 61)

If convergence afflicts molecular data in ways ³strong enough to overwhelm the 
historical signal,² then analyzing DNA and protein similarities may not provide 
the royal road to the true history of life, any more than classical lines of 
comparative evidence could.

18. Colin Patterson, David M. Williams, and Christopher J. Humphries, 
³Congruence Between Molecular and Morphological Phylogenies,² Annual Review of 
Ecology and Systematics 24 (1993): 153-188.

The authors, at the time of the publication of this paper all working at the 
British Museum of Natural History (Patterson is now deceased), argue that the 
widespread view that ³molecules confirm morphology² in evolutionary studies is a
myth: ³...in practice, we find that incongruence between molecular trees 
(generated from different data sets or by different analytical methods) is as 
striking or pervasive as is incongruence between trees generated by 
morphologists² (p. 153). They conclude that ³as morphologists with high hopes of
molecular systematics, we end this survey with our hopes dampened. Congruence 
between molecular phylogenies is as elusive as it is in morphology and as it is 
between molecules and morphology. (p. 179)

19. Michael K. Richardson et al., ³There is no highly conserved stage in the 
vertebrates: implications for current theories of evolution and development,² 
Anatomy and Embryology 196 (1997): 91-106.

Biology textbooks for decades have featured drawings purporting to show that 
vertebrate embryos begin development looking essentially the same, and only 
later diverge to their characteristic morphologies. Michael Richardson, a 
British embryologist, and an international team of co-workers inspected actual 
vertebrate embryos and found that the textbooks diagrams (which trace to the 
19th century German embryologist Ernst Haeckel) are false and misleading. There 
is no single stage of embryogenesis in vertebrates where all forms are similar: 
³The wide variation in morphology among vertebrate embryos is difficult to 
reconcile with the idea of a phylogenetically-conserved tailbud stage, and 
suggests that at least some developmental mechanisms are not highly constrained²
(p. 91).

20. Kensal E. van Holde, ³Respiratory proteins of invertebrates: Structure, 
function and evolution,² Zoology: Analysis of Complex Systems 100 (1998): 

Oxygen carriers such as hemoglobin are vitally important proteins throughout the
animals. But other oxygen-carrying molecules are utilized as well, such as 
hemocyanin (which uses a copper, not Fe-heme, binding site). The phylogenetic 
distribution of oxygen-carrying molecules is very puzzling, however, and cannot 
be easily fitted into current models of animal evolution. As Kensal van Holde 
(Biochemistry, Oregon State University) explains, ³the phylogenetic distribution
of the whole group of oxygen transport proteins cannot easily be reconciled with
many current models of metazoan evolution.² After reviewing the contradictions 
between the distribution of oxygen carriers and hypotheses of animal evolution, 
van Holde concludes that ³it seems likely that we need much more information 
before all parts of the puzzle can be fitted together² (p. 296).

21. Kenneth Weiss, ³We Hold These Truths to Be Self-Evident,² Evolutionary 
Anthropology 10 (2001):199-203.

Kenneth Weiss is the Evan Pugh Professor of Anthropology and Genetics at Penn 
State University. In this article, he argues that evolutionary biology relies 
far more on axioms -- unprovable assumptions -- than many biologists are willing
to admit. He writes:

The prevailing cosmology that greeted Darwin¹s Origin of Species in 1859 rested 
on the theologically based assumption that the universe was created at a single 
point in time by a purposive intelligence who selected a bestiary of species 
designed to be adapted to their environments. This was assumed to be given truth
rather than something one had to infer from observation. By comparison, in 
biology we believe we are practicing a rigorous, objective, empirical 
method-of-knowing that does not rest on wishful thinking. Yet much of our work 
rests on axioms -- conventional wisdom or laws of Nature, if you will -- that we
assume to be true, but cannot actually prove. (p. 199)

Weiss ends by saying ³It is healthy to be skeptical even of truths we hold to be
self-evident, and to ask: suppose it isn¹t true -- what would follow? Do we need
a theory of evolutionary biology?² (Please note that in his footnotes, Weiss is 
highly skeptical of creationism, and endorses what he calls ³the fact² of 

22. Carl Woese, ³The universal ancestor,² Proceedings of the National Academy of
Sciences USA 95 (1998): 6854-6859.

Probably no scientist has more influenced our current understanding of the base 
of the Tree of Life than the microbiologist Carl Woese of the University of 
Illinois. The widely-accepted tripartite division of life into the Archae, the 
Bacteria, and the Eukarya, is due to Woese¹s work using ribosomal RNA (rRNA) 
patterns. In this provocative paper, Woese suggests that Darwin¹s single Tree of
Life, terminating in a single common ancestor (often abbreviated LUCA, for the 
Last Universal Common Ancestor), may never have existed. ³It is time,² Woese 
argues, ³to question underlying assumptions² (p. 6855). The problem stems from 
the failure of molecules to provide a consistent story for the early history of 
life. ³No consistent organismal phylogeny has emerged from the many individual 
protein phylogenies so far produced,² Woese writes. ³Phylogenetic incongruities 
can be seen everywhere in the universal tree, from its root to the major 
branchings within and among the various taxa to the makeup of the primary 
groupings themselves² (p. 6854). Thus, if the LUCA existed, it was not an 
organism like any that we would recognize. ³The universal ancestor is not an 
entity, not a thing. It is a process characteristic of a particular evolutionary
stage² (p. 6858). The Tree of Life does not have a single root. Rather, stresses
Woese, ³we are left with no consistent and satisfactory picture of the universal
ancestor² (p. 6855), and biology must comes to grips with this.

Questions of Process

23. Robert L. Carroll, ³Towards a new evolutionary synthesis,² Trends in Ecology
and Evolution 15 (2000):27-32.

Robert Carroll is a professor in the Department of Biology and Curator of 
Vertebrate Paleontology at the Redpath Museum of McGill University (Montreal). 
In this article, Carroll argues that macroevolutionary changes cannot be derived
from microevolutionary processes:

Increasing knowledge of the fossil record and the capacity for accurate 
geological dating demonstrate that large-scale patterns and rates of evolution 
are not compatible with those hypothesized by Darwin on the basis of 
extrapolation from modern populations and species....The most striking features 
of large-scale evolution are the extremely rapid divergence of lineages near the
time of their origin, followed by long periods in which basic body plans and 
ways of life are retained. What is missing are the many intermediate forms 
hypothesized by Darwin, and the continual divergence of major lineages into the 
morphospace between distinct adaptive types. (p. 27)

Carroll concludes that a new evolutionary synthesis is needed, to explain such 
patterns as ³the extreme speed of anatomical change and adaptive radiation² of 
the Cambrian Explosion, when ³almost all of the advanced phyla [animal body 
plans] appeared² (p. 27).

24. Douglas Erwin, ³Macroevolution is more than repeated rounds of 
microevolution,² Evolution & Development 2 (2000):78-84.

Douglas Erwin is a paleontologist on the staff of the National Museum of Natural
History (at the Smithsonian), and one of the leading critics of claims that 
microevolutionary processes suffice to explain macroevolutionary patterns. In 
this article, Erwin challenges the standard view of evolution, and argues that 
other processes and mechanisms are needed:

Microevolution provides no satisfactory explanation for the extraordinary burst 
of novelty during the late Neoproterozoic-Cambrian radiation (Valentine et al. 
1999; Knoll and Carroll 1999), nor the rapid production of novel plant 
architectures associated with the origin of land plants during the Devonian 
(Kendrick and Crane 1997), followed by the origination of most major insect 
groups (Labandeira and Sepkoski 1993). (p. 81)

The gap between microevolution and macroevolution, Erwin contends, is real: 
³These discontinuities impart a hierarchical structure to evolution, a structure
which impedes, obstructs, and even neutralizes the effects of microevolution² 
(p. 82). Much more work is needed, Erwin concludes, before we can claim to 
understand macroevolution.

25. Scott F. Gilbert, Grace A. Loredo, Alla Brukman, and Ann C. Burke, 
³Morphogenesis of the turtle shell: the development of a novel structure in 
tetrapod evolution,² Evolution & Development 3 (2001): 47-58.

26. Olivier Rieppel, ³Turtles as Hopeful Monsters,² BioEssays 23 (2001): 

The origin of turtles, with their distinctive shells, has long been an 
evolutionary enigma. ³The turtle shell,² write Scott Gilbert (Embryology, 
Swarthmore College) and his colleagues, ³represents a classic evolutionary 
problem: the appearance of a major structural adaptation.² Could the 
characteristic features of turtles have arisen gradually, in a long series of 
Darwinian steps? ³The problem for an evolutionary biologist,² comments 
systematist and reptile expert Olivier Rieppel of the Field Museum (Chicago), 
³is to explain these transformations in the context of a gradualistic process² 
(p. 990). But the first turtle in the fossil record appears abruptly, fully 
turtle: ³The Chelonian Bauplan [turtle body plan] appears in the fossil record,²
Gilbert et al. observe, ³without intermediates, and the relationship of turtles 
to other amniote orders is not certain.² What inference should one draw from 
these patterns of evidence? ³The absence of intermediates or transitional forms 
in the fossil record,² speculate Gilbert et al. -- especially when the fossil 
record is coupled with the developmental and anatomical novelties exhibited by 
turtles -- ³could indicate that turtles arose saltationally² (p. 56). That is, 
turtles did not evolve by a gradual Darwinian process; as Rieppel describes this
hypothesis, turtles may be ³hopeful monsters.² (Neither Rieppel nor Gilbert and 
colleagues, however, provide a detailed model of this rapid evolutionary 
transition, but rather refer to the need for further research.)

27. Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff, ³Resynthesizing 
Evolutionary and Developmental Biology,² Developmental Biology 173 (1996): 

In this major statement about the pressing need for a new theory of evolution, 
biologists Gilbert (Swarthmore), Opitz (Montana State), and Raff (Indiana 
University) argue that while the neo-Darwinian synthesis was a ³remarkable 
achievement,² it fails to explain many of the most important phenomena of 

...starting in the 1970s, many biologists began questioning its adequacy in 
explaining evolution. Genetics might be adequate for explaining microevolution, 
but microevolutionary changes in gene frequency were not seen as able to turn a 
reptile into a mammal or to convert a fish into an amphibian. Microevolution 
looks at adaptations that concern the survival of the fittest, not the arrival 
of the fittest. As Goodwin (1995) points out, ³the origin of species -- Darwin¹s
problem -- remains unsolved.² (p. 361)

Under the new synthesis that these authors propose, in which the processes of 
development are integrated into evolutionary understanding, ³the role of natural
selection...is seen to play less an important role. It is merely a filter for 
unsuccessful morphologies² (p. 368).

28. George L. Gabor Miklos, ³Emergence of organizational complexities during 
metazoan evolution: perspectives from molecular biology, palaeontology and 
neo-Darwinism,² Mem. Ass. Australas. Palaeontols. 15 (1993): 7-41.

George Miklos is an evolutionary geneticist at the Centre for Molecular 
Structure and Function of the Australian National University. In this article, 
Miklos levels a major, across-the-board indictment of neo-Darwinism. The flavor 
of the indictment can be gathered from the opening six sentence of the abstract:

The popular theory of evolution is the modern synthesis (neo-Darwinism), based 
on changes in populations underpinned by the mathematics of allelic variation 
and driven by natural selection. It accounts more for adaptive changes in the 
colouration of moths, than in explaining why there are moths at all. This theory
does not predict why there were only 50 or so modal body plans, nor does it 
provide a basis for rapid, large scale innovations. It lacks significant 
connection with embryogenesis and hence there is no nexus to the evolution of 
form. It fails to address the question of why the anatomical gaps between phyla 
are no wider today than there were at their Cambrian appearance. It has no 
predictions about macromolecules and cellular evolution in the Archaean, about 
evolution via symbiogenesis, nor the manner in which cells and organisms alter 
and revise their genomic rules as they evolve. (p. 7)

Miklos¹s primary argument concerns the irrelevance -- to the solution of the 
problem of macroevolution -- of the scale of variation typically observed in 
neo-Darwinian studies, e.g., gene frequency (or allelic) shifts:

Allelic changes in natural populations are almost totally oblique to 
understanding the events that gave rise to the major metazoan body plans. 
Studies of speciation are targeting the evolutionary peripheries, and missing 
the significant metazoan issue -- the origin of complex forms. (p. 29)

Neo-Darwinians, Miklos contends, have been unwilling to reevaluate their theory 
in the light of contrary evidence:

The modern synthesis moved evolution theory into a mathematical siding from 
which there has been no return. Here is a theory which, as I have shown in this 
essay, does not touch upon any level of detail or mechanism that impinges on 
large scale evolutionary complexity or novelty. Whenever data have undermined 
its foundations, it is the data that have been considered inadequate. Thus the 
traditional gradualistic view is largely at variance with the fossil record, 
which is largely one of episodic change followed by stasis. (p. 29)

Evolutionary theory will need to break free of neo-Darwinism, Miklos concludes, 
to have any hope of explaining the deep puzzle that occupied Darwin, namely, how
did animals (and plants) themselves come to be? Here is his final paragraph:

Finally, it is necessary to acknowledge that after over a century of the 
dominant paradigm, the evolution of major complexities in the history of life 
has had very little to do with the origin of species. The seamless moving 
footway of neo-Darwinism that was to have smoothly transported us from allelic 
variation in natural populations to understanding body plans in different phyla 
has led to a cul-de-sac. The origin of phyla is not via speciation Œwrit large¹.
To understand what fuelled origins of phyla, the complexities that emerged long 
ago from macromolecular and supracellular complexes and from symbiogenic events 
will need to be understood via molecular embryology, where the quintessence of 
evolutionary truth is to be found. (p. 34)

29. Neil H. Shubin and Charles R. Marshall, ³Fossils, genes, and the origin of 
novelty,² in Deep Time (2000, The Paleontological Society), pp. 324-340.

Shubin (Paleontology, University of Chicago) and Marshall (Paleontology and 
Molecular Biology, UCLA) argue that the neo-Darwinian synthesis needs to come to
grips with new evidence that the theory never anticipated and has difficulty 

In the last 25 years, new data from genetics have dealt some profound surprises 
to the evolutionary biology community. Perhaps the most striking discovery is 
the extent to which major patterning genes and regulatory interactions are 
deeply conserved across vast expanses of time and phylogeny....Indeed, in many 
cases, the developmental role of these homologous genes is also conserved in 
creatures with different body plans. Strikingly, many homologous genes appear to
perform the same function in structures that share functional similarities but 
lack a common evolutionary origin. (p. 325)

Another puzzling problem is the Cambrian Explosion: ³The disconnect between 
rates of genetic and morphological change,² write Shubin and Marshall (p. 335), 
³is as vexing a problem for population geneticists as it is for 
paleontologists.² They conclude that evolutionists must bridge ³the gap between 
microevolution and macroevolution,² by seeking ³the mechanisms behind the 
production of morphological variation² (p. 338).

30. Keith Stewart Thomson, ³Macroevolution: The Morphological Problem,² American
Zoologist 32 (1992): 106-112.

Thomson (Oxford University) has long been disenchanted with the explanatory 
adequacy of neo-Darwinism. Macroevolution has resisted explanation, he argues:

While the origins of major morphological novelties remains unsolved, one can 
also view the stubborn persistence of macroevolutionary questioning, and 
particularly its revival in recent years, as a challenge to orthodoxy: 
resistance to the view that the synthetic theory tells us everything we need to 
know about evolutionary processes. (p. 106)

Although most evolutionary biologists, beginning with Darwin, saw evolutionary 
change as necessarily gradual, Thomson points out that ³no one has 
satisfactorily demonstrated a mechanism at the population genetic level by which
innumerable very small phenotypic changes could accumulate rapidly to produce 
large changes: a process for the origin of the magnificently improbable from the
ineffably trivial² (p. 107, emphasis in original).

31. Bärbel M.R. Stadler, Peter F. Stadler, Günther P. Wagner, and Walter 
Fontana, ³The Topology of the Possible: Formal Spaces Underlying Patterns of 
Evolutionary Change,² Journal of Theoretical Biology 213 (2001):241-274.

32. Günther P. Wagner, ³What is the Promise of Developmental Evolution? Part II:
A Causal Explanation of Evolutionary Innovations May Be Impossible,² Journal of 
Experimental Zoology (Mol Dev Evol) 291 (2001): 305-309.

In these companion papers, theoretical biologist Günther Wagner (Yale 
University) and his colleagues argue that neo-Darwinism fails to explain many 
important biological phenomena, and that the relationship of these phenomena ³to
the mechanistic theory of evolutionary change, as represented by population 
genetics, remains unclear and tense² (JTB, p. 242). They suggest that this 
failure of explanation stems from the underlying assumptions of neo-Darwinism, 
such as that any evolutionary change is readily accessible to natural selection.
Patterns of evidence, however, indicate that ³this fluidity is largely a fiction
and point at profound asymmetries in the accessibility of phenotypic and genetic
states² (JTB, p. 242), meaning that many evolutionary transitions may be all but
impossible. Going even further, Wagner contends that many important historical 
events in evolution may be forever inexplicable, because the conditions needed 
to understand those events -- in particular, the genetic background to the 
changes in question -- may be lost irretrievably. If this is the case, he 
writes, ³then it might be impossible to experimentally demonstrate exactly which
genetic changes caused the evolutionary innovation³ (JEZ, p. 308, emphasis in 

Questions about the Central Issue: the Origin and Nature of Biological 

33. Philip Ball, ³Life¹s lessons in design,² Nature 409 (2001): 413-416.

What might we learn from biological objects that could be applied to improving 
our own technologies? The research field of biomimetics tries to answer this 
question by looking closely at natural systems, and ³reverse-engineering² them 
for solutions to similar technological problems faced by humanly-constructed 
artifacts. Questions of scale and complexity, of course, arise immediately, as 
Philip Ball (an editor at the journal Nature) notes:

One of the biggest obstacles to taking full advantage of what nature has to 
offer is that the living world has an awesomely elaborate means of construction.
There is no assembly plant so delicate, versatile and adaptive as the cell. (p. 

The astonishing subtlety of biological designs beggars description; or, to put 
it another way, one cannot assume that every solution to a functional challenge 
will be intuitively obvious on first inspection. Consider, for instance, insect 

Specifically, insects are conjurors of the vortex. With deft flappings and 
rotations of their wings, they are able to manipulate the vortices shed from the
edges to control their motion in ways that flight engineers can only dream of: 
taking off backwards, for example, or landing upside down. By such means, 
insects subvert the ³conventional² aerofoil principles of flight, giving rise to
the canard that the bee is aerodynamically impossible. In essence, the flight of
the bumble-bee is a flight beyond the dynamic steady state: lift is generated at
particular, exquisitely timed moments during the flap cycle. By rotating the 
wing so that it is parallel to the ground on the downstroke but perpendicular on
the recovery stroke, an insect is able to recapture energy from the vortices 
shed from the wing edge. This reveals a new mechanism for flight that one could 
hardly have deduced from first principles, and which might be adopted for the 
development of miniaturized robotic flyers for remote sensing, surveying and 
planetary exploration. (p. 414)

Eventually, Ball argues, engineers seeking to learn from biology must turn to 
the realities of the microscopic realm. Synthetic silk, for instance, has yet to
become a commercially successful product, not because we do not understand the 
biochemistry or genetics of silk production, but because real silk gains its 
strength from more than its protein structure:

It is the weaving of strands in the spinneret that gives them their strength. 
The details of this process are not understood; but it may be that not until we 
can build an artificial, miniaturized spinning mechanism will silk be an 
industrial material.

This is why biomimetics must reach down to the microscopic and ultimately the 
molecular scale. Some of nature¹s best tricks are conceptually simple and easy 
to rationalize in physical or engineering terms; but realizing them requires 
machinery of exquisite delicacy. (p. 416)

Ball concludes that the horizon of knowledge opened by biomimetics is vast and 
continues to grow:

...fundamental research on the character of nature¹s mechanisms, from the 
elephant to the protein, is sure to enrich the pool from which designers and 
engineers can draw ideas. The scope for deepening this pool is still tremendous.
It is at the molecular scale, however, that we will surely see the greatest 
expansion of horizons, as structural studies and single-molecule experiments 
reveal the mechanics of biomolecules. If any reminder were still needed that 
nanotechnology should not seek to shrink mechanical engineering, cogs and all, 
to the molecular scale, it is found here. Nature¹s wheel -- the rotary motor of 
the bacterial flagellum -- never got any larger than this, nor is it fashioned 
from hard, wear-resistant materials, nor is driven electromagnetically or by 
displacement of a piston. But it is efficient, fast, linear and reversible. 
Somewhere there is a lesson in that. (p. 416)

34. Rodney Brooks, ³The relationship between matter and life,² Nature 409 
(2001): 409-411.

Rodney Brooks of the Artificial Intelligence Laboratory at MIT has long been a 
pathbreaking investigator in the construction of ³AI² (artificial intelligence) 
and ³Alife² (artificial life) systems. In this skeptical article, however, 
Brooks steps back from the bench to look critically at what AI and Alife 
research has actually demonstrated. He writes:

...both fields have been labelled as failures for not having lived up to 
grandiose promises. At the heart of this disappointment lies the fact that 
neither AI nor Alife has produced artefacts that could be confused with a living
organism for more than an instant. AI just does not seem as present or aware as 
even a simple animal and Alife cannot match the complexities of the simplest 
forms of life. (p. 409)

The failures of these fields, Brooks argues, requires a diagnosis:

We build models to understand the biological systems better, but the models 
never work as well as biology. We have become very good at modelling fluids, 
materials, planetary dynamics, nuclear explosions and all manner of physical 
systems. Put some parameters into a program, let it crank, and out come accurate
predictions of the physical character of the modelled system. But we are not 
good at modelling living systems, at small or large scales. Something is wrong. 
(p. 410)

After considering several modest ³fixes² for AI and Alife (e.g., incorrect 
parameters, lack of computing power, lack of complexity in models), Brooks turns
to a more challenging diagnosis: ³we might be missing something fundamental and 
currently unimagined in our models of biology² (p. 410). He argues:

We would then need to find new ways of thinking about living systems to make any
progress, and this will be much more disruptive to all biology. ... So what 
might be the nature of this unimagined feature of life? One possibility is that 
some aspect of living systems is invisible to us right now. The current 
scientific view of living things is that they are machines whose components are 
biomolecules. It is not completely impossible that we might discover some new 
properties of biomolecules or some new ingredient. One might imagine something 
on a par with the discovery of X-rays a century ago, which eventually led to our
still-evolving understanding of quantum mechanics. Relativity was the other such
discovery of the twentieth century, and had a similarly disruptive impact on the
basic understanding of physics. Some similar discovery might rock our 
understanding of the basis of living systems. (p. 410)

35. David W. Deamer, ³The First Living Systems: a Bioenergetic Perspective,² 
Microbiology and Molecular Biology Reviews 61 (1997): 239-261.

Could living systems have arisen without a means of transferring energy from the
environment to the primitive cell, in order to do the work characteristic of all
organisms? Biochemist and origin-of-life researcher David W. Deamer, of the 
University of California-Santa Cruz, argues that current models for the 
evolution of life itself neglect this critical question. To bring the point home
with clarity and force, Deamer suggests a thought experiment in which a 
prebiotic ³soup² of non-living chemicals is gradually made more complex, ³using 
what we know about the composition of a living cell² (p. 241). In no case, he 
argues, would a living system arise, without a means for capturing and 
transferring energy. He writes:

Imagine that on the early Earth, a complete system of catalytic and 
information-bearing molecules happened by chance to come together in a tide pool
that was sufficiently concentrated to produce the equivalent of the contents of 
our flask. We could model this event in the laboratory by gently disrupting a 
live bacterial culture, subjecting it to a sterilizing filtration step, and 
adding the mixture to the flask of nutrient broth. No living cells are present, 
but entire bacterial genomes are available, together with ribosomes, membranous 
vesicles, ATP and other energy-containing substrates, and thousands of 
functional enzymes. Once again, would a living system arise under these 
conditions? Although Kauffman might be optimistic about the possibilities, most 
experimentalists would guess that little would happen other than slow, 
degradative reactions of hydrolysis, even though virtually the entire complement
of molecules associated with the living state is present. The dispersion has 
lost the extreme level of order characteristic of cytoplasm in contemporary 
living cells. Equally important is that the ATP would be hydrolyzed in seconds, 
so that the system still lacks a continuous source of free energy to drive the 
metabolism and polymerization reactions associated with life. (p. 242)

Deamer suggests future directions of research to bring greater realism to 
origin-of-life theories, stressing that encapsulation (isolation from the 
environment) is a necessary condition for any plausible protobiont.

36. Michael J. Katz, Templets and the explanation of complex patterns, 
Cambridge: Cambridge University Press, 1986.

The first usage of the term ³irreducibly complex² in the scientific literature 
was not due to Michael Behe of Lehigh University (although Behe certainly put 
his stamp on the term, and has given it wide currency). Ten years before 
Darwin¹s Black Box was published, the theoretical biologist Michael J. Katz of 
Case Western Reserve University (Cleveland, Ohio) published an eight chapter 
scientific monograph with Cambridge University Press, entitled Templets and the 
Explanation of Complex Patterns (1986). In that publication, ³irreducible 
complexity² occurs as an index entry, and is explained in the text as follows:

In the natural world, there are many pattern-assembly systems for which there is
no simple explanation. There are useful scientific explanations for these 
complex systems, but the final patterns that they produce are so heterogeneous 
that they cannot effectively be reduced to smaller or less intricate predecessor
components. As I will argue in Chapters 7 and 8, these patterns are, in a 
fundamental sense, irreducibly complex...(pp. 26-27)

In context, it is abundantly clear that by ³irreducible complexity,² Katz refers
essentially to the same phenomena as does Behe. ³For some natural phenomena,² he
writes, ³there simply is no reduction to smaller predecessors. In these cases, 
the companion rule to Œorder stems from order¹ is that Œcomplexity stems from 
complexity¹² (p. 90). More fully:

...the unique characteristics of organisms are pattern characteristics. The 
first of these fundamental pattern characteristics is complexity. Cells and 
organisms are quite complex by all pattern criteria. They are built of 
heterogeneous elements arranged in heterogeneous configurations, and they do not
self-assemble. One cannot stir together the parts of a cell or of an organism 
and spontaneously assemble a neuron or a walrus: to create a cell or an 
organisms one needs a preexisting cell or a preexisting organism, with its 
attendant complex templets. A fundamental characteristic of the biological realm
is that organisms are complex patterns, and, for its creation, life requires 
extensive, and essentially maximal, templets. (p. 83)

Like Behe, Katz confronts the issue of the origin of life, and the dilemma 
raised for reductive or naturalistic explanation by the complexity of even the 
simplest organisms:

Today¹s organisms are fabricated from preexisting templets -- the templets of 
the genome and the remainder of the ovum [egg] -- and these templets are, in 
turn, derived from other, parent organisms. The astronomical time scale of 
evolution, however, adds a dilemma to this chain-of-templets explanation: the 
evolutionary biologist presumes that once upon a time organisms appeared when 
there were no preexisting organisms. But, if all organisms must be templeted, 
then what were the primordial inanimate templets, and whence came those 
templets? (pp. 65-66)

The parallels between Katz¹s argument, and those of design theorists such as 
Michael Behe, William Dembski, or Stephen Meyer, are so numerous and striking 
that if one did not know better, one might assume that a design theorist had 
written this (and dozens of other such passages in Katz¹s book):

Self-assembly does not fully explain the organisms that we know; contemporary 
organisms are quite complex, they have a special and an intricate organization 
that would not occur spontaneously by chance. The Œuniversal laws¹ governing the
assembly of biological materials are insufficient to explain our companion 
organisms: one cannot stir together the appropriate raw materials and 
self-assemble a mouse. Complex organisms need further situational constraints 
and, specifically, they must come from preexisting organisms. This means that 
organisms -- at least contemporary organisms -- must be largely templeted. (p. 

37. Claire M. Fraser et al., ³The Minimal Gene Complement of Mycoplasma 
genitalium,² Science 270 (1995): 397-403.

38. Clyde A. Hutchison et al., ³Global Transposon Mutagenesis and a Minimal 
Mycoplasma Genome,² Science 286 (1999): 2165-2169.

39. Eugene V. Koonin, ³How Many Genes Can Make a Cell: The Minimal-Gene-Set 
Concept,² Annual Review of Genomics and Human Genetics 1 (2000):99-116.

40. Jack Maniloff, ³The minimal cell genome: ŒOn being the right size,¹² 
Proceedings of the National Academy of Sciences USA 93 (1996): 1004-1006.

41. Arcady R. Mushegian and Eugene V. Koonin, ³A minimal gene set for cellular 
life derived by comparison of complete bacterial genomes,² Proceedings of the 
National Academy of Sciences USA 93 (1996): 10268-10273.

42. Scott N. Peterson and Claire M. Fraser, ³The complexity of simplicity,² 
Genome Biology 2 (2001):1-7.

These related articles explore the concept of a ³minimal genome,² and asks the 
question ³What is the minimal number of genes necessary to support cellular 
life?² (p. 1). Peterson and Fraser, who work at The Institute for Genomic 
Research (TIGR), which led one of two international efforts to map the human 
genome, explain that research on the simplest known living thing, the parasitic 
bacterium Mycoplasma genitalium, has revealed unexpected complexity at the 
foundation of life:

The fact that an estimated one third of the essential set of genes in this 
minimal genome are of undefined function is an important result that has at 
least two potential interpretations. First, it draws dramatically into question 
a basic assumption held by many biologists that the fundamental mechanisms and 
functions underlying cellular life have for the most part been identified and 
well characterized. If approximately 100 genes in the simplest functioning cell 
are of unknown function and are essential to basic cellular processes, this 
assumption becomes quite dubious....we have much work to do before we can claim 
to have a clear understanding of even the simplest cell and its functions. (p. 

Peterson and Fraser end by pointing to what they call an ³extremely interesting²
possibility, namely, ³that many gene functions have evolved independently more 
than once since the beginning of cellular life on the planet² (p. 7). Eugene 
Koonin, a leader in this field of research who works at the National Center for 
Biotechnology Information, explores the surprising discovery that only 
approximately 80 of the estimated 250 necessary genes are found ³in all life 
forms² (p. 99), suggesting a much greater degree of genetic diversity among 
organisms, in their basic functions, than had been suspected.

43. Leslie E. Orgel, ³Self-organizing biochemical cycles,² Proceedings of the 
National Academy of Sciences 97 (2000): 12503-12507.

How did basic metabolic pathways, such as the citric acid cycle, arise from 
non-biological precursors? Leslie Orgel of the Salk Institute for Biological 
Studies, one of the world¹s leading origin-of-life researchers, notes that all 
scenarios for the spontaneous origin of metabolic cycles ³have one feature in 
common: a self-organized cycle or network of chemical reactions that does not 
depend directly or indirectly on a genetic polymer² (p. 12503). In other words, 
starting with information-bearing molecules such as DNA or RNA is already too 
complex: the first metabolic system, then, must have originated in a much 
simpler state. Orgel is skeptical of such proposals, however:

Unfortunately, catalytic reactions of the required type in aqueous solution are 
virtually unknown; there is no reason to believe, for example, that any 
intermediate of the citric acid cycle would specifically catalyze any reaction 
of the citric acid cycle. The explanation of this is simple: noncovalent 
interactions between small molecules in aqueous solution are generally too weak 
to permit large and regiospecific catalytic accelerations [of the type required 
by living systems]. To postulate one fortuitously catalyzed reaction, perhaps 
catalyzed by a metal ion, might be reasonable, but to postulate a suite of them 
is to appeal to magic. (pp. 12504-12505)

Existing self-organization scenarios, therefore, appeal to a ³near-miracle² (p. 
12506), in which ³one must postulate a series of remarkable coincidences to 
conclude that all of the reactions are catalyzed on the same mineral and that 
each intermediate product is formed in the correct position and orientation² (p.
12506). Orgel concludes:

The novel, potentially replicating polymers that have described up to now, like 
the nucleic acids, are formed by joining together relatively complex monomeric 
units. It is hard to see how any could have accumulated on the early earth. A 
plausible scenario for the origin of life must, therefore, await the discovery 
of a genetic polymer simpler than RNA and an efficient, potentially prebiotic, 
synthetic route to the component monomers. The suggestion that relatively pure, 
complex organic molecules might be made available in large amounts via a 
self-organizing, autocatalytic cycle might, in principle, help to explain the 
origin of the component monomers. I have emphasized the implausibility of the 
suggestion that complicated cycles could self-organize, and the importance of 
learning more about the potential of surfaces to help organize simpler cycles. 
(p. 12507)

44. Eörs Szarthmáry, ³The evolution of replicators,² Philosophical Transactions 
of the Royal Society of London B 335 (2000): 1669-1676.

Any Darwinian scenario for the origin of biological complexity requires 
replicators: systems capable of storing and transmitting information with 
fidelity, yet also with some capacity for variation, to allow for adaptive 
change. In this theoretical analysis, Eörs Szarthmáry (of the Institute for 
Advanced Study of the Collegium Budapest) argues that the problem of the origin 
of replicators is unsolved, mainly because of what he calls ³the paradox of 
specificity² (p. 1669). In order for a self-organizing system (such as Stuart 
Kauffman¹s hypothetical autocatalytic protein nets) to exhibit more than very 
limited, and non-biological, heredity, it must contain a large number of 
different component types (i.e., molecules). But a large number of such types 
entails that harmful side reactions will follow: ³This is due to the fact that 
in a simple medium there can always be side reactions, stoichiometric and 
catalytic, which compromise the functioning of the network as a whole -- which 
might otherwise look good on paper² (p. 1672). As Szarthmáry notes,

A rather large number (n) of different polypeptide sequences seems to be 
required for the imagined functioning of these autocatalytic protein nets 
(Kauffman 1986). A higher-level analogy of the side-reaction plague readily 
arises. Calculations of probabilities about such systems always assume that a 
protein may or may not catalyse a given legitimate reaction in the system but 
that it would not catalyse harmful side reactions. This is obviously an error. 
Hence the paradox of specificity strikes again -- the feasibility of 
autocatalytic attractor sets seems to require a large number of component types 
(high n), whereas the plague of side reactions calls for small systems (low n). 
No satisfactory solution of this problem has yet been given. (p. 1673)

Szarthmáry summarizes numerous other difficulties for the origin of replicators,
such as (a) the need for a highly specific set of building blocks, and (b) 
chemical difficulties confronting any system of template replication, in the 
absence of specific enzymes. Consider (a):

There is an important precondition for successful replication of all molecular 
replicators--the environment must contain the right raw materials. This sounds 
trivial, but in fact it is not. Consider the case of RNA replication. This needs
activated ribonucleotides of the right conformation. One can imagine (and in 
fact synthesize) mirror images of the currently used nucleotides. An RNA 
molecule would not be able to replicate in a medium consisting of a mixture of 
the left and right mirror-image nucleotides. This obstacle to prebiotic 
replication is called ³enantiomeric cross-inhibition² (Joyce et al. 1987). 
Replication needs the right raw materials in the environment of the replicator. 
For contemporary nucleic acids this environment is highly evolved -- it is the 
cytoplasm of the cell, maintained to a large extent by the phenotypic effects of
the genes themselves on the ³vehicles² (Dawkins 1976) or ³interactors² (Hull 
1980) in which they are embedded and replicated. (p. 1673)

Or consider (b):

A common criterion for the replication process is that the two strands (template
and copy) must spontaneously separate. Since they are held together by hydrogen 
bonds (also necessary for replication) the strands cannot be too long or 
otherwise they would stick together for too long a time. Long pieces of nucleic 
acids can be replicated in the cell because enzymes of the replicase complex 
also ensure the unwinding of the strands -- this cannot be assumed in 
non-enzymatic [prebiotic] systems. (p. 1672)

Szarthmáry¹s review provides an excellent survey of the mechanistic difficulties
facing the modelling of prebiotic systems during their transition to true 
biological states.

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