Science Literature

Here is a paper that significantly shifts the focus of the debate about Neanderthal Man. What happened to the Neanderthals during the last glaciation? Did anatomically modern humans (AMH) slaughter them? Did they talk with them? Did they interbreed with them? To what extend did they exchange technologies and ideas? Finlayson and Carrion describe much of this debate as the expression of a "simplistic Neanderthal-AMH dichotomy".
After reviewing much data, they point out an interesting pattern: "An examination of the distribution of Aurignacian and transitional industries across Europe during the crucial time frame between 45 and 30 kya reveals a striking correspondence between location and the presence of sharp physiographical boundaries. This suggests that these industries, some made by Neanderthals (Chatelperronian) and others perhaps by AMHs (Aurignacian?), were independent regional responses to rapidly fluctuating ecological conditions. Their absence from more stable regions, such as south-western Iberia, supports this view. The changing circumstances and stresses experienced by human populations across the Palaearctic, most notably between the MLB and the plains, created a template for innovation."
Thus, instead of the emphasis being on culture associated with evolutionary change, the real issue is analysing the responses people made to their environment. "Technological innovations of the so-called Upper Palaeolithic can be understood as responses to living in vast open spaces rather than to the consequence of a cognitive revolution associated with an evolutionary change."
Of course, this presupposes that the Neanderthals were not much different from the other human groups around at the time. The authors claim that "Neanderthals were capable of behaviour that is regarded as modern". This may come as a surprise to those who have been brought up to think of Neanderthals as hairy brutes that could make little more than grunting noises to each other. Have we been misled by an evolutionary mindset? Is the key to understanding Neanderthals "ecology" rather than "brain wiring"?

Rapid ecological turnover and its impact on Neanderthal and other human populations
Clive Finlayson and Jose S. Carrion
Trends in Ecology & Evolution, Volume 22, Issue 4 , April 2007, Pages 213-222

Abstract: The latter part of the last glaciation, 50,000 - 12,000 years ago (kya), was characterized by a rapidly changing climate, cold conditions and corresponding vegetation and faunal turnover. It also coincided with the extinction of the Neanderthals and the expansion of modern human populations. Established views of modern human superiority over Neanderthals as the cause of their extinction are under attack as recent work shows that Neanderthals were capable of behaviour that is regarded as modern. As we discuss here, the exact nature of biological and cultural interactions between Neanderthals and other human groups between 50 kya and 30 kya is currently hotly contested. The extinction of the Neanderthals, and other modern human lineages, now appears to have been a drawn-out, climate-related affair.

Most of us know that aspirin derives from a naturally occurring chemical, salicylic acid, found in the bark of willow trees. Many of us know that the inhabitants of tropical rainforests are aware of the medicinal properties of a great number of leaves, roots, bark and other natural materials. What few of us realise is just how many of the drugs on pharmacy shelves derive from the natural world. In a review covering the past 60 years, two chemists have concluded that 70% of new drugs (never previously available as commercial products) are either derived from plants and animals or synthesised to mimic the natural product. This statistic is entirely in line with two previous reviews these authors had undertaken.
They write: "the continuing and overwhelming contribution of natural products to the expansion of the chemotherapeutic armamentarium is clearly evident, and as we stated in our earlier papers, much of Nature's "treasure trove of small molecules" remains to be explored, particularly from the marine and microbial environments." They make a particular point about microbially-produced substances: "We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore we consider that this area of natural product research should be expanded significantly."
In a recent entry to this literature blog, a link was made between "systems biology" and design theory. Both lead to the same scientific methodologies. Both emphasise the multidisciplinary character of research, and the importance of holistic (rather than reductionistic) thinking. The review authors have the same approach: "To us, a multidisciplinary approach to drug discovery, involving the generation of truly novel molecular diversity from natural product sources, combined with total and combinatorial synthetic methodologies, and including the manipulation of biosynthetic pathways (so-called combinatorial biosynthesis), provides the best solution to the current productivity crisis facing the scientific community engaged in drug discovery and development."
If the natural world is designed, and if mankind has a legitimate place within this designed world, the finding that natural medicinal products actually work is not surprising. Indeed, positive thoughts about design naturally follow.

Natural Products as Sources of New Drugs over the Last 25 Years
David J. Newman and Gordon M. Cragg
Journal of Natural Products, 70(3), 461-477, 2007. 10.1021/np068054v S0163-3864(06)08054-2

Abstract: This review is an updated and expanded version of two prior reviews that were published in this journal in 1997 and 2003. In the case of all approved agents the time frame has been extended to include the 251/2 years from 01/1981 to 06/2006 for all diseases worldwide and from 1950 (earliest so far identified) to 06/2006 for all approved antitumor drugs worldwide. We have continued to utilize our secondary subdivision of a "natural product mimic" or "NM" to join the original primary divisions. From the data presented, the utility of natural products as sources of novel structures, but not necessarily the final drug entity, is still alive and well. Thus, in the area of cancer, over the time frame from around the 1940s to date, of the 155 small molecules, 73% are other than "S" (synthetic), with 47% actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the antiinfective area being dependent on natural products and their structures. Although combinatorial chemistry techniques have succeeded as methods of optimizing structures and have, in fact, been used in the optimization of many recently approved agents, we are able to identify only one de novo combinatorial compound approved as a drug in this 25 plus year time frame. We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore we consider that this area of natural product research should be expanded significantly.

See also:
Mother Nature's Medicine Cabinet
Science Daily, March 20, 2007.

Phylogenomics makes use of "large quantities of genetic data (not just entire genomes) to build evolutionary trees, or phylogenies." The new discipline makes great claims, for it aims to "reshape systematics" using the extensive data sets emerging from genome mapping projects. One researcher explains its scope: "Genomes are giving a much better view of the tree of life on Earth" and "The revolution is just starting - every new genome is causing rethinking."
It may surprise some, but Linnaeus did not pioneer systematics with the tree of life in mind. It is not necessary to presuppose a common ancestor for all living things to be a scholar working in this field.
More importantly, waving "the banner of phylogenetics" must not be confused with delivering results. Because some say the revolution is just starting, this does not mean that they are right. "What has also become clear is that many problems cannot simply be battered into submission with more data."
To illustrate one problem: "Perhaps the most high-profile gaffe was the declaration by the Human Genome Project in 2001 that 100-200 genes in humans had come directly from bacteria." Lateral gene transfer (LGT) was invoked to explain the data. It was challenged by several "flabbergasted evolutionary biologists, [who] rapidly shot the claim down, showing that the genes in question were more likely to have been present in the common ancestor of humans and bacteria but then lost in other lineages."
What is surprising is that there has not been a similar response to the new explanation: for it implies that the relevant genes were present in the evolutionary descendants and were systematically lost in every branch and twig of the tree of life except for that leading to humans. This explanation is as contrived as LGT!
According to one expert quoted: "you can't do good genome analysis without evolutionary analysis." Linnaeus would not have agreed with this. He would have warned of the dangers of force-fitting the data into a predetermined mould. If you presuppose the tree of life, how could researchers ever conclude that they were studying a forest, not a tree?

Linnaeus at 300: We are family
John Whitfield
Nature 446, 247-249, (15 March 2007) | doi:10.1038/446247a
Updating the tree of life needs both the skills of evolutionary biologists and the data from genome-crunchers - the two ignore each other at their peril.

Medicinal research is the best funded area in biology, with large inputs of money from pharmaceutical companies as well as from research funding bodies. For longer than anyone can remember, "a reductionist focus has been the Holy Grail" in biological research. This has achieved results: "In medicine, tremendous scientific advancements have been made in understanding diseases from a reductionistic viewpoint." However, it appears that a turning point has arrived. "The success formula built on reductionism seems to have reached its limits and the pharmaceutical industry faces enormous challenges with productivity decreasing and development costs rapidly increasing."
Where next? Do we need a bolt-on to reductionism (so that reductionism is part of the solution), or do we conclude that reductionism is part of the problem and that a different methodology is needed?
The authors of the paper abstracted below have come to the view that Systems Biology is that "new strategic tool in Life Sciences". Systems thinking is a move to holism rather than reductionism. It is thus a complete change of direction, not an add-on.
"Understanding biology requires knowledge of connectivity in systems and their self-organization. [. . .] the need to map patterns of relationship is surfacing, as demonstrated in mammalian systems based on de novo measurements across transcriptomics, proteomics, and metabolomics. To achieve this crucial understanding of complex relationships in an intact system, there is a great need for reliable, high-quality experimental data beyond the cellular level."
"The most important step forward however is the paradigm shift needed to become a system thinking organization. [. . .] Such a paradigm shift will occur when a critical mass of global intelligence has embraced this concept of systems thinking."
All this is very interesting reading for Intelligent Design advocates. The philosophy of reductionism has long been identified as a negative influence when it ceases to be a tool and becomes a statement about the nature of reality. ID scholars have championed the cell, rather than DNA, as the most basic unit of living things. The ID approach is to see the importance of systems, whether they be complex specified systems or irreducibly complex systems. This is a real point of contact with systems biology: there is much common ground and this is to be welcomed. The methodologies being developed within systems biology are methodologies perfectly consistent with those emerging via design inferences.
The authors realise that a paradigm shift is urgently needed. Perhaps this is an area where funding agencies and employers will realise that ID biologists can assist with the development of systems thinking and will come to regard ID as an ally and an asset.

The Art and Practice of Systems Biology in Medicine: Mapping Patterns of Relationships
J. van der Greef, S. Martin, P. Juhasz, A. Adourian, T. Plasterer, E. R. Verheij, and R. N. McBurney
Journal of Proteome Research, ASAP Article 10.1021/pr0606530 S1535-3893(06)00653-1

Abstract: Systems biology has developed in recent years from a technology-driven enterprise to a new strategic tool in Life Sciences, particularly for innovative drug discovery and drug development. Combining the ultimate in systems phenotyping with in-depth investigations of biomolecular mechanisms will enable a revolution in our understanding of disease pathology and will advance translational medicine, combination therapies, integrative medicine, and personalized medicine. A prerequisite for deriving the benefits of such a systems approach is a reliable and well-validated bioanalytical platform across complementary measurement modalities, especially transcriptomics, proteomics, and metabolomics, that operates in concert with a megavariate integrative biostatistical/bioinformatics platform. The applicable bioanalytical methodologies must undergo an intense development trajectory to reach an optimal level of reliable performance and quantitative reproducibility in daily practice. Moreover, to generate such enabling systems information, it is essential to design experiments based on an understanding of the complexity and statistical characteristics of the large data sets created. Novel insights into biology and system science can be obtained by evaluating the molecular connectivity within a system through correlation networks, by monitoring the dynamics of a system, or by measuring the system responses to perturbations such as drug administration or challenge tests. In addition, cross-compartment communication and control/feed-back mechanisms can be studied via correlation network analyses. All these data analyses depend critically upon the generation of high-quality bioanalytical platform data sets. The emphasis of this paper is on the characteristics of a bioanalytical platform that we have developed to generate such data sets. The broad applicability of Systems Biology in pharmaceutical research and development is discussed with examples in disease biomarker research, in pharmacology using system response monitoring, and in cross-compartment system toxicology assessment.

Disillusionment with molecular clocks appears to be quite widespread. This paper draws attention to the great disparities that exist in the dates that emerge from these studies. The authors say that they await further work "with some nervousness, given that we suspect they might reveal that many past studies placed too much confidence in simple molecular clock analyses, and that their conclusions should thus be revisited."
Pessimism about the method is high. The worst case scenario is raised with the question: "is there likely to be so much uncertainty about molecular dating that the estimates are no longer useful? We fear that, for many current studies, the answer is yes."
The root problem is that the method has been built on Darwinian foundations. When legitimate concerns about these are addressed (see here), it may be possible do do something useful with the data.

Dates from the molecular clock: how wrong can we be?
Mario J.F. Pulquerio and Richard A. Nichols
Trends in Ecology & Evolution, Volume 22, Issue 4, April 2007, Pages 180-184

Abstract: Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. This research implies that many previous studies, even some of those using recently developed methods, might have placed too much confidence in their date estimates, and their conclusions might need to be revised.

Last sentence: We await the more rigorous type of assessment with some nervousness, given that we suspect they might reveal that many past studies placed too much confidence in simple molecular clock analyses, and that their conclusions should thus be revisited.

Evolutionary biologists have to squarely face the fact that living things look designed. However, is this appearance real (with the implication that there is an intelligent designer) or is it a subjective assessment without substance (with the implication that there are mechanisms for design emerging through natural causes)? The issue is not helped by those who try to trivialise the design argument. And Wedekind notes: "evolutionary biologists can struggle to find their best arguments when challenged by a well-prepared enthusiast of 'intelligent design'".
J. Scott Turner is an associate professor of biology at the State University of New York's College of Environmental Science and Forestry. He has written a book which is uninhibited in describing the harmony of structure and function as 'designedness'. He is aware that this will not please some colleagues, but argues that there is "no better way to open minds than to irritate them a bit".
Keywords for Turner's analysis are: "physiology", "homeostasis", and "self-organisation". He explains the concept of "Bernard machines". These both create and regulate environments, and ultimately are considered to lead to the "marvellous harmony of structure and function we observe in nature".
"But the author argues that life and evolution happen when Darwin machines act in concert with Bernard machines, which are the agents of homeostasis and can be seen, in their own particular way, as goal-seeking and purposeful. These are the 'tinkerer's accomplices' of the title."
People have been talking about self-organisation for many years, but with very little substance. It really is necessary to move from concepts to specifics. The problem is that decay appears to be a stronger trend than self-organisation, and promising starts do not get far. Furthermore, some regard the presence of homeostasis as a consequence of intelligent agency, which presupposes real design at the outset.

The interior designer
Claus Wedekind
Nature 446, 375, (22 March 2007) | doi:10.1038/446375a

Review of: The Tinkerer's Accomplice: How Design Emerges From Life Itself, by J. Scott Turner, Harvard University Press: 2007. 304 pp.

1st para: Sharing a broadly accepted idea or philosophical concept comes with a danger: after a period of indulgence in mutual affirmation, it is easy to forget how to effectively defend the concept against a smart and captious critic. Established politicians sometimes stumble and get lost in clumsy arguments when forced to defend the basic concepts of their politics against a cleverly presented and maybe radically different opinion. And evolutionary biologists can struggle to find their best arguments when challenged by a well-prepared enthusiast of 'intelligent design'. Non-physiologists, for example, might overlook the agents of homeostasis that lead, largely by themselves, to the marvellous harmony of structure and function we observe in nature.

A new eutriconodont mammal species, Yanoconodon, has been reported by a team of Chinese researchers.
The first point to make is that this is not an example of a transitional fossil. The animal has a number of specialised features and is described as "nested within crown mammals". The authors provide a cladogram of dental and skeletal characters of eutriconodonts, and the closest affinity is with Jeholodens. However, Yanoconodon has more thoracic ribs than Jeholodens, and Yanoconodon has lumbar ribs whereas Jeholodens does not. Whilst the authors discuss Hox gene mechanisms to alter the pattern of ribs, they do not attempt to locate Yanoconodon in any particular evolutionary lineage.
Rather, the new fossil has been hailed as illustrating an important evolutionary transition: detachment of the middle ear bones from the mandible. It is therefore better described as a fossil claimed to have a transitional structure associated with ear bones.
It is true that the authors favour the evolutionary transition scenario, but they are forced by the data to consider at least one alternative: that the definitive mammalian inner ear was present in "the common ancestor of monotremes, eutriconodonts and therians; but eutriconodonts re-evolved the middle ear attachment to mandible." (A polyphyletic approach introduces more options). The editors of Nature supplied a summary acknowledging that there is a legitimate debate about the significance of the find: "But the situation is not as clear-cut as it seems. The evolutionary relationships of the fossil suggest that either the 'modern' middle ear evolved twice, independently or that it evolved and was then lost in at least one ancient lineage." (In this comment, they are referring to monotremes and therians. The earbones of the duckbilled platypus emerge during development with a cartilaginous attachment to the jaw - much like Yanoconodon - but this attachment is reabsorbed as the animal grows thereby detaching the earbones).
It should be pointed out that this debate is not one where ID scholars might be expected to have a common view. Are evidences for design in the natural world affected by the earbones of Yanoconodon? The expectation would be that all the features of the animal would have functional significance, and that Darwinian mechanisms are not capable of achieving the specified complexity associated with the mammalian ear. Beyond that, let us explore the data without having to force everything into a Darwinian straitjacket! For those seeking a creationist comment, go here.

A new eutriconodont mammal and evolutionary development in early mammals
Zhe-Xi Luo, Peiji Chen, Gang Li, and Meng Chen
Nature 446, 288-293 (15 March 2007) | doi:10.1038/nature05627

Detachment of the three tiny middle ear bones from the reptilian mandible is an important innovation of modern mammals. Here we describe a Mesozoic eutriconodont nested within crown mammals that clearly illustrates this transition: the middle ear bones are connected to the mandible via an ossified Meckel's cartilage. The connected ear and jaw structure is similar to the embryonic pattern in modern monotremes (egg-laying mammals) and placental mammals, but is a paedomorphic feature retained in the adult, unlike in monotreme and placental adults. This suggests that reversal to (or retention of) this premammalian ancestral condition is correlated with different developmental timing (heterochrony) in eutriconodonts. This new eutriconodont adds to the evidence of homoplasy of vertebral characters in the thoraco-lumbar transition and unfused lumbar ribs among early mammals. This is similar to the effect of homeobox gene patterning of vertebrae in modern mammals, making it plausible to extrapolate the effects of Hox gene patterning to account for homoplastic evolution of vertebral characters in early mammals.

See also:
Editor's summary, An early look at mammals, Nature 446, 15 March 2007, vii.

Who can ever cease to be amazed at the complexity of cells and genetic systems? A Perspective essay in today's Science, concerned with "gene regulatory networks for development", confirms yet again the reality of complexity. The authors bring out the role of subcircuits in the gene regulatory network. These are "often of elegant and sometimes counterintuitive design, even more so, the ways they are combined in the overall network." The authors add: "Among the most fascinating aspects of gene regulatory networks are their design principles, for these are often interestingly different from what would seem the "simplest" solution."
The modular construction of these subcircuits is fascinating because it is at a much deeper level than the feedback circuitry we are more familiar with. "Thus, although subcircuits are indeed the modular functional components of developmental gene regulatory networks, they are to be distinguished from simpler "building blocks" or "motifs" that are used for many diverse developmental functions (e.g., feedforward or feedback elements, per se)."
The complexity goes even deeper: "As we have come to understand developmental gene regulatory networks, there arises an impression of "overlayered" circuit design--or more precisely, deployment of multiple subcircuits--that in different ways support the same end result."
What are we to make of the inter-dependent modular nature of regulatory networks? Is this the 'tinkering' model of Darwinism, or do we have the 'exquisite design' model of ID? "We may interpret this as we like--as overengineering; or as design deluxe, replete with bells and whistles; or as the expected result of an evolutionary process in which individual regulatory modules have been added in and overlain at different times." The authors plump for the 'tinkering' model. But even they appear to concede that what we have before us are irreducibly complex systems: "once integrated into the regulatory system, they are there to stay, barring evolutionary redirection". All I can say is that the hallmarks of 'tinkering' are noticeable by their absence! I'll go for the 'design deluxe' option!

Built to Run, Not Fail
Paola Oliveri and Eric H. Davidson
Science 315, 16 March 2007: 1510-1511.

On first encounter, gene regulatory networks for development often seem so complicated as to defy intuitive understanding. But the overall maze of gene interactions that they represent is actually composed of subcircuits that perform separate functions. The subcircuits are often of elegant and sometimes counterintuitive design, even more so, the ways they are combined in the overall network. As the underlying subcircuit structure is clarified, we see that gene regulatory networks in fact provide a direct and simply organized bridge from the phenomena of development to the detailed genomic programs that encode it. Among the most fascinating aspects of gene regulatory networks are their design principles, for these are often interestingly different from what would seem the "simplest" solution. Gene regulatory networks for development are the direct product of evolution, and the character of their design both illuminates evolution and is illuminated by it.

[snip]

Last para: We may interpret this as we like--as overengineering; or as design deluxe, replete with bells and whistles; or as the expected result of an evolutionary process in which individual regulatory modules have been added in and overlain at different times, so that some are more ancient and others more new (1). However, once integrated into the regulatory system, they are there to stay, barring evolutionary redirection. But the generality of this quality of developmental gene regulatory networks is emerging as a fact of life--it is what we see in modern animals. The consequences of evolutionary history determine the shape of the control apparatus that determines life processes. Perhaps in current system design we are seeing something of the grim pressures that modern lineages survived in past evolutionary bottlenecks--of the absolute necessity for lineage survival of genomic regulatory systems built to run and not to fail.

Carl Linnaeus features large this week in Nature. He is remembered as a towering figure whose impressive shadow looks likely to reach well beyond this 300 year anniversary. The Editorial draws attention to three distinctive contributions: "his systematic spirit, his stress on the concept of species, and the formal but adaptable conventions of nomenclature he introduced". Also, we read: "Nature is glad to celebrate his legacy in this special issue."
There is another aspect of Linnaeus that deserves our attention. The Father of Taxonomy considered that the living world was the product of a creator God: "Linnaeus believed in fixed species of knowable number created by God and observable by men." It should be pointed out that this summary reflects his early view; as he matured and developed in his thinking, he recognised the reality of speciation within distinct groups of organisms. But is his creation-oriented biology part of his legacy? Not in the opinion of the editors of Nature: "He would hopefully come round to evolutionary theory".
What if he failed to "come round"? What if he developed further his polyphyletic approach? What if he were to argue that the Tree of Life were a construct of ideology, not a result of empirical science? Would he then be disowned by the community of scientists who declare their pleasure in celebrating his legacy? Of course, these are all hypothetical questions. However, the deeper issue is this: Linnaeus did not separate his thinking into "public" and "private" compartments. He sought a unified understanding of the natural world. He was a theistic scientist. He was open to the possibility of seeing design in the living world, and he found it. He showed that design inferences were part of the early days of science, and that modern day attempts to banish intelligent design from the vocabulary of science take us away from the historic roots of our discipline. This is an aspect of Linnaeus' legacy that we do well not to overlook.

The legacy of Linnaeus
Editorial
Nature 446, 231-232 (15 March 2007) | doi:10.1038/446231b

Darwinists have never been comfortable with reports of "stasis". They have never been reconciled to Gould's statement that "Stasis is data". Instead, stasis is regarded as a paradox and as a problem to be solved. Estes and Arnold have contributed a significant new paper on the subject. In one paragraph, they review the evidence that stasis might have a genetic explanation and conclude that this refutes "the notion of omnipresent, internal constraints on evolution." However, their perspective is entirely Darwinian, and there is no engagement with structuralist thinking, or bau-plans or basic types. Darwinian theory makes no distinction between adaptations of traits and the development of novel structures, so the fact that "populations are often well equipped genetically to respond to at least short-term ecological challenges" is sufficient to settle the matter. Then "stabilising selection emerges as the leading contender among explanations for stasis."
Estes and Arnold employ the adaptive landscape concept to "evaluate the degree to which six evolutionary models fit the observed data." Three of these models are based on random variation, and these do not fit at all. In a News and Views article in Nature, Hendry comments "This conclusion will be reassuring, or perhaps just obvious, to the innumerable evolutionary biologists who believe that adaptation plays a central role in evolution". The other three models all involve a shift in the fitness peak of the adaptive landscape. In one case, the peak moves continuously in a particular direction. In the second case, there are two peaks separated by a valley. The third case is called the "displaced optimum" model; it has a single peak which jumps in a generation to a new location and stays there. "In the authors' estimation, this last model fits the data quite well."
Approaching a conclusion, Hendry explains the title of his article: "For some, any report of the death of this paradox will probably evoke the same reaction as the death of Elvis, with a large number of fans reluctant to accept its passing. But in the end, evolutionary biologists will probably converge on more pertinent questions, such as 'What generates and maintains adaptive zones in the first place?', and 'How do some lineages ultimately bridge the gap between different adaptive zones?'. In other words, these biologists can get back to the same questions that they have been puzzling over for 60 years!
The analogy with the death of Elvis is most unfortunate, because there is no valid comparison. Stasis is the conclusion of extensive analysis of data by specialists, not the emotive response of bystanders. The adaptive landscape, on the other hand, is a theoretical construct offered to illustrate adaptive change, but never validated by empirical research. The paper by Estes and Arnold provides theoretical modelling of reported data, with no analysis of the environmental factors changing the adaptive landscape, and no attempt to explain the changes in terms of adaptive responses to environmental factors. There are really so many loose ends to this work that the authors should not be allowed to get away with the idea that they have confronted "the predictions of alternative evolutionary models with the reality of data".
The paradox of stasis is not dead, nor is it in its death throes!

Resolving the Paradox of Stasis: Models with Stabilizing Selection Explain Evolutionary Divergence on All Timescales
Suzanne Estes and Stevan J. Arnold
American Naturalist, February 2007. Vol. 169, pp. 227-244.

ABSTRACT: We tested the ability of six quantitative genetic models to explain the evolution of phenotypic means using an extensive database compiled by Gingerich. Our approach differs from past efforts in that we use explicit models of evolutionary process, with parameters estimated from contemporary populations, to analyze a large sample of divergence data on many different timescales. We show that one quantitative genetic model yields a good fit to data on phenotypic divergence across timescales ranging from a few generations to 10 million generations. The key feature of this model is a fitness optimum that moves within fixed limits. Conversely, a model of neutral evolution, models with a stationary optimum that undergoes Brownian or white noise motion, a model with a moving optimum, and a peak shift model all fail to account for the data on most or all timescales. We discuss our results within the framework of Simpson's concept of adaptive landscapes and zones. Our analysis suggests that the underlying process causing phenotypic stasis is adaptation to an optimum that moves within an adaptive zone with stable boundaries. We discuss the implication of our results for comparative studies and phylogeny inference based on phenotypic characters.

See also:
Hendry, A. Evolutionary biology: The Elvis paradox. Nature 446, 147-150, (8 March 2007) | doi:10.1038/446147a
Abstract: Evidence for a universal driver of evolution across all timescales could mean that the venerable paradox of stasis is dead. But even with such evidence, some biologists would be reluctant to accept its passing.

The Ceratopsidae is the name given to a Family of four-legged herbivores from the Upper Cretaceous of Western North America. They are classified in two subfamilies: the Ceratopsinae (which includes the well-known Triceratops) and the Centrosaurinae (which includes Styracosaurus). These are all horned dinosaurs, with a diverse range of protrusions from the frill, from above the eyes and above the nose. The Ceratopsinae are associated with long brow horns whereas in the Centrosaurinae they are short. A new dinosaur find reveals a centrosaurine with long brow horns. Based on the stratigraphical position and a cladistic analysis, the animal has been identified "as the basal member of the Centrosaurinae".
The oldest known horned dinosaur is called Zuniceratops and had large horns. Consequently, "the newly found creature [is] an intermediate between older forms with large horns and later small-horned relatives" suggests Jim Kirkland, State of Utah paleontologist, who co-identified Zuniceratops in 1998. "He predicted then that something like Ryan's find would turn up. "Lo and behold, evolutionary theory actually works," he said."
The extraordinary diversity of the dinosaurs in general is no less apparent in the Ceratopsidae, all of which are documented from a few states of the US and parts of Canada. Variation on a theme is prominent. Evolutionists generally start by trying to trace a linear pathway, with clearly defined intermediates, but more data transforms the picture to a bush, with no obvious tree-like structure. So, although we read a comment like "evolutionary theory actually works", it does not carry much weight. "It is very surprising that a Centrosaur would have long brow horns," said Don Brinkman of the Royal Tyrrell Museum in Drumheller. If the prediction was substantial, one would expect people to say that they were expecting this discovery.
It is worth adding that the real debate over evolutionary theory is not about the positions and sizes of horns. This is just variation affecting existing traits and not controversial at all. Of far greater interest is the origin of novel structures, especially those exhibiting complex specified information. It will be a great day when Darwinists realise that they cannot simply lump together the origin of novelty with observations of variation of existing traits. Then we might witness some really interesting discourse about what evolutionary theory actually is and which aspects actually work!

A new basal centrosaurine ceratopsid from the Oldman Formation, Southeastern Alberta
Michael J. Ryan
Journal of Paleontology, 81(2), March 2007, pp. 376-396

Abstract: A new centrosaurine ceratopsid, Albertaceratops nesmoi, is described from the lower Oldman Formation (Upper Cretaceous) of southern Alberta, and is based on a single, almost complete skull. Referred material is described from equivalent beds in the Judith River Formation of north-central Montana. A limited phylogenetic analysis of the Ceratopsidae places the new taxon as the basal member of the Centrosaurinae and indicates that robust, elongate postorbital horncores that form a synapomorphy of (Ceratopsidae + Zuniceratops) are also present in Centrosaurinae.

See also:

Cleveland Museum of Natural History Scientist Discovers New Horned Dinosaur Genus
Cleveland Museum of Natural History Press Release, February 24, 2007

Dinosaur had yard-long horns over eyebrows
CNN News, March 5 2007.

Paleoanthropologists have always had plenty to debate, and a new genome comparison study is no exception. Whereas the majority view suggests that hominid line can be traced back to between 5 Ma and 7 Ma, the new study gives a more recent figure. "We apply the HMM [a statistical method] to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 ± 0.4 million years)." This is deemed by many as too late. Blair Hedges considers that the figure "is hard to defend because fossils practically reject it". Ian Tattersall says "it's inconceivable that you could have a common ancestor to both at 4 million years ago when you already have evidence in the hominid lineage that there were bipeds already around at that time."
The study raises again the whole question of what the genome comparisons are telling us. It gives particular relevance to the recent critique of Schwartz and Maresca noted here.

It would be a big step forward if the presuppositions and assumptions of every discipline involved in anthropology were more transparent, because there is often considerable difficulty distinguishing between data and interpretations of data.

Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model
Asger Hobolth, Ole F. Christensen, Thomas Mailund, Mikkel H. Schierup
PLoS Genetics, 3(2): e7 doi:10.1371/journal.pgen.0030007

Abstract: The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human-chimp ancestor and 45,000 ± 10,000 for the human-chimp-gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.

See also:

Gibbons, A., A Recent Split of Humans and Chimps? ScienceNOW Daily News, 27 February 2007.

Lloyd, R., First Humans: Time of Origin Pinned Down, LiveScience, 23 February 2007.

The assumptions underlying molecular clocks are all dependent on the "Darwinian model of continual and gradual change". What happens if these assumptions are probed, tested and subjected to critical scrutiny? This is the exercise undertaken by Schwartz and Maresca.
The first part of the paper addresses historical aspects of "molecular systematics" to better understand the "theoretical and methodological underpinnings." The authors are concerned to find out "how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central, especially to paleoanthropology." This they do with an incisiveness rarely appearing on the printed page of refereed journals. The MA (molecular assumption) is acknowledged to be dominant but to rest on theoretical rather than empirical foundations. "No doubt because it was completely Darwinian, the MA continued to dominate the increasingly influential field of what was now often called molecular systematics."
The authors go on to look at the topic of DNA hybridization, showing that the data may be telling us something about "primitive retention" rather than "closeness of relatedness". They show that although the authors of MA studies use the language of cladism, they are mistaken: "In light of this procedure of hypothesis testing, it is obvious that any molecular analysis based on the MA is not cladistic."
They show that comparisons based on structural genes can be interpreted in ways that are quite different from the MA advocates. "Phylogenetic relationships among metazoans might, therefore, be better revealed through comparing developmentally regulated genes, because changes in their expression can alter phenotypes."
It has been a major problem for Darwinism that its foundations are regarded as inviolable and a 'given'. "Our review [...] reveals that, no matter how sophisticated their mathematical models, molecular systematists have not questioned the basic assumptions upon which they are based. Thus, while refining computer programs to analyze molecular data phylogenetically continues apace [...] with statements of certitude about results following suit, no algorithm is more viable than the assumptions that inform it." The authors offer the hope that their critical review will open the way for a more integrated approach to systematics.
This is a paper that will disturb the Darwinists, but it will offer encouragement to all who want to see less ideology in evolutionary thinking and who want to follow the evidence wherever it leads.

Do Molecular Clocks Run at All? A Critique of Molecular Systematics
Jeffrey H. Schwartz and Bruno Maresca
Biological Theory, Fall, 2006, Vol. 1, No. 4, Pages 357-371 | doi:10.1162/biot.2006.1.4.357 (Open Access)

Abstract: Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the "molecular assumption."

See also:

Prof Questions Darwinian Dogma, Scienceagogo, 12 February 2007

"The genetic code is the mapping of 64 three-letter codons to 20 amino-acids and a stop signal." It stands out among possible competing codes in several ways. "First, the assignment of amino acids to codons appears to be optimal for minimizing the effect of translational misread errors." Errors in misreading a codon tend to have minimal effects on the translated protein. "Second, amino acids with simple chemical structure tend to have more codons assigned to them", as "they are required more often in protein assembly". But the researchers main interest in the paper below was the ability of the genetic code to carry parallel messages. The list is already impressive (and there is no reason why it should not be extended with research) - binding sequences of regulatory proteins that bind within coding regions, splicing signals that include specific 6-8 bp sequences within coding regions and mRNA secondary structure signals - all higher-order codes that ride over the protein forming code. "They found that the real genetic code could accommodate more arbitrary motifs in coding sequence than almost any of the other possibilities - it has a higher information content. One reason for the real genetic code's superiority is the fact that its stop codons, when frame-shifted, tend to form common codons, whereas in other codes frame-shifted stop codons form rarer codons or even other stop codons."
The authors appeal to selection to explain why the genetic code is optimal. The implication of this approach is that the selection had to take place before the Last Common Ancestor emerged on Earth. All this complexity had to be fine tuned in a single celled organism that predated all subsequent diversity. An information-based approach linked to Intelligent Agency deserves a fair hearing when seeking an explanation for optimal design.

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
Shalev Itzkovitz and Uri Alon
Genome Research, 2007 17: 405-412. doi 10.1101/gr.5987307(Open Access)

DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These "parallel codes" include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

See also:
Goymer, P., Evolution: The genetic code sees off rivals, Nature Reviews Genetics 8, 168-169 (March 2007) | doi:10.1038/nrg2076

There are many possible three-letter genetic codes that could adequately encode protein sequences, but what about the need to encode higher-order information on binding and splicing sites? New research shows that the actual genetic code is better than potential alternatives at encoding such information at the same time as encoding protein. [snip]

Evolution and multilevel optimization of the genetic code
Tobias Bollenbach, Kalin Vetsigian, and Roy Kishony
Genome Research, 2007 17: 401-404. doi 10.1101/gr.6144007

Abstract: The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors.

Last paragraph: "As we learn more about the functions of the genetic code, it becomes ever clearer that the degeneracy in the genetic code is not exploited in such a way as to optimize one function, but rather to optimize a combination of several different functions simultaneously. Looking deeper into the structure of the code, we wonder what other remarkable properties it may bear. While our understanding of the genetic code has increased substantially over the last decades, it seems that exciting discoveries are waiting to be made."