Science Literature

The first species to have its genome decoded by 'next-generation-sequencing' (NGS) machines is the giant panda (Ailuropoda melanoleuca). The individual animal was known previously to the world as the mascot of the 2008 Beijing Olympic Games. Scientists have been excited by the report because the NGS approach is significantly cheaper and faster than other methods. It is not the purpose of this blog to assess the robustness of the method, but it is important to be aware that the reported sequence utilizes previously determined genomes as a reference platform: dog and human genomes in this case.

"Using evidence-based gene prediction, the human and dog genes [. . .] were projected onto the panda genome, and the gene loci were defined by using both sequence similarity and whole-genome synteny information."

The iconic giant panda's genetic makeup reveals degradation (Source here)

The estimated size of the giant panda genome is said to be 2.40 Gb (compared with 2.45 Gb for the dog genome and 3.0 Gb for humans) making up about 21,000 genes (similar to humans). "Overall, we found that the quality of the predicted panda genes was comparable to that of other well-annotated mammalian genes." Although the panda eats only bamboo leaves, genes associated with carnivory are present in the panda:

"Of interest, our analysis of genes potentially involved in the evolution of the panda's reliance on bamboo in its diet showed that the panda seems to have maintained the genetic requirements for being purely carnivorous even though its diet is primarily herbivorous."

There was no trace of genes that encode enzymes for digesting cellulose, raising questions about how the panda can possibly survive on bamboo. The hypothesis proposed is that the bamboo diet "may instead be more dependent on its gut microbiome". Confirmation of this will require further work. A related dietary factor concerns the sense of taste. The authors refer to the five components of taste: sweetness, saltiness, sourness, bitterness and umami. The giant panda has lost the capability of sensing umami, which means that meat has become unappetizing.

"Umami is sensed through the T1R family. In the panda genome, T1R2 and T1R3 are in an intact form, but T1R1 has become a pseudogene - we found that [. . .] two panda T1R1 exons contain transcript errors."
"Two frameshift mutations occurred in the third and sixth exons of the panda T1R1 gene. The third exon contained a 2-bp ('GG') insertion; the sixth exon contained a 4-bp ('GTGT') deletion."

A possible genetic factor affecting the giant panda's low fecundity rate was identified. Nearly all of the mammalian reproduction genes were mapped, and "a putative pseudo follicle-stimulating hormone (FSH) [beta]-subunit gene (giant panda-FSHB2)" was noted. The authors comment:

"At this stage, whether the pseudo FSHB2 gene contributes to the reproduction features of the giant panda remains to be determined."

Some have considered whether the panda genome helps resolve the animal's taxonomic status. Although most place the panda in the bear family (Ursidae), a case has been made that it belongs elsewhere - in the raccoon family (Ailuridae). Since we do not have the genomes for any of these possible relatives, there is little more that can be said on the matter. However, even if other genomes were sequenced, does the "genome" tell us much about what makes a bear differ from a raccoon or a dog or a human? The genome can be described as the repository of housekeeping genes; it provides the materials needed for the organism to function - but something much more than this is needed to inform taxonomy. The ENCODE project (along with many others) has revealed rich functionality in the non-coding DNA (alias 'junk DNA'). Consequently, it is probable that the gene sequencers are just scratching at the surface of genetic information.

If the giant panda is correctly assigned to the Ursidae, the new research contributes significantly to the way we understand the speciation of this animal. Before genome sequencing, we could say that it has diversified significantly from ancestral Ursidae stock. It has a reduced number of chromosomes, 42, whereas most bears have 74. It has a wholly vegetarian diet and it has a modified sesamoid bone which it uses to strip bamboo leaves from stems. The panda genome findings provide the background for understanding herbivory: the panda still retains the genes for carnivory but mutations have destroyed the taste trigger for it to eat meat. Although the panda cannot make enzymes for digesting plant food, communities of gut microbes are the most likely explanation of its continuing survival. The reproduction problems experienced by giant pandas may also be linked to a mutation affecting follicle stimulation.

The overall picture is one of speciation/diversification linked to genetic degradation. Natural selection, which has often been portrayed as all-powerful and capable of building exquisitely complex structures, has failed to provide the giant panda with any enzymes for digesting plant food. We do not know whether the modified sesamoid bone is an evolutionary innovation, a part of the degradation story or information neutral. The News & Views essay that accompanies the research paper calls the panda China's "national treasure" - and so it is. However, from the perspective of genetics, the giant panda is not in a healthy state. Whatever else may be relevant, this case has strong affinities with speciation by gene pool reduction. From the perspective of Darwinism, the giant panda genome testifies to the failure of Darwinian mechanisms to overcome problems caused by mutations. From the perspective of design, we have a story of how a superbly designed carnivore has managed to survive the effects of genetic degradation. From a conservation perspective, without human intervention, the chances of long-term survival are slender.

There is also the finding that Jingjing's genome has a high degree of genetic diversity, but she is unlikely to be representative of the panda population taken as a whole. It is more prudent to assume that the relatively isolated panda enclaves harbour problems of inbreeding and that Jingjing is an example of the benefits of breeding across enclaves - further supporting the case for human intervention.

The sequence and de novo assembly of the giant panda genome
Li, R. et al.
Nature 463, 311-317 (21 January 2010) | doi:10.1038/nature08696

Abstract: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

See also:

Worley, K.C. and Gibbs, R.A. Decoding a national treasure, Nature 463, 303-304 (21 January 2010) | doi:10.1038/463303a

Qiu, J., Genome reveals panda's carnivorous side, 13 December 2009, Nature News | doi:10.1038/news.2009.1141

The claim that Rubisco is poorly designed or unintelligently designed was appearing in textbooks in the 1990s. The idea has been picked up recently in a News & Views piece by John Ellis. He writes that Rubisco "is a relic of a bygone age" and his essay has the title: "Tackling unintelligent design".

"Rubisco is the most important enyzme on the planet - virtually all the organic carbon in the biosphere derives ultimately from the carbon dioxide that this enzyme fixes from the atmosphere. But Rubisco is also one of the most inefficient enzymes on the planet. It evolved when the atmospheric composition was different from that of today, and its failure to adapt significantly to the modern atmosphere limits agricultural productivity."

RuBisCO has an active site (binding pocket) that binds ribulose-1,5-bisphosphate (RuBP) and catalyzes the reaction between RuBP and CO2 or O2. In the figure, the two large RuBisCO subunits (blue and cyan) sandwich an RuBP molecule (orange) in the active site. The site is gated by the C-terminus (yellow), lysine 128 (purple), and loop 6 (green), which undergo periodic conformational changes that open or close the site. Reactants enter and products escape while it is in an open state, and carbon-fixation reactions occur during the closed state. (Image credit: Paul Crozier, Sandia National Labs. Source here)

Over the past decade, the pendulum has swung away from the idea that Rubisco is unintelligent design. Its achievements are remarkable, as Griffiths (2006) explains:

"It is curious that Rubisco should fix CO2 at all, as there is 25 times more O2 than CO2 in solution at 25 degC, and a 500-fold difference between them in gaseous form. Yet only 25% of reactions are oxygenase events at this temperature, and carbon intermediates 'lost' to the carbon fixation reactions by oxygenase action are metabolized and partly recovered by the so-called photorespiratory pathway. Catalysis begins with activation of Rubisco by the enzyme Rubisco activase, when first CO2 and then a magnesium ion bind to the active site. The substrate, ribulose bisphosphate, then reacts with these to form an enediol intermediate, which engages with either another CO2 or an O2 molecule, either of which must diffuse down a solvent channel to reach the active site."

The analysis of Tcherkez et al. (2006) was significant for showing that Rubisco does not bear the marks of Darwinian tinkering and that research to genetic modify the enzyme to gain agricultural benefits can be expected to deliver only "modest improvements" in its efficiency of operation.

"Further, [our hypothesis] raises the possibility that, despite appearing sluggish and confused, most Rubiscos may be near-optimally adapted to their different gaseous and thermal environments. If so, genetic manipulation can be expected to achieve only modest improvements in the efficiency of Rubisco and plant growth. Such improvement would be limited to the magnitude of the scatter apparent in the correlations (Fig. 3), if the scatter represents incomplete optimization (see above). [. . .] Such adaptation in response to the changing atmosphere and temperature appears to have been instrumental in enabling the expansion of the biosphere to its current size."

Design theorists have drawn attention to three additional considerations:
1. A single-factor analysis of Rubisco is inadequate. The parameters considered to conclude the enzyme is poorly designed and inefficient are very limited. We should note that our perceptions of intelligent design are typically subjective, and most claims for poor design do not stand up to the test of time - further research leads to a greater appreciation of design (a good example being mammalian eye design). Furthermore, unintelligent design of architectures we deem sub-optimal should not be regarded as the only possible hypothesis. Multiple factors are likely to be relevant as chemosynthetic carbon fixation also makes use of Rubisco. It is employed by organisms living at hydrothermal vents and cold hydrocarbon seeps.
2. Photorespiration, the consumption of oxygen to produce a sugar that ultimately forms carbon dioxide during a series of reactions, may not be a mark of inefficiency, but the process may be useful to the plant. The null hypothesis for Design theorists is that processes have functionality. This hypothesis is not without some support: the process of photosynthesis is not just to capture CO2 and release oxygen because nitrate assimilation in plant shoots depends on photorespiration, as Rachmilevitch et al (2004) have shown.
3. Ecological considerations should be included in the analysis. If design is relevant to understanding the way plants work, we should consider not only the benefits to the organism (which limits the horizon for those with a Darwinian perspective) but also the biosphere as a whole. Rubisco's ability to capture CO2 increases with increasing CO2 content in the atmosphere, so its efficiency rises in a CO2-rich atmosphere. However, increasing oxygen levels in the atmosphere will reduce Rubisco's ability to capture carbon. So a negative feedback mechanism exists to regulate the relative concentrations of oxygen and carbon dioxide in the atmosphere. This is another example of design affecting the Earth's ecology - for more on this, go here.

Ellis was commenting on a paper by Liu et al. that reports on work to produce a Rubisco in vitro. In order to do this, the authors required two chaperone proteins, ATP and addition of 18 protein subunits (taken from a cyanobacterial Rubisco) to be introduced in the correct sequence to get yields of the enzyme. It is hoped that this procedure can be used to produce mutated versions that can be screened for improved effectiveness. It's all very interesting, but the biggest mystery is why people who expend so much intellectual energy on improving this remarkable molecule can live with the thought that "Rubisco is a superb example of unintelligent design for the modern world". Maybe research funds would be better spent exploring avenues identified using the presumption that this enzyme is optimally designed.

Tackling unintelligent design
R. John Ellis
Nature 463, 164-165 (14 January 2010) | doi:10.1038/463164a [restricted link]

Abstract: The key enzyme in photosynthesis, Rubisco, is a relic of a bygone age. The ability to assemble Rubisco in the test tube offers the prospect of genetically manipulating the enzyme to make it fit for the modern world.

Coupled chaperone action in folding and assembly of hexadecameric Rubisco
Cuimin Liu, Anna L. Young, Amanda Starling-Windhof, Andreas Bracher, Sandra Saschenbrecker, Bharathi Vasudeva Rao, Karnam Vasudeva Rao, Otto Berninghausen, Thorsten Mielke, F. Ulrich Hartl, Roland Beckmann & Manajit Hayer-Hartl.
Nature 463, 197-202 (14 January 2010) | doi:10.1038/nature08651 [restricted link]

Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO2 in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX2. RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX2. As revealed by the structure of a RbcL8-(RbcX2)8 assembly intermediate, RbcX2 acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL8 core assembly. Finally, addition of RbcS results in RbcX2 release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.

See also:

Griffiths, H., Designs on Rubisco, Nature 441, 940-941 (22 June 2006) | doi:10.1038/441940a [restricted link]

Rachmilevitch, S., Cousins, A.B., Bloom, A.J., 2004. Nitrate Assimilation in plant shoots depends on photorespiration. Proceedings of the National Academy of Sciences USA, 101(31), 11506-11510 | doi: 10.1073/pnas.0404388101 [abstract]

Tcherkez, G.G.B., Farquhar, G.D. and Andrews, T.J., Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized, Proceedings of the National Academy of Sciences USA, May 9, 2006, 103(19), 7246-7251 | doi: 10.1073/pnas.0600605103 [abstract]

"It seems we have all been guilty of defaming Neanderthal man" declared a recent Editorial in The Guardian. This comment was triggered by a report documenting evidence for the use of pigments and decorative shells by Neanderthals. This is claimed to have occurred many years before any direct contact with modern humans, thereby undermining any thought that the artefacts did not really represent Neanderthal culture. Personal adornment, using a variety of colours, implies an aesthetic sense and an appreciation of symbolism. Since Neanderthals have often been presented as lacking these "modern" traits, the new research demands a reappraisal.

This decorative shell likely adorned the neck of a Neanderthal (Image credit Joao Zilhao, Source here)

It may be helpful to describe the findings by reference to a design methodology. Two archaeological sites from the Murcia province of southern Spain have yielded artefacts. Apart from the usual stone tools and hearth features, there are a variety of perforated shells and a striking range of coloured pigments. Elsewhere in the world, such finds are associated with personal ornamentation.

Red coloured pigments are made from mixtures of siderite, goethite, hematite and nontronite. Yellow coloured colorants were of siderite and natrojarosite. These minerals are not found at levels where they could be collected by Neanderthals in the immediate environment, although the authors report sources for the red materials 3-5 km to the northwest, and the closest source for the yellow materials is 7 km to the east. The options are: Law (the minerals were deposited by hydrothermal processes locally); Chance (the materials have been carried to the area by water flow or some other mechanism) and Design (Neanderthals sourced the pigments and brought them to the site). However, after considering pros and cons of these options, the authors are in no doubt about the implications. They conclude: "These pigments can only be manuports". The Design inference is the most parsimonious.

A similar, but more complex, analysis of the perforated shells was made. The authors find no essential difference between their Spanish material and other finds from Africa and the Near East where the "symbolic implications of body painting and of the ornamental use of pigment-stained and perforated marine shells are uncontroversial". This has led to the authors claiming a high degree of confidence in their conclusions about the "modern" behaviour of Neanderthals. According to BBC News:

"Professor Zilhao explained that the findings were dated at 10,000 years before any contact between Neanderthals and modern humans. "To me, it's the smoking gun that kills the argument once and for all," he told BBC News. "The association of these findings with Neanderthals is rock-solid and people have to draw the associations and bury this view of Neanderthals as half-wits.""

Once the implications of the new research sinks home, a different light is shed on previously reported cultural artefacts. Take, for example, the occurrence of "pierced and grooved animal teeth in Neandertal-associated archeological cultures (such as the Chatelperronian of France)". Because of contemporaneous modern humans, this has been explained by "stratigraphic mixing" or "imitation without understanding". However, it could equally well be explained as "independent Neandertal innovation". This is the conclusion reached by the lead author and his team:

"When considering the nature of the cultural and genetic exchanges that occurred between Neanderthals and modern humans at the time of contact in Europe, we should recognise that identical levels of cultural achievement had been reached by both sides." (source here)

We have had a long-sustained exposure to the idea that Neanderthals were sub-human. They have been presented as slow, lumbering, dim-witted and brutish! Most people are likely to think that Neanderthals could not use words to speak. Will the new research change perceptions?

"It's very difficult to dislodge the brutish image from popular thinking," Professor Stringer told BBC News. "When football fans behave badly, or politicians advocate reactionary views, they are invariably called 'Neanderthal', and I can't see the tabloids changing their headlines any time soon."

The situation we find ourselves in has come about because the Darwinist explanation of human origins has been adopted by our culture. The Darwin origins myth requires a gradual evolution of both anatomy and culture - from ape to man. Neanderthal Man has been part of this story - he is the archetypal intermediary. Despite many evidences to the contrary, little has been done to remove the myth. Indications of cultural sophistication were interpreted as Neanderthals trading artefacts with modern humans, or imitating without understanding. This is a good example of 'saving the paradigm' in a Kuhnian sense, whereby the old paradigm clings on by force-fitting contrary evidences into the accepted theoretical model. It is time to discard the Darwinian mindset that presupposes gradual evolution. Let researchers be free to approach the evidence with multiple working hypotheses and engage in a more rigorous programme of hypothesis testing and analysis.

Symbolic use of marine shells and mineral pigments by Iberian Neandertals
Joao Zilhao, Diego E. Angelucci, Ernestina Badal-Garcia, Francesco d'Errico, Floreal Daniel, Laure Dayet, Katerina Douka, Thomas F. G. Higham, Maria Jose Martinez-Sanchez, Ricardo Montes-Bernardez, Sonia Murcia-Mascaros, Carmen Perez-Sirvent, Clodoaldo Roldan-Garcia, Marian Vanhaeren, Valentin Villaverde, Rachel Wood and Josefina Zapata
Proceedings of the National Academy of Sciences, published online before print January 11, 2010 | doi:10.1073/pnas.0914088107

Abstract: Two sites of the Neandertal-associated Middle Paleolithic of Iberia, dated to as early as approximately 50,000 years ago, yielded perforated and pigment-stained marine shells. At Cueva de los Aviones, three umbo-perforated valves of Acanthocardia and Glycymeris were found alongside lumps of yellow and red colorants, and residues preserved inside a Spondylus shell consist of a red lepidocrocite base mixed with ground, dark red-to-black fragments of hematite and pyrite. A perforated Pecten shell, painted on its external, white side with an orange mix of goethite and hematite, was abandoned after breakage at Cueva Anton, 60 km inland. Comparable early modern human-associated material from Africa and the Near East is widely accepted as evidence for body ornamentation, implying behavioral modernity. The Iberian finds show that European Neandertals were no different from coeval Africans in this regard, countering genetic/cognitive explanations for the emergence of symbolism and strengthening demographic/social ones.

See also:

Tyler, D. Images of evolution as secular icons, ARN Literature Blog (10 April 2009)

Tyler, D. The cognitive skills of Stone Age Man, ARN Literature Blog (29 June 2009)

Tyler, D. Darwinist thinking on the origin of religion, ARN Literature Blog (9 November 2009)

A year ago, Nature published an educational booklet with the title 15 Evolutionary gems (as a resource for the Darwin Bicentennial). Number 2 gem is Tiktaalik a well-preserved fish that has been widely acclaimed as documenting the transition from fish to tetrapod. Tiktaalik was an elpistostegalian fish: a large, shallow-water dwelling carnivore with tetrapod affinities yet possessing fins. Unfortunately, until Tiktaalik, most elpistostegids remains were poorly preserved fragments.

"In 2006, Edward Daeschler and his colleagues described spectacularly well preserved fossils of an elpistostegid known as Tiktaalik that allow us to build up a good picture of an aquatic predator with distinct similarities to tetrapods - from its flexible neck, to its very limb-like fin structure. The discovery and painstaking analysis of Tiktaalik illuminates the stage before tetrapods evolved, and shows how the fossil record throws up surprises, albeit ones that are entirely compatible with evolutionary thinking."

How one of the Devonian animals might have made the tracks (Source BBC News)

Just when everyone thought that a consensus had emerged, a new fossil find is reported - throwing everything into the melting pot (again!). Trackways of an unknown tetrapod have been recovered from rocks dated 10 million years earlier than Tiktaalik. The authors say that the trackways occur in rocks that: "can be securely assigned to the lower-middle Eifelian, corresponding to an age of approximately 395 million years". At a stroke, this rules out not only Tiktaalik as a tetrapod ancestor, but also all known representatives of the elpistostegids. The arrival of tetrapods is now considered to be 20 million years earlier than previously thought and these tetrapods must now be regarded as coexisting with the elpistostegids. Once again, the fossil record has thrown up a big surprise, but this one is not "entirely compatible with evolutionary thinking". It is a find that was not predicted and it does not fit at all into the emerging consensus.

"Now, however, Niedzwiedzki et al. lob a grenade into that picture. They report the stunning discovery of tetrapod trackways with distinct digit imprints from Zachemie, Poland, that are unambiguously dated to the lowermost Eifelian (397 Myr ago). This site (an old quarry) has yielded a dozen trackways made by several individuals that ranged from about 0.5 to 2.5 metres in total length, and numerous isolated footprints found on fragments of scree. The tracks predate the oldest tetrapod skeletal remains by 18 Myr and, more surprisingly, the earliest elpistostegalian fishes by about 10 Myr." (Janvier & Clement, 2010)

The Nature Editor's summary explained: "The finds suggests that the elpistostegids that we know were late-surviving relics rather than direct transitional forms, and they highlight just how little we know of the earliest history of land vertebrates." Henry Gee, one of the Nature editors, wrote in a blog:

"What does it all mean?
It means that the neatly gift-wrapped correlation between stratigraphy and phylogeny, in which elpistostegids represent a transitional form in the swift evolution of tetrapods in the mid-Frasnian, is a cruel illusion. If - as the Polish footprints show - tetrapods already existed in the Eifelian, then an enormous evolutionary void has opened beneath our feet."

In another blog, Ed Yong discussed the significance of the find and is obviously impressed by the endorsement of one seasoned researcher directly involved in trying to understand the evolution of tetrapods:

"Jenny Clack, the Cambridge scientist who discovered Acanthostega, has seen the Polish tracks for herself and finds them more convincing. Her only reservation is that the detailed prints don't have any trackways to show how their maker moved, while the trackways themselves consist of blobs. "But so do lots of previously known tracks," she says. "If you'd found those in other deposits in the last part of the Devonian, you wouldn't have any qualms about them." She'd like to see trackways of the detailed prints but she's nonetheless excited. "It's going to change all our ideas about why tetrapods emerged from the water, as well as when and where.""

Rethinking the why and where is another aspect of this explosive discovery. The first tetrapods have been recognised as animals that lived in water. People have wondered whether fins evolved into legs as the animals negotiated plant material in shallow waters, perhaps brackish or even freshwater. These ideas may still be applicable to Acanthostega and Ichthyostega, but they are not realistic for the new tetrapod trackways - which are found in marine tidal flat sediments.

"Niedzwiedzki and colleagues' apparently anachronistic Eifelian tetrapod trackways will thus shake up thinking about tetrapod origins. They show that the first tetrapods thrived in the sea, trampling the mud of coral-reef lagoons; this is at odds with the long-held view that river deltas and lakes were the necessary environments for the transition from water to land during vertebrate evolution."

The ID interest in this story is for at least two reasons. First, the case documents an example of a failed evolutionary prediction - although, for a while, evolutionists have claimed it as a triumph (see the blog by Casey Luskin on this). Second, the evolution of tetrapods is an important test case for the relevance of design thinking - we ask the question whether tetrapods are here by Design or whether Law+Chance processes are sufficient explanation. Research is proceeding assuming the latter option, but the new discovery suggests that pursuing multiple working hypotheses (including design-based options) might be more prudent.

Tetrapod trackways from the early Middle Devonian period of Poland
Grzegorz Niedzwiedzki, Piotr Szrek, Katarzyna Narkiewicz, Marek Narkiewicz & Per E. Ahlberg
Nature, 463, 43-48 (7 January 2010) | doi:10.1038/nature08623

Abstract: The fossil record of the earliest tetrapods (vertebrates with limbs rather than paired fins) consists of body fossils and trackways. The earliest body fossils of tetrapods date to the Late Devonian period (late Frasnian stage) and are preceded by transitional elpistostegids such as Panderichthys and Tiktaalik that still have paired fins. Claims of tetrapod trackways predating these body fossils have remained controversial with regard to both age and the identity of the track makers. Here we present well preserved and securely dated tetrapod tracks from Polish marine tidal flat sediments of early Middle Devonian (Eifelian stage) age that are approximately 18 million years older than the earliest tetrapod body fossils and 10 million years earlier than the oldest elpistostegids. They force a radical reassessment of the timing, ecology and environmental setting of the fish tetrapod transition, as well as the completeness of the body fossil record.

See also:

Janvier, P. & Clément, G. Muddy tetrapod origins, Nature 463, 40-41 (7 January 2010) | doi:10.1038/463040a

Dalton, R. Discovery pushes back date of first four-legged animal, Nature News, 6 January 2010 | doi:10.1038/news.2010.1

Yong, E. Fossil tracks push back the invasion of land by 18 million years, Not exactly rocket science, January 6, 2010

Darwin landed at the port of Bahia, Brazil, on 28 February 1832. Whilst his writings about the natural history of that part of the world have received much attention, "less well known is the effect Darwin had on the people of Latin America". The effect came through intermediaries - people who were inspired by Darwinism to engineer social change.

The first group of leaders was influential from the late 1880s. They were intellectuals and politicians who had already drank from the wells of secularism. They found Darwin's The Descent of Man compelling and were attracted to the eugenics theorising of prominent Darwinians.

"They soaked up the latest ideas from Europe, and read the works of philosophers such as Herbert Spencer and Francis Galton, Darwin's cousin and the inventor of eugenics. Most Latin Americans thought that society, like nature, evolved from primitive to complex structures, and saw the industrial societies of Western Europe as being more culturally sophisticated than their own."

The secularisation of knowledge in biology was Darwin's most significant achievement, but with it came the conviction that human society needs the same mechanisms (image source here)

Turning this into policy, they promoted mass migration from Europe "to 'whiten' and so 'evolve' their people". They "argued that 'whitening' their nations' stock through interbreeding was the only path to societal improvement". The result was spectacular: more than 11 million immigrants came from Britain, Germany, Ireland, Italy, Portugal and Spain. These people were encouraged to become land owners and to develop leadership roles.

"By 1900, people of European origin dominated society in Argentina and Uruguay. [. . .] European ideas and values spread across Latin America at the expense of Amerindian and African American ones, with the establishment of European-style cities and institutions."

The ideology pendulum swung away from this when the European continent disintegrated in World War I, followed some years after by economic turmoil.

"The death toll of the First World War demonstrated that Europeans had not evolved into superior human beings. A decade later, the Great Depression swept away the export economies underlying modernization in Argentina at least as much as it did in Mexico and Peru, belying the notion that the whitening of the population would lead to permanent social progress."

The intellectuals were still evolutionists at heart, but now it was the Lamarckian sympathies of Darwin that came to the fore.

[These leaders] "followed the 'soft inheritance' notion of French naturalist Jean-Baptiste Lamarck and countered that people's inheritable traits could be changed simply by altering their environment, including their education, diet and living conditions."

These voices came from the "cultural nationalists" who championed the idea of multicultural integration via literacy campaigns with a policy of racial and ethnic blending.

"Although Darwin wasn't specifically invoked in such theories, his body of thought was still influential; so much so that the cultural nationalists might today be described as having adopted their own brand of social Darwinism."

Then came World War II which "dealt a serious blow to notions of human history as a progressive process". Gradual evolutionary change was discarded and the intelligentsia embraced "social revolution as the solution to the region's problems". Although the author of the essay does not link this ideological shift to Darwinism, many communist leaders are known to have looked very favourably on Darwinian concepts. Instead of gradualism, they chose to emphasise survival of the fittest in an amoral world.

Latin America provides us with numerous examples of people taking Darwinian concepts and applying them to the social and political arena. Darwin himself did this in The Descent of Man and his followers have developed these ideas in ways that seem paradoxical today. Some promoted scientific racism and eugenics, whereas others worked for multicultural integration. Some justified capitalism whereas others advocated socialism. Some built their thoughts around gradualism and progress, yet others used survival of the fittest to engineer extinction and social revolution. There is enough in the history of Latin America to make anyone first question and then abandon the principles of Social Darwinism - yet even today there seem to be plenty of scholars who continue to think there is no alternative but to pursue Social Darwinism as the route for structuring social and political philosophy.

"Throughout, Latin America political thinkers shared an optimistic belief that these societies could and would 'evolve' in a positive direction - whatever that direction might be."

Some reflections on these historical developments seem justified.
First, there is an extraordinary malleability in the way Social Darwinism has been expressed. If there is the will, almost every social practice can be given the appearance of scientific respectability. What we do not see are the distinctive characteristics of science: of hypothesis testing, falsification, and the development of theory that can be used to make predictions.
Second, the concept of 'progress', when linked to Darwinism, is a clear indication that there has been an injection of human aspiration. As Darwin conceived his theory, there is no goal (or even a purposeful direction). The evolutionary process is a consequence of Law and Chance, neither of which give support to the "optimistic belief" of politicians about evolving their societies in a "positive direction". These politicians were seeking a place for Design within a theoretical framework that is incompatible with the concept of design. This superimposition of a Design layer on a Law+Chance system has become so widespread that one wonders how intellectuals can live with the incompatibility problem! If the exclusion of Design from evolutionary theory were more widely recognised, would Darwinian ideology be as popular as it appears to be?
This brings us to the third reflection - on subliminal Darwinism. Like the cultural nationalists, many people adopt Darwinism without being conscious of the source of their thinking. They have imbibed a worldview from their peers - without thinking it through for themselves. They are oblivious to the idea that Darwinism is a theory built upon a particular worldview and not just a science of origins. The long-term consequence of this should be cause for concern. Humans are creative, have values affecting behaviour, have a sense of justice and have aspirations. None of these characteristics fit harmoniously with a worldview that is made up of blind, unguided and stochastic processes. That is why many of us are disturbed by attempts to expand the exposure of children to Darwinism in primary school education. Whilst this may be defended by appeals to science, it does little to assuage concerns that what children will get is subliminal indoctrination in a Darwinian worldview.

Global Darwin: Multicultural mergers
Jurgen Buchenau
Nature, 462, 284-285 (19 November 2009) | doi:10.1038/462284a

Abstract: Latin Americans first saw evolution as a reason to 'whiten' their societies, then as a reason to take pride in their mixed lineage, says Jurgen Buchenau in the last of four pieces on Darwin's global influence.

See also:

The Idea of Race in Latin America, 1870-1940, Edited and with an introduction by Richard Graham, with chapters by Thomas E. Skidmore, Aline Helg, and Alan Knight. University of Texas Press, 1990.

Excerpt from Introduction:

Initiated in Europe, the classification and ranking of humankind into inferior and superior races profoundly influenced the development, indeed, the very creation of the sciences. Biology, medicine, psychology, anthropology, ethnology, and sociology were all to some degree shaped by an evolutionary paradigm. The spread of European colonialism and the rapid growth of the United States in the latter half of the nineteenth century brought additional and supposedly irrefutable proof of the validity of a scheme that placed the so-called primitive African or Indian at the bottom of the scale and at its top the "civilized" white European. Many social policies regarding education, crime, health, and immigration were informed by these dominant racial theories. Although the racialist conception of human beings began to lose its credibility from the early twentieth century, it was not until the Nazis began to apply those concepts to eugenics and to undertake massive extermination of the "inferior" races that most scientists firmly denounced the, by then, pseudo-scientific character of racial theories.

For comments on other essays in the Nature series, go here and here.

Organisms possess a wide variety of strategies for avoiding predation. Crypsis provides a means of avoiding detection; aposematism makes use of warning colouration; mimicry imitates an organism that has better defenses; masquerade "closely resembles inedible and generally inanimate objects". Graeme Ruxton and Michael Speed, who were coauthors of a book on this general theme, have recently coauthored a research paper on masquerade.

"Plants from the genus Lithops look remarkably like stones; stick insects resemble twigs; the Amazon fish Monocirrhus polyacanthus is visually almost indistinguishable from leaves, and birds from the family Nyctibiidae bear an uncanny likeness to tree stumps."

Leaf insects set a high standard for looking like something that's inedible (Credit: (Kirsty Wigglesworth/AP Photo, source here)

My personal favourite examples relate to stick insects and leaf insects. Not only do stick insects resemble the plants on which they live, they sway just as though they are being fanned by a gentle breeze. Furthermore, their eggs look exactly like their own fecal pellets. Newly emerged leaf insects have beautifully formed leafy appendages that allow them to blend in immediately with their surroundings. These characteristics, whilst remarkable, have not been seriously researched:

"one aspect of adaptive coloration has been almost completely ignored: masquerade."

The first research challenge is to determine whether masquerade is a distinctive phenomenon or another form of crypsis. The two relevant hypotheses are:
(a) The predator detects but misidentifies the prey (masquerade)
(b) The predator fails to detect the prey (crypsis)
The researchers set up a set of experiments using domestic chicks as predators and two species of twig-resembling caterpillars. The experimental area contained a hawthorn branch with twigs and leaves. Some experiments were undertaken with a branch that had been bound in purple cotton thread to change its visual appearance.

"Birds with prior experience of twigs took longer to attack both species of twig-resembling caterpillars, and handled them more cautiously, compared with birds that had either no experience of twigs or experience only of twigs whose visual appearance had been manipulated by binding them in colored thread. Our results show that masquerade functions to promote misidentification of the masquerading organism."

Thus far, the authors have demonstrated that hypothesis (a) above is substantiated. Then, in their paper, they proceed with an evolutionary explanation of the phenomenon.

"Our results show that predators' cognitive strategies (recognition and identification), rather than their sensory capabilities, are the selective force driving the evolution of masquerade and raise the possibility that predator cognition may be a more important selective agent than previously realized."

It is a fair conclusion to say that cognitive strategies are significant, as all the birds were able to sense the caterpillars. However, what is the rationale for saying that cognitive strategies have "driven the evolution of masquerade"? Can these experiments tell us anything about the origins of the phenomenon? They tell us that predation is affected by the predator's cognitive strategies, but not that these same strategies have driven the evolution of masquerade as an adaptive response. At best, this is an initial hypothesis awaiting testing. It is a hypothesis based on the assumptions of Darwinism - that masquerade is an adaptation driven by natural selection. To claim this as a conclusion is an indication that theory, rather than data, is dictating the outcome.

The examples of natural selection that we do have fall far short of showing the reasonableness of identifying it as the mechanism for explaining masquerade. We have finch beak length changes, lizard leg length changes, peppered moth colouration, and the like. To demonstrate the reasonableness of explaining masquerade in this way means having multiple factors - including behavioural - all responding to the same selection pressure. Such evidence may be forthcoming but, in the words of the authors (in a different context): "there is certainly no empirical evidence to support this theory". Instead, it is appropriate to propose multiple working hypotheses and proceed to construct ways of testing them. In particular, we can note here the hypothesis that organisms are designed with the potential for radiations linked to adaptive, developmental and epigenetic factors.

Masquerade: Camouflage Without Crypsis
John Skelhorn, Hannah M. Rowland, Michael P. Speed, and Graeme D. Ruxton
Science 327, 1 January 2010: 51.

Abstract: Masquerade describes the resemblance of an organism to an inedible object and is hypothesized to facilitate misidentification of that organism by its predators or its prey. To date, there has been no empirical demonstration of the benefits of masquerade. Here, we show that two species of caterpillar obtain protection from an avian predator by being misidentified as twigs. By manipulating predators' previous experience of the putative model but keeping their exposure to the masquerader the same, we determined that predators misidentify masquerading prey as their models, rather than simply failing to detect them.

See also:

Tyler, D., Stasis in the fossil record of leaf insects, ARN Literature Blog (14 January 2007)