Science Literature

A previous blog drew attention to negative feedback mechanisms in the Earth's climatic system as a mark (though not a proof) of design. An interesting study by Lindzen and Choi has recently appeared which gives an informative analysis of satellite data spanning 16 years (to 1999). These measurements provide evidence bearing on the Earth's radiation imbalance and climatic feedbacks. From the abstract:

"The observed behavior of radiation fluxes implies negative feedback processes associated with relatively low climate sensitivity. This is the opposite of the behavior of 11 atmospheric models forced by the same SSTs."

Figure 2 from the new paper. "The observed relationship between ocean temperature changes (x-axis) and radiation flux to space (y-axis) is contained in the graph with the red box around it. The other graphs depict the relationship as predicted by 11 different climate models." (Source here)

The data source is the Earth Radiation Budget Experiment (ERBE) which allows measurement of the heat energy emitted by the Earth. Solar energy drives the Earth's climatic system and the incoming radiation is that of a body with a temperature of about 6000 deg K. The Earth absorbs much of this heat energy and emits radiation corresponding to a temperature of about 255 deg K. In a state of equilibrium, the absorbed energy is balanced by the emitted energy.

The equilibrium state is altered by clouds and greenhouse gases (such as water vapour, carbon dioxide and methane). These materials act like an insulating layer, inhibiting energy emission. Equilibrium is restored when the effective temperature of the Earth rises. Carbon dioxide has been the focus of interest over the past two decades, and climate scientists have come to use the term "climate sensitivity" to define the equilibrium response obtained when doubling atmospheric carbon dioxide. The United Nation's Intergovernmental Panel on Climate Change (IPCC) estimates that climate sensitivity is in the range 1.5-5.0 deg C.

The hypothesis made by many climate scientists is that higher carbon dioxide levels increase the global temperature and this allows more water vapour to be held in the atmosphere. This leads to an increasing cloud cover and a greater blanketing effect: a positive feedback mechanism. Thus, the effect of the CO2 increase is amplified and global temperatures rise to restore equilibrium. This is the hypothesis that has been tested by Lindzen and Choi utilising the climate models currently favoured by climate scientists. The observed sea surface temperatures over the 16 year period have been fed into the models to calculate values for the heat energy radiated from the Earth. The results were compared with empirical observations derived from satellites. The findings, plotted in their Figure 2 (above), show that the model predictions are in marked contrast to the ERBE data. The authors point out that the latter reveal negative feedback mechanisms (as yet undetermined) in contrast to all the models which have positive feedback, described by the authors as "spurious positive feedback".

Lindzen and Choi go on to present revised climate sensitivity figures. Whilst the range of variation used in the models is 1.5-5.0 deg C, the authors say that their results "appear to demonstrate a climate sensitivity of about 0.5 deg C". This implies strong negative feedback. Furthermore, if greenhouse gases do warm the planet, their effects would not be distinguishable from natural climatic variations.

Scientists should have liberty to interpret the negative feedback mechanisms as a pointer to our planet's climatic system being designed for life. The Earth's climate is far more stable than the alarmists think. Their views are buttressed by incorporating positive feedback mechanisms into their models to amplify small climatic perturbations and, as Lindzen and Choi have shown, this approach is in tension with the empirical evidence.

It may be of wider interest to discuss a link between this topic and my earlier blog on "Darwin's boulders". The common thread is uniformitarianism adversely affecting the judgment of scientists. Much of climate science is concerned with the present and with short-term forecasting. However, not so many thousand years ago, all are aware of radically different climates during glacial periods. The causes of ice ages have been extensively discussed: some have favoured catastrophism whereas others offer uniformitarian explanations. Recently, the pendulum has swung very strongly towards acceptance of Milankovitch Cycles as the key to understanding glaciations. There are three dominant cycles, affecting the Earth's eccentricity, axial tilt and precession. The variations in solar energy relate to seasonality and geographic location.

Using these cycles, glaciations are said to occur because of predictable causal mechanisms affecting the Earth as it orbits the Sun. The mathematical formulas developed by Milutin Milankovitch are very suitable for incorporating into climate models and simulations, so they have proved to be attractive to climate scientists seeking to explain glaciations. Since the net annual solar radiation falling on the Earth is a constant, the irradiation differences identified by Milankovitch need to be amplified so that they can trigger large scale effects. This necessitates the use of positive feedback in model-building. The root problem is that the science that emerges is built on the assumption of uniformitarianism and model validation using empirical data has been far from rigorous.

This analysis of the way uniformitarianism is a hidden presupposition of much climate science is, of course, a personal view. ID is concerned with design inferences and there is no reason why ID scientists should not take different views on these particular issues. The reason why I am sharing these thoughts is because making design inferences about the Earth's climate system is not a no-go area, and my previous blog explained the basis for a prediction: that negative feedback mechanisms predominate. This is a testable prediction, as the research discussed in this blog has shown. It is just possible that if climate scientists were more alert to design issues, they would have been more critical of their own models (which demanded positive feedback and relative climatic instability). And it can be argued that the presumption of uniformitarianism (Lyell's legacy to the present generation) has not only led to flawed science, it has also cost billions of dollars in a misguided attempt to save the planet.

On the determination of climate feedbacks from ERBE data
Richard S. Lindzen and Yong-Sang Choi
Geophysical Research Letters, 36, L16705,2009 | doi: 10.1029/2009GL039628

Abstract: Climate feedbacks are estimated from fluctuations in the outgoing radiation budget from the latest version of Earth Radiation Budget Experiment (ERBE) nonscanner data. It appears, for the entire tropics, the observed outgoing radiation fluxes increase with the increase in sea surface temperatures (SSTs). The observed behavior of radiation fluxes implies negative feedback processes associated with relatively low climate sensitivity. This is the opposite of the behavior of 11 atmospheric models forced by the same SSTs. Therefore, the models display much higher climate sensitivity than is inferred from ERBE, though it is difficult to pin down such high sensitivities with any precision. Results also show, the feedback in ERBE is mostly from shortwave radiation while the feedback in the models is mostly from longwave radiation. Although such a test does not distinguish the mechanisms, this is important since the inconsistency of climate feedbacks constitutes a very fundamental problem in climate prediction.

See also:

Tyler, D. Was Lyell's "project simply the worldview of naturalism"? ARN Literature Blog, 6 July 2007.

As a young man aboard HMS Beagle, Charles Darwin was fascinated by erratic boulders. After completing his voyage, he wrote several papers about their origin. Tierra del Fuego was of particular interest, for he found boulder trains at different elevations at a place known as Bahia San Sebastian, which faces the Atlantic Ocean. Darwin actually delayed the survey work of HMS Beagle so he could gather more extensive information. On returning to the UK, he made the boulders the focus of two geological papers published in 1841. The route by which Darwin reached his conclusions is instructive for all of us involved in research today.

Some of "Darwin's Boulders" (Source here)

It is well known that Charles Lyell's writings were a major influence on Darwin. Captain Fitzroy acquired Volume 1 of Principles of Geology for the library of HMS Beagle. Darwin not only read it but afterward said that "it altered the whole tone of one's mind" and that, thereafter, he saw everything in the light of Lyell's ideas. He made a point of acquiring the other volumes as they were published. Lyell's approach to making geology a science was to relate all geological interpretations to the operations of present-day processes. He championed uniformitarianism as a methodological principle - and Darwin drank it all up. He followed Lyell's lead in explaining landscape evolution in terms of gradual, incremental changes of sea level.

"Darwin's thinking was profoundly influenced by Lyell's obsession with large-scale, slow, vertical movements of the crust, especially as manifested in his theory of submergence and ice rafting to explain drift. In turn, Lyell profited greatly from Darwin's observations, including uplift of the Pacific coast of Chile during the Talcahuano earthquake. Lyell celebrated these observations because they supported his idea of uniformitarianism - that continued small changes, as witnessed in the field, could account for dramatic changes of Earth's surface over geologic time."

Lyell had noted how sediments carried along by icebergs could be deposited far from their source, and Darwin extended the observations by documenting the way boulders were transported by icebergs. He then developed an ice-rafting model to explain erratic boulders. In 1845 he pointed out that if these boulders were close to glaciers, they were likely pushed into position, but if far from source, they were ice-rafted.

"Few geologists now doubt that those erratic boulders which lie near lofty mountains have been pushed forward by the glaciers themselves, and that those distant from mountains, and embedded in subaqueous deposits, have been conveyed thither either on ice-bergs or frozen in coast-ice."

Darwin supported this model for the Tierra del Fuego boulders using two arguments: first, that the land surface on which the boulders lay were free of mounds and ridges which might point to glacial action; and second, that the boulders were angular - which would not be expected if they were pushed such a great distance. Darwin "considered the possibility that glaciers could have extended" much further than they do today, but rejected the idea because it departed too much from uniformitarian thinking. Darwin's approach to interpreting landscape anomalies is described by the authors of a recent paper as "inductive reasoning". This is discussed further below.

The new research sets out to revisit "Darwin's Boulders" and to review the causal mechanism. The authors have mapped the Bahia San Sebastian train of boulders on the east coast (which number about 500) and also a second train at Bahia Inutil on the west coast (which number about 1000). All the boulders are medium-grained hornblende granodiorites, several hundred kilometres from the nearest source. The authors write:

"Of the three plausible mechanisms for emplacement of these distal erratics - iceberg rafting, stream-ice rafting, or direct deposition from glaciers - we support the latter. Overwhelming evidence for complete glaciation of Tierra del Fuego, from coast to coast, has been unchallenged for almost a century. It is unlikely that stream ice could have transported such large boulders over hundreds of kilometers while maintaining such a tight distribution, and there is no evidence of a capable fluvial environment in the immediate vicinity of either boulder train."

To expand on the relevant points: mapping of the surface sediments of Tierra del Fuego has revealed that the whole region has been glaciated. The boulder trains at Bahia San Sebastian train and Bahia Inutil have been mapped as resting on moraine crests. The "tight distribution" has been documented and ice-rafting has never been observed to result in anything like this. Direct deposition, however, is observed. Landslides onto glaciers can leave large boulders on the ice which can then be transported however far the glacier extends, leaving a linear train of blocks when the ice melts away.

I want now to return to the "inductive reasoning" comment noted earlier. Inductive reasoning starts with observations and philosophical premises, uses reason to identify patterns, which lead to the proposal of initial hypotheses. These can then be tested and confirmed hypotheses lead to theories. Darwin's observations were of angular erratic boulders, the ability of icebergs to carry large rocks over long distances, and relatively short glaciers in the upland areas. His philosophical premise was uniformitarianism. Put these together and the hypotheses were iceberg rafting or stream-ice rafting. The angularity of the boulders ruled out stream-ice rafting, so Darwin drew the conclusion that the mechanism was iceberg rafting.

The problems with this start with the philosophical premises. Once uniformitarianism was accepted as essential to science (as Lyell argued), Darwin felt honour-bound to adhere to it. His thinking became constrained. He was only prepared to work with hypotheses that were compatible with uniformitarianism - all else would be regarded as speculation or even antiscience. This led him to overlook data that was right in front of him: the "tight distribution" of the boulders that was inconsistent with the hypothesis. It also delayed the recognition of the glacial features that covered Tierra del Fuego.

The problem goes back to Francis Bacon, who wanted to move away from the deductive methodology of the Aristotelians and establish something more grounded in empiricism. Induction was a key stage in his methodology - but he underplayed the human dimension. Researchers have to bring philosophical premises to bear on their work. How can we avoid becoming slaves to our adopted premises? Uniformitarianism lasted a century before researchers accepted that catastrophism was just as viable as a philosophical presupposition. What matters is that we use these philosophical approaches to generate testable hypotheses. Multiple working hypotheses are to be commended as long as ways are found to put them to the test.

Charles Darwin never escaped uniformitarianism. It pervaded his geology - as is apparent from the example before us here. It entered his thinking about biological transformation: the natural selection of small incremental variations. (Unfortunately, this constraint is still with us today, as Darwinians are unwilling to concede anything significant to the theory of punctuated equilibrium or to evo-devo.) Darwin missed out in understanding heredity, because he was looking for gradual change rather than discontinuous variation. (For more on why Darwin did not discover the laws of inheritance, go here).

Philosophical premises are of crucial importance. We cannot afford to leave discussion of this to the philosophers. Scientists bring philosophical premises whether they know it or not - and, as Darwin demonstrated, it matters. This is why the issues raised by Intelligent Design are of such importance. Should design inferences be part of science? Those who say 'no' are united in the belief that design cannot be inferred in the natural world. They 'know' this, not because they have empirical evidence to show it, but because their philosophical starting point is naturalism. All causation must be by Law or by Chance, they say. ID advocates have repeatedly pointed out that this stance involves circular reasoning, because they can envisage no scientific test to prove or disprove design. Consequently, disproofs of design are always theological: 'God would not do it that way!' However, philosophical naturalism has within it the seeds of its own destruction: like Darwinism, it is a universal acid that eats up our humanity (consciousness and free agency), our values (all morality is relative and socially constructed) and ultimately our science. That's why ID advocates must persevere until the urgently needed changes come.

Enigmatic boulder trains, supraglacial rock avalanches, and the origin of "Darwin's boulders", Tierra del Fuego
Edward B. Evenson, Patrick A. Burkhart, John C. Gosse, Gregory S. Baker, Dan Jackofsky, Andres Meglioli, Ian Dalziel, Stefan Kraus, Richard B. Alley, Claudio Berti
GSA Today, December 2009, 19(12), 4-10.

Charles Darwin considered himself to be a geologist and published extensively on many geologic phenomena. He was intrigued with the distribution of erratic boulders and speculated upon their origins. In his accounts of the voyage of the HMS Beagle, Darwin described crystalline boulders of notable size and abundance near Bahia San Sebastian, south of the Strait of Magellan, Tierra del Fuego. Influenced by Charles Lyell's reflections upon slow, vertical movements of crust, submergence, and ice rafting to explain drift, Darwin proposed that the boulders of Bahia San Sebastian were ice-rafted. Benefiting from 170 years of subsequent study of the glacial history of Tierra del Fuego, petrography, and terrestrial cosmogenic nuclide measurements, we revisit the origin of "Darwin's Boulders" at Bahia San Sebastian. We suggest that they, as well as another train of boulders to the west, at Bahia Inutil, represent rock falls of Beagle-type granite from the Cordillera Darwin onto glacial ice flowing into the Bahia Inutil-Bahia San Sebastian lobe. These supraglacial rock avalanche deposits were subsequently elongated into boulder trains by glacial strain during transport and then deposited upon moraines. The cosmogenic nuclide exposure dates support the correlation of Andean glaciations with the marine oxygen isotope record and the glacial chronologies recently proposed for Tierra del Fuego.

Students of evolution are taught to avoid incorporating the idea of progress to the theory. Law + Chance do not allow the incorporation of an over-riding goal. One Evolution 101 course expresses it this way: "It is tempting to see evolution as a grand progressive ladder with Homo sapiens emerging at the top. But evolution produces a tree, not a ladder - and we are just one of many leaves on the tree." The Darwinian mechanisms of mutation + natural selection emphasise Chance over Law, with the corollary that the evolutionary process is unpredictable. Readers of Stephen Jay Gould will know that this was one of his favourite themes, to which he repeatedly returned. In a recent paper, Simon Conway Morris consciously challenges the status quo and points a way to a different perspective on evolutionary transformation:

"Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable."

Are humans an "evolutionary inevitability" or just one of many leaves on the Tree of Life? (Source here)

Conway Morris has wrestled with the question: why, if evolution is fortuitous and accidental, are there so many evidences of convergence? Over-specialisation has meant scientists escape the overwhelming evidence for convergence being ubiquitous. Their research "tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations". This needs to change, and the advocates of neo-Darwinism need to acknowledge the deficiencies of their theory.

"Here, I will suggest that one central tenet of the current neo-Darwinian synthesis, that evolution is for all intents and purposes open-ended and indeterminate in terms of predictable outcomes, is now open to question. Thus, not only is life suspended between permanently uninhabitable regions that are either locked into crystalline immobility or in continuous and chaotic flux, but that the lines of evolutionary vitality thread through a landscape that leaves evolution with surprisingly few choices. The basis of this view relies on the phenomenon of evolutionary convergence."

We can commend Conway Morris for his willingness to support "the heterodox idea" that there is more predictability in evolutionary biology than the Darwinians will admit. We need scholars who are prepared to think rather than operate within a theoretical straitjacket. However, what Conway Morris does not do is to critique the paradigm that makes "fortuitous and accidental" mechanisms the key to the mystery of life's origins. He thinks that "something is missing" and that he can bolt on something that will somehow turn these stochastic components into an engine for delivering "ubiquitous evolutionary convergence". He wants to do this by bringing in contributions from developmental biology and epigenetics. Key words for the new way of thinking include: emergent phenomena, self-organisation and nonlinear systems.

"[T]hese concepts can be melded with the currency of evolution in the form of developmental constraints (the role of which may be exaggerated) and epigenetics to suggest that indeed something is missing in the Darwinian synthesis."

Is something missing? Hardened Darwinists will interpret this as merely a refinement of their essential mechanisms: with an acknowledgment that living things are products of history: genetic variations and natural selection can only work with the source material that is there. This is how structuralism can be integrated within the evolutionary synthesis. But Darwinists are not showing any signs of acknowledging that anything significant is missing from their theory! The evolution of life is still essentially fortuitous, but the options open for transformation are constrained by history.

Conway Morris does not talk about mechanisms that challenge the "fortuitous" thesis. Rather, he gives numerous examples of striking convergences that allow him to suggest that evolutionary trajectories are predictable. However, the argument presupposes common ancestry and the early (existing in the Precambrian) appearance of life forms that exhibit "an extraordinary degree of complexity". His story effectively starts with complexity and it is this complexity that is transformed as the Tree of Life extends its branches. The process is described as an apparently "baffling series of self-organizations".

"In many cases, we also see that the particular molecules show a remarkable versatility of function in what appear to be unrelated contexts. It is most probable that these molecules are homologous, but in many cases the overall architecture and the iron constraints of active sites (or equivalents) suggest that convergence should not be automatically dismissed. It is also striking how in general the idea that primitive groups are simple, almost skeletal constructions in comparison to their descendants, is simply incorrect and in precursors as diverse as the last common ancestor of the eukaryotes or choanoflagellates we either infer or see an extraordinary degree of complexity. Rather than imagining that this arose by a series of conveniently cryptic prior stages, we may have to face the possibility that evolution involves what to us seem to be a baffling series of self-organizations."

None of the above is understood at the level of mechanism - Conway Morris is developing a theoretical model that tries to make sense of twigs without being able to trace the branches. "What we do not understand is how organisms assemble as exceedingly complex functional entities nor why they repeatedly navigate to convergent solutions." There is no insight here as to how complexity is built from simple precursors - just an appeal to self-organisation. This, however, is the weak point of the argument. The origin of biological information cannot be a matter of self-organisation because DNA is a code. The precursor molecules have physical and chemical bonds that permit all possible different codes to be carried. There is no innate process of organisation that can generate information.

Nevertheless, Conway Morris has put his finger on data that needs an explanation. Working within his adopted paradigm, Law (rather than Chance) must be invoked if there is to be predictability. This is the hope behind the appeal to self-organisation, developmental constraints and epigenetics. Will this deliver predictability? I think the answer to this is "yes" - but in a more limited sense than that intended by Conway Morris. Developmental biology has taken us beyond the genocentric view of organisms. For example, concentration gradients of morphogens regulate tissue differentiation and morphogenesis in multicellular organisms. Where a pattern of development can be described mathematically, the application area is limited to a limited range of organisms. These ideas can be applied, in principle, to predict diversification within the basic types of life, but beyond this, the empirical base is speculative.

This is where design thinking has enormous potential to move the discussion forward. If we allow Design to stand alongside Law and Chance, there are ways to move the discussion of biological information forward and to ensure theoretical ideas are both informed and constrained by empirical research. Conway Morris' descriptions of ID as "anti-evolutionary dogma" and "scientific fiction" fail to do justice to scholars who "in any other respect fail to manifest any obvious sign of mental instability".

How do we know that "convergence" is the right description of the phenomena described in this paper? Could some of them be design motifs? How can the different explanations of Law and Design be evaluated? This is a contribution ID scientists can bring to the table.

Evolution: like any other science it is predictable
Simon Conway Morris
Philosophical Transactions of the Royal Society B, (January 12) 2010 365, 133-145 | doi:10.1098/rstb.2009.0154

Abstract: Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology ('evolution explains evolution'). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein.

Ulrich Kutschera is a German biologist and Darwin scholar who has reached the conclusion that Darwin's 1859 treatise conveys a "philosophical imperative". By this is meant the strict separation of "scientific fact and theories from religious dogmas". Kutschera rejects the claims of some that "evolutionary theory and Bible-based myths are compatible". From an ID perspective, Kutschera's essay warrants a critical analysis because there are points of agreement and major areas of disagreement.

Sailing along with Darwin - Ulrich Kutschera is third from the right (Credit: N. Spencer, source here).

Let us start with the central claim that Darwin "strictly" separated scientific facts and theorising from religion. It is fair to say this was his stated approach - but did he achieve it? Darwin presented himself as working in the Baconian tradition, but how did he implement induction? In his writings, he makes frequent references to the religious concept of creation. Characteristic of his reasoning is that a Creator could not be responsible for the world portrayed in On the Origin of Species. Repeatedly, theological reasons are provided to support Darwin's conclusion. ID authors have drawn attention to this style of argument: notably Nelson (1998) and Hunter (2001).

Once it is acknowledged that theological arguments can be used in scientific discourse to reject design and advance evolution, then it follows that responses to these arguments which affirm design are also, in principle, legitimate within science. This is not, of course, what Kutschera and his colleagues want. Significantly, Darwin advocates never interact with ID authors about these matters.

Continuing with the core theme of Kutschera's paper, Darwin's metaphysical stance is described as philosophical naturalism. This means that only natural causes are admitted within science (although exceptions are permitted for archaeological science and forensic science where evidences of intelligent design are always of great interest). ID advocates have generally agreed with Kutschera regarding Darwin's philosophical naturalism, but not with the way he has reached this conclusion.

Kutschera presents the young Darwin as someone accepting the 'natural theology' of William Paley, but who gradually lost his Bible-based beliefs. This interpretation of events can only be followed if Darwin's autobiographical writings are regarded as authoritative. However, this leads to an approach to Darwin studies that is short on critical appraisal. This is significant because numerous statements made by Darwin appear to some of us as either inconsistent or incoherent. An example would be Darwin's explanation of his use of the word "Creator" in the last paragraph of the Origin - discussed below.

Without going into detail, an alternative interpretation of Darwin's spiritual pilgrimage is as follows. Darwin learned his naturalistic philosophy from his father and grandfather. It was reinforced during his time at Edinburgh University. However, he was forced to question these beliefs at Cambridge, where he was deeply influenced by Christians (notably John Stevens Henslow and Adam Sedgwick) and then on the Beagle (Robert FitzRoy). However, it was Charles Lyell, through his writings on geology, who had a more profound ideological impact and Darwin emerged from his travels fully signed up as an advocate of philosophical naturalism.

Another area where Darwin enthusiasts promote their own reading of history is the furor theologicus, highlighted in the title of Kutschera's article. The fury of theologians is supposed to have been poured on poor Darwin's head, making him insert the 'unscientific' word "Creator" in the last paragraph of the Origin. Darwin's 1863 letter to Hooker is quoted to reveal an author who had "long regretted" truckling to public opinion. What Kutschera does not discuss is why Darwin retained the offending words in every subsequent edition of his book. Also, Kutschera does not interact with Van Wyhe's (2007) paper on why Darwin did not publish the Origin before 1859. He shows (convincingly) that Darwin was not in the least troubled by being out of step with theologians or the public. His concern was to gain acceptance of his theory among his peers.

"[N]o unambiguous evidence has been found that Darwin was particularly concerned about a hostile reception. In fact, all of the evidence that does exist points to other forms of expected objections, gaps in the theory or its evidence for example. None of Darwin's written considerations of difficulties suggests an unwillingness or even a reluctance to go public." (Van Wyhe, 2007, p.184-5)

Darwin's ideas received far more criticism from fellow scientists than from theologians. What Kutschera totally fails to acknowledge is this scientific opposition to Darwinism. The furor theologicus is mentioned several times but never documented. The result is a distortion of history.

Kutschera views Darwinism through a filter of positivist philosophy. There is no recognition that Darwin adopted a theoretical framework of uniformitarianism and naturalism with which he interpreted the data. He claimed to be an inductive thinker, but demonstrated deduction. Nevertheless, Kutschera writes:
"[T]he attempt to depict evolution, labelled as "Darwinism", as though it were a political or religious ideology, [. . .] is a misrepresentation of the way scientists work and think. Evolutionary biology is a non-dogmatic system of modifiable theories that is based exclusively on empirical facts and data."

The real problem in this paper is not that it presents an air-brushed Darwin, but that it appears in a journal designed to be read by teachers and students. What is the message getting through to schools and colleges? Instead of help in developing a critical analysis of the issues, young people are fed with propaganda. These students ought to be assessing the cultural and philosophical underpinnings of Darwinism. They ought to be evaluating the effectiveness of the theory to explain empirical facts and data. Instead, it looks as though anyone seeking to apply critical thinking skills to Darwinism will be regarded as guilty of subverting science!

Darwin's Philosophical Imperative and the Furor Theologicus
U. Kutschera
Evolution: Education and Outreach, (December 2009) 2(4), 688-694 | DOI 10.1007/s12052-009-0166-8

Abstract: In 1859 Charles Darwin submitted a manuscript entitled "An Abstract of an Essay on the Origin of Species and Varieties through Natural Selection" to John Murray III, who published the text under the title On the Origin of Species. On many pages of this book, Darwin contrasts his naturalistic theory that explains the transmutation and diversification of animals and plants with the Bible-based belief that all species were independently created. On the last page of the first edition, published in November 1859, where Darwin speculated on the origin of the earliest forms of life from which all other species have descended, no reference to "the Creator" is made. In order to conciliate angry clerics and hence to tame the erupted furor theologicus, Darwin included the phrase "by the Creator" in the second edition of 1860 and in all subsequent versions of his book (sixth ed. 1872). However, in a letter of 1863, Darwin distanced himself from this Bible-based statement and wrote that by creation he means "appeared by some wholly unknown process." In 1871, Darwin proposed a naturalistic origin-of-life-concept but did not dare to mention his "warm little pond hypothesis" in the sixth definitive edition of the Origin (1872). I conclude that the British naturalist strictly separated scientific facts and theories from religious dogmas (Darwin's "philosophical imperative") and would not endorse current claims by the Catholic Church and other Christian associations that evolutionary theory and Bible-based myths are compatible.

See also:
Van Wyhe, J., 2007, Mind The Gap: Did Darwin Avoid Publishing His Theory For Many Years? Notes & Records of the Royal Society, 61, 177-205 | doi:10.1098/rsnr.2006.0171

With millions of eyes on Copenhagen, this seems an appropriate time to ask whether ID thinking has any relevance to understanding the Earth's environment. Can design concepts help us weigh the diverse and often conflicting messages? I think ID is helpful, because features of the Earth's environments and ecologies start to take on new meaning. In this blog, I am thinking particularly of negative feedback mechanisms. Human design engineers will use negative feedback to promote stability and positive feedback to amplify an input signal. They select the mechanisms they need to achieve the desired effect. By analogy, if the Earth is designed for life, we would expect to see negative feedback mechanisms predominating to achieve stable environments. What do we find?

Higher levels of carbon dioxide have accelerated the growth rates of quaking aspen, one of North America's most important and widespread deciduous trees (Source here)

In the scientific news recently are two research papers relevant to biological feedback mechanisms. The first concerns the quaking aspen (Populus tremuloides), a dominant species in many northern forest ecosystems. "Aspen growth has increased an average of 53% over the past five decades, primarily in response to the 19.2% rise in ambient CO2 levels."

"Trees are already responding to a relatively nominal increase in atmospheric carbon dioxide over the past 50 years," says Rick Lindroth, a UW-Madison professor of ecology and an expert on plant responses to climate change. [. . .] The study's findings are important as the world's forests, which cover about 30 percent of the Earth's land surface, play an important role in regulating climate and sequestering greenhouses gases. The forests of the Northern Hemisphere, in particular, act as sinks for carbon dioxide, helping to offset the increase in levels of the greenhouse gas, widely viewed as a threat to global climate stability.

A second study is concerned with the impact of fertilisers on the species diversity of grasslands. These chemicals more than double the availability of nitrogen and whilst this stimulates some plants to thrive, others are quickly out-competed and they die off.

"In a long-term open-air experiment, grassland assemblages planted with 16 species were grown under all combinations of ambient and elevated CO2 and ambient and elevated N. Over 10 years, elevated N reduced species richness by 16% at ambient CO2 but by just 8% at elevated CO2. This resulted from multiple effects of CO2 and N on plant traits and soil resources that altered competitive interactions among species. Elevated CO2 thus ameliorated the negative effects of N enrichment on species richness."

These are but two examples of negative feedback to promote stability. There have been many examples like this in the past, and there will be many more to come. Examples of positive feedback are rare. The effect this has in my mind is to reinforce the thought that the Earth's environments and ecosystems have a robustness about them. This means that when a catastrophe comes, like the eruption of Mt St Helens volcano, recolonisation rarely takes as long as was first anticipated. Whilst this does not prove the Earth is designed, the marks of design are easy to find and the evidence is fully consistent with design.

How does this relate to Copenhagen? A frequently heard message is that the Earth is heading for a doomsday crisis: rapid melting of ice caps, rapid sea-level rise, ocean currents that flip and runaway climate change, etc. These scenarios all invoke positive feedback mechanisms and avalanche processes. What seems to be overlooked is the dominance of negative feedback processes, many of which we are not yet aware of, that counter such dramatic changes. One way to handle such thinking is to analyse feedback mechanisms that we know are operating and check whether they are positive or negative. If mainly positive, the case for sustainable green energy is strong. However, if the findings show mainly negative feedback, it is fair to conclude that the predictors of doomsday are alarmists. We still need to work towards a sustainable future, but intelligent evolution (rather than revolution) will be the agenda.

Rising concentrations of atmospheric CO2 have increased growth in natural stands of quaking aspen (Populus tremuloides)
Christopher T. Cole, Jon E. Anderson, Richard L. Lindroth, Donald M. Waller
Global Change Biology, Published Online: Oct 22 2009 | DOI: 10.1111/j.1365-2486.2009.02103.x

Abstract: As atmospheric CO2 levels rise, temperate and boreal forests in the Northern Hemisphere are gaining importance as carbon sinks. Quantification of that role, however, has been difficult due to the confounding effects of climate change. Recent large-scale experiments with quaking aspen (Populus tremuloides), a dominant species in many northern forest ecosystems, indicate that elevated CO2 levels can enhance net primary production. Field studies also reveal that droughts contribute to extensive aspen mortality. To complement this work, we analyzed how the growth of wild aspen clones in Wisconsin has responded to historical shifts in CO2 and climate, accounting for age, genotype (microsatellite heterozygosity), and other factors. Aspen growth has increased an average of 53% over the past five decades, primarily in response to the 19.2% rise in ambient CO2 levels. CO2-induced growth is particularly enhanced during periods of high moisture availability. [. . .] Owing to aspen's role as a foundation species in many North American forest ecosystems, CO2-stimulated growth is likely to have repercussions for numerous associated species and ecosystem processes.

Elevated CO2 Reduces Losses of Plant Diversity Caused by Nitrogen Deposition
Peter B. Reich
Science, 326, (4 December 2009), 1399-1402 | DOI: 10.1126/science.1178820

Abstract: The interactive effects of rising atmospheric carbon dioxide (CO2) concentrations and elevated nitrogen (N) deposition on plant diversity are not well understood. This is of concern because both factors are important components of global environmental change and because each might suppress diversity, with their combined effects possibly additive or synergistic. In a long-term open-air experiment, grassland assemblages planted with 16 species were grown under all combinations of ambient and elevated CO2 and ambient and elevated N. Over 10 years, elevated N reduced species richness by 16% at ambient CO2 but by just 8% at elevated CO2. This resulted from multiple effects of CO2 and N on plant traits and soil resources that altered competitive interactions among species. Elevated CO2 thus ameliorated the negative effects of N enrichment on species richness.

See also:

Collins, S.L. Biodiversity Under Global Change, Science, 326 (4 December 2009), 1353-1354 | DOI: 10.1126/science.1183271

Devitt, T. Greenhouse gas carbon dioxide ramps up aspen growth. University of Wisconsin-Madison News (4 December, 2009)

The Galapagos Islands have long been recognised as the home of numerous endemic species, stimulating questions about how such species came into being. Those responding with answers have supported their views more by theory than observation. But Peter and Rosemary Grant are different, because they have pioneered longitudinal studies of the Galapagos finches, particularly on the small (and relatively isolated) island of Daphne Major. A newly reported study of an immigrant male ground finch (Geospiza fortis) covers the period 1981 to the present.

"We have followed the survival and reproduction of this individual and all of its known descendants, here termed the immigrant lineage, for seven generations (F0 to F6) spanning 28 years."

This finch's odd beak and song make it unpopular with the locals. (Credit: Peter Grant/PNAS, Source here)

The Grants have observed a clustering of male territories of the immigrant lineage and have established that these birds formed a new, albeit small, breeding population. The story is one of interbreeding followed by inbreeding. The authors consider they have gained an "important insight into the process of speciation" - although they hasten to add that they do not regard these birds as a new species.

"How many generations of exclusively within-group mating are needed before the group is recognized as a separate species that deserves taxonomic status? There is no nonarbitrary answer. We treat the endogamous group as an incipient species because it has been reproductively isolated from sympatric G. fortis for three generations and possibly longer."

This is not a story involving new mutations, or any significant genetic change outside the normal range of groundfinches. It is relevant to discussion of sympatric speciation, because the new population coexists with other medium groundfinches on the same island and interbreeding did take place in the earlier generations of the lineage. So what factors are associated with a barrier to interbreeding? The Grants identify two factors: one is morphological (immigrants have larger beak dimensions) and the other is song (immigrants differ from residents lower maximum frequency and higher note repetition rate).

"Our observations provide insight into speciation and hence, into the origin of a new species. They show how a barrier to interbreeding can arise behaviorally and without genetic change in sympatry. A necessary condition was prior ecological divergence, and introgressive hybridization was possibly another. Evidently it takes only a single diploid immigrant to start the process by breeding with a resident, and tolerance of the effects of inbreeding is needed to complete it."

These observations, and the emerging ecological perspective on speciation is interesting - but how does it relate to the broader issues faced by evolutionary biologists? In particular, does it help to understand how innovation occurs? The answer must be - no. There are no genetic changes that can be associated with novel characteristics and although this population is currently reproductively isolated, a few environmental traumas could easily lead to unification. Darwinism is exactly where it has always been - explaining the origin of complexity by appealing to theory and the imagination.

On the other hand, these data can be understood readily in terms of speciation by gene pool reduction. Although normally presented in terms of allopatry, this model considers the possible loss of alleles when a breeding population is split. The resultant populations may not have the genetic diversity of the parent population, and whilst this may be workable in the short-term, environmental change may reveal that the daughter population(s) are unfit and the end result may be extinction. Clearly, this perspective on the data has nothing to give Darwinism but it is compatible with several non-Darwinian perspectives on speciation.

Science reports of stories relevant to evolutionary theory can degenerate to the level of cheer-leading for a favoured cause. One account of the Grants' research refers to "a real-time record of evolution in action. In the PNAS paper, they describe something Darwin could only have dreamed of watching: the birth of a new species." For more, please refer to Jonathan Wells comments here.

The secondary contact phase of allopatric speciation in Darwin's finches
Peter R. Grant and B. Rosemary Grant
Proceedings of the National Academy of Sciences, Early Edition, Nov. 16, 2009 | doi 10.1073/pnas.0911761106

Abstract: Speciation, the process by which two species form from one, involves the development of reproductive isolation of two divergent lineages. Here, we report the establishment and persistence of a reproductively isolated population of Darwin's finches on the small Galapagos Island of Daphne Major in the secondary contact phase of speciation. In 1981, an immigrant medium ground finch (Geospiza fortis) arrived on the island. It was unusually large, especially in beak width, sang an unusual song, and carried some Geospiza scandens alleles. We followed the fate of this individual and its descendants for seven generations over a period of 28 years. In the fourth generation, after a severe drought, the lineage was reduced to a single brother and sister, who bred with each other. From then on this lineage, inheriting unusual song, morphology, and a uniquely homozygous marker allele, was reproductively isolated, because their own descendants bred with each other and with no other member of the resident G. fortis population. These observations agree with some expectations of an ecological theory of speciation in that a barrier to interbreeding arises as a correlated effect of adaptive divergence in morphology. However, the important, culturally transmitted, song component of the barrier appears to have arisen by chance through an initial imperfect copying of local song by the immigrant. The study reveals additional stochastic elements of speciation, in which divergence is initiated in allopatry; immigration to a new area of a single male hybrid and initial breeding with a rare hybrid female

See also:

Cressey, D. Darwin's finches tracked to reveal evolution in action, Nature News (16 November 2009) | doi:10.1038/news.2009.1089

According to James Pusey, writing in Nature, "Charles Darwin's banner was first unfurled in China during the Reform Movement of 1895-98, in response to China's defeat in the Sino-Japanese War." There were two groups seeking change: the reformers, who were loyal to the Manchu Qing Dynasty, and the revolutionaries, who wanted a clean break with the past.

"The watchword of the reform movement was 'bianfa', meaning 'change our institutions'. But the very word 'change' was anathema to the conservative officialdom of China. So reformers turned to Darwin as a foreign authority on change, presenting him not first and foremost as a natural scientist who had discovered an amazing fact of life, but as a political scientist who had discovered a cosmic imperative for change."

Some today see Darwin as inspiring revolution (Source here)

This led to a change in the way intellectuals approached ethics: reform meant that traditional codes of conduct were fast losing their appeal.

"Meanwhile, the Europeans waved Darwin's banner to justify imperialism. Dubbing themselves 'the fit', they declared their right to rule the 'unfit'. And some Chinese accepted this argument. Liang Qichao, one of the leading reformers, said in 1898: "If a country can strengthen itself and make itself one of the fittest, then, even if it annihilates the unfit and the weak, it can still not be said to be immoral. Why? Because it is a law of evolution.""

The reformers were very interested in democracy, but realized the people were totally unprepared to handle it. Their solution was to emphasise the step-by-step gradualism of Darwinism with direction and stability provided by an appeal to natural law. The revolutionaries also embraced Darwin, drawing inspiration from the thought that the "superior survive and the inferior are defeated". "The man who introduced Darwinian evolution to the reformers of 1895 was Yan Fu."

"Yan wanted democracy for China - even anarchic democracy, without presidential rule. In Whence Strength? his call for reform was revolutionary: "Establish a parliament at the capital and let each province and county elect its own officials." But 'Darwin' held him back from real revolution. Yan believed that step-by-step progress was a fixed natural law, so stages had to be taken in order. America had skipped constitutional monarchy and gone straight to democracy, but a resulting class war, he felt, would be their undoing. "Should we, then, now throw away all loyalty to our ruler?" he asked in his essay. "We most certainly should not! Because the time has not arrived. ... Our people are not yet ready to rule themselves.""

The reformers and the revolutionaries debated vigorously "with both sides wildly waving Darwin's banner" The leaders of these movements imbibed the message of scientific racism coming from America and Europe and presented themselves as 'fit' to rule.

"Sadly, both camps also accepted the pervasive Western view that Darwin had proven races unequal - that one race was 'fitter' and therefore better than another. The reformers had originally done so to disassociate themselves from those who had fallen prey to the imperialists, such as the Africans and Indians. But in their exile in Japan, reformers and revolutionaries alike turned angrily on the Manchus as scapegoats, labelling them evolutionary low life, whose 'unnatural' conquest of the Han Chinese was responsible for China's peril."

The tensions after the end of World War I were extreme. The traditional pacifist Chinese philosophies were perceived as weak and this led to a philosophical and political vacuum. In their place came Marxism: this "seemed to them the fittest faith on Earth to help China to survive".

"This was not, of course, all Darwin's doing, but Darwin was involved in it all. To believe in Marxism, one had to believe in inexorable forces pushing mankind, or at least the elect, to inevitable progress, through set stages (which could, however, be skipped). One had to believe that history was a violent, hereditary class struggle (almost a 'racial' struggle); that the individual must be severely subordinated to the group; that an enlightened group must lead the people for their own good; that the people must not be humane to their enemies; that the forces of history assured victory to those who were right and who struggled.
Who taught Chinese these things? Marx? Mao? No. Darwin."

Ideas have legs and ideas walk. These developments are possible because Darwinism is more than a scientific theory: it is fundamentally a philosophical stance about the nature of reality. The materialism that underpins the Darwinian worldview has spawned scientific racism + eugenics in the West, and revolutionary fervor in the East. We should help the next generation understand and recognize the significance of such matters, and encourage them to ask questions about the philosophical roots of science.

Global Darwin: Revolutionary road
James Pusey
Nature 462, 162-163 (12 November 2009) | doi:10.1038/462162a (Restricted access link)

In China, under the threat of Western imperialism, interpretations of Darwin's ideas paved the way for Marx, Lenin and Mao, argues James Pusey in the third in our series on reactions to evolutionary theory.

Earlier this year, Eugene Koonin published a masterly analysis of the impact of genomics on evolutionary thinking. This proved to be too meaty a study for a concise blog, and my initial draft was abandoned. Happily, a shorter overview has now been published, and this abstracts salient points from the research paper. Koonin notes that the 1959 Origin centennial was "marked by the consolidation of the modern synthesis" but subsequent years have witnessed great changes which have undermined its credibility.

"The edifice of the modern synthesis has crumbled, apparently, beyond repair."

It is time for a paradigm change - but neoDarwinists are stuck because they have so much philosophical baggage holding them down (Image credit: Shaun Curry/AFP/Getty Images, Source here)

Koonin uses the metaphor of "the landscape of evolutionary biology". There are three distinct revolutions have occurred over the past half-century: the molecular, the microbiological and the genomic revolutions.

"[T]his year is the perfect time to ask some crucial questions: how has evolutionary biology changed in the 50 years since the hardening of the modern synthesis? Is it still a viable conceptual framework for evolutionary thinking and research?"

The molecular revolution culminated, says Koonin, in the neutral theory, which means that purifying selection is more common than positive selection. The microbiological revolution brought the world of prokaryotes into the domain of evolutionary biology, but it then became apparent that the concepts of Darwinism and the modern synthesis "applied only to multicellular organisms". The genomic revolution revealed that the living world was "a far cry from the orderly, rather simple picture envisioned by Darwin and the creators of the modern synthesis". In particular, it is now interpreted as an "extremely dynamic world where horizontal gene transfer (HGT) is not a rarity but the regular way of existence, and mobile genetic elements that are vehicles of HGT are ubiquitous".

"The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the tree of life as we knew it but also another central tenet of the modern synthesis inherited from Darwin, namely gradualism. In a world dominated by HGT, gene duplication, gene loss and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable."

Koonin is serious in saying that all the concepts of the modern synthesis are in need of a fundamental overhaul.

"Moreover, with pan-adaptationism gone forever, so is the notion of evolutionary progress that is undoubtedly central to traditional evolutionary thinking, even if this is not always made explicit.
The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking. In the postgenomic era, all major tenets of the modern synthesis have been, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the modern synthesis is gone."

Koonin tentatively identifies two candidates to fill the vacuum left by the discarded modern synthesis. The first of these appears to emphasis the role of chance; the second appears to emphasise law.

"The first is the population-genetic theory of the evolution of genomic architecture, according to which evolving complexity is a side product of non-adaptive evolutionary processes occurring in small populations where the constraints of purifying selection are weak. The second area with a potential for major unification could be the study of universal patterns of evolution such as the distribution of evolutionary rates of orthologous genes, which is nearly the same in organisms from bacteria to mammals or the equally universal anticorrelation between the rate of evolution and the expression level of a gene. The existence of these universals suggests that simple theory of the kind used in statistical physics might explain some crucial aspects of evolution."

It is not difficult to predict that Koonin's analysis will not be received quietly by the very vocal leaders of evolutionary biology. They are still entrenched in neoDarwinism and show no signs of conceding any ground to anyone. From a design perspective, Koonin's analysis of the changing landscape of evolutionary biology is spot on. His two candidates for moving forward the theoretical framework are interesting - but lack any recognition of purposeful design in nature. Dembski's design filter concept is relevant here: there are features in the biological world that are best understood in terms of stochastic processes; there are other features that are best understood in terms of natural law; but there are also features that require a design perspective in order to understand them. It is the latter element, prominent in the thinking of design-orientated scientists, which needs to be part of any discussion of where evolutionary biology is heading.

The Origin at 150: is a new evolutionary synthesis in sight?
Eugene V. Koonin
Trends in Genetics, 25(11), November 2009, 473-475.

Abstract: The 200th anniversary of Charles Darwin and the 150th jubilee of the On the Origin of Species could prompt a new look at evolutionary biology. The 1959 Origin centennial was marked by the consolidation of the modern synthesis. The edifice of the modern synthesis has crumbled, apparently, beyond repair. The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution.

Darwinian evolution in the light of genomics
Eugene V. Koonin
Nucleic Acids Research, 2009, 37(4), 1011-1034 | doi:10.1093/nar/gkp089

ABSTRACT: Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

Darwin was a great composer of metaphors, of which "natural selection" is the best known. Today, few are aware of negative responses from scientists uncomfortable with Darwin's imagery. One of these was Alfred Russel Wallace, the co-originator of evolution by natural selection.

"Wallace remarked, in his article Mr Darwin's Metaphors Liable to Misconception (1868), that the Malthusian progressions and struggle for existence were self-evident "facts". Yet because natural selection seemed to personify a perceptive and forward-thinking selector, or god, he urged Darwin to replace the term with "survival of the fittest". [See also here]
Darwin, however, had brushed him off. "Everyone knows what is meant and is implied by such metaphorical expressions," he had demurred. "And they are almost necessary for brevity"."

Does "natural selection" have the dominant role in unravelling Darwin's entangled bank? (source here)

In a perceptive essay, Daniel Todes focuses attention on the reactions of Russian biologists to Darwin's writings. Many of these naturalists "were evolutionists before 1859", so they did not dissent from common ancestry. However, their experiences of the living world were quite different from Darwin and Wallace, who drew their inspiration from densely populated tropical forests and related habitats. They witnessed a struggle for existence that matched the description Thomas Malthus had given of human communities. Using the same logic, Darwin and Wallace were stimulated to think about winners and losers in populations of animals and plants. The Russian scientists lived in a different world.

[They] "investigated a vast under-populated continental plain. For them, nature was not an "entangled bank" - the image Darwin took from the Brazilian jungle. It was a largely empty Siberian expanse in which overpopulation was rare and only the struggle of organisms against a harsh environment was dramatic."

The Russian response to living in a harsh environment was to develop "the language of communalism - stressing not individual initiative and struggle, but the importance of cooperation within social groups and the virtues of social harmony." The analysis of Malthus did not match the biological communities in their part of the world, so Darwin's metaphor of the "struggle for existence" was not, in their view, well grounded.

"Russian political commentators of the left, right and centre reviled Malthus as an apologist for predatory capitalism and soulless individualism." [. . .]
"[F]ew Russians shared Darwin and Wallace's respect for Malthus, and [. . .] many saw the struggle for existence as an infusion of the British enthusiasm for individualistic competition into natural science. Darwin's theory, as Danilevskii put it, was a "purely English doctrine"."

Dissent did not apply just to the "struggle for existence" metaphor. Natural selection was equally controversial. The Russians wanted to give more emphasis to concepts like the "harmony of nature" and "cooperation". Many of them advocated "the theory of mutual aid". Indeed, Todes says that it became a "staple of Russian evolutionary thought".

"Darwin too had called attention to such cooperation, but the theory of mutual aid went further. It held that the central aspect of the struggle for existence is an organism's struggle with abiotic conditions, that organisms join forces in this struggle, that such mutual aid is favoured by natural selection, and that cooperation so vitiated intraspecific competition as to render it unimportant in the origin of new species."

This essay highlights issues which have been discussed often by design-orientated scientists. These are identified below.

1. Scientific criticism of natural selection as an evolutionary mechanism. It will come as a surprise to many that dissent about the role of natural selection comes from within science. Such dissent was present in Darwin's day and it is still significant. This blog has drawn attention to relevant papers here and here. Those who portray requests for a 'critical evaluation of the role of natural selection' as religiously motivated are living in denial of history and are undermining the integrity of science.

2. Scientific analysis of harmony within the natural world. Due to the dominance of Darwinism, ecological studies have been imbalanced. Evidences of populations regulating their own numbers and of cooperative behaviour have been underplayed or reinterpreted in terms of a "struggle for survival".

3. Science is not a culture-free discipline. Objectivity is a worthy aspiration but it cannot be fully realised because scientists are unaware of most of the cultural norms they bring to their work. Since many aspects of culture are linked to religious/secular convictions, it is absurd when individuals and organisations try to set up demarcation arguments to separate science from ideology (whether religious or atheistic).

"Researchers bring their life experiences and culture with them into the field and laboratory, and in the course of their investigations actively originate, interpret, develop and reject metaphorical pathways. As is shown by the reception of Darwin's theory in Russia, the deployment and criticism of metaphors are part of the ineffably human process by which scientists mobilise their experiences and values to explore the infinite complexity of nature."

Global Darwin: Contempt for competition
Daniel Todes
Nature 462, 36-37 (5 November 2009) | doi:10.1038/462036a (restricted access here)

Darwin's idea of the 'struggle for existence' struck a chord with his fellow countrymen. But Russians rejected the alien metaphor, says Daniel Todes, in the second of four weekly pieces on reactions to evolutionary theory.

See also:

Todes, D.P. Darwin's Malthusian Metaphor and Russian Evolutionary Thought, 1859-1917, Isis, 78(4), December 1987, 537-551

This topic forces us to assess the relationship between science and spirituality: is the invisible spiritual realm generated from the material or should it be considered as having a separate existence? Is religion a phenomenon that can ultimately be explained by science in naturalistic ways, or does religion represent a dimension of reality that cannot be directly probed by the methodologies of science? In an essay in Science, Elizabeth Culotta writes:

"[I]n the past 15 years, a growing number of researchers have followed Darwin's lead and explored the hypothesis that religion springs naturally from the normal workings of the human mind. This new field, the cognitive science of religion, draws on psychology, anthropology, and neuroscience to understand the mental building blocks of religious thought."

Neanderthal burial, considered to be 60,000 years old (Kabara, Israel). Material culture analysis can stimulate hypotheses but the interpretations can easily be dominated by researcher presuppositions. (Source here)

Darwin approached the topic from the perspective of his thesis on the origin of species. He looked for evidence that religion itself could be explained by small incremental steps in human cognition and social structure. He started his "story" with the idea that primitive people had no belief system in an all-powerful God. He wrote: "There is no evidence that man was aboriginally endowed with the ennobling belief in the existence of an Omnipotent God. On the contrary there is ample evidence, derived not from hasty travellers, but from men who have long resided with savages, that numerous races have existed and still exist, who have no idea of one or more gods, and who have no words in their languages to express such an idea." But if the enquiry starts at a much more rudimentary level of spirituality, the emerging picture is different:

"If, however, we include under the term "religion" the belief in unseen or spiritual agencies, the case is wholly different; for this belief seems to be almost universal with the less civilised races. Nor is it difficult to comprehend how it arose. As soon as the important faculties of the imagination, wonder, and curiosity, together with some power of reasoning, had become partially developed, man would naturally have craved to understand what was passing around him, and have vaguely speculated on his own existence." (Source here)

Culotta quotes the above passage to illustrate the thought that "to Charles Darwin, the origin of religious belief was no mystery". Yet those following in Darwin's footsteps have been puzzled, because humans put extraordinary resources into "elaborate religious buildings and rituals, with no obvious boost to survival and reproduction". Her article suggests that while there is no consensus yet among scientists, "potential answers are emerging from both the archaeological record and studies of the mind itself".

Archaeology certainly offers some data that is potentially relevant: geometric designs interpreted as an indication of symbolic behaviour; deliberate burials of the dead pointing to "the birth of metaphysical anguish", and carved figurines suggestive of shamanism. The problem with all these is that the metaphysical messages are read in different ways by scholars: these artefacts may stimulate thoughts about belief systems, but they are not hard evidence that reveals the minds of our ancestors.

Cognitive psychologists often start with children, who are said to reflect innate, rather than cultural, biases. It is not difficult to show that "young children prefer "teleological" or purpose-driven, explanations rather than mechanical ones for natural phenomenon". This leads them to perceive nature as purposefully designed by a designer. For children older than age 5, the researchers refer to the "theory of mind" which is our understanding that other humans have intentions, desires and beliefs like us.

"If you suspect that an agent was responsible for some mysterious event, it's a short step to thinking that the agent has a mind like your own. "Higher order theory of mind enables you to represent mental states of beings not immediately or visibly present, and who could have a very different perspective than your own," says Barrett. "That's what you need to have a rich representation of what it might be like to be a god." (It's also what is needed to have a functional religion, because people need to know that others share their beliefs.) As Darwin put it, humans developing religion "would naturally attribute to spirits the same passions, the same love of vengeance, or simplest form of justice, and the same affections which they themselves feel.""

Although these cognitive models are regarded as building on Darwinian foundations, there is a recognition that they have not provided satisfactory answers. One researcher is quoted as saying: "Deriving belief from the architecture of the mind is necessary but not sufficient". What drives all this? What gives religion the fitness to survive? The adaptationist approach of Darwinism comes to the rescue:

[Religion] "promotes cooperative behavior among strangers and so creates stable groups. Other researchers hypothesize that religion is actually adaptive: By encouraging helpful behavior, religious groups boost the biological survival and reproduction of their members. Adhering to strict behavioral rules may signal that a religion's members are strongly committed to the group and so will not seek a free ride, a perennial problem in cooperative groups."
[. . .]
But others [. . .] counter that this adaptationist explanation is itself light on data. "It is often said that religion encourages or prescribes solidarity within the group, but we need evidence that people actually follow [their religion's] recommendations," says Boyer. "The case is still open."

So the "potential answers" Culotta mentions at the outset have the word potential in bold and the rest is in the imagination. What is strikingly lacking in these studies is any questioning of the materialist mindset of the researchers. The most significant way they follow Darwin is in excluding any thought that intelligent design issues need to be addressed before we can properly understand humanity. Indeed, the researchers set up a culture that portrays teleology as anti-science. Culotta reports on the findings of cognitive psychologists working with some undergraduate students:

"When the undergrads had to respond under time pressure, they were likely to agree with nonscientific statements such as "The sun radiates heat because warmth nurtures life." "It's hard work to overcome these teleological explanations," says Kelemen, who adds that the data also suggest an uphill battle for scientific literacy. "When you speed people up, their hard work goes by the wayside." She's now investigating how professional scientists perform on her tests. Such purpose-driven beliefs are a step on the way to religion, she says. "Things exist for purposes, things are intentionally caused, things are intentionally caused for a purpose by some agent. ... You begin to see that a god is a likely thing for a human mind to construct.""

These attitudes are deeply worrying, because the researchers have started with the premise of philosophical naturalism. If a teleological perspective is correct, these researchers have no way of discovering the truth. When we look at the radiation that life needs to be sustained, and then look at the radiation emitted by the sun, the match is superb. It is perfectly reasonable to make design inferences and to test teleological hypotheses.

The real problems are with researchers who say that the material processes that create the physical bodies of animals and plants are no different in essence from the material processes that create religion and morality. We can make a prediction that these researchers will continue to grope around in the dark, looking for a answers but never finding them. In the end, they will conclude that religion, morality and consciousness are spandrels.

On the Origin of Religion
Elizabeth Culotta
Science, 6 November 2009, 326, 784 - 787 | DOI: 10.1126/science.326_784

How and when did religion arise? In the 11th essay in Science's series in honor of the Year of Darwin, Elizabeth Culotta explores the human propensity to believe in unseen deities. No consensus yet exists among scientists, but potential answers are emerging from both the archaeological record and studies of the mind itself. Some researchers, exploring religion's effects in society, suggest that it may boost fitness by promoting cooperative behavior. And in the past 15 years, a growing number of researchers have followed Darwin's lead and explored the hypothesis that religion springs naturally from the normal workings of the human mind. This new field, the cognitive science of religion, draws on psychology, anthropology, and neuroscience to understand the mental building blocks of religious thought.

Sooner or later, students of abiogenesis will encounter Darwin's 1871 letter to Joseph Hooker with his speculations on the spontaneous generation of life. He was returning some pamphlets which triggered the reaction: "I am always delighted to see a word in favour of Pangenesis, which some day, I believe, will have a resurrection." The next paragraph has his "big if" dream:

"It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, - light, heat, electricity &c. present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed."

Bon appetit Mr Darwin! (Source here)

When taken alongside other comments Darwin made on this theme, it is clear that his public stance was to be cautious. The science of his day was unable to say anything positive about spontaneous generation. He felt the power of Pasteur's experiments which brought to an end all the earlier speculations about life emerging from non-life. The authors of a paper reviewing Darwin's thinking summarises the "big if" in this way:

"In the absence of any real corroborative evidence, it is impossible to guess what Darwin thought about the nature of the first living beings. In any case, Darwin's remarks should not be read to imply that he was thinking in terms of prebiotic chemistry, but rather that he recognized that the chemical gap separating organisms from the non-living was not insurmountable."

Also to be considered is the reference to a "Creator" in the last sentence of all the editions of his magnum opus bar the first:

"There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." (Source on page 490 here)

Does this mean that Darwin was a Deist, invoking the Creator to explain the first cells that can be called living? What is this "breathing" he refers to? Is it a link with the biblical account of origins? Why was the "Creator" absent from the 1st edition but present thereafter? The authors draw attention to Darwin's own explanation, contained in an 1863 letter to Hooker and shortly afterwards another to the Athenaeum, based on the profound ignorance within science of any route for life to have emerged from non-life:

"[to Hooker] But I have long regretted that I truckled to public opinion & used Pentateuchal term of creation, by which I really meant "appeared" by some wholly unknown process. - It is mere rubbish thinking, at present, of origin of life; one might as well think of origin of matter."
[to the Athenaeum] "Now is there a fact, or a shadow of a fact, supporting the belief that these elements, without the presence of any organic compounds, and acted on only by known forces, could produce a living creature? At present it is to us a result absolutely inconceivable. Your reviewer sneers with justice at my use of the "Pentateuchal terms", "of one primordial form into which life was first breathed": in a purely scientific work I ought perhaps not to have used such terms; but they well serve to confess that our ignorance is as profound on the origin of life as on the origin of force or matter."

In the light of these comments, it is curious that Darwin did not drop the word "Creator" in subsequent editions. Whatever regrets he expressed in 1863, they were not deep enough to excise the injudicious word. The authors note the consistency in Darwin's view that science did not have any insights into spontaneous generation. They show from his comments to Haeckel, from the apochryphal account of Darwin's encounter with fossils in a meteorite, and from several other comments made in letters, that Darwin was publicly silent because he could find no basis in science for making any positive statements.

"As for myself I cannot believe in spontaneous generation & though I expect that at some future time the principle of life will be rendered intelligible, at present it seems to me beyond the confines of science." (Letter 5282, 1866)
"I have met with no evidence that seems in the least trustworthy, in favour of the so-called Spontaneous generation. I believe that I have somewhere said (but cannot find the passage) that the principle of continuity renders it probable that the principle of life will hereafter be shown to be a part, or consequence of some general law; but this is only conjecture and not science." (Letter to Wallich, 1882)

This being said, the authors are also at pains to point out that Darwin was consistently predisposed to the origin of life being a wholly natural phenomenon. "Although he insisted over and over again that there was no evidence of how the first organisms may have first appeared, he was firmly convinced it was the outcome of a natural process that had to be approached from a secular framework."

"The intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable." (2nd Notebook, 1837)
"Though no evidence worth anything has as yet, in my opinion, been advanced in favour of a living being, being developed from inorganic matter, yet I cannot avoid believing the possibility of this will be proved some day in accordance with the law of continuity. [. . .] If it is ever found that life can originate on this world, the vital phenomena will come under some general law of nature." (Letter 13711, 1882)

The "secular framework" of Darwin resulted from his adoption of philosophical materialism. He was a child of Enlightenment rationalism, along with Lyell, Huxley and Hooker. He knew that some others wanted to put his ideas into a theistic or a deistic framework, but Darwin always resisted this. His explanation of using the word "Creator" ("I truckled to public opinion") simply reinforces the conclusion that Darwin's science was wholly secularised. It is surprising, therefore, to read this comment of the authors about people who misread Darwin:

"Indeed, a careful examination and critical reading of his public and private writings shows that what appear to be contradictory opinions on the problem of the emergence of life are the result of texts read out of context, sometimes maliciously, as shown by some publications of creationist groups and advocates of the so-called intelligent design."

It is remarkable how often such comments appear in scholarly work, nearly always unsupported by references or quotes. On this occasion, as is generally the case, the charge is erroneous and entirely misplaced. By and large, creationist and ID scholars have exactly the same understanding of Darwin's secular framework as the authors of this paper. Where they differ is in thinking that this secular framework is profoundly wrong and is an inappropriate foundation for science. Here is an example of an ID advocate who gives the same interpretation of events as the authors:

"Nor should we be misled by a sop Darwin attached to later editions of his Origin of Species. The first edition ended with the famous flourish: "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one [. . .]" To smooth ruffled feathers, later editions read: "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one [. . .]" Some are fooled by this sop even to this day. But what did Darwin himself say about this little addition? "I have long regretted that I truckled to public opinion & used [a] Pentateuchal term of creation, by which I really meant 'appeared' by some wholly unknown process."" (Wiker, B. 2009)

Those who should be accused of taking Darwin out of context are the Theistic Evolutionists, who do not want to acknowledge Darwin's philosophical materialism. They generally refer positively to Darwin's reference to a Creator and try to suggest that Darwinism can be harmonised with Theism. Examples include Richard Aulie, Darwin and spontaneous generation, Journal of the American Scientific Affiliation, 22, 1970, 31-33 (cited by the authors!), William Phipps, Darwin, the Scientific Creationist, Christian Century, 1983, 809-811, Denis Alexander, Creation or Evolution - do we have to choose? Monarch Books 2008, and Nick Spencer, Darwin and God, SPCK 2009. The latter two names are associated with the "Rescuing Darwin" project, funded by The Templeton Foundation, which seeks to find a harmony between Darwinism and God's creative process. For some Christian comment on the project, go here.

As a final thought, Darwin was intellectually honest enough to see the difference between his philosophical materialism (which demanded some form of spontaneous generation) and empirical science (which gave no support for it). My question is: when does it become reasonable to use the findings of abiogenesis research as evidence against spontaneous generation? We have a large body of evidence today and it is telling us something! Some of us have concluded that the materialist paradigm cannot succeed because it fails to recognise the importance of biological information. The question (When does it become reasonable?) is never asked by philosophical materialists because they cannot entertain the notion that causation may be intelligent.

Charles Darwin and the Origin of Life
Juli Pereto, Jeffrey L. Bada and Antonio Lazcano
Origins of Life and Evolution of Biospheres, 39(5), October, 2009, 395-406 | doi 10.1007/s11084-009-9172-7

Abstract: When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that "the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable". Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organic compounds could lead to the appearance of organisms. Although he favored the possibility that life could appear by natural processes from simple inorganic compounds, his reluctance to discuss the issue resulted from his recognition that at the time it was [not] possible to undertake the experimental study of the emergence of life.

See also:

Dawkins, R. There is Grandeur in this View of Life, The Edge (30 September 2009)

Wiker, B., What were Darwin's Religious Views? Discovery Institute (1 May 2009)

Alongside all the public interest in sporting prowess, recent research has added significantly to our knowledge of how the human body actually works. Many characteristics we take for granted now appear to be critical success factors. Take, for example, our toes. We do not need long toes, like monkeys and apes, because our toes are not used for grasping branches. But are they vestigial - withered remnants of once-grand appendages? The answer is: most definitely not! Whilst it is possible to walk comfortably with longer toes, running is different. Increase toe length by just 20% and there is a doubling of the peak digital flexor impulses and the mechanical work required.

An image like this shows just how different the human foot is from the apes (Source here)

It emerges that the human body has numerous traits that all support the ability to run. In an informative piece in the New York Times, author Parker-Pope refers to the research into short toes saying that it:

"showed that the short toes of the human foot allowed for more efficient running, compared with longer-toed animals. Increasing toe length as little as 20 percent doubles the mechanical work of the foot. Even the fact that the big toe is straight, rather than to the side, suggests that our feet evolved for running. "The big toe is lined up with the rest, not divergent, the way you see with apes and our closest non-running relatives," Dr. Bramble said. "It's the main push-off in running: the last thing to leave the ground is that big toe." Spring-like ligaments and tendons in the feet and legs are crucial for running. (Our close relatives the chimpanzee and the ape don't have them.) A narrow waist and a midsection that can turn allow us to swing our arms and prevent us from zigzagging on the trail. Humans also have a far more developed sense of balance, an advantage that keeps the head stable as we run. And most humans can store about 20 miles' worth of glycogen in their muscles."

A few years ago, one of the authors, Daniel Lieberman, was involved in a related study. This was concerned with the gluteus maximus, said to be the the largest muscle in the human body. Parker-Pope also reports on this work, which found that the gluteus maximus is primarily engaged during running.

"Your butt is a running muscle; you barely use it when you walk," Dr. Lieberman said. "There are so many features in our bodies from our heads to our toes that make us good at running."

There would appear to be potential for clarifying the use of this muscle. It is important for posture, and another has made the comment: "As all weightlifters know, the primary purpose of the gluteus maximus is to raise the body from a deep squat." There is more to be said on these matters.

A noticeable element of this research is that the data are consistently interpreted in terms of natural selection pressures acting on natural variation. This is nothing unusual, because most biologists working in this field have come to accept Darwinism as their interpretative paradigm. Richard Dawkins speaks for many when he wrote in The Blind Watchmaker (Chapter 3) that "We have seen that living things are too improbable and beautifully designed to have come into existence by chance." Natural selection is perceived as giving direction to hereditable variation and results in incremental adaptation. This is how Lieberman and his colleagues approach the 'evolution' of short toes:

"The data suggest that having longer pedal phalanges, in the hallux and to some extent in the lateral toes, increases digital flexor force and work and might contribute to an increased risk of overuse injury during running. Although these effects presumably have negligible fitness consequences for habitually shod recent-modern humans who do not run long distances daily, they might have been significant enough to impose the kind of selective pressures that led to the observed changes in phalangeal size and shape during human evolution. For example, partial foot remains recovered at Hadar, Ethiopia, suggest that, by 3.6 million years ago, the lateral phalanges of A. afarensis were shorter than in the African great apes, but approximately 40% longer and more curved than in modern humans. This intermediate phalangeal morphology is thought to reflect a mixed behavioral repertoire comprising substantial arboreality and facultative terrestrial bipedalism."

What makes this a matter for concern is that no one appears to be talking about testing alternative hypotheses. It is as though the Darwinian explanation wins by default, and this does not make for healthy science. In particular, one hypothesis that is held by a great many people but is not admitted to academic debate, is that the human body is a product of intelligent design. The strength of this approach rests (a) in the holistic character of the alleged design; (b) the exquisite nature of the various characteristics; and (c) the claim that some of these features are irreducibly complex. (as in chapter 2 of Stuart Burgess' book The Origin of Man.

There are ways to test the Darwinian hypothesis. The presumed ancestor had elongated foot bones, illustrated here. To transform this stage to a short-toed human foot by natural selection demands gradual change and this is how the hypothesis can be tested. Where is the evolutionary pathway? Incidentally, the australopithecine feet should not be compared with the African great apes (as Lieberman) but with other ancestral apes contemporary with Australopithecus afarensis. This same line of reasoning about hypothesis testing means that design-based predictions of abrupt appearance can also be evaluated. Are evolutionists willing to allow this testing process to occur? Is this a debate that can be permitted in academic literature and in educational contexts?

Almost invariably, in the past, the idea that ID leads to testable hypotheses is blocked by the philosophical principle that all causes in science must be natural (law or chance). Despite repeated efforts to point out this is a metaphysical block, not one required by science, few take the time to address the point. However, it is encouraging to find some shifts in opinion from time to time. An example, surprising to most of us, is the concession Richard Dawkins gave to John Lennox in a debate last year.

"The deist god would be one that I think it would be [pause] one could make a reasonably respectable case for that. Not a case that I would accept, but I think it is a serious discussion that we could have." (The audio of this exchange can be accessed via http://www.fixed-point.org)

This is a welcome acknowledgement. For those wanting more input on this, the day after the debate, Melanie Phillips had an article in Spectator Magazine drawing attention to the significance of Dawkins' admission. The offer of a serious discussion is welcome. ID scientists do not ask for anything more than the freedom to present a respectable case. What is needed is for academics to abandon their doctrinaire attachment to methodological materialism in science.

Another perspective on this issue is to consider what needs to be done to build a robot that walks and runs. This task certainly focuses the mind and clarifies the issues. For an insight into the state-of-the-art, go here. PETMAN is wearing normal athletic shoes and exhibits a normal heel-to-toe gait. This robot is the product of intelligent design: many man-hours of effort by highly skilled scientists and engineers. Those who think natural selection acting on natural variations would do well to consider the immensity of the task they are expecting Darwin's mechanisms to accomplish.

Walking, running and the evolution of short toes in humans
Campbell Rolian, Daniel E. Lieberman, Joseph Hamill, John W. Scott and William Werbel
Journal of Experimental Biology 212, 713-721 (2009) | doi: 10.1242/jeb.019885

Abstract: The phalangeal portion of the forefoot is extremely short relative to body mass in humans. This derived pedal proportion is thought to have evolved in the context of committed bipedalism, but the benefits of shorter toes for walking and/or running have not been tested previously. Here, we propose a biomechanical model of toe function in bipedal locomotion that suggests that shorter pedal phalanges improve locomotor performance by decreasing digital flexor force production and mechanical work, which might ultimately reduce the metabolic cost of flexor force production during bipedal locomotion. We tested this model using kinematic, force and plantar pressure data collected from a human sample representing normal variation in toe length (N=25). The effect of toe length on peak digital flexor forces, impulses and work outputs was evaluated during barefoot walking and running using partial correlations and multiple regression analysis, controlling for the effects of body mass, whole-foot and phalangeal contact times and toe-out angle. Our results suggest that there is no significant increase in digital flexor output associated with longer toes in walking. In running, however, multiple regression analyses based on the sample suggest that increasing average relative toe length by as little as 20% doubles peak digital flexor impulses and mechanical work, probably also increasing the metabolic cost of generating these forces. The increased mechanical cost associated with long toes in running suggests that modern human forefoot proportions might have been selected for in the context of the evolution of endurance running.

See also:

Lieberman, D.E., Raichlen, D.A., Pontzer, H., Bramble D.M. and Cutright-Smith, E., The human gluteus maximus and its role in running, Journal of Experimental Biology 209, 2143-2155 (2006) | doi: 10.1242/jeb.02255

Parker-Pope, T., The Human Body Is Built for Distance, New York Times (October 26, 2009)

Darwinius masillae is the magnificently preserved Ida, the "eighth wonder of the world" unveiled earlier this year: "our Mona Lisa" and an evolutionary "Rosetta Stone". Afradapis is a newly discovered adapoid from Egypt, known from fossilised jaws and teeth. The controversies surrounding Ida have been the subject of comment here and here. A newly published cladistic analysis of 360 morphological features found in 117 living and extinct primates comes down on the side of Ida being more closely related to lemurs and lorises rather than ancestral to anthropoids.

Darwinius was proposed to be on the right branch - an ancestor of apes and humans - but the new study puts it as a dead end on the left branch (Source here)

One of the criticisms of the original report of Darwinius is that the authors did not provide a comprehensive cladistic analysis, but only referred to anthropoid-like characters. That analysis is still not forthcoming, but a new paper by Seiffert and colleagues considers dentition and jaw morphological features for a comprehensive set of primates, including Darwinius. The claim for anthropoid-like characters is put in a new light, because so many adapiform animals (ancestors of lemurs and lorises) have them.

"It has long been known that some adapiform lineages evolved derived morphological features that are also seen in living and extinct anthropoids (for example, fused mandibular symphyses, upper canines with mesial grooves, enlarged and spatulate upper and lower incisors, short and tall rostra). The phylogenetic significance of these features has been a source of ongoing debate for decades."

Their significant finding is that Afradapis (their newly reported fossil species - an undisputed adapiform) has numerous anthropoid-like characters. This leads the authors to conclude that evolutionary convergences are in plentiful supply.

"Of all known fossil prosimians (including Darwinius), Afradapis provides perhaps the most detailed examples of derived anthropoidlike adaptations in its dental and mandibular morphology. As is the case for many of the morphological features that some have argued link adapiforms to anthropoids, however, the anthropoid-like features of Afradapis (fused mandibular symphysis with transverse torus, deep mandibular corpus, deep masseteric fossa, large upper molar hypocones, absence of P2/2 and presence of an enlarged P3 with a honing facet for the upper canine) are not present in the most primitive undoubted fossil anthropoids, such as Biretia and Proteopithecus, indicating that the features are likely to have been acquired through convergent evolution."

The implication, then is that the Darwinius team have been misled by characters that have turned out not to be diagnostic of anthropoid affinities. This conclusion has been picked up and discussed by many commentators, such as Gibbons:

"When they scored Ida and Afradapis against those other primates, Seiffert and colleagues found that adapids do share some traits with anthropoids, such as the loss of a third upper and lower premolar. But these traits evolved more than once among primates, the team reports tomorrow in Nature. They are the result of convergent evolution, which is the acquisition of the same biological trait in unrelated lineages - and, thus, do not indicate inheritance of the trait from a shared ancestor."

Several significant consequences follow from this research. Not least is the reminder that tracking human ancestors by identifying missing links is an exercise fraught with methodological difficulties. As has been previously noted, human evolution data can be likened to a pointillist painting. Like a pointillist painting, evolution is only apparent from a distant vantage point. Close up, we see masses of data, but no coherent picture.

Another issue to address concerns convergent evolution and the problems this phenomenon creates for cladistic analyses. How do we know what characters are primitive and what are derived? Here is an opportunity for human interpretation to be concealed behind a scientific analysis. The extent to which convergences can be invoked raises suspicion in the minds of some:

"One of the researchers who studied Ida, however, responds that Ida and Afradapis look more like the group that gave rise to anthropoids than the group that gave rise to lemurs and lorises - and that there are too many traits to dismiss as convergent evolution. "The complete convergence postulated for Afradapis seems implausible to me," says paleontologist Philip Gingerich of the University of Michigan, Ann Arbor."

The best outcome of all this is for scientists to demonstrate more humility in handling data. So many seem to grasp at some data and brandish 'evidence' as though it provides a definitive answer to controversy. But this is not how data should be handled in research. Data needs to be interpreted and history shows that there is always more than one way of interpreting it. If we can all adopt a 'multiple working hypotheses' approach when using the scientific method, it will be progress indeed.

Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates
Erik R. Seiffert, Jonathan M. G. Perry, Elwyn L. Simons & Doug M. Boyer
Nature 461, 1118-1121 (22 October 2009) | doi:10.1038/nature08429

Adapiform or 'adapoid' primates first appear in the fossil record in the earliest Eocene epoch (~55 million years (Myr) ago), and were common components of Palaeogene primate communities in Europe, Asia and North America1. Adapiforms are commonly referred to as the 'lemur-like' primates of the Eocene epoch, and recent phylogenetic analyses have placed adapiforms as stem members of Strepsirrhini, a primate suborder whose crown clade includes lemurs, lorises and galagos. An alternative view is that adapiforms are stem anthropoids. This debate has recently been rekindled by the description of a largely complete skeleton of the adapiform Darwinius, from the middle Eocene of Europe, which has been widely publicised as an important 'link' in the early evolution of Anthropoidea. Here we describe the complete dentition and jaw of a large-bodied adapiform (Afradapis gen. nov.) from the earliest late Eocene of Egypt (~37 Myr ago) that exhibits a striking series of derived dental and gnathic features that also occur in younger anthropoid primates [. . .] The specialized morphological features that these adapiforms share with anthropoids are therefore most parsimoniously interpreted as evolutionary convergences. [. . .]

See also:

Gibbons, A., New Primate Fossil Poses Further Challenge to Ida, ScienceNOW Daily News (21 October 2009)

Dalton, R., Fossil primate challenges Ida's place, (21 October 2009), 461, 1040 | doi:10.1038/4611040a

Shallow water light ranges from the ultraviolet to red (wavelengths 360 nm - 650 nm). Going deeper, the extremes disappear and the spectrum narrows to a blue (approx 480 nm). Of the fish species whose colour vision has been tested to date, all except one can see in the ultraviolet (UV). The exception is the scabbardfish, which is the subject of a new research paper. The authors find that the fish that are sensitive to UV have a pigment that absorbs UV light, but the scabbardfish lacks this pigment and has, instead, a pigment that is violet-sensitive.

The scabbardfish (Lepidopus fitchi) is now the only fish known to have switched from ultraviolet to violet vision, or the ability to see blue light. (Credit: Carol Clark, Emory University) (Source ScienceDaily)

The researchers have looked at the molecular structure of the relevant pigments and their absorption spectra.

"[T]hey used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.
"Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted," Yokoyama says."

The hypothesis is that the shift from UV to violet vision was adaptive. Since the lampfish is also a benthopelagic marine fish, the adaptation explanation must also address why the lampfish has retained UV vision.

"Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light."

The researchers found several other amino acid sequence variants that could not be linked to any change in function. This stimulated some salutary comments from the authors:

"It is very common that evolutionary biologists infer the possibility of adaptive evolution of various genes by using computer programs, which compare the nonsynonymous and synonymous nucleotide substitutions per site. However, these analyses not only predict a significant number of false-positives but also fail to predict many positively selected sites; consequently, the positively selected amino acid changes inferred by the statistical methods must be tested by using experimental methods."

In the Press Release, Yokoyama is quoted as saying: "Evolutionary biology is filled with arguments that are misleading, at best". The research team is to be commended for connecting changes in amino acid sequences with changes in phenotypes and then relating all to the living environments. This is good science and a big contrast from the story-telling approach. Adaptation can be studied in a rigorous way, and analyses like this are a demonstration of what is possible.

The words "evolutionary" and "evolution" are used by the authors in their paper. It is strange that evolutionary biology has a fixation of the e-word when there are so many different meanings given to it. In this case, we have a study of adaptive change involving the change of a single amino acid in the opsin protein. This can be understood as a means of the organism becoming fine-tuned to its environment. Darwinian mechanisms appear to be adequate for understanding the data. It should not be necessary to point out that 'fine-tuning' is qualitatively different from 'constructing' the visual apparatus of the organism. Fine-tuning is only possible when the eye is functioning. This point can be better appreciated when the change involves the deletion of existing biological information - as it is in this case. Adaptation is not the route to create biological novelties: microevolution is not macroevolution.

There is a design-orientated way of approaching these data. What if organisms are designed to vary so that they can adapt to changes in their environment? In such cases, mechanisms for fine-tuning can be understood as designed mechanisms, thereby shifting the focus away from the biological world being the product of chance + necessity and towards a world resulting from purposeful intelligent agency.

Evolutionary replacement of UV vision by violet vision in fish
Takashi Tada, Ahmet Altun and Shozo Yokoyama
Proceedings of the National Academy of Sciences, October 13, 2009, 106(41), 17457-17462 | DOI: 10.1073/pnas.0903839106

Abstract: The vertebrate ancestor possessed ultraviolet (UV) vision and many species have retained it during evolution. Many other species switched to violet vision and, then again, some avian species switched back to UV vision. These UV and violet vision are mediated by short wavelength-sensitive (SWS1) pigments that absorb light maximally ([lamda]max) at approximately 360 and 390-440 nm, respectively. It is not well understood why and how these functional changes have occurred. Here, we cloned the pigment of scabbardfish (Lepidopus fitchi) with a [lamda]max of 423 nm, an example of violet-sensitive SWS1 pigment in fish. Mutagenesis experiments and quantum mechanical/molecular mechanical (QM/MM) computations show that the violet-sensitivity was achieved by the deletion of Phe-86 that converted the unprotonated Schiff base-linked 11-cis-retinal to a protonated form. The finding of a violet-sensitive SWS1 pigment in scabbardfish suggests that many other fish also have orthologous violet pigments. The isolation and comparison of such violet and UV pigments in fish living in different ecological habitats will open an unprecedented opportunity to elucidate not only the molecular basis of phenotypic adaptations, but also the genetics of UV and violet vision.

See also:

Seeing Blue: Fish Vision Discovery Makes Waves In Evolutionary Biology, ScienceDaily (17 October 2009)

Tyler, D. Adaptations affecting dim-light vision in vertebrates, ARN Literature blog (10 September 2008)

When I took a course leading to the Certificate of Higher Education, we had some lecture inputs on psychology. The rationale was to show how educational strategies can be informed by the findings of psychologists. My abiding memory of these lectures concern the way the thinking of Sigmund Freud was presented: I was astounded that the lecturer was so uncritical of Freundianism. It was as though the great man was an oracle and we were expected to absorb his words rather than appraise them. At the time of taking the course, I was aware that Freud was no scientist. He did not test out his ideas using an experimental approach. Rather, he used his ideology-based theory as a filter through which to interpret the data. It was a useful experience for me - reinforcing the distinction between ideology and empirically based science.

In view of this, I welcomed reading the concerns expressed in an editorial in the current Nature. The opening paragraph reads:

"Anyone reading Sigmund Freud's original works might well be seduced by the beauty of his prose, the elegance of his arguments and the acuity of his intuition. But those with a grounding in science will also be shocked by the abandon with which he elaborated his theories on the basis of essentially no empirical evidence. This is one of the main reasons why Freudian-style psychoanalysis has long since fallen out of fashion: its huge expense - treatment can stretch over years - is not balanced by evidence of efficacy."

Disillusionment with Freud has not led to a better understanding of humanity (source here)

The stimulus for the editorial was a report issued by a report into the current status and future prospects of clinical psychology in the US. This found that a very high proportion of practitioners put more emphasis on their personal experience than on scientific evidence. This leads to a situation where craft practices prevail and interest in science is low. The US is not alone with these problems: go here and here.

"[M]any psychologists continue to use unproven therapies that have no clear outcome measures - including, in extreme cases, such highly suspect regimens as 'dolphin-assisted therapy'."

Questions are raised in the Editorial about the educational programmes leading to professional qualifications. The American Psychological Association is the accrediting body for the United States and Canada. However:

"The APA requires that such courses have a scientific component, but it does not require that science be as central as some members would like. In frustration, representatives of some two-dozen top research-focused graduate-training programmes grouped together in 1994 to form the Academy of Psychological Clinical Science (APCS), with a mission to promote scientific psychology."

The Editorial points out the scientific advances that could support clinical psychology: neuroimaging, molecular and behavioural genetics, and cognitive neuroscience. However, the link between the science and clinical practice is not explained, and it is worth asking whether the lukewarmness of practitioners towards science is because they have not been able to translate the science into therapeutic interventions. These practitioners are pragmatists: they are looking for therapies that they can use. They will not need to be brow-beaten into using scientific psychology if the findings are relevant to their profession.

Without wishing to denigrate in any way the empirical work being done in science laboratories, there is a problem with the theoretical framework adopted by most researchers. Here is one psychologist writing about free-will and his perception of science:

"[T]here can be no such thing as free will for the committed scientist, in his or her professional life. Thus, science itself presupposes that every phenomenon has a cause. We may speak of "spontaneous combustion" or a "spontaneous abortion" or even "spontaneous applause", but in each of these cases, some cause is more than likely . . . it is essential to a sober, naturalistic worldview." (Source here)

In this quote, the writer says that "science itself presupposes that every phenomenon has a cause", but he means that every phenomenon has a natural cause. He refers to a naturalistic worldview. Now this is a real problem. Instead of science being a search for truth, the writer is using science to pre-empt discussion about causation. But what if there are intelligent causes as well as natural ones? How would naturalistic science ever know? The author quotes Daniel Dennett approvingly:

"By trying to answer the questions, by sketching out the non-miraculous paths that can take us all the way from senseless atoms to freely chosen actions, we open up handholds for the imagination. The compatibility of free will and science . . . is not as inconceivable as it once seemed."

The issue is not one of introducing the miraculous to science (which is an impossible scenario) but insisting that there is continuity from senseless atoms to conscious humanity. By excluding intelligent causation, naturalistic science is making a statement about the nature of reality. The assertion does not emerge by the use of the scientific method, but is a dogmatic imposition. Unfortunately, this materialistic mindset is widespread among behavioural geneticists and neuroscientists. If their philosophical stance is wrong, and there are no checks and balances in their science, then they will never understand the human condition. This does not give confidence that their work will lead to therapeutic interventions that will help patients.

This is not to defend "unproven therapies" but to flag up a problem not mentioned in the Editorial. Freud imposed theory onto data, but so also does naturalistic science. We need to be encouraging a science that is free to explore the evidence wherever it leads and which builds into its methodologies the means to challenge its most cherished presuppositions.

Current Status and Future Prospects of Clinical Psychology
Timothy B. Baker, Richard M. McFall, and Varda Shoham.
Psychological Science in the Public Interest, 9(2), November 2008, 67-103.

Excerpt from Summary: Clinical psychologists' failure to achieve a more significant impact on clinical and public health may be traced to their deep ambivalence about the role of science and their lack of adequate science training, which leads them to value personal clinical experience over research evidence, use assessment practices that have dubious psychometric support, and not use the interventions for which there is the strongest evidence of efficacy. Clinical psychology resembles medicine at a point in its history when practitioners were operating in a largely prescientific manner.

Psychology: a reality check
Editorial
Nature 461, 847 (15 October 2009) | doi:10.1038/461847a

Abstract: If clinical psychology in the United States wants to remain viable and relevant in today's health systems, it needs to publicly embrace science.

For more blogs on the nature of humanity, go here, here and here.

Evolutionary theory does not boast of many laws, and those that do are not universal by any means. One of these is Dollo's law, which is said to date back to about 1890. It is really a hypothesis about the non-reversibility of evolutionary pathways. The authors of new research considered the relevance of the law to the molecular evolution of a protein structure and reported a significant constraint preventing reversibility.

"The extent to which our observations concerning the evolutionary reversibility of glucocorticoid receptors can be generalized to other proteins requires further research. We predict that future investigations, like ours, will support a molecular version of Dollo's law: as evolution proceeds, shifts in protein structure-function relations become increasingly difficult to reverse whenever those shifts have complex architectures [. . .]"

A few restrictive mutations meant the key would not turn (Source here)

A description of the work is provided by Carl Zimmer in The New York Times:

"Dr. Thornton and his colleagues [. . .] studied a protein called a glucocorticoid receptor that helps humans and most other vertebrates cope with stress by grabbing a hormone called cortisol and then switching on stress-defense genes. By comparing the receptor to related proteins, the scientists reconstructed its history. Some 450 million years ago, it started out with a different shape that allowed it to grab tightly to other hormones, but only weakly to cortisol. Over the next 40 million years, the receptor changed shape, so that it became very sensitive to cortisol but could no longer grab other hormones. During those 40 million years, Dr. Thornton found, the receptor changed in 37 spots, only 2 of which made the receptor sensitive to cortisol. Another 5 prevented it from grabbing other hormones. When he made these 7 changes to the ancestral receptor, it behaved just like a new glucocorticoid receptor.
Dr. Thornton reasoned that if he carried out the reverse operation, he could turn a new glucocorticoid receptor into an ancestral one. So he and his colleagues reversed these key mutations to their old form. To Dr. Thornton's surprise, the experiment failed. "All we got was a completely dead receptor," he said."

To find out why the receptor was inactive, the researchers looked for other mutations - and found 5. These were described as "restrictive" because when attempts were made to return the receptor to its supposed ancestral form, the additional mutations acted as blocks.

"Dr. Thornton argues that once the restrictive mutations evolved, they made it practically impossible for the receptor to evolve back to its original form. The five key mutations could not be reversed first, because the receptor would be rendered useless. Nor could the seven restrictive mutations be reversed first. Those mutations had little effect on how the receptor grabbed hormones. So there was no way that natural selection could favor individuals with reversed mutations."

Some significant comments on this research have been made by Michael Behe here and here. These comments are highly relevant to discussions of mechanisms of evolutionary transformation. At the outset, Behe said that the work was interesting and the conclusion was reasonable -

"but the result was exceedingly modest and well within the boundaries that an intelligent design proponent like myself would ascribe to Darwinian processes. After all, the starting point was a protein which binds several steroid hormones, and the ending point was a slightly different protein that binds the same steroid hormones with slightly different strengths. How hard could that be?"

Behe's central point is that the evolutionary pathway was relatively easily disrupted by a few other mutations, so it is not satisfactory to think that Darwinian processes can find a way over every hurdle. The conclusions of his first post are as follows:

* The central point of The Edge of Evolution was that if several amino acids of a protein must be changed before a certain selective effect is available, then that is effectively beyond the reach of Darwinian processes. Bridgham et al (2009) confirm that conclusion. [. . .]
* There is no reason to think the protein studied by Bridgham et al (2009) is unusual in its difficulty of developing a binding site for even a relatively closely-related substance. In fact, in the absence of strong opposing data, that should be the default, reasonable assumption.
* That same reasonable assumption counts strongly against any two unrelated proteins easily developing a binding site for each other.
* That reasonable assumption therefore negates all woolly Darwinian evolutionary scenarios where critical protein binding sites are assumed without justification to pop up when needed (such as, say, in the building of multiprotein structures like the cilium or flagellum).
* Thus the work strongly supports the conclusion of Edge that Darwinian processes are highly unlikely to have built the complex molecular machinery of the cell.

The conclusion of the second post is this:

"The bottom line is that, for a given evolutionary task, at best only a handful of proteins will likely be helpful to evolve, at worst none may help. To calculate the probability of, say, a helpful protein-protein interaction developing in response to any particular selective pressure, it's mistaken to gratuitously multiply odds by the total number of proteins in a cell. Combined with the point made by Bridgham et al (2009), that even tiny structural/functional changes may not be achievable by random mutation/selection, these considerations pretty much squelch the likelihood of Darwinian processes doing much of significance during evolution."

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
Jamie T. Bridgham, Eric A. Ortlund & Joseph W. Thornton
Nature 461, 515-519 (24 September 2009) | doi:10.1038/nature08249

The extent to which evolution is reversible has long fascinated biologists. Most previous work on the reversibility of morphological and life-history evolution has been indecisive, because of uncertainty and bias in the methods used to infer ancestral states for such characters. Further, despite theoretical work on the factors that could contribute to irreversibility, there is little empirical evidence on its causes, because sufficient understanding of the mechanistic basis for the evolution of new or ancestral phenotypes is seldom available. By studying the reversibility of evolutionary changes in protein structure and function, these limitations can be overcome. Here we show, using the evolution of hormone specificity in the vertebrate glucocorticoid receptor as a case-study, that the evolutionary path by which this protein acquired its new function soon became inaccessible to reverse exploration. Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent 'restrictive' mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

See also:

Behe, M. Nature Publishes Paper on the Edge of Evolution, Evolution News & Views, 30 September 2009

Behe, M. Nature Paper Reaches "Edge of Evolution" and Finds Darwinian Processes Lacking, Evolution News & Views, 7 October 2009

Dolgin, E. Protein burns its evolutionary bridges, Nature News, 23 September 2009 | doi:10.1038/news.2009.940

In a Commentary essay, Carl Woese and Nigel Goldenfeld provide an analysis of biological thought that differs profoundly from that presented by those celebrating the Bicentenary of Darwin's birth and, incidentally, the recently published AP Biology Standards.

"This is the story of how biology of the 20th century neglected and otherwise mishandled the study of what is arguably the most important problem in all of science: the nature of the evolutionary process. This problem [ . . ] became the private domain of a quasi-scientific movement, who secreted it away in a morass of petty scholasticism, effectively disguising the fact that their primary concern with it was ideological, not scientific."

Procrustes was slain on his own bed by Theseus: an analogy for the microbial world liberating biology from the "Procrustean bed of dogma" that goes under the name of neo-Darwinism (source here)

The authors want to see biology liberated "from the Procrustean bed of dogma on which it has been cast for so long". A radical overhaul is warranted. The issues are comparable to the "transformation of the physical sciences" in the early 20th Century. This is when the foundations of Newtonian mechanics were undermined and the certainties of that approach were replaced by relativity theory and the statistical uncertainties of quantum mechanics. Just as physics then had to accept that there was much more to learn, so also biology today.

"Although 2009 will be marked by a plethora of celebrations on the subject of evolution, most of the attention is being bestowed on the personalities and historical circumstances surrounding the theory of natural selection, as if this and its synthesis with genetics in the first decades of the 20th century marks the culmination of the theory of evolution. It does not. The MMBR (Microbiology and Molecular Biology Reviews) community has been at the forefront of defying the standard wisdom; and thus it is, in many ways, its story that we now wish to tell."

This blog will refer to some of the themes developed in the essay. The first of these is reductionism. Newtonian physics is described as "deterministic reductionism, and safe in its completeness" and there is a direct link to neo-Darwinism: "the petrified form of evolution that emerged from the modern synthesis". This had adverse consequences for the study of living things: "Organisms, like pinatas, were there to be burst open in order to get at the (biochemical) goodies within - a view of microorganisms that, with justification, persists today among some subfields of microbiology."

"The discipline [of microbiology] clearly had a foundational issue. Biochemistry was simply not sufficient to serve as the basis upon which the study of the microbial world could rest. Neither the organism nor its ecology could be satisfactorily encompassed by this reductionistic perspective - an objection that could also be raised against all the sum-of-the-parts disciplines, such as molecular biology and genetics."

The second theme is the prokaryote hypothesis. In 1962, Stanier and van Niel sought to move microbiology on by declaring all bacteria to be prokaryotes. In their view, all bacteria shared a common cellular organisation and this allowed a common ancestry to be inferred. Woese and Goldenfeld write: "This notion, that all bacteria shared a common cellular organization, was to stand firmly in the path of microbiology's development for the better part of half a century." In their view, the assertion that "all bacteria were prokaryotes was an eminently testable hypothesis", but the microbiology community perceived the hypothesis as "the answer". Indeed, it became an axiom of microbiology. The test of the hypothesis came when Woese looked much more closely at the molecular properties of bacteria and recognised two distinct types: the archaebacteria and the eubacteria. Subsequent research widened the gap when it was realised that there was actually no common cellular organisation.

"[T]here were [. . .] many fundamental molecular properties in which the bacteria (declared to be synonomous with prokaryotes by Stanier and van Niel) differed from one another. The "archaebacteria (Archaea) had finally appeared on the scene, and their molecular properties were as distinct from those of the "eubacteria" (Bacteria) as either one's were from those of the Eukarya. The prokaryote hypothesis had been proven false."

The third theme relates to the concept of the gene. The root problem here is reductionism, but the consequences for genetics have been far-reaching. The mindset of the scientists was highly mechanistic.

"In this Newtonian world, the study of biology becomes a highly derived subdiscipline of the basic science of physics - in effect, an engineering enterprise; there is nothing "fundamental" about it. Biology becomes a study of machines made of assemblages of parts and the interactions among them, an exercise in describing, but not explaining, things as they are. [. . .] A discipline whose perspective is that of classical 19th century physics is inherently incapable of dealings with the problems of a nonlinear world, which is nonreductionist, nondeterministic (acausal), and works in terms of fields and emergent properties, not a static world of particles with linear relationships among them."

As a result, genetics was dominated by concepts of templating and translating that underplayed the "incredible and complex mechanism that can extract information (pattern) from the sequence of one type of macromolecule and "express", i.e., store, most of it as the structure (sequence pattern) of another macromolecule of a different type". Neo-Darwinism cannot deliver answers, because its vision of biology is fundamentally flawed.

"This turn in the road (of applying reductionist metaphysics to the understanding of the biological world) would become a superhighway that dead-ended before it reached molecular biology's ultimate goal, that of understanding the essence of "livingness" and directly answering the question of how molecules come to life."

This sense of biology entering a cul-de-sac is pronounced. Woese and Goldenfeld want to see a different approach to evolutionary thinking: for them, it is the key to moving the discipline forward. Their perception of the Modern Synthesis is that it has led to (a) stagnation (no new ideas) and to (b) safeguarding the consensus (looking after vested interests).

"The basic understanding of evolution, considered as a process, did not advance at all under its tutelage. The presumed fundamental explanation of the evolutionary process, "natural selection", went unchanged and unchallenged from one end of the 20th century to the other. Was this because there was nothing more to understand about the nature of the evolutionary process? Hardly! Instead, the focus was not the study of the evolutionary process so much as the care and tending of the modern synthesis. Safeguarding an old concept, protecting "truths too fragile to bear translation" is scientific anathema."

There is much more in this essay - happily it is open access. The vision of Woese and Goldenfeld warrants further discussion, as do their comments on the significance of horizontal gene transfer. However, this blog has an educational focus. Why are educationalists so keen to make neo-Darwinism the central pillar of evolutionary theory? Why are the AP Biology Standards affirming things that are here so vigorously contested? Why should students be given the impression that evolutionary theory is robust and settled? Woese and Goldenfeld comment:

"What makes the treatment of evolution by biologists of the last century insufferable scientifically is not the modern synthesis per se. Rather, it is the fact that molecular biology accepted the synthesis as a complete theory unquestioningly - thereby giving the impression that evolution was essentially a solved scientific problem with its roots lying only within the molecular paradigm."

Returning to the Procrustean bed of dogma, it is important to realise the significance of this imagery. Biology has been lying on a bed which has led to emasculation. To draw on the other images in the title, biology needs to be delivered from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis. These theoretical constructs have had serious negative effects on biological science, and yet we still teach them uncritically! In summary:

"Dogmatic thinking has prevailed all too often in our account, with disastrous consequences for the progress of the fields of microbiology, molecular biology, and the study of the evolutionary process. It led to the stagnant and scientifically invalid notion of the prokaryote; it led to the redefinition of the problem of the gene; and through a slavish adherence to the modern evolutionary synthesis, it led to a premature declaration of victory in the struggle to understand the evolutionary process."

How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis
Carl R. Woese and Nigel Goldenfeld
Microbiology And Molecular Biology Reviews, 73(1), March 2009, 14-21 | doi:10.1128/MMBR.00002-09

There must be no barriers for freedom of inquiry. There is no place for dogma in science. The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors.
-J. Robert Oppenheimer, The Open Mind, p. 114 (1955)

First sentence: This is the story of how biology of the 20th century neglected and otherwise mishandled the study of what is arguably the most important problem in all of science: the nature of the evolutionary process.

See also:

Tyler, D. Teaching goals for Advanced Placement Biology, ARN Literature Blog (21 September 2009)

Many schools in the US are introducing the Advanced Placement (AP) program which sets out to mirror "an introductory college course". Schools perceive these courses as "a marker for a quality education". Inevitably, teething problems have arisen and have highlighted issues of a pedagogological nature.

"[Reports have found a] flawed approach to teaching science: too much emphasis on facts and memorization and too little attention to the underlying concepts and how science is actually practiced."

With some topics, critical thinking is conflated with knowing the right answers! (source here)

Particular problems arose because AP exam successes give exemption from other introductory courses. Colleges wanted everything covered by those courses to be incorporated in the relevant AP course. One of the organisers said: "AP teachers have had to resort to memorization and factual recall as a way to cover everything that could be on the exam". This is, by most accounts, not the way to design courses. Happily the situation is changing.

The revised approach for science is built on understanding concepts, direct experience of experimentation via laboratory work, and developing an appreciation of how scientists conduct research.

"The new courses will emphasize conceptual knowledge, updated regularly and learned by doing, along with teaching how scientists ask and answer important questions."

A chemistry teacher is quoted to show the differences between rote-learning and the revised approach:

Instead of drilling students on how to apply a particular algorithm, he says, "I'd much rather that students are able to explain the underlying concept to me, in English, and show me they understand something about how nature builds the stuff around us."

It has to be said that such comments echo discussions that have been taking place over many years in colleges of education. These contemporary developments in the US are a reflection on the bureaucratisation of education and the need to tick the right boxes when developing and delivering courses. Another factor may be the way the media presents intellectual prowess: competitions to find the best 'brain' or the person with the most expertise invariably probe knowledge that is memorised. Concepts, and the application of concepts, do not lend themselves to true/false responses needed to sustain the interest of viewers or listeners.

Biology is reported to be the first of the AP Science sources to be revised according to the new emphasis. The big ideas for this discipline have been identified and these set the agenda for structuring the experiences of students.

"[the] big ideas [. . .] include evolution, the storage and transmission of information, and the use of energy to carry out essential functions. That's followed by a series of core principles. One new wrinkle links content knowledge to the actual practice of science. The final layer is a set of performance expectations: what students should know, understand, and be able to do to demonstrate their mastery of the subject."

Of the three big ideas listed, the link between concept and application is straightforward for two of them. Information storage and transmission provides a solid foundation for genetics, developmental biology and systems biology. Similarly, the production of energy and its use provides the conceptual framework for the operation of cellular machines, physiology and metabolism. There is a problem, however, with evolution as a "big idea". This is partly because the word has a fuzzy meaning and is understood in different ways by different people. It is also partly because evolution belongs to the realm of history whereas the other two big ideas are rooted in empiricism. Historical science and empirical science do not have identical methodologies and students grappling with these ideas need to be able to recognise the differences when they link "content knowledge to the actual practice of science". There are serious issues here: why do so many biologists think that observations of peppered moths or deer mice have a bearing on the origin of moths or mice? The answer to this question is: they have not learned the skill of linking the "actual practice of science" with relevant theoretical concepts.

The debate for our consideration is not 'should evolution be taught?' but 'how should evolution be taught?' It is not that evolutionary theory should be dropped (as controversial) but that evolutionary theory should be taught critically - in a way that makes same use of critical faculties as is normal for the empirical sciences. Some of us regard Design as a 'big idea' in biology. Nothing in biology makes sense except in the light of design. We find it strange that whilst design is often mentioned by advocates of evolution, it is only done to reject it summarily. These evolutionists have no intention of finding the best expression of design thinking and subjecting it to critical scrutiny - they are generally content to speak of Rev William Paley or the writings of Charles Darwin. Modern exponents of design thinking are rarely mentioned and their analyses of evidence are typically deemed not worthy of consideration. We consider this situation unhealthy for science. Evolutionists (generally of a Darwinian mindset) are claiming a central role for evolutionary concepts but are resisting all attempts to rigorously scrutinise their claims.

The new standards for AP courses are to be welcomed in principle. The emphasis on concepts and their application to the real world is the right way to go. However, the biology standards have a yielded too much ground to doctrinaire Darwinism. For the details, go here. The AP Biology standards have statements like:

* Natural selection is the major driving mechanism of evolution because the essential features of the mechanism contribute to the change in the genetic makeup of a population over time.
* Although natural selection is usually the major mechanism for evolution, genetic variation in populations can occur through other processes, including mutation, genetic drift, sexual selection and artificial selection.
* Scientific evidence - including emergent diseases, chemical resistance and genomic data - supports the idea that evolution occurs for all organisms and that evolution explains the diversity of life on the planet.
* New species arise when two populations diverge from a common ancestor and become reproductively isolated.

All these statements can be challenged scientifically - yet the AP document presents them in the sections headed "enduring understanding". This is where the intention to develop the critical skills of students is not matched by the text of the standards. Students taking AP Biology courses will be delivered a non-negotiable package of Neo-Darwinian evolutionary theory. Let's hope the students are alert to these issues: after being encouraged to develop critical skills in the empirical sciences, they learn that these skills must not be used to question the Darwinian framework for understanding the diversity and unity of life!

Revisions to AP Courses Expected to Have Domino Effect
Jeffrey Mervis
Science, 325, 18 September 2009: 1488-1489.

First para: Last month, Jeffrey Lamb began teaching Advanced Placement (AP) chemistry for the first time at Woodmont International Baccalaureate High School in Piedmont, South Carolina. The public school's decision to offer the course reflects the explosive growth of the AP program, a suite of 38 courses intended to mirror an introductory college course.

See also:

Tyler, D., Liberating biology from a Procrustean bed of dogma, ARN Literature blog (25 September 2009)

A cave in the Republic of Georgia has yielded over 1000 fragments of flax that are being interpreted as the oldest example of humans using textile fibres in utilities and garments. The samples come from various dated horizons, the oldest considered to be about 34,000 years before the present. Whereas other archaeological sites of a similar (slightly younger) age have provided impressions of textile materials, the new find pin-points flax and carries the implications of humans gathering the stems, removing the fibres, processing the fibres to make yarns and then using the yarns to either sew skins, to create ropes or even to weave textiles for use in garments.

"This was a critical invention for early humans. They might have used this fiber to create parts of clothing, ropes, or baskets - for items that were mainly used for domestic activities," says Bar-Yosef. "We know that this is wild flax that grew in the vicinity of the cave and was exploited intensively or extensively by modern humans."

A selection of fibres from Dzudzuana Cave, Georgia (Source here)

There are two evidences to support weaving. The first is that a "few of the fibers are colored and appear to have been dyed". "The color range includes yellow, red, blue, violet, black, brown, green, and khaki." The range of colours suggests intentional colouration rather than chance contact with colourants. The second line of evidence relates to organisms that are associated with decaying textiles, as well as the "spores of the Chaetomium fungus, usually growing on clothes and other textiles and unfortunately destroying them". Michael Balter summarises this point as follows:

"The team thinks the flax was used to make garments as well as woven baskets, because it was associated with skin beetles and moth larvae that infest decaying textiles, as well as spores of a fungus known to grow on clothes. The team also found a few twisted and colored fibers of wool from a goat species whose bones were found in the cave."

The significance of the find is that it contributes to the discussion of "when hominins started looking modern and when they began acting modern". In a blog on reports of shells used as jewellery, Michael Balter describes two positions:

"[S]ome scientists [. . .] argue that modern human cognition, including language and other complex symbolic behavior, needed the additional kick-start of a genetic mutation about 50,000 years ago. Yet an increasing number of researchers have come to think that Homo sapiens was capable of modern behavior from the very beginning of its history. Whether those behaviors show up in the archaeological record, these researchers say, depends on a variety of factors unrelated to genetics, such as how big and widespread early human populations were and what environmental challenges they faced."

Ultimately, underlying philosophies influence the way researchers think: some are evolutionary gradualists and predict the slow transformation of culture from animal to human traits. These people are happy to invoke a mutation that switches on self-awareness, or consciousness, or similar. A mutation is, after all, a link in the chain constructed by gradualism. Others go with punctuated equilibrium and abrupt appearance. They typically do not have a mechanism, but they argue they are doing justice to the evidence. It hardly needs to be said, but the history of studies of Palaeolithic culture shows that examples of human traits and human behaviour are being found earlier and earlier in time. The newly reported research is just the latest example of this.

ID thinking has a bearing on these debates. Humanity cannot and should be explained purely in terms of physics and chemistry. Yet Darwin's portrayal of the descent of man was calculated to by-pass design. Evolutionary gradualists are in the Darwinian tradition and they bring this philosophical position to their science. They are not free to follow the evidence wherever it leads, because they 'know' that complexity has to be constructed incrementally. ID does not forcefit design to be the solution to every question researchers ask, but it does allow non-naturalistic avenues to be explored. If Homo sapiens is the product of design, then our species should have been capable of modern behavior from the very beginning of its history. Furthermore, if research confirms modernity, then we do not need to apologise for not invoking a material cause. Those waving a magic wand are those who conjour up a "mutation" or some other simplistic device to transform an ape into a human.

30,000-Year-Old Wild Flax Fibers
Eliso Kvavadze, Ofer Bar-Yosef, Anna Belfer-Cohen, Elisabetta Boaretto, Nino Jakeli, Zinovi Matskevich, and Tengiz Meshveliani
Science, 325, 11 September 2009: 1359.

A unique finding of wild flax fibers from a series of Upper Paleolithic layers at Dzudzuana Cave, located in the foothills of the Caucasus, Georgia, indicates that prehistoric hunter-gatherers were making cords for hafting stone tools, weaving baskets, or sewing garments. Radiocarbon dates demonstrate that the cave was inhabited intermittently during several periods dated to 32 to 26 thousand years before the present (kyr B.P.), 23 to 19 kyr B.P., and 13 to 11 kyr B.P. Spun, dyed, and knotted flax fibers are common. Apparently, climatic fluctuations recorded in the cave's deposits did not affect the growth of the plants because a certain level of humidity was sustained.

See also:

Balter, M., Clothes Make the (Hu) Man, Science, 325, 11 September 2009: 1329.

Balter, M., Drawing a Bead on Ancient Symbolic Behavior, Origins Blog, 28 August 2009

Archaeologists discover oldest-known fiber materials used by early humans, EurekAlert (10 September 2009)

The launch of Ida, alias Darwinius masillae, in May this year was unprecedented. It raised eyebrows across the whole range of media-savvy people. Whilst scientists have learned how to capture the interest of the media and promote their work, this particular indulgence was a shock and it was quickly recognised as hype.

"Indeed, Ida has had the public impact of an asteroid. The debut of Darwinius was a media juggernaut: the scientific paper, a public unveiling by New York City's Mayor Bloomberg, a Web site, coverage in People magazine, a television special, and the book all appeared within a week. On the day of the announcement, the traffic at the Web site exceeded that for www.sciencemag.org. But has this fossil rocked our understanding of primate evolution?"

David Attenborough narrated the documentary on Ida, Uncovering Our Earliest Ancestor: The Link (source here)

Thus far, the book has received little attention from the scientific literature. Science has remedied this with an incisive review that leaves readers in no doubt that big mistakes have been made.

"Of the book's nine chapters, the first three and final are written by Young in a sensational style: "Hurum pulled out one final key card and opened the door.... Geffen was stunned." These parts are the most entertaining or, depending on one's point of view, disturbing. Ida is a reprise of the seamier side of paleontology: the exploitation, with the complicity of major museums, of our natural heritage for profit."

The reference to "profit" draws attention to the purchase price of the fossil: reputed to be "a stunning $750,000". The reviewer was one of the signatories to a letter in Nature that expressed "[o]utrage at [the] high price paid for a fossil". When palaeontologists join the ranks of fossil traders, their integrity is suspect. As an Editorial in Nature said: "such arrangements introduce conflicting incentives that can all too easily undermine the process of the assessment and communication of science."

The reviewer is not impressed with the attention to detail that is displayed by coauthor Colin Tudge. This again stimulates comments about the whole process of launching Ida to the world.

"Tudge also offers a tour of primate ecology, behavior, and evolution that is often inaccurate and at times misleading. (For example, he misstates the age of the earliest New World monkey by 6 million years and that of the African anthropoid fossil Apidium by 10 million years.) Why are there so many errors? Perhaps because the book had no scientific editor to check facts or demand reviews that would have uncovered these inaccuracies. The book was rushed out, and the whole project from purchase of the fossil up to the media blitz was cloaked in secrecy."

The palaeontological expertise provided by Philip Gingerich is called into question. This is at the heart of the technical analysis of Ida's significance.

"In short, the interpretation favored by Gingerich and described by Tudge is incompatible with a basal split of anthropoids from lemurs and lorises. Adapoids cannot simultaneously be the source of lemurs, lorises, and anthropoids to the exclusion of tarsiers because tarsiers and anthropoids form a clade. So Darwinius cannot be both an adapoid and a monkey ancestor.
[. . .]
So, Link's premise, that Ida is our ancestor, is fallacious. Ida is a lemur. While the search for anthropoid origins goes on, we shouldn't look for human ancestors in Darwinius or its close relatives."

Why is this relevant to a blog addressing issues of Intelligent Design? A previous blog drew attention to some of the reasons for taking an interest in this case. The science community does not like being confronted by a fait accompli: it expects and demands peer review. It does not welcome situations where the judgment of scholars could be influenced by financial commitments. It does not welcome teams who want to control the publicising of their work by publishing their own resources (documentary, book and web site) contemporaneously with publishing their research. The review by Kay is valuable because it articulates very well the human face of science. The big question is whether this represents the tip of an iceberg (and there is much more of this under the surface) or whether it is exceptional. In my assessment, the Ida-team has overstepped the mark but what they have done is not that unusual. Science does not have the objectivity that the textbooks claim. That is why it is essential to have vigorous debate within science. That is why the questions raised by Intelligent Design are important and why it can only be healthy for science to engage in meaningful dialogue.

Much Hype and Many Errors
Richard F. Kay
Science 28 August 2009: 1074-1075.

Summary: This account of Darwinius masillae, its discovery, and its importance was rushed into print as part of the hype surrounding the public announcement of the work.

Book reviewed- The Link: Uncovering Our Earliest Ancestor by Colin Tudge, with Josh Young Little, Brown, New York, 2009. 304 pp. ISBN 9780316070089.

In the past few years, studies of fossil feathers have yielded some surprising and unexpected results. How do graphic artists know what colours to use when illustrating extinct birds? The answer has been: we don't know - we use artistic licence. The new research has not yet provided different answers to this question, but methodologies are in place which should allow more definitive statements to be made in the future.

This Middle Eocene fossil feather had iridescent colours (source here)

Pigment colours are derived from melanin. These are produced within organelles called melanosomes that have a shape not dissimilar to bacteria. Since researchers were expecting to find bacteria rather than melanosomes, bacteria are what they reported - until last year.

"Melanins are synthesized in a special class of pigment cells (melanocytes) and are packaged within organelles (melanosomes) that vary in morphology between tissues, colours and organisms; the chemically inert structure is not fully understood. Wuttke (1983) interpreted the aligned oblate bodies that constitute the fossil feathers of the Messel Oil Shale as lithified bacteria. This interpretation was extrapolated to fossil feathers from other localities. Our recent investigation of a colour-banded feather from the Cretaceous Crato Formation of Brazil led us to interpret the oblate bodies as eumelanosomes, which contain black melanin (Vinther et al. 2008)."

Examples like these demonstrate the importance of multiple working hypotheses in science to avoid the danger of confirmation bias. If there is only one hypothesis on the table, there is a strong temptation to 'fit' the data to the hypothesis (rather than test the hypothesis using data). An example of this phenomenon was pointed out here. These considerations are significant for the application of design thinking within science. At very least, ID provides information-based alternatives to naturalistic hypotheses to account for biological complexity - as is discussed below.

The melanosomes have implications for plumage colouration. Modern-day examples show an association with black, brown, red and buff colours. The new research reports the "laminar nanoscale organization of melanosomes in feather barbules" that is associated in modern birds with iridescence. The melanosome layer lies underneath a very thin covering of keratin.

"These nanostructures produce a structural colour by interference among light waves scattered by the keratin layer and the underlying layer of melanosomes. [. . .] Feathers with this type of colour-producing nanostructure generally appear black with a glossy or oily iridescent sheen. Depending on the thickness of the keratin layer (from approx. 100 to over 300 nm), the iridescent colour varies in reflectance from saturated ultraviolet or blue to an oily appearance. The most distinctive feature of these nanostructures is the highly uniform superficial layer of closely packed melanosomes. The melanosomes may be rod shaped as in some passerines, galliform birds and the fossils described here or flattened as seen in some ducks and swifts."

The "dense external layer of melanosomes" in the fossil feather is now perceived as diagnostic of structural colour. The original hue of the feather cannot be determined because the outer keratin layer has been degraded. However, coauthor Julia Clark says that the reported research is just "proof of concept" and many more insights into colouration lie ahead.

The authors think that "[t]his type of thin-film nanostructure has evolved numerous times in passeriform and non-passeriform birds". The appearance of this phenomenon in diverse groups points, in their minds, to evolutionary convergence. However, it could be argued (as it is here) that structural colour has a high level of complex specified information.

Some types of colour may point to irreducible complexity. If so, it would seem desirable to adopt a multiple working hypotheses approach and consider design explanations alongside convergence. It is not without significance that the fossil feather documented in this paper is from the Messel Shale (considered to be 40 Ma). It demonstrates the kind of stasis we would expect from a complex specified system. The pattern of abrupt appearance of mature structures is not unusual and the implication is that complexity emerges rapidly (not gradually). The claim for convergence should be understood as an inference from theory, as yet unvalidated by testing.

Inevitably, evolutionary theorists have sought to relate this work to dinosaur 'feathers' and to the 'consensus' view that birds evolved from feathered dinosaurs. Zimmer comments on the ambitions of palaeontologists to extend the methodology to dinosaur feathers. He might have said that such detailed work could reveal fundamental differences between dino-feathers and bird feathers, but he did not. He might have acknowledged the controversial aspects of the dino-bird scenario (see here) but he did not. Rather, he wrote: "It is possible that dinosaurs evolved these colors before they evolved the ability to fly". I see in this an indication that not only the origin of feathers, but also the origin of structural colour, needs to be pushed back earlier and earlier, in order to allow time for such complexity to originate by natural processes.

Structural coloration in a fossil feather
Jakob Vinther, Derek E. G. Briggs, Julia Clarke, Gerald Mayr and Richard O. Prum
Biology Letters, published online before print August 26, 2009, doi:10.1098/rsbl.2009.0524

Abstract: Investigation of feathers from the famous Middle Eocene Messel Oil Shale near Darmstadt, Germany shows that they are preserved as arrays of fossilized melanosomes, the surrounding beta-keratin having degraded. The majority of feathers are preserved as aligned rod-shaped eumelanosomes. In some, however, the barbules of the open pennaceous, distal portion of the feather vane are preserved as a continuous external layer of closely packed melanosomes enclosing loosely aligned melanosomes. This arrangement is similar to the single thin-film nanostructure that generates an iridescent, structurally coloured sheen on the surface of black feathers in many lineages of living birds. This is, to our knowledge, the first evidence of preservation of a colour-producing nanostructure in a fossil feather and confirms the potential for determining colour differences in ancient birds and other dinosaurs.

See also:

Ancient Bird's Feathers Had Iridescent Glow, livescience.com (August 26 2009)

Zimmer, C. First Trace of Color Found in Fossil Bird Feathers, New York Times (August 31, 2009)

The deer mouse is described as one of the "most abundant and widespread mammals in North America" and normally has a dark coloured pelt. The Sand Hills of Nebraska are home to a sub-population of deer mice (Peromyscos maniculatus) with a light-coloured fur that matches the local habitat. The potential for understanding more about adaptive change and the genetics of hair colour has attracted the attention of researchers.

"To unravel evolutionary mechanisms in the wild, we must estimate the fitness advantage of adaptive alleles and infer their source, either as new or pre-existing variation."

Pale-coated deer mouse on a dark soil (Source here)

Based on what is already known about pigment-producing cells at the base of mammalian hair follicles, the gene Agouti was identified as responsible for the different phenotypes. In the house mouse (Mus musculus), it is known that knockouts of Agouti result in dark hairs, whereas overexpression of Agouti leads to light colours. It is also known that "light alleles are generally dominant to dark ones". Significantly, the crosses between dark and light coloured deer mice produced light-coloured offspring. Empirical work pointed unambiguously to Agouti expression as the underlying cause of the two phenotypes (referred to in the paper as wildtype and wideband phenotypes). Sequencing analysis led to the identification of 20 nucleotide differences between the dark and light mice. Of these, two stood out as prime candidates for a genetic mechanism: "a conservative amino acid substitution (Arg37Lys) and a serine deletion (residue 48), both in exon 2". After more detailed investigations, the authors report:

"On the basis of these results, we cannot determine whether the serine deletion, a linked mutation, or both cause wide bands and light coats. [. . .] Nonetheless, the haplotype containing the serine deletion[. . .] explains a substantial amount of ecologically relevant phenotypic variation."

Deer mouse with the darker coat colour. (Source here. For more images, go here)

Further research concluded that "selection is probably acting on the wideband Agouti haplotype". Also, "both population genetic data and predation experiments suggest that selection for light color is strong, and our estimates fall within the range of selection coefficients for other color polymorphisms, including beach mice, pocket mice, ladybirds, and land snails."

Allowing all this, what can be said of this example of adaptive change?
First, selection demonstrably acts on phenotypes that affect the ability of organisms to survive and reproduce. In this case, the phenotype relates to coat colour and its ability to provide camouflage, thus avoiding predation.
Second, the genetic variation involved is linked to a "single amino acid deletion" in the Agouti gene. Deletions are not infrequently found in cases of natural selection. By contrast, additions are rare. Information loss is the norm.
Third, both types of deer mouse interbreed readily. Coat colour is not a factor in mate selection. "Therefore, we hypothesized that light and dark mice interbreed with ample opportunity for recombination between the wideband and wild-type alleles." We are not looking at new species or sub-species here.
Fourth, the adaptive changes are inferred to have been rapid. The authors consider this worthy of comment because they consider the genetic changes to be de novo (i.e. natural selection was not acting on a pre-existing allele).

In the light of these comments, natural selection can be identified as a factor of relevance in ecological studies. Over generations, organisms adapt to their environment and become more optimised to local conditions.

What this research does not do is lend support to Charles Darwin's claim that evolution by natural selection is the key to understanding the development of biological complexity and the origin of species. the genetic changes associated with the modified coat colour are attributed to the deletion of a single amino acid in the Agouti gene - there is no increase in information and no move towards specified complexity. It is necessary to point this out because some (e.g. the BBC report) are suggesting this research is so important for evolutionary theory that it deserves iconic status.

"Rival icon. In some respects, the dune-living deer mice are similar to the famous peppered moths of northern England. For decades, the peppered moths (Biston betularia) have been heralded as one of the best-examples known of a wild animal adapting to its environment due to natural selection. [. . .] "In both species, changes in colour evolve rapidly due to selection by visually-hunting predators," says Prof Hoekstra. But the study by Dr Linnen and Prof Hoekstra's team takes our undertaking of natural selection to a much deeper level. The selection pressure on the moths was technically artificial, caused by pollution produced by people. Whereas the selection causing the pale mice is truly natural. What is more, the scientists have found the gene responsible, and worked out exactly how long it took to evolve and take hold in the population. "Despite the fact that the peppered has been an icon of 'evolution in action', we do not yet know the genetic changes involved," says Prof Hoekstra. "Once researchers find the pigmentation gene responsible for moth colour change, they can do the same types of analyses we have done. It will be really interesting to compare these estimates between mice and men."

Like so many other studies of natural selection, Darwinists think that if they can only demonstrate natural selection in action, their theory is verified. Of course, this is fallacious for the reasons pointed out above. The deer mice example demonstrates ecological adaptation, and does not provide any insight into the origin of complex specified information. To say that the deer mouse example is an icon of evolution is like saying 'if we can only generate amino acids in a reducing atmosphere, we will have shown that the first living cell could have arisen by natural processes'. It is like saying 'if we can show that oxygen levels elevated significantly in the Early Cambrian atmosphere, we will have explained the Cambrian Explosion'. We need these discussions to mature - there is no dispute over natural selection as a driver of adaptive change in ecological systems, but if it is to be presented as a key mechanisms for the creation of biological complexity, the quality of argument needs to be improved by many orders of magnitude!

On the Origin and Spread of an Adaptive Allele in Deer Mice
Catherine R. Linnen, Evan P. Kingsley, Jeffrey D. Jensen, and Hopi E. Hoekstra
Science, 28 August 2009, 325: 1095-1098 | DOI: 10.1126/science.1175826

Adaptation is a central focus of biology, although it can be difficult to identify both the strength and agent of selection and the underlying molecular mechanisms causing change. We studied cryptically colored deer mice living on the Nebraska Sand Hills and show that their light coloration stems from a novel banding pattern on individual hairs produced by an increase in Agouti expression caused by a cis-acting mutation (or mutations), which either is or is closely linked to a single amino acid deletion in Agouti that appears to be under selection. Furthermore, our data suggest that this derived Agouti allele arose de novo after the formation of the Sand Hills. These findings reveal one means by which genetic, developmental, and evolutionary mechanisms can drive rapid adaptation under ecological pressure.

See also:

Walker, M. Mouse set to be 'evolution icon', BBC News (27 August 2009)

Can there be any student of palaeontology who does not have some awareness of the fossils from the Burgess Shale? With their exquisite preservation, including soft body parts, these animals have provided a window into Middle Cambrian life that has only recently been supplemented by other material. Charles Doolittle Walcott is the person who discovered the most significant fossil site. By 1917, his collection numbered 65,000 fossils. His publications set the scene for subsequent debates about the significance of these animals.

"Walcott's 1909 discovery was not the first, but the best Burgess Shale site. By his collections and publications, Walcott contributed more than anyone, before or since, to drawing back the curtain obscuring our view of the life of the Cambrian world. For this alone, he deserves the glory of this month's centennial celebrations."

The Darwinian model of evolutionary transformation does not explain the explosion of life in Cambrian seas (source here)

My interest in this blog is not the history of the discovery, but the significance these fossils have for palaeontological thinking. Three phases of understanding can be identified.

1. Walcott's interpretations. From today's vantage point, it is easy to underestimate the challenge facing this pioneer. Numerous fossil animals were collected by Walcott that had no identifiable living descendants. Nevertheless, he made every effort to find meaningful links to defend his classification of the organisms. Collins draws attention to a 1911 paper on soft-bodied animals: 4 sea cucumbers, 1 jellyfish and some annelid worms.

"Walcott's identifications did not fare well. Only one of the sea cucumbers is still thought to be a sea cucumber, and the jellyfish is now known to be part of an extraordinary arthropod. Of the 12 annelid worms, only one is still recognized as such. Walcott was on more familiar ground with his publication of arthropods in 1912 but, even here, many of the 8 genera he described are now known to belong to classes different to those which he assigned them."

2. Whittington's reinterpretations. For over 40 years, little work was done on Walcott's collection. Then, in the late 1960s, Harry Whittington and colleagues took up the challenge. They were more ready to recognise "unknown affinities" and acknowledge the weirdness of some Cambrian animals.

"This was the first time that anyone had questioned Walcott's implicit assumption that Cambrian animals belonged to groups alive today. [. . .] None of Walcott's contemporaries, nor indeed the scientists who followed him, questioned Walcott's assumption that the Burgess Shale animals belonged to living animal groups; not until Whittington."

Enter Stephen Jay Gould in 1989 with the publication of Wonderful Life. Apart from retelling the story of the Burgess Shale fauna to a new generation of readers, Gould developed three major arguments, summarised below.

The first pointed out significant human factors affecting the way palaeontological work is done. Walcott was criticised "for 'shoehorning' his animals into known groups, so delaying the true understanding of the Burgess Shale fossils".

Second, Gould claimed to recognise new body plans (phyla) in the "weird wonders" revealed by the Whittington group. This, he claimed, pointed to contingency and chance being dominant factors in the history of life. It did not escape the notice of some that this perspective fitted well into Gould's Marxist/atheist worldview.

Third, Gould wanted to point out the incompatibility between the history of life as revealed by the fossils (the sudden appearance of new body plans) and the theoretical understanding of life's diversity provided by Darwinism (which requires gradualism and incremental branching patterns).

3. Desmond Collins' fieldwork and revised classifications. Starting in 1975, Collins (the author of the Nature essay) led "18 seasons of fieldwork and excavation in the Burgess Shale". Many new localities were found, 3 new faunas, plus "a flood of new specimens" in the period 1983-2000. New forms were described and old forms were re-described.

"Today, we have returned mostly to Walcott's practice of classifying Burgess Shale animals in living animal groups, but the groups are different. There are some extinct classes, such as the Dinicarida, but very few extinct phyla. Five of Gould's weird wonders have been classified, only one in a new phylum."

Collins has provided us with a helpful overview with which as assessment of the issues raised by Gould can be made. We shall look at each of the three arguments in turn.

First, the issue of Walcott's "shoehorning". Collins choice of word is different: he refers to Walcott's "misadventures". Clearly, mistakes were made - but not only by Walcott! It can be argued that Gould himself shoehorned the Burgess Shale data to fit a story that matched his 'contingency' worldview. He wanted to be able to say that if the tape of life were ran again, life's history would look very different.

Second, the dramatic explosion of novel body plans in the Cambrian, many of which went nowhere and became extinct. The re-classification of Collins' et al has reduced the number of new phyla to one. This undermines Gould's contingency argument. If the logic of Gould's argument is valid, then the re-evaluation of the data implies that we have no grounds for thinking that re-running the tape of life will lead to the emergence of unfamiliar phyla. Gould drew conclusions relating to humanity:

"Homo sapiens, I fear, is a "thing so small" in a vast universe, a wildly improbable evolutionary event well within the realm of contingency. Make of such a conclusion what you will." (page 291).

Significantly, arguments against contingency have been developed by one of Whittington's colleagues - and one of the characters appearing in Wonderful Life - Simon Conway Morris, Professor of Evolutionary Palaeobiology at the University of Cambridge. These arguments, based partly on the Burgess Shale fossils and partly on the phenomenon of convergence, appear in his book The Crucible of Creation (1998). It should not be necessary to say that a design-orientated understanding of these data is entirely consistent with the approach taken by Conway Morris.

"I hope that by now I have persuaded you that whatever importance is attached to the Burgess Shale, it is not in the operation of either historical contingency or in the fable of re-running the film of the history of life." (page 205)

Thirdly, the challenge to Darwinism because of the Cambrian Explosion of life forms. Although Gould's claims regarding additional phyla are no longer defensible, this particular argument still stands. Darwinism predicts gradualism and increasing diversification (Gould's cone of increasing diversity in Chapter 1). The pattern of diversification and decimation (Gould's inverted cone) is still to be found in the Burgess Shale organisms. The fundamental incompatibility between the evidence and Neodarwinism means that Darwin's theory have very little to offer us as an explanation of the origin of diversity and organic complexity.

"Additional Cambrian material is now coming from the Chengjiang fauna in China (particularly new chordates, the group that includes humans), and the Sirius Passet fauna in Greenland. Along with the Burgess Shale animals, they demonstrate that virtually all animal groups alive today were present in Cambrian seas."

Gould drew conclusions of a theological nature when he argued from science that we live in the realm of contingency and are ourselves the product of contingency. Yet few challenged his philosophy of history. And few pointed out that his advocacy of purposelessness in the Cosmos was incompatible with his promotion of the strict separation of science and religion (as non-overlapping magisteria). Now that the consensus in science has moved on, we can see that Gould's Burgess Shale argument for contingency was flawed and that the opposite conclusion is warranted: that the history of life suggests purpose and meaning in the Cosmos. For more on these issues, please refer to Meyer's paper on the evidences for design apparent in the Cambrian Explosion and also the film Darwin's Dilemma.

Misadventures in the Burgess Shale (Restricted access)
Desmond Collins
Nature 460, 952-953 (20 August 2009) | doi:10.1038/460952a

One hundred years after Charles Doolittle Walcott found a wealth of Cambrian fossils in the Rocky Mountains of British Columbia, Desmond Collins reflects on the bumpy road of their classification.

See also:

Gould, S.J. Wonderful Life, Hutchinson Radius, 1989.

Morris, S.C. The Crucible of Creation, Oxford University Press, 1998.

Recent years have seen significant advances in our knowledge of the biology of extinct placoderm fish. These animals are now regarded as the earliest vertebrates capable of live birth. Embryos have been found inside pregnant fish alongside evidence for the presence of an umbilical cord (go here and here). The latest reported find concerns the male reproductive organ necessary for internal fertilisation.

The females of Incisoscutum ritchiei bore live young following internal fertilisation (source here)

The background to the discovery of the male organ is interesting in its own right. Males have "penis-like pelvic claspers similar to those found in fossil Ptyctodontida (a group of unarmoured placoderms) and in sharks".
The fossil revealing this organ was found in 2001, but the pelvic clasper was labelled as the pelvic girdle. Second author Kate Trinajstic explained

"at the time, we didn't realize that live births were possible. [. . .] [E]arlier this year [. . . we] looked at this specimen with a new set of eyes. As soon as [Per Ahlberg] got it under a high power microscope, we both realised we had found the missing clasper".

This provides a striking example of human factors affecting the outworking of the scientific method. We are familiar with the idea of scientists gathering data in order to test hypotheses, but much less aware of the way worldviews and paradigms affect what we see as data and what hypotheses we consider to be worthy of testing. When placoderms were considered "primitive", no one was looking for unborn embryos or for the means to achieve internal fertilisation. This was not a hypothesis entertained by the researchers. Even when they looked at a male clasper, they did not recognise what it was. However, once internal fertilisation and live births became accepted (the new paradigm for placoderm biology), the researchers were alerted to new possible explanations of fossil material. Per Ahlberg is quoted as saying: "It provides a pedigree of nearly 400 million years for the "advanced" and seemingly specialized reproductive biology of modern sharks".

Design thinking is like this. Once one accepts the legitimacy of making design inferences within science, the data looks rather different. With the new paradigm, evidences of design appear to be pervasive. Evolutionary presumptions about the "primitiveness" of so-called stem organisms no longer seem coherent. Complex specified information diagnostic of design can be found everywhere we look.

Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires
Per Ahlberg, Kate Trinajstic, Zerina Johanson & John Long
Nature 460, 888-889 (13 August 2009) | doi:10.1038/nature08176

Recent finds demonstrate that internal fertilization and viviparity (live birth) were more widespread in the Placodermi, an extinct group of armoured fishes, than was previously realized. Placoderms represent the sister group of the crown group jawed vertebrates (Gnathostomata), making their mode(s) of reproduction potentially informative about primitive gnathostome conditions. An ossified pelvic fin basipterygium discovered in the arthrodire Incisoscutum ritchiei was hypothesized to be identical in males and females, with males presumed to have an additional cartilaginous element or series forming a clasper. Here we report the discovery of a completely ossified pelvic clasper in Incisoscutum ritchiei (WAM 03.3.28) which shows that this interpretation was incorrect: the basipterygium described previously is in fact unique to females. The male clasper is a slender rod attached to a square basal plate that articulates directly with the pelvis. It carries a small cap of dermal bone covered in denticles and small hooks that may be homologous with the much larger dermal component of the ptyctodont clasper.

See also:

Abstractions, Nature 460, 780 (13 August 2009) | doi:10.1038/7257780b

Sharks: Missing Piece Of Fossil Puzzle Found, ScienceDaily (July 14, 2009)

Water striders are found all over the world, moving effortlessly over the surfaces of ponds, lakes and rivers. Fossil Gerridae and Hydrometridae date back to the Upper Paleocene and fossil Veliidae and Mesoveliidae have been discovered in Lower Cretaceous rocks. This implies an origin in the Middle Cretaceous or earlier followed by relative stasis. The insects belong to the Infra order Gerromorpha and all have piercing and sucking mouth parts. Although there is remarkable diversity of leg lengths and shapes, the group is distinguished by the relative lengths of their mid and hind legs. "The mid-legs are disproportionately long and function as oars, whereas the hind-legs are shorter and function as rudders."

A water strider showing its long mid-legs (source here)

The researchers were aware that the "Hox gene Ultrabithorax (Ubx) is known to play multiple roles in defining specific morphological differences among the segments along the anteriorposterior body axis in arthropods, including appendage size, shape, and function". Consequently, testing the role of Ubx became an objective of their research: does this gene affect the leg dimensions of these insects?

Of the three pairs of legs, the front legs are designated L1, the mid-legs L2 and the hind-legs are L3. In the presumed ancestor, the ground plan is L3>L2>L1. The Gerromorpha have L2>L3>L1. The changes are associated with adaptation: locomotion on water surfaces. The research involved mapping early stage development and identifying events where Ubx is expressed.

"Our results show that Ubx establishes the appendage ground plan in water striders through elongating L2, and through multiple functions that establish the identity of the third thoracic segment, including the shortening of L3. In other insects that present the common L3>L2>L1 appendage ground plan such as O. fasciatus and Acheta domesticus, Ubx is expressed in L3 only and functions to elongate its size. Therefore in the novel L2>L3>L1 ground plan of water striders, Ubx has evolved a new expression domain but maintained its ancestral elongating function in L2, whereas in L3, Ubx has maintained its ancestral expression domain but evolved a new shortening function."

In an accompanying press release, Professor Locke Rowe expresses surprise that the one gene had two opposite functions. At the present stage of the research, there is no insight yet into the way this gene operates and why it is different from other insect ground plans.

"To our surprise, we discovered that Ultrabithorax performs opposite functions in different limbs. It lengthens the mid-legs but shortens the hind-legs to establish this unusual body plan that allows water striders to glide on the water surface."

So far, so good. This is all interesting stuff. But then the focus shifts from development (involving empirical studies) to evolution (which goes into the realm of history). The press release continues:

"Determining how these major evolutionary changes happen is a central goal of evolutionary biology, explained Rowe. "Many have marveled at the ability of water striders to walk on water, and we are excited to have discovered the gene that has affected this evolutionary change." "

This research can be understood in terms of the evo-devo approach: small genetic changes affecting early development can achieve significant evolutionary transformations in adult organisms. Let us suppose that the authors are right in thinking that the "evolution of a novel appendage ground plan in water striders is driven by changes in the Hox gene Ultrabithorax". The novelty is in the relative lengths of the mid and hind legs. This is not a new organ and there appears to be no change in the complexity of the specified information.

We need to be realistic in our assessment of what has been achieved. In a blog, Cornelius Hunter writes about this research: "Incredibly, evolutionists were quick to add their gratuitous, scientifically meaningless, interpretation of the findings. [. . .] How cogent. This would be like entering an automobile manufacturing plant, finding the robot that installs the doors, and claiming to have discovered how the doors evolved." There are likely to be many other characteristics of water striders that need to be in place before there is a functioning organism. Perhaps these need to be analysed in some detail before getting too excited by the Ubx story.

Evolution of a Novel Appendage Ground Plan in Water Striders Is Driven by Changes in the Hox Gene Ultrabithorax
Abderrahman Khila, Ehab Abouheif, Locke Rowe
PLoS Genetics, 5(7): e1000583, 2009 | DOI: 10.1371/journal.pgen.1000583

Abstract: Water striders, a group of semi-aquatic bugs adapted to life on the water surface, have evolved mid-legs (L2) that are long relative to their hind-legs (L3). This novel appendage ground plan is a derived feature among insects, where L2 function as oars and L3 as rudders. The Hox gene Ultrabithorax (Ubx) is known to increase appendage size in a variety of insects. Using gene expression and RNAi analysis, we discovered that Ubx is expressed in both L2 and L3, but Ubx functions to elongate L2 and to shorten L3 in the water strider Gerris buenoi. Therefore, within hemimetabolous insects, Ubx has evolved a new expression domain but maintained its ancestral elongating function in L2, whereas Ubx has maintained its ancestral expression domain but evolved a new shortening function in L3. These changes in Ubx expression and function may have been a key event in the evolution of the distinct appendage ground plan in water striders.

See also:

Luke, K. U of T scientists identify gene that enables water striders to glide across water, University of Texas Press Release (August 13, 2009)

The general public is led to think that Charles Darwin magnificently solved the problems associated with the emergence of biological complexity. Many opinion-formers write confidently about the revolution triggered by the publication of "On the origin of species" in 1859. These people have developed a 'consensus' position which they use to convince scientific societies, policy makers, funding agencies and educationalists that any dilution of Darwinism is a retrograde step, ushering in a dark age for science. What will they make - and what will we make - of an essay in Nature Physics that talks about breaking with "many of the presuppositions of traditional evolutionary thinking" and highlights its message with these words:

"A coming revolution may go so far as to unseat Darwinian evolution as the key explanatory process in biology."

The dynamics of interacting populations of viruses and bacteria (Source here)

The essay is a contribution to cross-disciplinary thinking. It starts with an awareness of collective phenomena in modern physics. Thinking has moved away from reductionism and is adopting a holistic interactionism. The new focus is:

"- on the fundamentals of phase transitions and other ordering phenomena in condensed-matter systems, on pattern formation out of equilibrium, and on the rich cooperative dynamics of granular and glassy systems, polymers and other forms of 'soft matter', or charge carriers in high-temperature superconductors and other exotic materials."

The writer, Mark Buchanan, sees a parallel between physics and biology. The tools of physics and engineering are already being used to understand interacting networks within biological systems:

"It now seems clear that biology may also have a second act linked to the widespread importance of collective phenomena. The explosion of genetic and proteomic data, of course, has ushered in the era of systems biology, as biologists have come to recognize the need to gain a more holistic understanding of the functioning of organisms."

However, it is horizontal gene transfer that is perceived to be ushering in the overthrow of Darwinism. This is because all the mechanisms that are being seriously discussed to account for the data invoke environmental influences/drivers. Buchanan argues that the phenomenon can be regarded as confirmed, even though our understanding of mechanisms is in its infancy.

"The clear impact of horizontal gene transfer on bacterial evolution has been established only fairly recently using large-scale genome sequencing, and in the context of a small number of bacteria. Biologists have only begun exploring the various environmental factors that promote or limit horizontal gene transfer, and know almost nothing of how this mechanism of genetic sharing influences the overall logic of the evolutionary process itself."

Why does this take us beyond Darwinism? It is because the mechanisms of Darwinian evolution are inherently reductionistic, with individual life forms struggling for survival in competition with other individuals. Within Darwinian theory, the environment acts as a filter, allowing the fit to live on. Horizontal gene transfer (HGT) moves us away from individuals and towards breeding populations, and the environment becomes a driver of genetic change rather than a passive filter. The tree of life now looks like an unstructured bush (for more, see here).

"[T]he apparent ubiquity of horizontal gene transfer implies that microorganisms have an impressive capacity to actively alter their genomes in response to environmental stresses or opportunities, and this capability is intimately linked to their involvement in a larger community in which the diversity of genetic material resides. Consequently, [. . .] the basic concept of an organism as an isolated biological entity with a unique genetic make-up makes little sense in the bacterial world, as the genetic repertoire of an entire population, as well as foreign species, is available to any individual within it."

Talk of unseating Darwinian evolution has not gone down well with some. Larry Moran quotes some of Buchanan's visionary words and declares: "This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it." However, we could do with more substance in arguments against this essay. Darwinism is inherently reductionistic and it can devise ways of framing HGT to fit into its own mental models. But what it cannot easily do is adopt the holistic perspectives that are emerging everywhere. This is why some of us find a framework of design to be compelling. Design provides a coherent context for systems biology, for biomimetics, and for many other contemporary areas of research. Furthermore, although our understanding of HGT is imperfect and in its infancy, design thinking provides a warrant for inferring the origin of genes capable of being transferred, and for understanding the roles played by HGT in populations.

Collectivist revolution in evolution
Mark Buchanan
Nature Physics, 5(8), (August 2009), 531-531 | doi:10.1038/nphys1352 (Text here)

Last few sentences: The conjecture is that horizontal gene transfer was indeed required for the present genetic code to take the form it has, and that the emergence of life most likely went through a series of stages, with the early stage more Lamarckian in character, and only the latter stages becoming more Darwinian.
Exploring that point in greater detail will be a task for a new kind of biology, one that breaks with many of the presuppositions of traditional evolutionary thinking, and explores the potential for rich and surprising dynamics in a collective setting. It will almost surely benefit from the ideas and experience of physics, which has already experienced its own collectivist revolution.

Toucans are able to alter the flow of blood through their large bills, which make-up 30-50% of their body area. The effect is very significant: the toucan bill is now understood to make a major contribution to temperature regulation.

The Toco Toucan(Source and video here)

The newly published research needs to be considered in the context of history: for many people have wondered about the unusually large beak (the toucan has the largest bill relative to the body size of birds). The authors draw attention to previous speculation:

"In the hall of animal oddities, the toucan's enlarged bill is the avian example of exaggeration, being a source of debate since Buffon labeled it a "grossly monstrous" appendage. Even Darwin was intrigued, stating that "toucans may owe the enormous size of their beaks to sexual selection, for the sake of displaying the diversified and vivid stripes of colour with which these organs are ornamented". More recent explanations for the oversized bill include fruit peeling, nest predation, social selection in the context of territorial defense, and, finally, serving as a visual warning."

Since this is Darwin's year, it is worth highlighting his comments which were made as part of an argument for sexual selection. The justification of his interpretation is (a) that the idea is not incredible; and (b) that there is no greater improbability in thinking toucans have large beaks because of sexual selection than in thinking male pheasants should be "encumbered with plumes" for the same reason.

"This leads me to remark that it is not at all incredible that toucans may owe the enormous size of their beaks to sexual selection, for the sake of displaying the diversified and vivid stripes of colour, with which these organs are ornamented. The naked skin at the base of the beak and round the eyes is likewise often brilliantly coloured; and Mr. Gould, in speaking of one species, says that the colours of the beak "are doubtless in the finest "and most brilliant state during the time of pairing." There is no greater improbability in toucans being encumbered with immense beaks, though rendered as light as possible by their cancellated structure, for an object falsely appearing to us unimportant, namely, the display of fine colours, than that the male Argus pheasant and some other birds should be encumbered with plumes so long as to impede their flight."
(Darwin, C. R. 1871. The descent of man, and selection in relation to sex. London: John Murray. Volume 2. 1st edition. Chapter 16. The quoted words are on page 227).

The reason why many have not found this hypothesis convincing is that both male and female toucans excel in bill size, and both sexes have bills that are brightly coloured. The other hypotheses that have been explored have not fared any better. Take the fruit peeling idea: toucans eat fruit, but is there an advantage in having a large bill to do this? There are many other frugivorous birds, but none display notable large bills. Before moving on to consider the new research, it is worth pausing to reflect on the adaptationist paradigm. What Darwinists have done is persuade people to think that plausible speculations deserve to be considered as science. The tried-and-tested empirical approach is replaced by just-so stories, which become the basis of adaptationist 'science'. People have the view that Darwin's strength was his detailed knowledge of empirical observations, but this case may help to illustrate why this image is false. Darwin's theory did not emerge from the data but was brought in as an interpretative screen through which the data was viewed. There were numerous places where the fit was not good, but people did not perceive them because of Darwin's skill in telling persuasive stories.

The researchers have documented the function of thermoregulation after noting the network of blood vessels between the horny and bony parts of the toucan bill. They chose to work with the toco toucan because it has the largest bill of all the toucans.

"The bill has a network of superficial blood vessels supporting the horny ramphotheca. Therefore, the toucan's bill combines all the important features of a candidate thermal radiator: It is enlarged, uninsulated, and well vascularized. It is, however, crucial that blood flow be adjustable in order to control heat exchange from the bill. We examined whether the toucan's bill can operate as a thermal window for heat loss, capable of being "opened" within and above the thermal neutral zone and "closed" to conserve metabolic heat at lower temperatures. We used infrared thermography to examine the effects of changing ambient temperature on the heat exchange profile of different regions of the bird's body."

The findings were spectacular:

"The bill radiated a great deal of heat at high temperatures and when the toucan flew, indicating that, like elephants and rabbits do with their ears, the toucans flush their bills with blood to cool down. At lower temperatures, the difference between air temperature and bill temperature dropped, meaning that the toucans were restricting blood flow to their bills. Based on its size, a toucan's bill can theoretically account for anywhere from 5% to 100% of the bird's body heat loss [. . .]. When the toucan is in flight, its bill is the most efficient heat-shedder ever reported, losing four times more heat than the bird produces while at rest. That's about four times more efficient than either elephants' ears or ducks' bills."

The earlier explanations assumed adaptation, whether the trait is the consequence of sexual selection, fruit peeling, nest predation, social selection - territorial defense or visual warning. These analyses are now revealed as over-simplistic. They all assume that the only thing to be explained is the large bill. Once a driver for adaptive change is found, a new just-so story is invented. The new explanation is full of complexity: the bill has an internal structure involving vascularity, and the bird has the ability to control the flow of blood so as to achieve thermoregulation. This is an integrated system with feedback mechanisms - and this is not amenable to the 'one driver - one trait' mentality that has dominated the thinking of adaptationists. These systems, however, fit readily within the design paradigm because here we recognise complex specified information.

Heat Exchange from the Toucan Bill Reveals a Controllable Vascular Thermal Radiator
Glenn J. Tattersall, Denis V. Andrade, and Augusto S. Abe
Science, 325, 24 July 2009: 468-470.

Abstract: The toco toucan (Ramphastos toco), the largest member of the toucan family, possesses the largest beak relative to body size of all birds. This exaggerated feature has received various interpretations, from serving as a sexual ornament to being a refined adaptation for feeding. However, it is also a significant surface area for heat exchange. Here we show the remarkable capacity of the toco toucan to regulate heat distribution by modifying blood flow, using the bill as a transient thermal radiator. Our results indicate that the toucan's bill is, relative to its size, one of the largest thermal windows in the animal kingdom, rivaling elephants' ears in its ability to radiate body heat.

See also:

Price, M. A Bird With a Big Air-Conditioning Bill, ScienceNOW Daily News (23 July 2009)

Some icy winds are blowing through the corridors of academia. What we are seeing is the linking of the intellectual 'consensus' with power, peer esteem and funding. The freedom to follow the evidence wherever it leads is being steered into a 'freedom' to strengthen the consensus (but not to question it). These issues are raised in a retirement interview with Thomas Bouchard, the Minnesota psychologist known for his study of twins raised apart. He pointed out the way this was affecting his own discipline (although I'm omitting references to specific issues):

"But we still have whole domains we can't talk about. One of the great dangers in the psychology of individual differences is self-censorship." [. . .]
"But people had enormous amounts of data [showing this] that they didn't publish because it did not fit the prevailing belief system." [. . .]
"There are a lot of people who simply won't talk about those things. Academics, like teenagers, sometimes don't have any sense regarding the degree to which they are conformists."

The human face of academia - and of science (source here)

These issues were picked up by Nicholas Wade in The New York Times. He recognised that Dr Bouchard was describing a situation that is widespread.

"Journalists, of course, are conformists too. So are most other professions. There's a powerful human urge to belong inside the group, to think like the majority, to lick the boss's shoes, and to win the group's approval by trashing dissenters.
"The strength of this urge to conform can silence even those who have good reason to think the majority is wrong. You're an expert because all your peers recognize you as such. But if you start to get too far out of line with what your peers believe, they will look at you askance and start to withdraw the informal title of "expert" they have implicitly bestowed on you. Then you'll bear the less comfortable label of "maverick", which is only a few stops short of "scapegoat" or "pariah"."

Wade wanted to make the point that scientists are not exempt from this human tendency. Indeed, it is vital for science that they guard against it.

"Conformity and group-think are attitudes of particular danger in science, an endeavor that is inherently revolutionary because progress often depends on overturning established wisdom." [. . .]
"The academic monocultures referred to by Dr. Bouchard are the kind of thing that sabotages scientific creativity."

A bit of history of science will help here. Why is it that science did not flower after the young plant started so well among the ancient Greeks? Why did Islamic science falter in the Middle Ages? Why did Chinese science not get beyond some promising technological innovations? The answer is that in each case, the thinking of the scholars was dominated by a consensus ideology. Instead of testing ideas by reference to the natural world, they showed their allegiance was to Aristotelian philosophy (or to the equivalent in the cases of the Arab and Chinese cultures). Why did science develop in 17th Century Europe? It is because the scientists were consciously throwing off Aristotelianism and resolving to test their theories of the natural world by reference to observations of nature. The experimental method was the hallmark of their enquiries. Many have seen the Christian culture of those days as the handmaiden to science: they had come to distrust the unaided power of the human mind. One such scholar is Peter Harrison, whose book The Fall of Man and the Foundations of Science brings a refreshing perspective on this period of history:

"The strength of Harrison's argument is his insistence that experimental science grew out of the acute awareness that attaining knowledge is not an easy, natural process. In a postlapsarian world, strategies must be devised to overcome the inherited infirmities of original sin, as well as circumscribe the difficulties of apprehending nature, which had become less intelligible since the Fall. A scientist would have to create controlled environments so that experiments could be performed and repeated, and naturalia observed and described."

We need a fresh appraisal of developments in contemporary society. Scientists who step outside the 'consensus' are given a rough ride. Science leaders are being perceived by the public as arrogant. They are behaving like priests who understand their role to dispensers of knowledge. Bill Dembski refers to a "powerful new caste of scientists who have appointed themselves the guardians of humanity and the priests of a new social order." He continues:

"Scientists are as fallible as the rest of us, as are their scientific theories. Indeed, the history of science is filled with failed scientific theories that once were confidently asserted and now have been radically modified or even abandoned (see Thomas Kuhn's "The Structure of Scientific Revolutions"). The new scientific priesthood, however, has raised the stakes considerably for the mischief that science can do. In claiming to find and then resolve problems that threaten to overwhelm humanity, they have invaded the political scene, commanding vast research moneys and attempting to force on the wider population government-sanctioned programs for social control."

In the light of these trends, it is not surprising that ID scientists are regularly portrayed as enemies of reason and as subversive influences in the academic world. He/she who has eyes to see, let them see.

Behavioral Geneticist Celebrates Twins, Scorns PC Science
Constance Holden
Science 325, 3 July 2009, 27 | DOI: 10.1126/science.325_27 (restricted access)

Last month, the Behavior Genetics Association held its annual meeting in Minneapolis, home of the world-famous Minnesota Study of Twins Reared Apart. Attendees took the occasion to honor psychologist Thomas Bouchard, the man who started it all. Bouchard, 71, is retiring after 40 years at the University of Minnesota, Twin Cities, and has moved to Steamboat Springs, Colorado. Bouchard spoke with Science at the meeting; his comments have been edited for clarity and brevity.

See also:

Wade, N. Researcher Condemns Conformity Among His Peers, The New York Times, (Tierneylab, 23 July 2009).

Popular science magazines, television programmes and many educational resources convey the message that birds are descendants of the dinosaurs. Every year brings new evidence from the Jehol Biota of northeastern China that is claimed to strengthen the scientific case. Feathered dinosaurs have started to adorn the pages of National Geographic and elsewhere. A lavishly illustrated book with the title Feathered Dinosaurs has been published recently by Oxford University Press. For many the issue is settled: any dissent is regarded as inexcusable. So it is noteworthy that a leading dissenter, Alan Feduccia (from the Department of Biology, University of North Carolina), has reviewed the book in Trends in Ecology & Evolution.

A picture is worth a thousand words - but is it true? (source here)

As many are aware, the Jehol Biota includes avian fossils, but these have not gained the headlines. Proto-feathers and dino-birds have been centre stage. Feduccia notes:

"New tantalizing material has resulted in unprecedented understanding of the early avian radiation, but has also provided a bonanza for paleontological speculation and controversy."

After a few complimentary words, Feduccia switches on critical analysis mode. He points out that the selective reading of evidence, together with ignoring of counter evidence, has led to an imaginary world masquerading as science.

"Although Long and Schouten promote the orthodoxy of 'feathered dinosaurs', compelling evidence for any proto-feathers in these fossils has always been lacking, and new evidence shows that the filamentous fibers on the small 'feathered dinosaur' Sinosauropteryx represented a complex mesh work of supportive skin collagen fibers; and the body outline on the specimens encloses the fibers. Furthermore, new evidence suggests that feathered microraptors and other groups of plumed maniraptorans are derivatives of the early avian radiation that produced an aviary at all stages of flight and flightlessness."
"The small theropod Compsognathus, 'compys' of Jurassic Park, is depicted with a covering of down-like proto-feathers, and modeled after the roadrunner; it is given an expanded throat sac 'critical for temperature regulation' and a pattern of small spots and bars for camouflage. Yet, there is no evidence for any type of feathers in the 'compys' (and, in fact, evidence to the contrary) or for endothermy; unfortunately, no references are provided in the text to papers marshalling evidence contrary to the dogma of feathered dinosaurs, part of an alarming trend in paleontology towards censorship by lack of citation."

Feduccia considers that history is repeating itself. In the 1860s, "Thomas Huxley envisioned a dinosaurian origin of birds via the flightless ratites" but was effectively rebuffed by Richard Owen who pointed out that the ratites were derived forms, with pedomorphic traits. This was confirmed in 1956, in the work of Gavin de Beer.

"[Owen's] statement should also provide a cautionary note for advocates of today's bird origin orthodoxy, which, among myriad problems, calls for all the sophisticated avian aerodynamic flight architecture to have evolved as exaptations, in earth-bound theropod dinosaurs: '. . . science will accept the view of the Dodo as a degenerate Dove rather than as an advanced Dinothere.'"

The closing paragraph returns to an appreciation of the book, and ends with a sentiment that will be shared by many:

"Feathered Dinosaurs is, despite my reservations on interpretation, a beautiful book, and the life poses of the Mesozoic menagerie are dazzling. The 'Fantasia' of feathered theropods aside, depictions of the Early Cretaceous birds are truly exceptional, the best to date. I particularly recommend the images of the flightless oviraptorosaurs. Hopefully, this book will help lead a new generation of students to go beyond the current unchallengeable orthodoxy of feathered dinosaurs to unravel the long-kept secrets of the Mesozoic."

A colorful mesozoic menagerie
Alan Feduccia
Trends in Ecology & Evolution, 24(8), August 2009, 415-416 | doi:10.1016/j.tree.2009.03.002

Review of:
Feathered Dinosaurs: The Origin of Birds by John Long, illustrated by Peter Schouten. Oxford University, Press. 2009. hbk (280 pages) ISBN 978 0 19 537266 3

See also:

Tyler, D.J. Dino skin shows no trace of protofeathers, ARN literature Blog (11 January 2008)

According to C.R.C. Paul, "the search for gradual change in the fossil record is a cautionary tale". The instigator of the search was, of course, Charles Darwin, whose theory predicted that a pattern of small incremental changes would be found in the fossil record as well as in contemporary life forms. It is well known that Darwin did not find what he was looking for. On the Origin of Species included a whole chapter (X) to explain how the theory could be reconciled with the fossil record, using the argument of its "extreme imperfection". This argument held sway for over 100 years. Palaeontologists adopted Darwin's explanation, presenting the few cases of gradual change that they did manage to identify as a great achievement.

[Paul refers to the] "belief that the fossil record should contain abundant evidence of gradual evolutionary (i.e. morphological) change, which we all accepted (myself included) until Eldredge and Gould (1972) proposed the alternative punctuated equilibrium model."

The fossil record provides an important test for Darwinian gradualism - but what weight can we give to the evidence we find? (Source here)

During this 100 year period, some examples of "genuine evolutionary trends" were reported but, Paul points out, "there are far too few of them". Even the classic trend examples "do not bear close scrutiny". The cases of Micraster, Zaphrentis and Gryphaea are not as robust as once was thought.

"[F]or over 100 years palaeontologists sought examples of evolutionary trends in the fossil record and yet they remain stubbornly rare. In contrast, no one reported examples of stasis during this interval. We did not even have a name for lack of morphological change - it was regarded as lack of information."

So strong was the focus on gradual change that few found morphological stasis interesting. It was not even deemed worthy of reporting. Published litereature became biased in favour of gradual transformation. A major characteristic of the fossil record - stasis - was neglected until Eldredge and Gould launched Punctuated Equilibrium in 1972.

"In over a century the very rare examples that were found were accepted as evidence of a general pattern in the fossil record, whereas the more abundant patterns, unbiased random walks and stasis, were ignored. The analyses of Paul (1999) and Hunt (2006, 2007) are very different, yet both agree that trends are rare in the fossil record. With the benefit of hindsight it seems amazing that it took so long for us to recognize that the vast majority of fossil species do not change significantly throughout their stratigraphical ranges."

Paul draws attention to the analytical approach of Hunt, whose methods are described as "robust".

"Hunt (2007) analysed the frequency of the three patterns in a large sample (251 characters in 51 taxa), covering benthonic and planktonic microfossils and macrofossils (mammals, fish and molluscs), as well as size, shape and other characters. He found that in only 13 characters (5.2%) was directional change (trends) best supported, whereas unbiased random walks and stasis were best supported in 123 (49%) and 115 (45.8%) cases. Hunt commented that since there was an historical bias in favour of trends, 5% was probably an overestimate."

The remainder of Paul's paper is concerned with the probability of fossilisation. He concludes that most animals with skeletons are likely to have become fossilised. Impoverishment of the record is linked to active erosion of fossiliferous strata.

Darwin regarded the fossil evidence as potentially providing a valid test of his theory. He predicted gradual transformation. Since he did not observe it, he invoked "extreme imperfection" to preserve the theory. This explanation is no longer credible. The fossil record must now stand as evidence that refutes Darwinian gradualism. Those examples of gradual morphological change represent, at best, 5% of observed trends, but it is possible they are simply extreme cases of random walk trajectories. In a eureka moment of clear thinking, Stephen Jay Gould declared that Neodarwinism "as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy". Those who represent analyses like this as religiously motivated and out of bounds for consideration in school science lessons are doing a great disservice to education and to the students they claim to be defending.

The Fidelity of The Fossil Record: The Improbability of Preservation
C. R. C. Paul
Palaeontology, May 2009, 52(3), 485-489 | doi 10.1111/j.1475-4983.2009.00872.x

Abstract: The fidelity of the fossil record reflects how accurately it preserves the history of life. Since Darwin's time any mismatch between our theories and the fossil record has been attributed to the imperfections of the record. For over a century scarcity of gradual evolutionary trends was explained in this way until the punctuated equilibrium model was proposed. A null hypothesis that all morphological patterns in the fossil record are unbiased random walks can be rejected because it predicts far more apparent trends than exist. Current best estimates suggest that trends occur in at most 5% of characters. When an organism dies either it becomes fossilized or it doesn't. To be confident a species has not been preserved the probability against preservation must be significantly larger than the total number of individuals of that species that ever existed. For skeletized species preservation was the norm not the exception. Nevertheless, fossils must then avoid subsequent destruction and be discovered to be useful.

See also:

Gould, S.J. The Structure of Evolutionary Theory, Harvard University Press, 2002, page 1004 (for reflective comments on the effective death of Neodarwinism quote).

Hunt, G., 2007. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proceedings of the National Academy of Sciences of the United States of America, 104(47), (November 20), 18404-18408 | doi: 10.1073/pnas.0704088104

Synopsis Of The Second Chapter Of Nature's IQ By Balazs Hornyanszky and Istvan Tasi
ISBN 978-0-9817273-0-1
By Robert Deyes
ARN Correspondent

Defense, Disguise, Perception is the descriptive title that Hornyanszky and Tasi have chosen for the second chapter of their book Nature's IQ. And the delivery of the facts is as convincing and thought-provoking as ever. Coupled with its vivid illustrations, the chapter lays out a set of arguments that are easily accessible to the expert and non-expert reader alike. The underlying principle of their text is simple- intelligent design lies at the heart of many of nature's phenomena.

As Hornyanszky and Tasi show from the onset, the natural world is replete with innovative defense mechanisms that afford potential prey with the protection they need. For many of those doing the eating, an aversion towards highly toxic prey such as the poisonous sea snake is one that is deeply ingrained into their instinctive fabric. It has to be. After all, one bite-sized morsel taken out of a creature such as a sea snake would be lethal to most prospective predators. The fire-bellied toad cautions all who might dare nibble at its poisonous flanks by flipping onto its back and displaying the red and black markings on its belly.

Warning-style markings are of course common-place throughout nature as are rapidly deployed disguises or masquerades that ward off would-be attackers. Many a high school student will learn about eye spots on moth and butterfly wings, designed as they are to give the impression that a much larger, potentially dangerous beast lies waiting. Bearers of such disguises often times exhibit associated behaviors only showing their disguises when threatened. The copper-band butterfly fish has the astonishing ability to move backwards so as to make the eye spot on its large tail look as if it really is at the front.

In the case of the American four-eyed frog, white and black nodes on its back stand out as realistic three-dimensional imitations of much larger mammalian and cephalopod eyes. These frogs exhibit the extraordinary ability to turn their backs to wherever danger is lurking, lifting their hind legs into a position that makes their fake eyes look all the more face-like and therefore less enticing for the hungry onlooker. For evolution pundits this theatrical act defies their version of the story of life since, in the words of Hornyanszky and Tasi "the simultaneous appearance, via chance mutations, of the pseudo-eyes and the knowledge of just what to do at precisely the right moment is, to put it mildly, highly improbable" (p.30).

As artful masters of disguise go, the treehopper Umbonia spinosa takes some beating. Making the most out of its thorn-like dorsal protrusion, this particular insect instinctively flattens its underlying body against the stems of rose bushes to avoid detection. The Atlantic Halibut about which Darwin himself wrote in The Origin Of Species, maintains its anonymity by also lying flat, camouflaged against the sand covered sea bottom. How would either of these creatures know that to lie still in their respective environments is the best way to eschew the grasp of a predator?

For these and all their earlier examples, Hornyanszky's and Tasi's intelligent design inference shines through as they reason in favor of irreducibly complex, genetically inherited systems that require both phenotypic and behavioral traits in order to achieve their respective functions. Knowledge of the most appropriate behaviors is not something that is learned but rather is genetically hard-wired into these creatures from birth. In order for such behaviors to be effective, they must have appeared in tandem with the phenotypic traits with which they are so evidently associated. Therein lies the designed IQ that we observe in many fauna.

Horyanszki's and Tasi's superb treatise is a 'must read' for all who are interested in the ongoing debates over the origin of animal behaviors. It is bound to shake the unquestioned acceptance of the Darwinian story of life that today pervades many a field of science.

For more information and to order Nature's IQ go to http://www.arn.org/arnproducts/php/book_show_item.php?id=129

Foraminifera are protozoans with a hard calcareous shell. There are two major groups: benthic and planktic. Benthic organisms live on the sea floor whereas planktic are buoyant and live in the upper water layer as part of the plankton. Their shells, although mostly microscopic, are much studied because they are found in profusion in oceanic sediments. The geological history of the benthic forams goes back to the Early Cambrian, but planktic species first appear in Mid-Jurassic sediments.

"Traditionally, all planktic foraminifera have been seen as monophyletic [Suborder Globigerinina], descended from a single Early-Middle Jurassic ancestor, similar to the monophyletic origins of other planktic groups."

Streptochilus globigerus (credit: Kate Darling, source here)

Six years ago, Hart and colleagues reviewed evidence bearing on the ancestor of the planktic forams and suggested that its evolution was triggered by an oceanic anoxic event in the Early Jurassic. They introduce their paper with an acknowledgement of the problems:

"In a recent review of the earliest planktic Foraminifera (Globigerinina) Simmons et al. (1997) report that the origins of the group are '. . . still shrouded in uncertainty'."

The new research by Darling and colleagues has found that a planktic species, Streptochilus globigerus, is genetically the same as a benthic species, Bolivina variabilis. This is the first time such a lifestyle has been recognised in foraminifera. The technical term is tychopelagic.

"The word "tychopelagic" is used to describe organisms that usually live as benthos but can survive and grow in fairly large numbers as plankton and may be advected well offshore into open ocean assemblages. Such a lifestyle is known from diatoms, but until now has never been documented for foraminifera."

The implications are many. First, the sharp line drawn between benthic and planktic forams needs to be erased. The issue of buoyancy suddenly becomes secondary. The previous stance - that planktic forams were a radical evolutionary innovation - needs to be discarded. "Interestingly, buoyancy is generally assumed to be one of the major constraining evolutionary traits on the passage from benthos to plankton."

Secondly, the monophyletic radiation of planktic forams, with examples of both punctuated and gradual changes, needs to be re-examined. If tychopelagic forams are common, everything goes into the melting pot.

"The Cenozoic planktic foraminiferal phylogeny of microperforates, the group containing biserial and triserial forms, has generally presented taxonomists with problems. Many of these genera and species show discontinuous stratigraphic records, making ancestor-descendant patterns difficult to reconstruct. This could be the result of a lack of observation of the small forms, in a size fraction that commonly is not included in study. In our view, however, such ancestor-descendant relations simply do not exist."
[. . .]
"Appearances of biserial and triserial planktic forms in the geological record should therefore not be considered as necessarily discrete punctuated evolutionary events but as a series of excursions of expatriated tychopelagic microperforates into the planktic domain."

Thirdly, the concept of recolonisation has been underplayed by evolutionary biologists. They get as far as colonisation, but perceive this as a process of gradual adaptation under the influence of natural selection. They have given little thought to inbuilt capabilities of rapid adaptation to new environments - perhaps because this could be understood as a designed capability. Nevertheless, the authors of the new research recognise the ecological advantages possessed by tychopelagic organisms.

"The ability to survive in both planktic and benthic habitats should be seen as an extraordinary ecological adaptation for long-term survival. After mass extinctions in the plankton, e.g., as caused by bolide impacts and oceanic anoxic events, tychopelagic species are able to repopulate the pelagic realm and evolve into purely planktic forms."
[. . .]
"We thus argue that radiation and repopulation of the empty niche in the plankton after the end Cretaceous mass extinction may at least in part have occurred from benthic tychopelagic species rather than from nerito-planktic ones."

This research provides another angle on the hypothesis outlined in a previous blog that the fossil record has more to do with ecology and the colonisation/recolonisation of habitats than it has to do with evolutionary transformation.

Surviving mass extinction by bridging the benthic/planktic divide
Kate F. Darling, Ellen Thomas, Simone A. Kasemann, Heidi A. Seears, Christopher W. Smart and Christopher M. Wade
Proceedings of the National Academy of Sciences USA, online before print July 2, 2009, doi: 10.1073/pnas.0902827106 (abstract)

Abstract: Evolution of planktic organisms from benthic ancestors is commonly thought to represent unidirectional expansion into new ecological domains, possibly only once per clade. For foraminifera, this evolutionary expansion occurred in the Early-Middle Jurassic, and all living and extinct planktic foraminifera have been placed within 1 clade, the Suborder Globigerinina. The subsequent radiation of planktic foraminifera in the Jurassic and Cretaceous resulted in highly diverse assemblages, which suffered mass extinction at the end of the Cretaceous, leaving an impoverished assemblage dominated by microperforate triserial and biserial forms. The few survivor species radiated to form diverse assemblages once again in the Cenozoic. There have, however, long been doubts regarding the monophyletic origin of planktic foraminifera. We present surprising but conclusive genetic evidence that the Recent biserial planktic Streptochilus globigerus belongs to the same biological species as the benthic Bolivina variabilis, and geochemical evidence that this ecologically flexible species actively grows within the open-ocean surface waters, thus occupying both planktic and benthic domains. Such a lifestyle (tychopelagic) had not been recognized as adapted by foraminifera. Tychopelagic are endowed with great ecological advantage, enabling rapid recolonization of the extinction-susceptible pelagic domain from the benthos. We argue that the existence of such forms must be considered in resolving foraminiferal phylogeny.

See also:

Tiny marine organism lives double life to survive extinction, Planet Earth Online, 1 July 2009.

Hart, M.B., Hylton, M.D., Oxford, M.J., Price, G.D., Hudson W. and Smart, C.W., The search for the origin of the planktic Foraminifera, Journal of the Geological Society, 160, 2003, 341-343.

More and more people are realising that the living world is like a treasure trove packed full with engineering marvels. The agenda of biomimetics is to actively research the potential of applications inspired by animals and plants. The human body supplies some of these design ideas, and the one considered in this blog concerns the inner ear, or cochlea. Undoubtedly, researching organs like this leads to a new appreciation of the sophistication of biological systems.

Sound is collected in the outer ear, travels through the ossicles (or bones) of the middle ear and delivers pressure waves through the oval window of the cochlea (the inner ear) (Source here)

The people involved in the newly published work describe the cochlea as "an amazing sensory instrument that transforms sound frequencies into spatially and temporally-varying excitation patterns of the auditory nerve". It is particularly interesting to electrical engineers because: "It performs this task over a wide range of input frequencies and amplitudes using very little power. In humans, the approximate values of these performance metrics are three decades, 120 dB, and 14 W, respectively". The mechanism is described thus:

"The cochlea is a hydro-mechanical system; incoming sounds set up travelling waves on the basilar membrane (BM) and in the fluids that surround it. The properties of the BM scale approximately exponentially with position: The membrane gradually becomes wider and less stiff, and resonates at lower frequencies. Thus, high frequency sounds excite responses towards the beginning, or basal part, of the cochlea, while low frequency sounds excite responses towards the end, or apical part. In other words, the cochlea uses a frequency-to-space transformation to perform audio spectral analysis."

There is broader medical interest in any research with potential relevance to problems of deafness. Cochlear implants have been available for some years. They give some benefit to people whose hearing is impaired, but do not restore normal hearing. Electrodes are implanted to stimulate the the cochlear nerves using electrical impulses generated from sound reaching the subject. For an brief overview of the history of cochlea implants, go here. For more technical information, a paper by Kissiah (2007) is helpful.

However, medical applications are beyond the scope of the reported research. The researchers have their sights on constructing an electronic cochlea - not implanting electrodes but making a complete system. They are interested in radio-frequency devices, not audio-frequency applications. Their goal is to achieve a high speed of operation, an ability to handle a wide range of input frequencies and a reduced power requirement in use.

"The human ear is a very good spectrum analyzer," said Rahul Sarpeshkar, a professor at MIT who co-authored the paper [. . .]. "We copied some of the tricks the ear does, and mapped those onto electronics."
[. . .] To detect electromagnetic waves instead of pressure waves the MIT scientists used circuits, in place of cilia. Starting on the outside edge of the 1.5-mm by 3-mm-chip are tiny squares, each one corresponding to a different size radio wave.
As they spiral into the center, the squares become larger and larger. The outer spiral detects the highest energy, shortest frequency waves, while the center circuits detect less energetic, longer frequency waves.

The team have produced an "electromagnetic ear". This detects a very wide range of frequencies with no more energy than is used by a typical cell phone. What they have done is to combine an analogue spectrum analyser with digital signal processing. This reduces the power requirement to about 1% of a purely digital system.

"A simple cell phone takes 300 millivolts to detect one carrier wave," Sarpeshkar said. "We can do all 50 carrier frequencies with 300 millivolts." Other devices do exist that can examine a range of radio frequencies. They just require much more power to do so. The low power usage of the electromagnetic ear means it would be ideal for portable electronic devices.

One assessment of this work is as follows: "People have tried to construct electronic cochlea before, but this is the first demonstration that imitates the amplification we think happens in the ear to produce a device that works." The team is now working on RF transmission as well as signal analysis, because this has the best potential for commercial exploitation.

Since the discovery of DNA, it has been increasingly popular to refer to life as "digital". Darwinists, particularly, have latched onto this concept, because their mechanism (incremental changes filtered by natural selection) can be understood in terms of digital mutations. Artificial life software like Avida is 100% digital, and enthusiasts consider that their digital world gives them the power to experiment in an unprecedented way. One researcher, Richard Lenski, is quoted thus:

"It's also the power to manipulate almost any variable one can imagine, to measure variables with absolute precision, to store information that then allows one to trace back a complex chain of events, and to take evolved organisms and subject them to new sorts of analyses that one might not even have anticipated when first collecting the data."

But what if life is both digital and analogue? What if analogue information is independent of digital information? These are questions that Darwinians do not ask because they stretch beyond the horizon of the gradualist paradigm. What if analogue systems point to complex specified information that cannot be modified gradually without ruining functionality? The case of the RF silicon cochlea is significant. This device was only developed by the focused effort of intelligent design engineers. When we consider the human cochlea, we need to ask the question whether it could have been developed by digital tinkering or whether the sophisticated design principles embedded in the physical structure of the organ point to an explanation involving intelligent agency.

A Bio-Inspired Active Radio-Frequency Silicon Cochlea
Mandal, S.; Zhak, S. M.; Sarpeshkar, R.
IEEE Journal of Solid-State Circuits, June 2009, 44(6), 1814-1828 | doi: 10.1109/JSSC.2009.2020465

Abstract: Fast wideband spectrum analysis is expensive in power and hardware resources. We show that the spectrum-analysis architecture used by the biological cochlea is extremely efficient: analysis time, power and hardware usage all scale linearly with N, the number of output frequency bins, versus Nlog(N) for the Fast Fourier Transform. We also demonstrate two on-chip radio frequency (RF) spectrum analyzers inspired by the cochlea. [. . .] Our work, which delivers insight into the efficiency of analog computation in the ear, may be useful in the front ends of ultra-wideband radio systems for fast, power-efficient spectral decomposition and analysis. Our novel rational cochlear transfer functions with zeros also enable improved audio silicon cochlea designs with sharper rolloff slopes and lower group delay than prior all-pole versions

See also:

Bland, E. Human ear inspires universal radio antenna, Discovery Channel (June 8, 2009)

Is Life Analog or Digital? A Question for Edge discussion group from Freeman Dyson (2001)

Paul Knauth and Martin Kennedy have been studying isotopic signatures in carbonate sediments. Indeed, they have "examined the chemical composition of all known limestones dating from the Neoproterozoic era, which stretched from 1 billion years ago up to the start of the Cambrian." The ratio of carbon-13 to carbon-12 is a frequently measured parameter, because plants preferentially absorb carbon-12. Similarly, freshwater is depleted in oxygen-18, oxygen isotope ratios are also interesting. "So sediments deposited in these conditions have a recognisable carbon-12 to oxygen-18 ratio." Significantly, the authors report that the 'modern' signature for land-derived sediments goes back - not to the Ordovician (where the record of land plants begins) - but to 850 Ma (which is Late Precambrian).

"Knauth says the balance of carbon-12 to oxygen-18 in the limestones is "screaming" that they were laid down in shallow seas that received extensive rainwater run-off from a land surface thick with vegetation."

"Screaming" is a strong word, but data itself does not scream. An interpretation placed on that data, however, can provide a compelling argument. The question to be addressed is whether that argument is strong, or whether the researchers are just shouting.

Was a moss and liverwort filled world responsible for oxygenating the atmosphere? (Source here)

There are several strands for analysis in this research. The first is whether the isotope ratios are best interpreted in the terms suggested. As well as the positive evidence from isotope fractionation, the researchers report finding a sparsely populated area of their data plots - which they named the "forbidden zone."

"If previous interpretations of carbon isotope data were correct, there would be no forbidden zone on these cross plots," Knauth said. "The forbidden zone would be full of Neoproterozoic data."
"These zones show that the isotopic fingerprints in limestone we see today started in the late Precambrian and must have involved the simultaneous influx of rain water that fell on vegetated areas, infiltrated into coastal ground waters and mixed with marine pore fluids. During sea level drops, these coastal mixing zones are dragged over vast geographic regions of the flooded continents of the Neoproterozoic," Knauth said. "Vast areas of limestone can form in these mixed pore fluids."

It will be interesting to find out what others make of this interpretation, but my initial reaction is that the argument is strong. The main objection thus far appears to be the lack of fossil evidence for vegetated land surfaces. This blog proceeds on the basis that the researchers have documented isotopic evidence strongly suggesting vegetated areas in the Neoproterozoic.

The second strand of analysis is concerned with the relationship between the evidence for vegetated land and the Cambrian explosion. The abstract includes the comment: "This facilitated a rise in O2 necessary for the expansion of multicellular life". The paper expands slightly with the words: "The terrestrial expansion of an extensive, simple land biota indicated by the isotope data may thus have been a critical step in the transition from the Precambrian to the Phanerozoic world". The press release accompanying advance publication says that the researchers "believe they have found the trigger for the Cambrian explosion". This, and the Science Daily reports suggest that the problem of the Cambrian Explosion may have been solved. "It was a massive greening of the planet [that] virtually set the table for the later explosion of life through the development of early soil that sequestered carbon, led to the build up of oxygen and allowed higher life forms to evolve". The New Scientist story says that the plants "turned the hitherto barren Earth green, created the first soils and pumped oxygen into the atmosphere, laying the foundations for animals to evolve in the Cambrian explosion that started 542 million years ago".

It has to be said that the Cambrian Explosion needs to be addressed on two fronts: biological and environmental. The new work adds nothing to the conundrums faced by biological science: the emergence of new body plans, complex organs and organelles. What it does do is contribute to the environmental story. If marine animals are to thrive, they need oxygenated waters. Accompanying this is the need for conducive water chemistry, suitable temperatures, appropriate food supplies, etc. Nevertheless, with these elements all present, life will not simply emerge to fill the space! To think this is to make the same mistake as the abiogenesis researchers who seem to think that if the building blocks are assembled, life just happens! The same problem is faced by astrobiologists: they get excited about finding a planet in the habitable zone with water - but this is just the environmental dimension. It provides a necessary but not sufficient condition. Real solutions are only obtained by the generation of complex specified information - which is the hallmark of intelligent design.

If it is the case that biological diversification is triggered by environmental factors, it can be argued that this is an indication of design in the workings of the natural world. Create a suitable environment, and it is filled with living things! Maybe the story of life on Earth is governed by ecology: where conditions are appropriate, the animals and plants that can live in those environments move in to colonise them. Ecology, rather than evolution from primitive ancestors, may be the key to understanding the development of living things.

The late Precambrian greening of the Earth
L. Paul Knauth & Martin J. Kennedy
Nature advance online publication 8 July 2009 | doi:10.1038/nature08213

Many aspects of the carbon cycle can be assessed from temporal changes in the 13C/12C ratio of oceanic bicarbonate. [. . .] Here we compile all published oxygen and carbon isotope data for Neoproterozoic marine carbonates, and consider them in terms of processes known to alter the isotopic composition during transformation of the initial precipitate into limestone/dolostone. We show that the combined oxygen and carbon isotope systematics are identical to those of well-understood Phanerozoic examples that lithified in coastal pore fluids, receiving a large groundwater influx of photosynthetic carbon from terrestrial phytomass. Rather than being perturbations to the carbon cycle, widely reported decreases in 13C/12C in Neoproterozoic carbonates are more easily interpreted in the same way as is done for Phanerozoic examples. This influx of terrestrial carbon is not apparent in carbonates older than ~850 Myr, so we infer an explosion of photosynthesizing communities on late Precambrian land surfaces. As a result, biotically enhanced weathering generated carbon-bearing soils on a large scale and their detrital sedimentation sequestered carbon. This facilitated a rise in O2 necessary for the expansion of multicellular life.

When Earth greened over
Explosion of animal life could have been triggered by blanket of vegetation.
Eric Hand
Nature 460, 161 (8 July 2009) | doi:10.1038/460161a

Abstract: A thick, green carpet of photosynthetic life, on the scale of that seen today, exploded across Earth 850 million years ago - much earlier than thought - a new study suggests.

Professor Michael Reiss is Director of the Institute of Education, University of London. He gained notoriety last year for being sacked by the Royal Society for failing to say the 'right' things about creationism and ID in the context of school science education. Previous blogs have covered this story: here and here.

A new paper in the journal Evolution provides an opportunity to restate or retract. Reiss is unrepentant - he restates his case! His critics are almost all advocates of the "conflict" view of the relationship between science and religion. Ian Barbour is quoted approvingly: "In scientific materialism, science swallows religion. In biblical literalism, religion swallows science." There are strengths and weaknesses in Reiss' paper and this blog seeks to provide some constructive discussion of relevant issues.

Mirror, mirror on the wall - How do I look? (source here)

In his discussion of the nature of science, Reiss draws attention to the work of Robert Merton and Karl Popper. Whilst there is much of value here, he writes, "most historians and philosophers of science would argue that there is more to the nature of science". He considers the "seminal contributions" of Thomas Kuhn and the concept of scientific paradigms, plus the related analysis of research programs by Lakatos. More recently, science has become "more influenced by politics; it is more industrialized; and it is more bureaucratic." Then comes the conclusion:

"The effect of these changes is to make the boundaries around the city of science a bit fuzzier. [. . .] Of course, if one accepts the contributions of the social study of science one finds these boundaries fuzzier still."

Whilst all this is helpful, it is not clear to me how this affects the subsequent argument of the paper. The paradigms affecting evolutionary biology are not analysed; nor the research programs of scientists involved with origins research. The fuzzy boundaries are not mentioned again. Reiss could have taken the opportunity to show the defenders of "scientific materialism" where they fit into the analysis - thereby constricting their comfort zone - but he does not. Later, he says that creationism "is not really a science in that its ultimate authority is scriptural and theological rather than the evidence obtained from the natural world". Creationists, of course, do not see any incompatibility between their ultimate authority and working with evidences from the natural world - but that is another discussion. If ultimate authority is an issue, what can be said of the many advocates of "scientific materialism"? What shall we make of Richard Lewontin's oft-quoted maxim: "Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door."? Does this statement imply that Lewontinism 'is not really a science in that its ultimate authority is philosophical materialism rather than the evidence obtained from the natural world'?

Let us move on to the worldview issue. Reiss draws on the work of others to provide a working definition: "A worldview constitutes an overall perspective on life that sums up what we know about the world, how we evaluate it emotionally, and how we respond to it volitionally." He applies this to student convictions about creationism or intelligent design, recognising that these students are not just confused about the details.

"A value of the worldview perspective is that it indicates the extent to which a belief in creationism or intelligent design for many students is not just a simple misconception to be remedied by some straightforward science teaching, as a belief that most of the mass of a plant comes from material extracted from soil might be, but rather a whole way of understanding the world - a "world view"."

The implications for science teaching are far reaching. It means that conflict strategies are counter-productive because students find them threatening and this is not a good learning environment. Teachers need to realise that they are there to teach, not to indulge in personal crusades against what they perceive as nonsense and ignorance.

"I do believe in taking seriously and respectfully the concerns of students who do not accept the theory of evolution while still introducing them to it. Although it is unlikely that this will help students who have a conflict between science and their religious beliefs to resolve the conflict, good science teaching can help students to manage it - and to learn more science."

There is wisdom in this approach. The problem comes if teachers (or the scientific community) think that they do not need to think about their own worldviews and their effect on scientific work. So often, teachers and science leaders retreat into a positivist stronghold and embark on a discourse to emphasis their objectivity. They completely forget Reiss' earlier discussion of the nature of science. Unfortunately, Reiss also appears to overlook the wider relevance of these issues. This point is picked in a blog on the Truth in Science web site:

"What is disappointing is that Reiss, in common with most evolutionists (whether secular or theistic) regards science as something separate from religion. He constantly contrasts 'religious worldviews' with 'the scientific worldview' as if science is a faith-free zone. However, the last half-century or so of work in the history and philosophy of science has abundantly shown that in each and every discipline of science, the facts are seen in terms of a theory, against the frame of reference of a paradigm (research programme), within a philosophical view of reality, and from a religious stance."

To conclude, it is worth looking at the application of Reiss' approach to school science teaching. The issue has become alive this week because the Assessment and Qualifications Alliance in the UK has set a GCSE biology exam paper with a question exploring the students' understanding of different theories of origins. The essence of the question was reported by The Daily Telegraph:

Pupils were presented with four "theories of how new species of plants and animals have developed". These included creationism, which is commonly known as the belief that the Earth and its species were created suddenly by God within the last 10,000 years, and intelligent design, its more recent off-shoot. Pupils were also presented with Darwinism and Lamarckism, the theory of organic evolution advanced by the French naturalist Lamarck.
They were then asked to match each theory with a sentence.
Pupils were supposed to place creationism with the observation that "fossils of all the different kinds of animals appear suddenly in the rocks, with no evidence of ancestors".
They should also have identified intelligent design as theory based on the "complicated way in which cells work".

Reaction has been rapid, and the AQA says it has withdrawn the question. The scientific materialists insist that only Darwinism and Lamarckism are entitled to be called scientific and that there is no case for putting creationism and ID at the level of "theory". ID scientist, Dr Steve Meyer, is quoted as saying: "The exam board should be commended, not attacked, for exposing students to competing ideas about the origin and development of life."

My interest is in whether the exam question was informed by the stance taken by Michael Reiss or whether it is a further example of muddled thinking. If worldview thinking is to be taken seriously, then the same evidence is likely to be handled differently by the science that emerges from each worldview. For example, whereas an evolutionist considers classification to be a matter of tracing ancestor-descendant relationships, a design theorist is open to the idea that some of the pattern may be better explained by design. We have the same data - but different interpretations. However, in the examination question, matching a theory with a sentence suggests that data brings its own interpretation. Data then is perceived as "magic bullets" to prove or disprove a particular theory. But this is not good science and it is not informed by worldview thinking. What might be more appropriate is to match different interpretations of the same data to theories springing from different worldviews.

Clearly, there is a lot of work to be done in developing a better understanding of the philosophy of science, and how philosophical materialism, theistic materialism, creationism and ID can relate meaningfully to science. Reiss is to be commended for proposing an approach that keeps the opportunity to dialogue open.

The Relationship Between Evolutionary Biology And Religion
Michael J. Reiss
Evolution, 63(7), July 2009, 1934-1941 | doi: 10.1111/j.1558-5646.2009.00714.x

ABSTRACT: Belief in creationism and intelligent design is widespread and gaining significance in a number of countries. This article examines the characteristics of science and of religions and the possible relationship between science and religion. I argue that creationism is sometimes best seen not as a misconception but as a worldview. In such instances, the most to which a science educator (whether in school, college or university) can normally aspire is to ensure that students with creationist beliefs understand the scientific position. In the short term, the scientific worldview is unlikely to supplant a creationist one for students who are firm creationists. We can help students to find their evolutionary biology courses interesting and intellectually challenging without their being threatening. Effective teaching in this area can help students not only learn about the theory of evolution but better appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science, and the ways in which scientific knowledge differs from other forms of knowledge.

Synopsis Of The First Chapter Of Nature's IQ By Balazs Hornyanszky and Istvan Tasi
ISBN 978-0-9817273-0-1
By Robert Deyes
ARN Correspondent

Ethology, the field of biology that attempts to explain the origins of animal behavioral patterns, has traditionally focused on two possible sources for such patterns- those that are inherited and those that are environmentally induced. For the former of these two, the Darwinian mechanism is that which is most commonly advanced. The underlying axiom barely needs repeating- inherited behaviors have been acquired through gradual changes as a result of environmental selective pressures. In his 1973 Nobel lecture entitled Analogy As A Source Of Knowledge, Konrad Lorenz made his case in favor of the link between Darwinian gradualism and animal behavior. And yet in Nature's IQ, authors Balazs Hornyanszky and Istvan Tasi blast such a gradualistic inference and re-interpret the evidence in favor of the intelligent design alternative.

For many key anatomical features found in nature, a necessary behavioral pattern must be present if a desired function is to be fulfilled. The prominent bioluminescent bulb of the anglerfish for example must exhibit a slow waving motion if it is to lure its prey. As Hornyanszky and Tasi so vividly illustrate, any intermediate behavior on the way to becoming the fully-fledged comportment we see today, would have been inappropriate and insufficient for catching unsuspecting fry. In effect, anglerfish are endowed with an IQ that must have appeared at once and in parallel with its predatory anatomy if it were to provide any selective advantage.

We see the same principle playing out in the trap-like lures of other creatures such as the decoy scorpion fish, the Argentine Horned frog and the copper-head snake. Most prominent of all is the alligator snapping turtle which holds its mouth open for extended periods of time while waiting for a victim to catch sight of its worm-like wriggling tongue. The New Guinean dung spider is able not only to assume the appearance of bird droppings but also produce a characteristic 'dropping' smell as a way of enticing and trapping insects that normally feed on such a delectable meal. Hungry Egyptian vultures repeatedly throw stones at ostrich eggs as they try to access their next meal- a behavior that has been conclusively shown to be integral part of the vulture's genetic constitution.

Hornyanszky and Tasi maintain that for all such cases, both the anatomical features and the accompanying behaviors must have arisen all at once if the observed functions were to have been achieved. In short they build on biochemist Michael Behe's showcase volume Darwin's Black Box by inferring that many such anatomical-behavioral functional units are irreducibly complex and thereby inaccessible to a progressive accumulation of random mutations.

Hornyanszky's and Tasi's case in favor of intelligent design is made all the more compelling through the wealth of examples that they draw on as well as the rich illustrations that accompany many of these examples. In all, the first chapter of Nature's IQ provides a firm foundation in support of the Intelligent Design case and sets the tone for the chapters that follow.

For more information and to order Nature's IQ go to http://www.arn.org/arnproducts/php/book_show_item.php?id=129

Apparently, journalism faces something of an identity crisis, not least science journalism. The 6th World Conference of Science Journalists was held in London last week. Before it started, it was said that many attendees will be "wondering if this is journalism's swan song". An Editorial in Nature asked whether the role of science journalists is that of cheerleader ("to explain new scientific findings to the masses" and "for making the case for a thriving research enterprise to public and politicians alike") or a watchdog ("to cast a fair but sceptical eye over everything in the public sphere - science included").

The one question not being asked is: are science journalists letting us down? (Link to source here)

The root problem is that readers are deserting in significant numbers and with that comes declining advertising revenue. "Readers - and small ads, once a reliable earner - are migrating to the Internet." Science journalists and other specialists are being replaced by press releases:

"This contraction is perhaps particularly bad news for journalists with specialist beats such as science - the kind of journalists who need an informed understanding of what they are writing about, and know which experts can provide context, and where appropriate criticism, of new results. But publishers tend to see that kind of expertise as a luxury when money is tight, especially when the same space can be easily filled with material from press releases and wire services."

What is singularly lacking from the Editorial comment is any discussion of ideology and worldviews. It is the concern of many of us that significant issues are waiting to be explored but the traditional media are just not interested. Denyse O'Leary puts her finger on the problem here, when she writes:

"Believing that materialism is the truth, many journalists assumed that their role was to promote materialism at the expense of traditional, spiritually oriented ideas about human nature. Journalism consciously modelled itself on science, with "objectivity" as a new standard. Journalism would provide trenchant criticism of the religious outlook that it replaced."

This situation has become unstable over the past decade because of the increasing problems of maintaining a materialist worldview. Opinion polls show that a majority of people are not persuaded by the design-free media output. They are increasingly aware of evidence for design! In a second post on this topic, O'Leary writes:

"But most science journalists are not really aware of this stuff because their template for understanding issues is simply to reinterpret all problems as support for materialism, with Darwinism as its creation story. For example,
* Fine-tuning of the universe = That proves that many flopped universes exist!
* Cells as super-computers = That just shows what Darwinism can do!
* Origin of life? = Harvard will spend $50 million on "the answer"!
* Hard problem of consciousness = Science (materialism) will solve it [no end date for evaluation of project suggested]
Almost all coverage of the intelligent design controversy in major media is provided by people who cannot acknowledge any problem with materialism. They think you must be a fraud or just plain stupid if you raise problems that cannot even exist, in their opinion. And remember, as far as they are concerned, their opinion is science."

For most part, science journalism reflects the materialistic philosophy that is promulgated by science leaders and science organisations. Busy journalists often produce reports that are popularised versions of the press releases issued by the researchers, with little attempt to evaluate the significance of the research. This year, Ida has provided a clear example of the problem. Darwin dissenters have a tough time getting their message across. Repeatedly, I have learned of scientists being interviewed and they have pointed out that their objections are based on scientific evidence - only to find that the media report paints their views as an expression of their religious convictions. The thought that the mainstream view is an expression of a materialistic worldview seems never to have occurred to these journalists.

The editorial closes with some fine words that are worth repeating:

"Science and journalism are not alien cultures, for all that they can sometimes seem that way. They are built on the same foundation - the belief that conclusions require evidence; that the evidence should be open to everyone; and that everything is subject to question. Both groups are comprised of professional sceptics. And whether it's directed towards an experiment or a breaking news story, each can appreciate the other's critical eye."

The word "everything" is important. We know that many science leaders and science organisations do not accept that materialism is "subject to question". They are not prepared to either re-assess their own presuppositions or to allow anyone with different presuppositions to represent science. Until this situation changes, these people should not be surprised that readers vote with their feet and find other media that does not ram an alien ideology down their throats.

Cheerleader or watchdog?
Editorial
Nature 459, 1033 (25 June 2009) | doi:10.1038/4591033a

Abstract: Science journalism is under threat. What can scientists do to help?

See also:

For more on materialism in science, go here, here and here.

Brainard, C. NSF "Underwriting" Coverage. . ., The Observatory (July 01, 2009)

Quacks, hacks and pressing problems with press releases, The Guardian (30 May 2009)

The world of human phylogeny has been hit by a bombshell. Although scholars and textbooks are presenting chimpanzees as man's closest relatives, Grehan and Schwartz have revived the case for orangutans. They consider hominoids to be comprised of two sister clades: the human-orangutan clade (dental hominoids) and the chimpanzee-gorilla clade (African apes). They claim that humans and orangutans "share a common ancestor that excludes the extant African apes". Since it is received wisdom that chimps are the nearest relative to humans because we share over 98% of their genes and since humans are referred to as the "third chimpanzee", the ramifications of the new paper are immense!

Mr. Jiggs, a six-year-old orangutan at London Zoo, is capable of mopping his own quarters (credit B. A. Stewart and D. S. Boyer, source here)

Conceptual upheavals of this magnitude are unlikely to happen without major methodological modifications. This is the main concern of this blog. The authors do not start with DNA similarities but with morphological data. They note that, originally, the DNA comparisons were interpreted in the light of morphological analyses, but:

"Neither of two oft-cited morphological studies claiming to corroborate the interpretation of molecular data as supporting a close relationship between chimpanzees and humans took into consideration or provided justification for excluding most of the morphological features that have been documented as being shared uniquely by humans and orangutans."

The authors proceed to critique previous studies for the way they selected characters for cladistic analysis. They point out that these approaches incorporated characters considered to be derived within the ingroup "in spite of the fact that the feature is also common in the outgroup".

"Although a range of morphological studies have claimed to support a closer relationship between humans and chimpanzees or African apes, these studies have relied on many of the characters that we found to be problematic, and thus demonstrate how entrenched error becomes as it is unquestioningly passed on from and incorporated into one study after another."

Those familiar with the Kuhnian analysis of the practice of science will discern features here of 'working within the paradigm', with presuppositions unintentionally closing off avenues of enquiry. Conscious of the limitations of other work, Grehan and Schwartz explain and justify their selection of characters. One of their additional objectives was to include numerous fossil apes within their study.

"Our analysis of relationships between living and fossil taxa is based on a character matrix limited to hard-tissue characters that have been sufficiently well described in the literature to permit verification, and whose claimed character states as well as unique occurrence within a large-bodied hominoid clade we could corroborate via a broad outgroup comparison."

It is worth noting that their conclusion has deep roots. Schwartz was making points like this in 1984. His book The Red Ape appeared in 1987 and in a revised form in 2005. The paper has not come from authors who have suddenly hit on a quirky idea but it represents the mature judgment of two respected scholars.

What then shall be said of the DNA similarity data? The analysis of the authors is scathing. The key points are, in their own words:

"But the widely accepted notion that the 'greatest overall molecular similarity' is synonymous with 'most closely related' derives not from any empirical evidence but merely from the acceptance without question of the 'molecular assumption': namely, most recently divergent taxa will be most similar in their proteins and DNA because they will have shared a longer lineage of molecular change prior to their divergence and that the pace of molecular change was clocklike in nature. Nevertheless, despite claims to the contrary, the demonstration of molecular similarity does not a priori equate with a demonstration of homology, which must precede any hypothesis of phylogenetic relationship because a demonstration of similarity alone is only phenetic and must be subject to rigorous phylogenetic enquiry."

They cite previous work by Schwartz & Maresca that was the subject of a blog here. They argue that the published studies lack objectivity and have embedded tautologies. The New Scientist report summarises the argument against chimp/human genetic similarities by quoting one of the authors:

"Grehan, however, argues that this is not scientifically justified. He points out that traditional taxonomy makes a distinction between two types of similarity - "derived novelties" and "primitive retentions". Derived novelties are traits shared by two closely related species and are taken to have evolved in a recent common ancestor. Primitive retentions are older traits with a deeper evolutionary past shared by a larger group of species.
The problem with molecular systematics, says Grehan, is it fails to distinguish between the two. "It does not matter that more DNA similarities may be found between humans and chimpanzees if these similarities are really primitive retentions," he says."

A third element of the new paper is to set the argument for the human/orangutan relationship in a biogeographical context. Whereas the consensus view understands an emergence of humanity "out of Africa", there is a need for these issues to be addressed for the dental hominoid clade. The authors do this utilising data relating to the fossil species included in their analysis.

The significance of the paper is that the arguments relate to cladism (which is very widely used for assigning probabilities to evolutionary relationships) and phylogenomics (which is a standard tool for establishing evolutionary relationships). The authors have challenged the scientific consensus with some cogent and penetrating arguments. It is not just a dispute about the meaning of data, but how that data is selected and what presuppositions the researchers bring to their work. As such, the new paper provides us with a very important case study and sets the agenda for potentially very interesting discussions about methodology. If this is properly done, it will be to the health of the science community. Scientists with an openness to ID will welcome this debate, because many of critiques made by Grehan and Schwartz link directly to issues that concern us.

Evolution of the second orangutan: phylogeny and biogeography of hominid origins
Grehan, J.R. and Schwartz, J. H.
Journal of Biogeography, advance online 22 June 2009 | doi 10.1111/j.1365-2699.2009.02141.x (abstract)

Main conclusions: Humans and orangutans share a common ancestor that excludes the extant African apes. Molecular analyses are compromised by phenetic procedures such as alignment and are probably based on primitive retentions. We infer that the human-orangutan common ancestor had established a widespread distribution by at least 13 Ma. Vicariant differentiation resulted in the ancestors of hominids in East Africa and various primarily Miocene apes distributed between Spain and Southeast Asia (and possibly also parts of East Africa). The geographical disjunction between early hominids and Asian Pongo is attributed to local extinctions between Europe and Central Asia. [. . .]

See also:

Lawton, G. Could the orang-utan be our closest relative? New Scientist, 17 June 2009

Humans and Orangutan, Buffalo Museum of Science web resource.

Research into the skeletal remains of Stone Age Man has been undertaken in parallel with work to clarify the cultural and cognitive skills of these people. The dominant paradigm has been gradualism linked to the slow transformation of ape-like creatures into Modern Man. Darwinism has influenced the way people have approached the data and the interpretations they have placed on findings.

Papers are regularly published which point out the earliest example of a cultural trait: use of fire, hunting using spears, artefacts (like jewellery) indicating the presence of aesthetic values, Venus figurines, and so on. Two recent examples are noted in this blog.

Musical instruments like these allow inferences to be made about the cognitive skills of the users (Source here)

The first example concerns hafted spears, which are said to date back to 200,000 years ago. These are compound tools, where a sharp, hard point is hafted to a shaft. Archaeologists recognise that this invention has implications for our understanding of the minds of the spear-makers. The newly reported discovery is of spears where the hafting was found to be associated with a number of naturally occurring materials. Why were these materials located at the join? By an extensive programme of experimentation, the researchers came to the view that the artisans were using the materials as adhesives, and that the manufacturing process demonstrated a high level of abstract thinking.

"Wadley et al. identified naturally available materials (acacia gums and beeswax) that could be combined with ochre (found as residue on the tools), after which they experimented with various combinations to find the most effective mixture. They also tried different techniques for producing the actual haft, including the use of fire for rapid drying of the adhesives. With the most effective procedure in hand they could then ask themselves what an artisan needed to understand in order to conceive of and execute this task. "We propose that these artisans were exceedingly skilled; they understood the properties of their adhesive ingredients and they were able to manipulate them knowingly". In particular the artisans needed to understand the properties of their ingredients (e.g., cohesiveness), to be able to judge the effects of temperature, to be able to switch attention back and forth between separate rapidly changing variables, and to be flexible enough to adjust to the variability inherent in naturally occurring ingredients."

In a Commentary on the paper, Wynn points out that the reasoning that leads to such a conclusion must be "based on a sequence of inferences, each of which must be explicit and persuasive if the argument as a whole is to be credible." He spells out the details of that reasoning process, "borrowed loosely from Botha's detailed critique of an archaeological argument for the use of syntactical language by people at Blombos Cave 77,000 years ago." The merit of this approach is that observations and inferences can be clearly identified and each step can be scrutinised carefully. Archaeologists have new avenues to explore, which is very exciting.

"Most of the focus in this debate has been on the role language and symbolism but, as Wadley et al. make clear, there is more to modern cognition than language and the use of symbols. Indeed, language has proven to be a particularly intractable topic for archaeologists, a point made cogently by Botha. By focusing on activities that tax reasoning ability and are also visible archaeologically, such as hafting, archaeologists are in a better position to contribute to an understanding of the evolution of the modern mind."

The second paper concerns the finding of musical instruments. "Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication." Previously, the oldest instriument was about 30,000 years ago, but the new finds come from a site dated at about 35,000 years. Some of the reported comments are as follows:

"It's becoming increasingly clear that music was part of day-to-day life," he said.
"Music was used in many kinds of social contexts: possibly religious, possibly recreational - much like we use music today in many kinds of settings."
The researchers also suggest that not only was music widespread much earlier than previously thought, but so was humanity's creative spirit.
"The modern humans that came into our area already had a whole range of symbolic artifacts, figurative art, depictions of mythological creatures, many kinds of personal ornaments and also a well-developed musical tradition," Professor Conard explained.

The first general point I want to make is that the procedures described (for making inferences from archaeological data) are not dissimilar from the procedures used by Intelligent Design scholars for making inferences about design in nature. These procedures are not arbitrary or poorly conceived, but rigorous and evidence-based (and exciting!). This is why the objections most often heard are based on demarcation arguments: 'Design is not part of Science'. Clearly, in archaeology, design is part of science!

The second general point concerns the creeping awareness that Stone Age men were far more "modern" than we have given them credit for. The problem is that most scholars understand consciousness, capacity for abstract thought and aesthetics as emergent properties of evolving animals. They do not allow the thought that these capabilities might be present by design. So, the data is moulded to fit a slow evolutionary transformation and other ways of interpreting the data are neglected. To show that design perspectives can propose hypotheses that can be tested, here is possible scenario. All these Stone Age men are human and have essentially modern cognitive skills. However, they lived in environments where they needed to adopt survival strategies and this prevented the flowering of sedentary communities and limited evidences of creativity. The prediction is that evidences of modernity will continue to be found, pushing the appearance of cultural artefacts earlier and earlier in time.

Implications for complex cognition from the hafting of tools with compound adhesives in the Middle Stone Age, South Africa
Lyn Wadley, Tamaryn Hodgskiss and Michael Grant
Proceedings of the National Academy of Science USA, Published online May 11, 2009 | doi: 10.1073/pnas.0900957106

Abstract: Compound adhesives made from red ochre mixed with plant gum were used in the Middle Stone Age (MSA), South Africa. Replications reported here suggest that early artisans did not merely color their glues red; they deliberately effected physical transformations involving chemical changes from acidic to less acidic pH, dehydration of the adhesive near wood fires, and changes to mechanical workability and electrostatic forces. Some of the steps required for making compound adhesive seem impossible without multitasking and abstract thought. This ability suggests overlap between the cognitive abilities of modern people and people in the MSA. Our multidisciplinary analysis provides a new way to recognize complex cognition in the MSA without necessarily invoking the concept of symbolism.

New flutes document the earliest musical tradition in southwestern Germany
Nicholas J. Conard, Maria Malina, Susanne C. Munzel
Nature (online 24 June 2009) | doi:10.1038/nature08169 (Abstract)

Considerable debate surrounds claims for early evidence of music in the archaeological record. Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication but, owing to the scarcity of finds, the archaeological record of the evolution and spread of music remains incomplete. Although arguments have been made for Neanderthal musical traditions and the presence of musical instruments in Middle Palaeolithic assemblages, concrete evidence to support these claims is lacking. Here we report the discovery of bone and ivory flutes from the early Aurignacian period of southwestern Germany. These finds demonstrate the presence of a well-established musical tradition at the time when modern humans colonized Europe, more than 35,000 calendar years ago. Other than the caves of the Swabian Jura, the earliest secure archaeological evidence for music comes from sites in France and Austria and post-date 30,000 years ago.

See also:

Ghosh, P. 'Oldest musical instrument' found, BBC News, 25 June 2009.

Wynn, T. Hafted spears and the archaeology of mind, Proceedings of the National Academy of Science USA, 2009 | doi: 106:9544-9545 (Extract)

By Robert Deyes
ARN Correspondent

The summer of 2000 promised to be very exciting for ornithologists and paleontologists alike as they flew into Beijing for the fifth quadrennial meeting of the Society of Avian Paleontology and Evolution (Ref 1). The setting was most appropriate given the richness of fossils that have been unearthed in Chinese soil. The central theme of the meeting lay in trying to resolve the question of whether birds had really evolved from dinosaurs (Ref 1). However, rather than a harmonious discussion with the constructive disagreement that one might expect from any scientific 'get-together' aimed at resolving discrepancies in data, the meeting did nothing but expose an underlying discord (Ref 1).

While some scientists such as Berkeley's John Hutchinson and Yale ornithologist Richard Prum were frustrated over issues that they considered long resolved, others were much more skeptical about the certainty of the facts. Storrs Olson, head of ornithology at the National Museum of Natural History, weighed in by accusing Prum of engaging in "ideological mumbo-jumbo" when Prum claimed that feathers had the same evolutionary origin as "hair like integuments found on dinosaur fossils" (Ref 1). So strong was Olson's feeling against the evolutionary link drawn between birds and dinosaurs that throughout the meeting he and others wore badges stating their case: "BIRDS ARE NOT DINOSAURS" (or B.A.N.D for short; Ref 1). University Of North Carolina paleontologist Alan Feduccia, well known for his discussions on temporal discrepancies between bird and dinosaur fossils, was similarly uncertain about the dinosaur-bird link. Feduccia made his uncertainty public to the sound of accusations claiming a creationist undertone (Ref 1).

With the latest evidence Olson and his 'BAND of merry men' appear to have been vindicated. New data on how birds breathe makes the dinosaur-bird link untenable. According to a recent study, the unique thigh bone and muscle structure in birds' legs play a key role in preventing lung collapse (Ref 2). For birds, that need about twenty times more oxygen than say reptiles, such structural support is crucial to survival (Ref 2). Theropod dinosaurs from which birds are thought to have descended, did not sport such a fixed thigh bone structure and are therefore not viable candidates for a hypothetical bird ancestor (Ref 2).

Of course the impasse over how birds evolved extends well beyond thigh bones and muscles. In fact, the origin of feathers continues to be a formidable stumbling block for 'evo-philes'. To further understand the difficulty that the feather poses to the assumed evolutionary transition from dinosaurs to birds, consider the feather's structural foundations. What we know is that the central rachis (or shaft) of the feather branches off into smaller barbs and barbules. The barbules are equipped with tiny hooklets at their ends that interlock with ridges in the posterior barbules to form an impervious, tightly-held vane (Ref 3).

From an aerodynamic standpoint, the arrangement of the feathers in the overall shape of the wing makes for an aerofoil that displays minimal levels of turbulence (Ref 3). The ability to change the geometry and shape of such an aerofoil makes it ideally suited for the various tasks that the bird has to perform such as landing, soaring and flapping. From a molecular and cellular perspective, the story is no less fascinating. The feather follicle, from which the central rachis projects, contains specific zones of epithelial cells specialized in the formation of each of the components of the feather (Ref 4). The molecular mechanisms by which such cell specialization is achieved have also been elucidated in recent years (Ref 4). Through concentration gradients and a highly-regulated activation of specific genes, the morphogenesis and development of a feather is a very tightly-controlled affair (Ref 4).

With such a realization, we begin to get a sense of why it was that twenty three years ago biologist Michael Denton so emphatically decried the step-by-step, unguided evolutionary origin of wings (Ref 3). As Oregon State University Professor John Ruben humorously quipped, "a velociraptor did not just sprout feathers and fly off into the sunset" (Ref 2). The wing- the perfect aerofoil- must meet rigorous criteria before it can provide the necessary lift (Ref 4). No slight fraying of dinosaur scales would have done the job.

Seemingly oblivious of these intractable challenges, some scientists have gone all out to prop up their evolutionary meanderings by focusing on the three-fingered limbs of theropod dinosaurs and modern day birds (Refs 5,6). Paleontologists Xing Xu and James Clark for example recently published on two specimens of a 156 million-old, toothless-beaked, herbivorous theropod called Limusaurus inextricabilis that, they maintain, is a Darwinian-style 'missing link' (Refs 5,6).

One factor that has long been a source of consternation is that the finger digits of theropods and birds do not appear to match. While theropods seemingly carried digits 1,2 and 3 of the pentadactyl arrangement, birds display what scientists believe to be digits 2,3 and 4 (Refs 5,6). Xu and Clark have ruffled feathers by claiming that theropod digits have historically been misidentified. Based on their study of L. inextricabilis, they contend that just like in birds early theropods would have had digits 2,3 and 4 (Refs 5,6).

Such a conclusion is not without its critics. In fact prominent Yale evolutionary geneticist Gunter Wagner has questioned the numbering assignments of bird digits adding that bird wings might be based on digits 1,2 and 3 after all (Ref 5). Wagner cites fundamental aspects of embryonic development in support of his case. University of California paleontologist Kevin Padian has similarly suggested that the digit morphology of L. inextricabilis might represent nothing more than an "oddly reduced hand", commensurate with its herbivorous lifestyle (Ref 5).

Today, nine years after the Beijing meeting, Olson would seemingly be justified in wearing his famous badge. For him and others, the 'B.A.N.D' does indeed play on. To be sure, contemporary evidence shows birds to be a distinct phyletic group not easily integrated into a man made evolutionary scheme. While evolutionists point proudly to the apparent anatomical similarities between birds and dinosaurs, they themselves admit to the pressing need to resolve crucial questions about the origin of flight, the evolution of feathers and the conversion to endothermy (Ref 7).

These are not side questions designed to obfuscate discussions, but rather questions that are central to the matter at hand. In light of such facts, perhaps a more radical message needs to be conveyed that echoes the beat of a different mantra: BIRDS ARE REALLY BIRDS (or B.A.R.B for short). It is perhaps time to re-examine our most treasured notions of bird evolution.

Literature Cited
1. Rex Dalton (2000), Feathers fly in Beijing, Nature, Volume 405, p.992

2. See 'Discovery raises new doubts about dinosaur-bird-links', http://www.eurekalert.org/pub_releases/2009-06/osu-drn060809.php

3. Michael Denton (1986), Evolution: A Theory in Crisis, Adler and Adler Publishers, Bethesda Maryland, 1st Edition, pp. 202-208

4. Mingke Yu, Ping Wu, Randall B. Widelitz, Cheng-Ming Chuong (2002), The morphogenesis of feathers, Nature, Volume 420, pp.308-312

5. Matt Kaplan (2009), Dinosaur's digits show how birds got wings, 17 June 2009, Nature, doi:10.1038/news.2009.577

6. Xing Xu, James M. Clark, Jinyou Mo , Jonah Choiniere, Catherine A. Forster, Gregory M. Erickson, David W. E. Hone, Corwin Sullivan, David A. Eberth, Sterling Nesbitt, Qi Zhao, Rene Hernandez, Cheng-kai Jia, Feng-lu Han, Yu Guo (2009), A Jurassic ceratosaur from China helps clarify avian digital homologies, Nature 459, pp.940-944

7. See 'Are Birds Really Dinosaurs?', http://www.ucmp.berkeley.edu/diapsids/avians.html

In 2002, a team of Argentinian geologists published a paper on what they considered to be the oldest bird tracks. The lead researcher was quoted as saying: "The first and most striking feature of these fossil footprints is the overall resemblance with modern bird footprints". In commenting on the finds, Martin Lockley, a respected palaeontologist, said: "what is commendable here is that the Argentineans have presented their material well and these footprints seem to be distinctly bird-like and different from any known dinosaurs walking around at the time".

a) Footprints are numerous in this slab of the Santa Domingo Formation.
b) The arrows point to a track of footprints. Visible in each print of the track is the hallux, the digit that points backwards in birds. (Credit: Ricardo Melchor, Source here).

During the intervening years, the Argentinians have worked on their find and numerous related themes. For example, they have published "the first comprehensive ichnotaxonomic review of the Triassic tetrapod track record in Argentina, including previous accounts and new material recently discovered, and an analysis of its composition and stratigraphic distribution." They have analysed depositional environments and looked a a whole range of fossil traces. Most recently, they have used a modern-day locality to study trackways left by birds and compared them with previously-found fossil material. Their study is thorough and authoritative. Rather than review the details, we shall go straight to their conclusions:

"The presence of flight trace fossils (Volichnia), i.e. footprints with elongated hallux impressions that are interpreted as representing low angle landing, associated with probing marks and a similar morphology of Gruipeda dominguensis with tracks of modern shorebirds, strongly suggest an avian affinity for the producers of the fossil tracks."

The claim for bird tracks in these rocks is no longer tentative. After rigorous examination, the fossil evidence points clearly to birds feeding and moving about in a "low-gradient fluvio-lacustrine setting under semi-arid climate". The problem this poses is integrating this with other knowledge regarding fossil birds. These deposits are thought to predate Archaeopteryx by 55 Ma. They conflict dramatically with those who claim that birds evolved from theropod dinosaurs. Consequently, these traces are very controversial. The authors back off from confrontation by saying: "in consequence, the Santo Domingo track site would be younger than supposed".

However, the geological Period associated with these rocks may not be dismissed easily. There are three independent pointers to age and the lithology is also typical of rocks known as New Red Sandstone. The authors write:

"The track surface belongs to the Santo Domingo Formation, which is considered of Late Triassic-Early Jurassic age. This age is based on characteristic fossil wood remains, on a 40Ar/39Ar radiometric age from interbedded basalt flows, and palaeomagnetic studies. The formation reaches a minimum thickness of c. 1950 m and is in fault contact with Carboniferous igneous and sedimentary rocks. The Santo Domingo Formation is a red bed succession that displays, from base to top, a transition from alluvial fan, fluvial braided (with calcretes), ephemeral fluvial and shallow lakes, and eolian environments."

Whilst it is perfectly reasonable to revisit the question about assigned age, it is no less reasonable to revisit the supposed theropod-bird evolutionary transition. In particular, it is worth noting the research of BAND scholars (Birds Are Not Dinosaurs). One of these is John Ruben, who with colleagues (1997), compared the respiratory structures of modern birds, mammals, and crocodiles with those reconstructed from the fossils of early birds and theropod dinosaurs. There are big differences. Theropod dinosaurs appear to have crocodile-like diaphragms. Birds, however, lack a diaphragm and make use of pelvis and chest movements to breathe. The differences are so marked that, it is claimed, there are "fundamental problems" with the proposal that diaphragm-less birds evolved from dinosaurs with diaphragms. For more, go here.

Ruben has co-published another challenging study recently, related to avian respiration.

"It's been known for decades that the femur, or thigh bone in birds is largely fixed and makes birds into "knee runners," unlike virtually all other land animals, the [Oregon State University] experts say. What was just discovered, however, is that it's this fixed position of bird bones and musculature that keeps their air-sac lung from collapsing when the bird inhales. Warm-blooded birds need about 20 times more oxygen than cold-blooded reptiles, and have evolved a unique lung structure that allows for a high rate of gas exchange and high activity level. Their unusual thigh complex is what helps support the lung and prevent its collapse."

Like his analysis of the diaphragm in respiration, Ruben interprets the new findings in terms of a fundamental clash between the designs of birds and the design of dinosaurs. It is unreasonable to postulate an evolutionary transition.

"The implication, the researchers said, is that birds almost certainly did not descend from theropod dinosaurs, such as tyrannosaurus or allosaurus. The findings add to a growing body of evidence in the past two decades that challenge some of the most widely-held beliefs about animal evolution. "For one thing, birds are found earlier in the fossil record than the dinosaurs they are supposed to have descended from," Ruben said. "That's a pretty serious problem, and there are other inconsistencies with the bird-from-dinosaur theories.
"But one of the primary reasons many scientists kept pointing to birds as having descended from dinosaurs was similarities in their lungs," Ruben said. "However, theropod dinosaurs had a moving femur and therefore could not have had a lung that worked like that in birds. Their abdominal air sac, if they had one, would have collapsed. That undercuts a critical piece of supporting evidence for the dinosaur-bird link."

It will be a good day for science when these evidences get featured in educational materials and in media presentations. However, other factors affect this:

"Frankly, there's a lot of museum politics involved in this, a lot of careers committed to a particular point of view even if new scientific evidence raises questions," Ruben said. In some museum displays, he said, the birds-descended-from-dinosaurs evolutionary theory has been portrayed as a largely accepted fact, with an asterisk pointing out in small type that "some scientists disagree."

Application of neoichnological studies to behavioural and taphonomic interpretation of fossil bird-like tracks from lacustrine settings: The Late Triassic–Early Jurassic? Santo Domingo Formation, Argentina
Jorge F. Genise, Ricardo N. Melchor, Miguel Archangelsky, Luis O. Bala, Roberto Straneck and Silvina de Valais
Palaeogeography, Palaeoclimatology, Palaeoecology, 272(3-4), 15 February 2009, 143-161 | doi 10.1016/j.palaeo.2008.08.014

Abstract: The purpose of this study is to apply neoichnological observations to the behavioural and taphonomic interpretation of a Late Triassic-Early Jurassic track surface from the Santo Domingo Formation (Argentina) containing hundreds of bird-like tracks and trackways. [. . .] Field observations allowed to distinguish twenty one behaviours that produced distinct traces and four modern footprint types (1 to 4) related to specific substrate conditions. In particular, the preferential formation of bird tracks parallel to the waterline, also confirmed by studies on droppings and invertebrate fauna of the pond, and other associated sedimentary features (ripple marks, wrinkle marks, mud drape thickness) and trace fossils were important for recognition of the shoreline in the fossil example. [. . .]. Five of the behaviours recognised in the modern pond were inferred from the sixteen trackways distinguished on the fossil track surface, including walking, walking with a zig-zag path, short runs, probing, and landing with legs directed forward (possible trace of flight). The recognition of traces of flight (Volichnia), probing marks, and tracks showing morphology similar to modern shorebirds (G. dominguensis), strongly suggest an avian affinity for the producers of the fossil tracks and, in consequence, the Santo Domingo track site would be younger than supposed.

Cardio-pulmonary anatomy in theropod dinosaurs: Implications from extant archosaurs
Devon E. Quick, John A. Ruben
Journal of Morphology, Early View 20 May 2009 | doi 10.1002/jmor.10752

Abstract: Although crocodilian lung and cardiovascular organs are markedly less specialized than the avian heart and lung air-sac system, all living archosaurs possess four-chambered hearts and heterogeneously vascularized, faveolar lungs. In birds, normal lung function requires extensive, dorsally situated nonvascularized abdominal air-sacs ventilated by an expansive sternum and specially hinged costal ribs. The thin walled and voluminous abdominal air-sacs are supported laterally and caudally to prevent inward (paradoxical) collapse during generation of negative (inhalatory) pressure: the synsacrum, posteriorly directed, laterally open pubes and specialized femoral-thigh complex provide requisite support and largely prevent inhalatory collapse. In comparison, theropod dinosaurs probably lacked similarly enlarged abdominal air-sacs, and skeleto-muscular modifications consistent with their ventilation. In the absence of enlarged, functional abdominal air-sacs, theropods were unlikely to have possessed a specialized bird-like, air-sac lung. The likely absence of bird-like pulmonary function in theropods is inconsistent with suggestions of cardiovascular anatomy more sophisticated than that of modern crocodilians.

See also:

Discovery raises new doubts about dinosaur-bird links, EurekAlert, 9 June 2009.

Towards the end of the 17th Century in England, there was a fascinating debate between philosophers (scientists) and theologians about mountains. The question concerned their significance in our understanding of the natural world. Thomas Burnet triggered the debate by publishing "Sacred Theory of the Earth" in 1681 (in Latin) and in 1684 and 1690 (in English). This book was pioneering in its day in that it proposed a concordance between Biblical history and natural philosophy as well as arguing against Aristotle's eternalism.

"The book begins with the earth's creation from Chaos and goes on to explain the earth as paradise, the deluge, the destruction of the earth by fire and its eventual restitution at the end of time. What Burnet set out to do was to reconcile the scriptural account of the earth's history with recent sorts of natural philosophical explanations for them. His own preference was for a model of creation and physical causation that owed a great deal to the works of Rene Descartes. The different stages in the earth's history were illustrated in the book's beautiful frontispiece."

The frontispiece of the first volume of Burnet's Theory (Source here)

Burnet was taken to task by numerous scholars: "John Ray [botanist], the Newtonians John Keill and William Whiston, the scholar Richard Bentley and John Woodward [geologist]". They responded at two levels. The first area of concern was theological (which we will not consider further here), and the second was concerned with natural philosophy - particularly related to mountains.

Burnet presented mountains as a consequence of the Deluge, thereby associating them with God's judgment on human sinfulness. After the Deluge, the surface of the Earth was "a broken and confus'd heap of bodies" and mountains presented "the image or picture of a great Ruine".

"Burnet was unequivocal in his claim that mountains 'do not consist of any proportion of parts that is referable to any design, or that hath the least footsteps of Art or Counsel'."

His adversaries did not deny the Biblical narrative of Creation, the Antediluvian Earth, the Deluge and the Modern era - but they did not agree about design! Their writings reveal them demonstrating that mountains have uses (functionality) and that mountains are aesthetically pleasing (not ugly). It appears that the quest to strengthen functionality arguments stimulated scientific enquiry (particularly in understanding the role of mountains in the water cycle).

"Ray, Bentley, Keil and others set about enumerating all the different 'uses' of mountains that they could think of. Their discussions ranged from the role of mountains as alpine habitats, their supposed role in regulating the weather, and they even touted mountains as useful natural frontiers between nations. Perhaps most important to posterity are their inclusion of early explanations of the water cycle. Research carried out by Edmund Halley on St Helena into the possible role of mountains in the water cycle provided Burnet's critics with ammunition to prove that mountains were indeed useful, or perhaps even essential to the very preservation of human life on earth."

Regarding aesthetic arguments, Burnet found it easier to make a case for the ugliness of mountains by comparing them with the mountains of the Moon. If we viewed the Earth from afar, "look'd upon with a good Glass [telescope]",the mountains would appear "rude and ragged". In countering this argument, there was some incredulity with the idea of being elevated to so high a vantage point , but the main objection appealed to the aesthetics of landscape painting and gardening.

"The two key pieces of terminology used by Burnet's opponents to describe the place of mountains in the landscape were 'prospect' and 'variety'. [. . .] In seventeenth-century English discourse the word 'prospect' could be used interchangeably with 'landscape painting' and referred to landscape paintings made through the formal practices of mathematical perspective. [. . .] 'Variety' was the most important aesthetic consideration in contemporary discussions of landscape art. Early English theorists of landscape art praised mountains for their contribution to landscape paintings that would otherwise lack variety and fail to stimulate onlookers. Burnet's critics put this exact argument to use in their criticism of his aesthetic."

Wragge-Morley, the author of this analysis, points out that "the difference between seeing the truth about the design of mountains, and seeing nothing at all, lay in a simple perspectival shift". One person looks at a relief map of the globe and sees lumps and scars; another brings the perspective of landscape art and sees beauty, grandeur and majesty.

"This in turn could lend weight to an argument for or against their utility, which could in turn have ramifications for one's view of their theological meaning."

The history of ideas provides much food for thought, and this "strange and surprising debate" is no exception. There appear to be at least two applications that are relevant to our own day and to contemporary debates about design. First, Wragge-Morley's comments on perspective could be applied to design thinking generally. This is the explanation why some look at the natural world and see design everywhere, whereas others witness the same objects and declare them to be design-free. These perspective differences do not reflect on people's ability to think rationally, but rather point to underlying metaphysical differences affecting both thinking and scientific practice. In his essay, Wragge-Morley does not enlarge on these aspects, but he does draw attention to Burnet's interest in Cartesian philosophy which would be a good launching point for further analysis.

Second, this case-study reveals the way design-based thinking triggered research into functionality. Making a design inference actually stimulated enquiry, because intelligent design suggests purpose and meaning. This is a principle of general application, and it is an effective response to those who claim that ID is a science-stopper. The claim is entirely polemical, unsupported by evidence. A modern-day example is Junk DNA. Darwinian biologists regarded it as garbage and it was not targeted for research. Those brave scientists who were prepared to challenge the paradigm by postulating functionality found that they were stumbling on a treasure-trove of cellular information! (Go here and here).

It is worth pointing out, in conclusion, that design thinking is not lacking in theoretical development. This debate about mountains predated natural theology and William Paley: differences in emphasis can be traced through this period. The modern resurgence of design-thinking is not a return to Paley's watchmaker arguments. Finding complexity and functionality is not enough to confirm design. We recognise that some functionality can be introduced by natural processes: a fallen tree can provide a bridge over a river, but that does not mean the functionality was designed. Today, we talk more about information, and refer to complex specified information when making design inferences.

A strange and surprising debate: mountains, original sin and 'science' in seventeenth-century England
Alexander Wragge-Morley
Endeavour, Volume 33, Issue 2, June 2009, Pages 76-80 | doi:10.1016/j.endeavour.2009.05.001

It could come as a shock to learn that some seventeenth-century men of science and learning thought that mountains were bad. Even more alarmingly, some thought that God had imposed them on the earth to punish man for his sins. By the end of the seventeenth century, surprisingly many English natural philosophers and theologians were engaged in a debate about whether mountains were 'good' or 'bad', useful or useless. At stake in this debate were not just the careers of its participants, but arguments about the best ways of looking at and reckoning with 'nature' itself.

In this Bicentennial year of Darwin's birth, there are many who want to drive a wedge between Darwinism as a scientific theory and Darwinism as a philosophical, social or political theory. Here in the UK, we have a Templeton Foundation-funded project called "Rescuing Darwin" which seeks to do exactly this. Darwinism, it is claimed, is essentially a scientific theory and it needs to be rescued from the atheists, the social-engineers and others who are taking it far beyond the domain of science. Here is an excerpt from the report "Rescuing Darwin".

"Social Darwinism did not have the monopoly on interpreting evolution. Indeed, in its time evolution has been used in support of every "ism" imaginable, including socialism, capitalism, racism, eugenics, feminism, theism and atheism. As George Bernard Shaw once remarked, Darwin "had the luck to please everybody who had an axe to grind". The key point is that, from the earliest times, evolution was understood - and sometimes rejected - as a philosophical, social or political theory, rather than simply a biological one." (page 25)

This strategy of presenting Darwinism as science with no philosophical or ideological baggage deserves to be critiqued and challenged. Many of us argue that science necessarily implies a philosophical underpinning, and that metaphysical foundation inevitably affects the way science is practised. This blog, however, is concerned with the evidence from history. What was Darwin's own thinking about laissez-faire social Darwinism? Does he deserve to be rescued from those who have inappropriately applied his science to the workings of human society? Or is he being expelled from his own house?

Will the real Darwin please stand up! (Source here)

In an incisive essay, Richard Weikart contributes to the scholarly answers to these questions. There have been some who say that "social Darwinism was an essential part of Darwin's theory". Others have denied that social Darwinism ever existed, and still others who "blame Herbert Spencer for originating and popularizing social Darwinism". The essay concerns the relationship between Spencer's and Darwin's social views over time.

"That is the task I set for myself, as I explore the following questions: How much influence did Spencer exert on Darwin's social thought and vice-versa? What did Spencer and Darwin think about each others' views of social evolution, especially as it related to laissez-faire economic theory? Was Spencer a social Darwinist? Was Darwin a social Darwinist?"

Both men were influenced by Thomas Malthus's population theory. Both used and developed arguments first made by Malthus. Weikart's analysis is that the views of Spencer and Darwin provide a striking example of convergent evolution.

"Because laissez-faire economic ideals were so prominent in English intellectual and political life in the mid-nineteenth century, it should come as no surprise that Darwin and Spencer imbibed these ideas independently. Their thinking about human society was shaped heavily by mid-Victorian economic values and concepts such as competition, division of labor, and adaptation."

Spencer's thinking was developed earlier than Darwin's, although Spencer's views can be described as Lamarkian. After reading Darwin, he incorporated selection into his thinking.

"Thus long before he read Darwin, Spencer (1851, 324) embraced the position that laissez-faire was necessary to ensure biological progress, not only by stimulating some people to improve themselves (Lamarckism), but also by society "excreting its unhealthy, imbecile, slow, vacillating, faithless members" (Darwinian selection)."

Although there are hints of Darwin's thinking on these matters before 1871, it was not until the publication of "The Descent of Man" that we have something more substantial to refer to.

"But would not the evolution of morality, based on what Darwin called social instincts, ameliorate the struggle for existence among humans? Would it not temper the struggle for existence with moral sentiments that would make humans cooperate? Yes, Darwin explained, when he forthrightly broached the subject in the last half of chapter five, in a section entitled, "Natural Selection as affecting Civilised Nations." In this section Darwin explained his views about how his theory impinged on human society. If one wants to know whether or not Darwin was a social Darwinist, especially in relation to laissez-faire economics, this is the section to examine."

After reviewing the views of different scholars and making his own arguments, Weikart concludes that:

"Though Darwin's advocacy of laissez-faire economic competition was neither as vocal nor as radical as Spencer's, he clearly viewed economic competition as an integral part of the human struggle for existence, and he insisted that governments should foster, not reduce, competition."

So, it is concluded that both men were social Darwinists and that they had come to their views largely independently. Darwin made no attempt to distance himself from Spencer on these matters.

"Despite any differences between them, Darwin and Spencer were both laissez-faire social Darwinists. They both used biological arguments to justify economic policies designed to sharpen human competition. They warned against government involvement or legislation that would significantly reduce economic competition because they thought this would result in biological deterioration. They developed these ideas in a common intellectual and social context where laissez-faire economics was economic orthodoxy. Spencer was certainly the first of the two to publish his social Darwinist ideas, if it is appropriate to use this term before 1859. Spencer's laissez-faire views were also even more radical than Darwin's since his opposition to government intervention was far more radical than most laissez-faire proponents. Darwin's views were more in line with mainstream laissez-faire economics."

The take-home message is this: Darwinism is NOT a purely scientific theory. The science cannot be divorced from the underpinning philosophy. Projects like "Rescuing Darwin" are fundamentally flawed and philosophically naive. Educationalists have a duty to introduce students to these issues in a way that encourages critical thought and analysis.

Was Darwin or Spencer the Father of Laissez-Faire Social Darwinism?
Richard Weikart
Journal of Economic Behavior and Organization, 71, 2009, 20-28 | doi:10.1016/j.jebo.2007.06.011

Abstract: This article explores the way that Darwin and Spencer integrated laissez-faire ideas into their evolutionary biology, and how they then extrapolated from their evolutionary theories to social and economic thought. It argues that Darwin and Spencer developed laissez-faire social Darwinism independently, making both important progenitors of it.

The journal Science carries an interview with Eugenie Scott, who is executive director of the National Center for Science Education. She is presented as a tireless warrior, who is to be found "on the frontlines of the contentious battle over teaching evolution in U.S. public schools." She refers to her opponents as "the enemy". They are diverse: "creation science, intelligent design [ID], and antievolution" protagonists. Those of us who follow these issues are well aware of the stance Scott takes and the arguments she brings. This blog is concerned with the way Science presents her thinking as mainstream, with no attempt to provide analysis or to suggest that Scott's thinking deserves to be critiqued.

We have reached a situation today where any criticism of Darwinism is repackaged as an assault on science. To frame the issues in this way is to close down discussion and critical analysis. It is a problem, not only for ID scientists and creation-based scientists, but also for evolutionary biologists who accept that Darwinism does not deliver the mechanisms needed to accomplish biological transformation. For more on this, go here and here. Darwinians like Scott have a blind spot: they have so equated their cherished theory with 'science', that they are unable to appreciate that some of us want a genuine scientific debate about mechanisms: what they can achieve and what their limitations are.

Research has shown that 10% of blind dogs have blurred vision but this appears to make no difference to their day-to-day duties. It is thought that the animals compensate by relying more on smell and hearing. There is a useful analogy here with science leaders. (Source here)

This blind spot spills over into education. "Besides periodic assaults on science standards as we recently saw in Texas, we are concerned about antievolution legislation in different states under the guise of academic freedom bills." Scott does not admit that the principle of academic freedom implies the right to bring criticism of Darwinism into the classroom. Consequently, "academic freedom" advocates are painted as subversive to science. There are ideological agendas behind this opposition to developing the critical minds of students (for more, go here).

A revealing Q&A concerned the relevance of evolutionary theory for practicing scientists. The answer given by Scott is actually very weak. Instead of pointing out examples of relevance, she makes a sweeping statement about seeing the "big picture":

Q: Why is it important to teach evolution? Can't doctors and most life scientists do their jobs without accepting evolution?
E.S.: You can be a mechanic without understanding the niceties of the internal combustion engine. [But] wouldn't you rather go to a mechanic who has the big picture?

This fails to interact with those scientists who are prepared to say that evolutionary theory is more of a surficial veneer than an underpinning framework (go here). Also, it fails to do justice to the place of design in medicine: those who consider the human body to be designed have had a good track record for helping to cure ailments, whereas reductionistic biology tends to focus on symptoms rather than causes and the emerging field of Darwinian medicine is largely untried and untested (go here and here).

One further area where Scott needs to be challenged is in her understanding of the philosophy of science. She appears to think that science transcends philosophy. When talking about what scientists should not do, her argument envisages scientists drawing philosophical ideas from science. Some draw atheism; some draw theism. Here is the relevant part of the interview:

"What university scientists should not do is to force students to choose between religion and science. If a professor were to say that evolution proves there is no God, that's not just bad philosophy of science, it ensures that a significant number of students will stick their fingers in their ears.
When explaining biological questions, such as the evolution of the eye, there is no need to say that God had nothing to do with it. It's an irrelevant comment. I don't think a classroom is an appropriate place to try to create more atheists any more than it is an appropriate place to create more fundamentalist Christians."

A major element of the analysis contributed by ID scholars is that philosophy underpins science. This is not an exclusive emphasis by any means - for this view is common among philosophers of science. The problem is that few ask questions about the ideological underpinnings of science and whether different ideologies matter. Is it fairer to say "evolution proves there is no God" or "atheism leads to a science of origins where there is no purpose, guidance or any role for a Creator"? There is plenty of evidence for "bad philosophy of science", but it is evident at a deeper level than acknowledged by Scott. For more, go here.

What shall we say about Scott's approach to explaining "biological questions, such as the evolution of the eye". Notice that she does not refer to the functioning of the eye (which is a question for empirical science) but rather to the evolution of the eye (which is a question for historical science that presumes the eye has evolved). The philosophical issues needing consideration are affected by the questions asked. Scott says: "there is no need to say that God had nothing to do with it. It's an irrelevant comment." From a scientific perspective, the issue concerns causation. What causes are legitimate to consider within science? We are familiar with the role of natural law within science. We are also aware of chance events which need statistical description rather than physical or chemical laws. The controversial area of causation concerns intelligent agency (design). ID advocates do not think that it is irrelevant to consider the possibility of intelligent causation and have proposed various tests to distinguish law, chance and design. The unwillingness of Scott to acknowledge that design can be even considered within science is a reflection on the philosophy of science she has adopted: a metaphysical presupposition that prohibits design from being discerned. This metaphysical stance creates the blind spot. For more, go here.

The real concern is not that Scott holds these views (for we live in the free world where we protect academic freedom). It is problematical because Science did not think it appropriate to provide a forum for dialogue with scientists who have a different philosophy of science. To pretend that there is no debate over these issues is folly. For a recent contribution relating to the policy adopted by the Texas State Board of Education, go here.

Eugenie Scott Toils in Defense of Evolution
Yudhijit Bhattacharjee
Science 324, 5 June 2009: 1250-1251 | DOI: 10.1126/science.324_1250b

1st para: As executive director of the California-based National Center for Science Education, anthropologist Eugenie Scott has spent the past 2 decades on the frontlines of the contentious battle over teaching evolution in U.S. public schools. [. . .] Last week, Scott won the inaugural Stephen Jay Gould Prize from the Society for the Study of Evolution, only weeks after Scientific American ranked her among the country's top 10 science and technology leaders for her self-described role as "Darwin's golden retriever." Scott spoke to Science last week about where things now stand.

See also:

Hunter, C. Pure Dogma, Darwin's God (blog), 4 June 2009.

Mcleroy, D. State curriculum ensures only science taught in science classes, The Eagle, May 31, 2009

The blogosphere seems to have realised that there is more hype than substance about the alleged status of Darwinius masillae. In itself, this is reassuring. Providing critical thought about the claims is not just the province of Darwin-doubters. For a selection of relevant links, try ScienceNOW, The Times, Livescience and Ergo Sum Daniel. An overview of the hype is elsewhere on the ARN site, Nature published some quotes that illustrate the "frenzy", and an Editorial in Nature refers to the media communicating a "drastic misrepresentation" of the significance of Ida and what the research team actually claim in their research paper. My interest in adding some thoughts is to tease out some of the scientific issues stimulated by the fossil find.

Ida under the spotlight (Credit: Tyler Lang, Source here)

Today, lemurs are found only on Madagascar and the neighbouring Comores Islands. Fossil lemurs are known: although Madagascar is the dominant source. A significant find in the year 2001, dated at 30 Ma (which makes it earlier than all the African lemurs), comes from Pakistan. This raised questions about whether lemurs originated in Asia rather than Africa. The Messel Pit in Germany has yielded eight fragmentary specimens of primates. A lemur-like species named Godinotia is one of these. Ida is recognisably a fossil lemur and she also comes from the Messel Pit. This confirms that questions need to be asked about the past geographical spread of these animals and also suggests that the model of the lemur ancestors being marooned on Madagascar with subsequent diversification is over-simplistic.

The term "missing link" has been used to publicise the fossil find. The term has fallen out of favour because Darwinists are committed to gradualism, and it follows that every fossil represents a link in the chain from an ancestral form to descendants. For them, it is misleading to refer to one particular fossil as a transitional form because every fosil is transitional in some sense. Advocates of Punctuated Equilibria reject this. They consider species to have a distinct identity: they are born, they live, they die (extinctions). Within their paradigm, it is reasonable to talk about forms that are transitional between one distinct species and another.

To get an evolutionary perspective on human ancestors, we can turn to Richard Dawkins' book The Ancestor's Tale. In a pilgrimage back in time, Dawkins leads his readers to rendezvous with human ancestors. He traces the phylogeny back through the apes and, at Rendezvous 5 about 25 Ma ago, we meet the common ancestor of apes and Old World monkeys. Going back further, at Rendezvous 6 about 40 Ma ago, the apes/Old World monkeys branch meets the New World monkeys branch. Going back further, at Rendezvous 7 which Dawkins puts at 58 Ma ago, the apes/monkeys (anthropoid) branch meets the tarsiers branch. It is only at Rendezvous 8 (associated with a date of 63 Ma) that we reach the ancestor of all primates. The two branches here are the haplorhine primates (apes/monkeys/tarsiers) and strepsirhine primates (mostly lemurs). It is this ancestral "link" that the researchers are claiming to have found: the common ancestor of all primates, including humans. (Note the mismatch on time - Ida is dated as 47 Ma).

The media hype passed lightly over these technical details: the headlines say the missing link is ancestral to humans! When asked about the mismatch between the technical paper and the media headlines, lead author Hurum said:

"I don't think a discussion of Haplorhines [tarsiers, apes, monkeys and humans] and Strepsirhines [the suborder of primates comprising lemurs and lorises] would be easy in popular science. You need to simplify it down to more understandable words. Of course in that you lose a little bit of the scientific terms, but really I think the message is very, very much the same in what we are doing popularly and scientifically."

The claim of the researchers is that the newly described fossil is not just another fossil lemur, but an animal that is ancestral to both lemurs and haplorhines. This requires a redrawing of the family tree and it conflicts with the thinking of numerous other researchers in the field. Norman MacLeod and Angela Milner make some interesting comments about the structure needed for a convincing argument:

"So is Ida another of these great "missing links"? Perhaps - but there is a problem. In order to be recognised as a true ancestor, a fossil must have no truly unique aspects: it must have passed all of its characteristics on to its daughter species, albeit in an altered form. [. . .] On this qualification, the Tiktaalik and Archaeopteryx both fall down as true missing links: both have unique features that have not been passed on to any living creatures. In other words, despite their enormous importance, they are not true ancestors, but belong to small branches of the tree of life whose form is close to that of the true ancestor.
Is the same true of Ida? Well, her fossil's status as a missing link is controversial in a slightly different way. Ida lacks some of the features common to modern lemurs, but does not appear to possess any features unique to our own lineage of anthropoid primates. This renders Ida's evolutionary status ambiguous, at best."

Further technical discussion is provided by Brian Switek, and his points are picked up and endorsed by many others.

"The bottom line is that the hypothesis that Darwinius is closer to anthropoids than tarsiers or omomyids does not have strong support. Even though the authors of the paper constructed a very simple cladogram they did not undertake a full, rigorous cladistic analysis to support their claims. I am baffled as to how they could stress the significance of this fossil without undertaking the requisite research to support their hypothesis.
Is Darwinius important to understanding primate evolution? Of course! It is an exceptionally preserved specimen that could do much to aid our understanding of adapid evolution and paleobiology. The grand claims about it being our ancestor, though, cannot be upheld as true. The researchers simply did not do the work to support their case."

Hurum was asked about what it would take to persuade other palaeontologists that he is right, and Hurum commented that work is in progress that will convince them. This illustrates the problem with creating a media frenzy. The editorial in Nature suggests that a "hyped-up fossil find highlights the potential dangers of publicity machines". Darwin sceptics are accustomed to such media manipulation. The headlines proclaim the advance in evolutionary understanding, but with the passing of time, the significance of the find decreases exponentially. We may yet find that this superbly preserved fossil lemur is within the range of variation observed in living and fossil lemurs and is more suited to provide evidence of stasis within the lemur basic type.

Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology.
Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, Smith, B.H.
PLoS ONE, 2009, 4(5): e5723 | doi:10.1371/journal.pone.0005723

From the Abstract: Darwinius masillae represents the most complete fossil primate ever found, including both skeleton, soft body outline and contents of the digestive tract. Study of all these features allows a fairly complete reconstruction of life history, locomotion, and diet. Any future study of Eocene-Oligocene primates should benefit from information preserved in the Darwinius holotype. Of particular importance to phylogenetic studies, the absence of a toilet claw and a toothcomb demonstrates that Darwinius masillae is not simply a fossil lemur, but part of a larger group of primates, Adapoidea, representative of the early haplorhine diversification.

See also:

Media frenzy, Editorial, Nature 459, 484 (28 May 2009) | doi:10.1038/459484a

So could Ida be the true missing link? By Norman MacLeod and Angela Milner, The Daily Telegraph, 26 May 2009

Poor, poor Ida, Or: "Overselling an Adapid", by Brian Switek, Laelaps (blog), May 19, 2009

In an essay in Science's series in honour of the Year of Darwin, John Travis explored the evolution of the immune system. He hits the ground running by recounting the Dover trial and the encounter between biochemist Michael Behe as witness and lawyer Eric Rothschild. A dramatic moment was recalled. Behe had claimed that "The scientific literature has no answers to the question of the origin of the immune system." Rothschild came prepared: he started to bring out journal articles, books, and book chapters, which he said demonstrated research on the evolutionary origins of immunity. Behe was unimpressed. "They're wonderful articles. [. . .] They simply just don't address the question that I pose," he responded. Travis reports that the judge believed Rothschild and rejected Behe's testimony:

The judge, John E. Jones, found Behe's responses revealing. Behe "was presented with 58 peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution," the judge wrote in his decision. Jones concluded that ID proponents set "a scientifically unreasonable burden of proof for the theory of evolution." Score one for evolution, which is now taught without competition from ID in Dover schools.

Exhibit A. This stack of evolutionary immune research literature was used in the Dover trial. (Credit: Nick Matzke/National Center For Science Education, Source Science)

One only has to read Travis' essay to realise that answers have been proposed but are still being evaluated. Some perceive a sudden and dramatic assembly of the immune system and others look for gradual change. Here is a taste of the tensions:

"The basic idea of an immune 'big bang' in the vertebrates has led to a variety of oversimplifications and conceptual problems," says Rast. "Whatever the actual evolutionary pathway that led to the very complex vertebrate adaptive system, it was surely a gradual progression that co-opted many preexisting immune mechanisms."

There is no doubt that many immunologists have written about the origin of the immune system. Judge Jones was impressed by that. But academics do not weigh student essays to award marks - they look at the arguments presented. This principle must also apply to research papers. Speculation does not count as evidence! Furthermore, when the presuppositions of the research exclude design, these do not count either when evaluating alternatives that include design. As an example, consider Marchalonis et al (2006): these words are taken from the Introduction.

"At the onset, we emphasize that evolution is a stochastic or accidental process building upon the spontaneous generation of mutations followed by natural selection based upon survival to reproduce under external/environmental conditions. Our conceptual approach, thus, differs fundamentally from the theoretical approach presented by Cohn, because we adhere to the principle that 'in evolutionary systems there is no design'."

Dr Behe submitted a letter of response to Science, but has been informed that his letter was not of sufficient interest to publish. The Darwinians are quick to claim a victory over these issues but are simply not able to get beyond speculations about the origin of the immune system. Here is Behe's last paragraph.

In my court testimony I cited the then-new article by Klein and Nikolaidis, "The descent of the antibody-based immune system by gradual evolution" (Proc. Natl. Acad. Sci. USA 102:169-174, 2005), which first disputed the big bang hypothesis. In it the authors candidly remark, "Here, we sketch out some of the changes that the emergence of the AIS entailed and speculate how they may have come about." Valuable as it might be to science, however, speculation is not data, let alone an experimental result. Students are poorly served when they are not taught to distinguish among them.

On the Origin of The Immune System
John Travis
Science, 324, 1 May 2009: 580-582.
Did the immune system evolve to keep out harmful organisms, or is it like a bouncer at a nightclub, trained to allow the right microbes in and kick the less desirable ones out? In the fifth essay in Science's series in honor of the Year of Darwin, John Travis explores the evolution of the immune system.

See also:

Behe, M.J. Letter to Science (unpublished), Amazon Blog, 21 May 2009

Marchalonis, J.J. et al. The antibody repertoire in evolution: Chance, selection, and continuity, Developmental & Comparative Immunology, 30(1-2), 2006, 223-247 | doi: 10.1016/j.dci.2005.06.011

It is good advice to be wary of anyone purporting to represent the consensus in science. Those who speak the loudest about scientific consensus are often advancing other agendas. A good example can be derived from what people say about the 'scientific method'. Anyone practising science needs to know what it is, but in the real world, the progress of science often departs from the norm. Paul Dirac was a case in point. He was a theoretical physicist at Cambridge University who, in 1928, developed the maths that described the quantum behaviour of electrons. This led to the conclusion that it must be possible for an electron to have a positive charge. Later, Dirac described it as an "anti-electron" and when it was discovered in 1932 it was named the positron. The following year, Dirac received the Nobel Prize for his work. The first biography of this genius has been published recently and an informative review appears in the current Nature.

The unconventional Paul Dirac (Credit: Bettmann/Corbis, Source here)

Several characteristics of Dirac's work do not fit well with the consensus way of doing science. First, Dirac was a pure theoretician. He was not an experimentalist (although, later in life, this changed). He did not show any interest in stimulating a quest to find the positron.

"Although he commented that it could be made transiently in experiments, he was surprisingly circumspect, more concerned with the difficulties of detection than the inevitability of its existence. He made no suggestion as to how experimentalists might make it, or recognize it. He was away in the United States later that year when Robert Millikan gave a talk at the University of Cambridge, UK, showing Anderson's images of particle tracks from cosmic rays - including some that looked like those of electrons but which curved the wrong way in a magnetic field. No one associated these tracks with Dirac's holes."

Second, not brought out in the Nature review, but nicely described in other essays, Dirac was a theoretician who thought that elegant theory, beautiful maths and good science go together. Dirac was confident in his theoretical work, not because it had been confirmed empirically, but because it satisfied his aesthetic sense of the relationship between physics and the real world.

[Waldegrave]: "And yet Dirac's brand of theoretical physics, and the way he saw the world, was so close to philosophy. He was convinced that the more beautiful an equation, the more likely it was to be accurate - in other words, he saw a picture of the world that was of such beauty that it had to be true."
[and]
[Carey] "Even his fellow physicists complained that he worked in a deliberately mystifying private language. For his part, he insisted that the quantum world could not be expressed in words or imagined. To draw its picture would be "like a blind man sensing a snowflake. One touch and it's gone". Its beauty revealed itself only in mathematical formulae."

But the greatest contrast between the consensus scientific method and Dirac's research experience is found in the route to reach radical or revolutionary conclusions. Dirac was working on the frontiers of relativistic quantum theory and he was pioneering in his foresight of the "mirror world of antimatter". His colleagues were rather sceptical.

By 1932, the holes had become a joke. At a meeting in Copenhagen, when Bohr lost his patience and confronted Dirac with: "Do you believe all that stuff?", he simply replied, "I don't think anyone has put a conclusive argument against it."
[and]
[Waldegrave]: His great equation for the electron - an improbable marriage of relativity and quantum theory - only worked if you assumed that there was such a thing as an "anti-electron". His colleagues mocked the idea, but Dirac stuck to his guns: the maths was so harmonious that reality had to reflect it.

The hallmark of any revolutionary idea in science is that, before the transformation, the community of scientists are sceptical about the new ideas, with some expressing outright disagreement. After the change, the community applauds the new research - which becomes the new orthodoxy. The 'scientific method' knows nothing of this punctuated change, for it portrays an incremental step-by-step approach towards increasing knowledge. To explain scientific revolutions, we need something more. The analysis of Thomas Kuhn provides such an explanation, forcing us to think through the meaning of scientific paradigms. According to Kuhn, any community of researchers share a set of assumptions, concepts, values, and practices. This is their way of viewing the world and, generally, is exempt from being questioned or changed. Much can be done from within this conceptual framework, but observations will be found that create tensions or understanding. These tensions are the drivers for a paradigm shift, and the process of change can be traumatic.

Paul Dirac's pioneering work in quantum physics led to him sharing with Erwin Schrodinger the 1933 Nobel Prize for physics. This was awarded "for the discovery of new productive forms of atomic theory". He was Lucasian professor of mathematics at Cambridge from 1932 to 1969. His appreciation of beauty in the mathematics of the physical world is reminiscent of one of his predecessors in the Lucasian Chair. Isaac Newton had great confidence in the inverse square law of gravity. This confidence came because of his commitment to design in nature. Dirac is said to have been an atheist, but he is also reported to have said: "God used beautiful mathematics in creating the world".

These thoughts on the scientific method are being contributed because there are many strident voices insisting on what science is and what it is not. The claim that 'ID is not science' crops up repeatedly. Books and articles are published regularly making grandiose claims about the crisis facing science if students are even exposed to design-based thinking. What characterises them all is that they fail to engage with what ID scholars are actually saying. ID scientists are interested in truth. They operate within a different paradigm than scientists starting out with a materialistic philosophy. If there is a commitment to truth-seeking on all sides, then there has to be some way for scientists with different paradigms to interact meaningfully. Isaac Newton and Paul Dirac held the same professorial chair at Cambridge University - perhaps that provides a lesson for us all.

Paul Dirac: a physicist of few words
Frank Close
Nature 459, 326-327 (21 May 2009) | doi:10.1038/459326a

A detailed biography argues that the Nobel prizewinner's notorious reticence delayed experimentalists from discovering the antimatter that would confirm his elegant theory.

According to one commentator, the newly published research provides "one of the great advances in prebiotic chemistry". The media have captured the excitement with headlines like "Chemist Shows How RNA Can Be the Starting Point for Life" (New York Times), "Molecule of life emerges from laboratory slime" (New Scientist) and "How RNA got started" (Science News). These are strong statements and they deserve closer attention. What is going on in the field of OOL research?

Artistic portrayal of the 'RNA World' dream (Credit: Nicolle Rager Fuller & National Science Foundation, Source here)

The first point worth making is that new advances are often shown to be significant by referring to the lack of progress that had earlier characterised the field. This is often a surprise to the general public, who are typically fed a story that the problems are largely cracked and abiogenesis researchers are confident of tying up the loose ends in the near future. Wade's report refers to the solution of "a problem that for 20 years has thwarted researchers trying to understand the origin of life - how the building blocks of RNA, called nucleotides, could have spontaneously assembled themselves in the conditions of the primitive earth." Van Noorden explains the problem like this:

"An RNA polymer is a string of ribonucleotides, each made up of three distinct parts: a ribose sugar, a phosphate group and a base - either cytosine or uracil, known as pyrimidines, or the purines guanine or adenine. Imagining how such a polymer might have formed spontaneously, chemists had thought the subunits would probably assemble themselves first, then join to form a ribonucleotide. But even in the controlled atmosphere of a laboratory, efforts to connect ribose and base together have met with frustrating failure."

Abiogenesis researchers adopt either 'law' or 'chance' as causal explanations. They have rejected 'design' (not because it does not work, but because they insist on all causation being material). The new research is driven by a confidence in 'law'. The researchers are chemists. For them, the origin of life is a matter of chemistry. Thus, Sutherland, the lead author, is quoted as saying:

"My ultimate goal is to get a living system (RNA) emerging from a one-pot experiment. We can pull this off. We just need to know what the constraints on the conditions are first."
[and]
"My assumption is that we are here on this planet as a fundamental consequence of organic chemistry, so it must be chemistry that wants to work."

What, then, has been achieved? The researchers have synthesised both pyrimidine ribonucleotides (but not the purine ribonucleotides). As Van Noorden described it, they have "shown that it is possible to build one part of RNA from small molecules". They have not formed RNA molecules; they have not addressed the chirality problem, they have not generated any biological information and they have not made RNA do anything of biological significance, let alone become clothed with a membrane and undergo replication. Nevertheless, what they have done can be applauded as an elegant example of systems chemistry. A specific bond was needed between the Ribose and the Nucleobase, and a decade of research proved that the bond was not going to form directly. So what the researchers did was to create the bond and then turn the components on each side of the bond into the desired building blocks of the Ribonucleotide. Phosphate, which previously caused problems for OOL researchers, becomes a catalyst. Szostak's News and Views essay draws attention to the elegance of their approach:

"But in a remarkable example of 'systems chemistry', in which reactants from different stages of a pathway are allowed to interact, Powner et al. show that phosphate tames the combinatorial explosion, allowing oxygenous and nitrogenous reactants to interact fruitfully."
[. . .]
"The penultimate reaction of the sequence, in which the phosphate is attached to the nucleoside, is another beautiful example of the influence of systems chemistry in this set of interlinked reactions. The phosphorylation if facilitated by the presence of urea; the urea comes from the phosphate-catalysed hydrolysis of a by-product from an earlier reaction in the sequence."

It is good chemistry, but does it achieve a major advance in abiogenesis research? Questions can certainly be raised. The researchers argue that they are not starting with any unrealistic initial conditions: "We don't use any way-out scenarios - all the conditions are consistent with what we know about early Earth." However, this is disputed.

"The flaw with this kind of research is not in the chemistry. The flaw is in the logic - that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro, a chemist at New York University.
[and]
Dr. Robert Shapiro [. . .] said the recipe "definitely does not meet my criteria for a plausible pathway to the RNA world." He said that cyano-acetylene, one of Dr. Sutherland's assumed starting materials, is quickly destroyed by other chemicals and its appearance in pure form on the early earth "could be considered a fantasy."
[and]
"But while this is a step forward, it's not the whole picture," [James] Ferris [of the Rensselaer Polytechnic Institute in Troy, N.Y.] points out. "It's not as simple as putting compounds in a beaker and mixing it up. It's a series of steps. You still have to stop and purify and then do the next step, and that probably didn't happen in the ancient world."

It can be argued that the chemical reactions documented actually yield products that are intelligently designed. The experimental conditions are engineered to selectively accumulate some reaction products (by fractional crystallisation) and selectively destroy others (by the influence of UV radiation). These conditions are considered more plausible in Darwin's hypothetical "little warm pond". Indeed, Wade's report says: "Dr. Sutherland's report supports Darwin". This is significant because the emphasis in abiogenesis research has shifted in recent years to other scenarios - notably at mid-ocean ridge locations. Those who find themselves impressed with the potential of this research would do well to reflect on the way the chemistry is engineered to achieve the outcomes and the associated fine tuning of environmental factors. These are not Darwinian emphases!

Of the other limitations mentioned above, the chirality problem is noted in Wade's report:

"A serious puzzle about the nature of life is that most of its molecules are right-handed or left-handed, whereas in nature mixtures of both forms exist. Dr. Joyce [an expert on the chemical origin of life at the Scripps Research Institute in La Jolla, Calif.] said he had hoped an explanation for the one-handedness of biological molecules would emerge from prebiotic chemistry, but Dr. Sutherland's reactions do not supply any such explanation."

For those of us more familiar with 'design' as a causal explanation, this work does not dent the arguments already in place to demonstrate the futility of explaining life without design. Notably, the idea that life is just a matter of chemistry simply fails to engage with the information necessary for a cell to function as a biological entity. We are impressed by the systems chemistry reported, but find it such a shame that the hype surrounding the research is driven by the quest to explain life without a designer. Sutherland has ambitions to make a compelling case for chemical evolution: "That is the goal of my career", he says. A more worthy goal, although probably with less hype, would be to apply his undoubted talents to address contemporary conundrums facing the human race.

Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions
Matthew W. Powner, Beatrice Gerland, John D. Sutherland
Nature 459, 239-242 (14 May 2009) | doi:10.1038/nature08013

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively, and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis - cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate - are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

See also:

Luskin, C. Scientists Say Intelligent Designer Needed for Origin of Life Chemistry, Evolution News & Views, 7 July 2009.

Szostak, J.W., Origins of life: Systems chemistry on early Earth, Nature 459, 171-172 (14 May 2009) | doi:10.1038/459171a

Van Noorden, R., RNA world easier to make, Nature News, 13 May 2009 | doi:10.1038/news.2009.471

Wade, N., Chemist Shows How RNA Can Be the Starting Point for Life, New York Times, 14 May 2009.

The new find "will either be nothing or the biggest revolution in paleontology ever". These words were spoken by a palaeontologist in response to newly published research. He was commenting on a report of well-preserved tissues and primary collagen sequences recovered from the femur of a plant-eating dinosaur identified as a hadrosaur. It followed several years of intense activity by Mary Schweitzer and colleagues, whose previous papers on soft tissues in dinosaur bones were met with great scepticism. Last year, it seemed as if the claim had met its final rebuttal when the soft tissues were suggested by the same palaeontologist quoted above to "have come from bacterial contamination". However, the new research appears to have answered the critics very effectively.

Multiple hadrosaur red blood "cells" surrounded by white, fibrous matrix (Credit Mary H. Schweitzer, Source here)

The authors were well aware that their newly reported work adds fuel to the fire of controversy. They start their abstract by reminding readers about it and they end their paper with comments addressing the "appropriate skepticism" of earlier work. The problem is this: all direct measurements of the degeneration of biomolecules suggest timescales of hundreds or thousands of years (depending on environmental conditions). Indirect measurements, based on detecting biomolecules in artefacts of known age, suggest that the upper limit is less than a million years. Yet, the biomolecules detected in dinosaurs are considered to be 80 million years old. Two orders of magnitude justifies considerable skepticism!

Consequently, the authors have gone to great lengths to address concerns of contamination - particularly by the invasion of bacteria to form biofilms. The femur they have used came from an articulated hindlimb of a hadrosaur. The pes elements, tibia and fibula were collected in 2006, so they knew the femur was still embedded in rock. The following year, the rock containing the femur was removed, taking care that the fossil bone "was not exposed in the field". Every effort was made to prevent contamination so that all the materials examined were representative of the fossil itself. The researchers found a variety of morphological evidences that indicated they were handling fossil material of significance. "The variation in texture, microstructure, and colour of dinosaur material is consistent with extant tissues and not plausibly explained by biofilms". A battery of tests followed, with replication by another lab, leasing to some very convincing findings. Many critics of the earlier work are acknowledging the substantial nature of the new research. Service writes:

"Both groups then independently performed biochemical and antibody-binding studies that showed evidence of collagen as well as laminin and elastin, two proteins found in blood vessels."
[McIntosh, a critic of the earlier work, is quoted as saying:] "I'm not saying it's true. But I cannot right now make a plausible argument that it's not true." He adds: "The door is closing on plausible alternatives."

Yet another aspect of the newly published research is a comparison of the hadrosaur collagen sequences with collagen from birds, reptiles, mammals, amphibians and with the previous sequences obtained for T. rex. The findings from this comparison have captured headlines across the world. The emerging phylogenetic tree first places the two dinosaurs adjacent to the birds - subsequent to the branching point with reptiles. Undoubtedly, both dinosaur sequences are fragmentary. "The eight peptide sequences for collagen alpha1 type I and collagen alpha2 type I represent 7.8 and 2.5% of the full-length sequence for related organiosms, respectively." Nevertheless, whilst acknowledging this, the authors regard their analysis as a significant output.

"The amount of missing data in B. canadensis and T. rex sequences relative to extant samples resulted in relatively low resolution within Dinosauria, but even so, the phylogenetic relationship of recovered B. canadensis sequences supports the species' placement within Archosauria, closer to birds than Alligator."

In view of this, the sequence comparisons can and will be critiqued. Comment at this stage may be premature (although go here for further thoughts on the matter). From a design perspective, there is another angle on sequence comparisons worth considering. Instead of interpreting sequences in terms of evolutionary pathways, with similarities mapping ancestor/descendant relationships, similar sequences may actually correlate with similar functionalities. So, for example, similarities between dinosaur and avian collagen may result from similar design requirements relating to size/weight/strength criteria. These similarities are not evidences for birds and dinosaurs belonging to the same clade, but they are evidences for birds and dinosaurs having common physiological and anatomical design features.

One further point relates to the 'god-of-the-gaps' style of argumentation. ID scientists are unfairly charged with finding a gap in knowledge and filling it with a miracle (whereas design arguments are actually based on evidence - not the lack of it). With dinosaur soft tissue preservation, the shoe is on the other foot. All the knowledge we have points to the impossibility of detecting any protein sequences from dinosaurs. On these grounds, many were intensely sceptical of the T. rex analysis. Now that collagen sequences have been confirmed by replication, the challenge is to explain what was previously considered impossible. The authors conclude their paper with the words: "still unknown is the chemistry behind such preservation". On the basis of what we know, the creationist claim that the dinosaurs are not millions of years old might seem the more parsimonious. The point I am making is that 'god-of-the-gaps' charges are misdirected whenever people argue from evidence, and that most instances of the use of the phrase reveal its role as a rhetorical tool.

Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis
Mary H. Schweitzer, et al.
Science, 324, 1 May 2009: 626-631.

Abstract: Molecular preservation in non-avian dinosaurs is controversial. We present multiple lines of evidence that endogenous proteinaceous material is preserved in bone fragments and soft tissues from an 80-million-year-old Campanian hadrosaur, Brachylophosaurus canadensis [Museum of the Rockies (MOR) 2598]. Microstructural and immunological data are consistent with preservation of multiple bone matrix and vessel proteins, and phylogenetic analyses of Brachylophosaurus collagen sequenced by mass spectrometry robustly support the bird-dinosaur clade, consistent with an endogenous source for these collagen peptides. These data complement earlier results from Tyrannosaurus rex (MOR 1125) and confirm that molecular preservation in Cretaceous dinosaurs is not a unique event.

See also:

Service, R.F. 'Protein' in 80-Million-Year-Old Fossil Bolsters Controversial T. rex Claim, Science 324, 1 May 2009: 578.

New Data from 80-Million-Year-Old Dinosaur Demonstrates Ancient Protein Is Preserved, Beth Israel Deaconess Medical Center Press Release, 30 April 2009.

Tyler, D. T. rex - spectacular findings - wrong message. ARN Literature Blog (29 April 2008)

The transition from fish to land animal is regarded by many as well documented: it is number two in Nature's presentation of "15 evolutionary gems". Some of the names given to members of the tetrapod lineage are quite well known: Panderichthys and Tiktaalik, Ichthyostega and Acanthostega, for example.

"Open any paleontology text or children's book on prehistoric animals, and you will find something between fish and tetrapod, forelimbs or fins planted on the land, tail receding into the water, eyes cast hopefully forward. These images encapsulate an episode of vertebrate history spanning the latter half (390 to 360 million years ago) of the Devonian, the waning days of the "Age of Fishes.""

The first animals deemed to be tetrapods (rather than fish) are called Ichthyostega and Acanthostega. They both come from rocks from Greenland. Until recently, Acanthostega was considered to be the most primitive tetrapod, and Ichthyostega was considered to have more derived characters. New research has placed Ichthyostega before Acanthostega in evolutionary development. Whilst this appears a very minor tweaking of the story, there are more important issues raised by the change. Before discussing these, it is worth reminding ourselves that the tetrapod evolution story has morphed dramatically with time. The quotation above represents the 'conquest of the land' model, with fish-like animals crawling out of the water. However, more recent work has exploded this hypothesis. All the Devonian tetrapods have characteristics that suggest they were aquatic and that fin-limbs evolved for negotiating their way through underwater obstacles. Somehow, the hypothesis goes, these structures were co-opted for terrestrial use.

Painting of Acanthostaga at home in the water (Credit Janice McCafferty, Source here)

The researchers examined the humeri of Ichthyostega and Acanthostega. They could not do this by extracting the fossil bones and examining them visually. To avoid damaging them, they utilised computed tomography (CT) scanning to sense the shape of the fossils remotely. Then the animals were "reconstructed" using imaging software, The first significant discovery was that some of the rocks contained juvenile forms of Ichthyostega - previously known only as adults. Interest then focussed on the upper arm bones, or humeri. In his commentary article, Friedman writes:

"Found in both the forelimbs of tetrapods and the lobed fins of their "fish" relatives, the humerus is the single bone that links the appendage to the body. It is a complicated, festooned with bumps and ridges marking muscle origins and insertions. Because humeri are integral to the pectoral appendages, they record the biomechanical signature of the shift from fins to weight-bearing limbs."

The researchers obtained four sets of data: juvenile and adult Ichthyostega humeri, and juvenile and adult Acanthostega humeri. This allowed them to assess developmental differences between the two animals as they matured. An overview of the findings is provided in the press release (which cites Callier as first author):

"Anatomies can morph as animals move towards adulthood, Callier said. And such shifts can help scientists deduce when in development the animal acquired the terrestrial habit. The fossils suggest that Ichthyostega juveniles were aquatically adapted, and that the terrestrial habit was acquired relatively late in development. The fossils bore evidence that the muscle arrangement in adults was better suited to weight-bearing, terrestrial locomotion than the juvenile morphology. It is possible that Ichthyostega came out of the water only as a fully mature adult.
In contrast, in Acanthostega "there is less change from the juvenile to the adult. Although Acanthostega appears to be aquatically adapted throughout the recorded developmental span, its humerus exhibits subtle traits that make it more similar to the later, fully terrestrial tetrapods," Callier said."

This creates an unexpected situation: subtle traits in the humerus of Acanthostega place it nearer the fully terrestrial tetrapods, but other characters point to an aquatic existence. Resolving this tension results in some surprising speculations:

"Ironically, the shape of Acanthostega's limb's, in both adult and the newly-discovered juvenile forms, is more "paddle-like" than Ichthyostega's, Callier said. "They would have been really good swimmers. So, although Acanthostega had limbs with digits, we don't think it was really terrestrial. We think even the adults were aquatic."
"If Ichthyostega is actually more primitive than Acanthostega, then maybe animals evolved towards a terrestrial existence a lot earlier than originally believed," she said. "Maybe Acanthostega was actually derived from a terrestrial ancestor, and then, went back to an aquatic lifestyle.""

Some may consider this situation unconvincing, with rather too much speculation about subtle morphological traits. Nevertheless, since there is a presumption of evolutionary transformation, these data have to be fitted into a coherent framework. Earlier in the fossil record, there are fish and no tetrapods; later in the fossil record, there are clear signs of terrestrial tetrapods - so, it is inferred, there has to be a transition between them. The more we now of the fossil record, however, the more difficult it is to identify an evolutionary branch. Instead of a tree, we see a bush. But this means that the quest for missing links will be elusive. We cannot identify ancestors and descendants in the data accessible to us. This changes the nature of the debate. As Friedman says:

"After 150 years of paleontological research dedicated to filling the gap between fishes and tetrapods, it is time to move past the simple formula of "the next missing link" and confront broader questions about tetrapod origins. The field has come far from its pre-Darwinian roots and ancestor-descendant daisy-chains, and now yields a profusely branching tree and correspondingly nuanced scenarios of terrestrialization, including that proposed by Callier et al: in a very real sense, a tangled bank."

According to Viviane Callier: "If there is one take-home message, it is that the evolutionary relationship between these early tetrapods is not well resolved". To that we can add the need to abandon talk of "ancestor-descendant daisy-chains" and to recognise the role of evolutionary presuppositions in the analysis of data.

Contrasting Developmental Trajectories in the Earliest Known Tetrapod Forelimbs
Viviane Callier, Jennifer A. Clack, and Per E. Ahlberg
Science