Science Literature

Animations of the kinesin motor protein have captured something of the astounding orchestration of processes within the cell. We already know quite a lot about the microtubules on which kinesin “walks”. Protofilaments made of tubulin assemble to form a sheet which then folds to form the microtubule structure. The join of the two edges of the sheet has not been previously considered very interesting. Andreas Hoenger is quoted as saying: "Until now the function of the seam has been unknown and it has been largely ignored as an odd and irrelevant part of the microtubule lattice. Our experiments now reveal it as a central spot where microtubule stability can be regulated."
New research has identified a protein Mal3p that plays a crucial role in assembly of the microtubules, described as a molecular “zipper”. Cellular controls on this protein lead to assembly, disassembly and rapid switching. There are indications that the same protein “could also play a more active role in transportation”. A remarkable photograph of an opening microtubule is here.
Although the new studies have involved yeast cells, the Mal3p protein is widely found in different organisms, and the results are considered likely to be of general relevance.
Every new advance in understanding the molecular machines within the cell reveals complex specified information and strengthens the case for ID.

The Schizosaccharomyces pombe EB1 Homolog Mal3p Binds and Stabilizes the Microtubule Lattice Seam
Linda Sandblad, Karl Emanuel Busch, Peter Tittmann, Heinz Gross, Damian Brunner, and Andreas Hoenger
Cell, 127(7), 29 December 2006, Pages 1415-1424

Summary: End binding 1 (EB1) proteins are highly conserved regulators of microtubule dynamics. Using electron microscopy (EM) and high-resolution surface shadowing we have studied the microtubule-binding properties of the fission yeast EB1 homolog Mal3p. This allowed for a direct visualization of Mal3p bound on the surface of microtubules. Mal3p particles usually formed a single line on each microtubule along just one of the multiple grooves that are formed by adjacent protofilaments. We provide structural data showing that the alignment of Mal3p molecules coincides with the microtubule lattice seam as well as data suggesting that Mal3p not only binds but also stabilizes this seam. Accordingly, Mal3p stabilizes microtubules through a specific interaction with what is potentially the weakest part of the microtubule in a way not previously demonstrated. Our findings further suggest that microtubules exhibit two distinct reaction platforms on their surface that can independently interact with target structures such as microtubule-associated proteins, motors, kinetochores, or membranes.

See also:
Kikkawa, M. and Metlagel, Z. A molecular ‘zipper’ for microtubules,
Cell, Volume 127, Issue 7, 29 December 2006, Pages 1302-1304.

Roadworks on the motorways of the cell
EurekAlert, 28 December 2006.

"Another dogma in cell biology seems about to be toppled: If a mutation in a gene doesn't change the basic sequence of building blocks, then it has no effect." This introduces Beckman's news report of some recent research. A silent mutation is a single letter change in a codon that nevertheless produces the same amino acid. According to co-author Kimchi-Sarfaty: "We were all educated that silent mutations should be ignored, and people really don't pay attention to them." However, this entered education because of the dominance of theory rather than the strength of evidence. The new paper provides enough data to show that many areas of molecular biology need to be revisited. "This may be a generalizable phenomenon that may lead to changes in function we haven't been thinking about" said co-author Gottesman.
The authors draw attention to possible medical implications, "raising the possibility that mutations that do not change coding sequence may contribute to disease by a similar mechanism". But the findings are also relevant to genome similarity measures (particularly humans and chimps) and also the detection of signatures of natural selection in genome sequences (based on the neutral theory of molecular evolution). They allow us to anticipate some revisions to previously reported findings.
Perhaps the most interesting comment comes from Pearson: "Biologists have realized that the genetic code harbours a layer of information that they have largely ignored. Again." This needs to be digested. Why has this layer of information been ignored? Why did it become a "dogma in cell biology"? The answer seems to be that the mindset of molecular biologists is to assume simplicity rather than complexity in the genetic code. This mindset is driven by the thought that cellular information is ultimately mindless and a product of natural forces. This new research allows us once again to ask whether it is time to assume complexity rather than simplicity because design inferences allow us to recognise intelligent agency in the genetic code.

A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity
Chava Kimchi-Sarfaty, Jung Mi Oh, In-Wha Kim, Zuben E. Sauna, Anna Maria Calcagno, Suresh V. Ambudkar, Michael M. Gottesman.
Science Online December 21, 2006, DOI: 10.1126/science.1135308

Abstract: Synonymous Single Nucleotide Polymorphisms (SNPs) do not change the coding sequences, and, therefore, are not expected to change the function of the protein in which they occur. Here, we report that a synonymous SNP in the Multidrug Resistance 1 (MDR1) gene, part of a haplotype previously linked to altered function of the MDR1 gene product, P-glycoprotein (P-gp), nonetheless results in P-gp with altered drug and inhibitor interactions. Similar mRNA levels and protein, but altered conformations were found for wild-type and polymorphic P-gp. We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of co-translational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.

See also:

Choi, C.Q. "Silent" mutations are not always silent, The Scientist, 21st December 2006.
http://www.the-scientist.com/news/home/38329/

Pearson, H. Silent mutations speak up, news@nature.com: 21 December 2006; | doi:10.1038/
http://www.nature.com/news/2006/061218/full/061218-12.html

Beckman, M. The Sound of a Silent Mutation, ScienceNOW Daily News, 22 December 2006
http://sciencenow.sciencemag.org/cgi/content/full/2006/1222/2

Amato, I. Silent No Longer, Chemical & Engineering News, January 22, 2007, Volume 85, Number 04, pp. 38-40.

"The more scientists study the genetic code, the more it reads like poetry. In a poem, every word, every line break, even every syllable can carry more than a literal meaning. So too can the molecular letters, syllables, and words of the genetic code carry more biologically relevant meanings than they appear to at first.
Now, a cadre of researchers is discovering intriguing depths of meaning in "synonyms" in the genetic code - very short wordlike sequences, or codons, that translate into exactly the same amino acids during the construction of a protein. Scientists are finding that synonymous codons influence the temporal pattern by which a messenger RNA (mRNA) molecule bearing genetic specifications from a cell's nucleus is translated by machinelike ribosomes into protein molecules." [snip]

Lactose tolerance is the trait that allows children to digest their mother’s milk, and this makes it an essential character during infancy. However, the gene for making lactase (the enzyme responsible for converting lactose to digestible products) may be switched off after weaning. Thus, many adults in the world have no interest in consuming milk. Research into adult lactose tolerance in sub-Saharan Africa is the theme of a news feature by Erika Check in Nature. This work reveals that people groups who rely on cattle for survival all have lactose tolerance. This has led to a reconstructed history of the lactose persistence mutation driven by selection. It involves rapid establishment of the trait in genetically related groups and, with three lactase persistence mutations, the phenomenon is described as a good example of “convergent evolution”. This research is being hailed as a “textbook example” of evolutionary processes affecting humans.

Distinguishing between different meanings of the word “evolution” does not seem to be widespread outside ID literature. It is relevant to this case: lactose persistence is not a novelty but the retention of a trait present in infancy. There is no new genetic information: although the word “mutation” is used, it refers to switch inactivation. These genetic changes do not, for example, do anything to explain the origin of lactase, nor do they illuminate the origin of any genetic novelty. Consequently, they fit into a category of “evolution” known as “microevolution” or “minor genetic variations”. They have no bearing on mechanisms for achieving large scale evolutionary transformations.

What can a design perspective contribute to this? At very least, it allows some interesting questions to be asked: are we dealing here with a lactose persistence mutation or a lactose intolerance mutation? Are there different mechanisms for achieving lactose intolerance? Why should lactose tolerance be lost in hunter/gatherers? Is the cost of producing lactase so high? Why a genetic switch when the trait could be kept as a vestigial genetic system? Put another way, is it “normal” or “abnormal” for adults to have milk with their muesli?

Human evolution: How Africa learned to love the cow
Erika Check.
Nature, 444, 21/28 December 2006), 994-996. ¦ doi:10.1038/444994a

Lactose Tolerance in East Africa Points to Recent Evolution
By NICHOLAS WADE
New York Times: December 11, 2006
http://www.nytimes.com/2006/12/11/science/11evolve.html

Convergent adaptation of human lactase persistence in Africa and Europe
Sarah A Tishkoff, Floyd A Reed, Alessia Ranciaro, Benjamin F Voight, Courtney C Babbitt, Jesse S Silverman, Kweli Powell, Holly M Mortensen, Jibril B Hirbo, Maha Osman, Muntaser Ibrahim, Sabah A Omar, Godfrey Lema, Thomas B Nyambo, Jilur Ghori, Suzannah Bumpstead, Jonathan K Pritchard, Gregory A Wray & Panos Deloukas
Nature Genetics, Published online: 10 December 2006 | doi:10.1038/ng1946

A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past ~7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits—animal domestication and adult milk consumption.

Crustaceans are found as marine organisms in Cambrian rocks. Hexapods are documented in freshwater and terrestrial environments, but no earlier than the Devonian. “A key problem is the almost complete absence of fossils that connect hexapods to the other major arthropod subphyla”, that is Crustacea, Myriapoda and Chelicerata. In the absence of fossilized transitional forms, there are few constraints for theories of insect evolution and “hexapods have been phylogenetically linked to all of these major arthropod taxa”. Recent research, involving “morphological and molecular-based studies” has concluded “that hexapods originated within the crustaceans rather than as a sister group”. It claims this makes sense of several lines of evidence and there is clearly a desire to have an evolutionary story.
What makes this science rather than speculation? Reasoned argument + critical thought + circumstantial evidence might be characteristics used to justify the legitimacy of this work as science. However, there is very little primary data, and very little scope for the testing of hypotheses and for falsification. There is no benefit to humanity in sight. All the common objections to ID as science (except for one) apply to this research. And ID has amply demonstrated the use of reasoned argument + critical thought + circumstantial evidence. What objection is the exception? It is that all causation within science is natural. That’s the real stumbling block. But is not a problem for science. It is a problem for secularized science.

The Origin of Insects
Henrik Glenner, Philip Francis Thomsen, Martin Bay Hebsgaard, Martin Vinther Sorensen, and Eske Willerslev
Science 314, 22 December 2006: 1883-1884.

First para: Although hexapods--those arthropods having six legs, including insects--are the most diverse group of contemporary animals in terms of biological niches and number of species, their origin is highly debated. A key problem is the almost complete absence of fossils that connect hexapods to the other major arthropod subphyla, namely Crustacea, Myriapoda (such as centipedes and millipedes), and Chelicerata (such as scorpions and spiders). Over the years, hexapods (insects, springtails, proturnas, and diplurans) have been phylogenetically linked to all of these major arthropod taxa (1).

According to some educationalists, science teachers face a curious paradox. “In our culture, schools are designed to present established understandings, not to promote discovery of new knowledge. […] The ensuing culture of conformity with established knowledge is the very antithesis of scientific inquiry.” Instead of experiencing science as an exhilarating quest for truth, students feel the burden of learning lots of textbook knowledge.
The article cited below focuses attention on how classrooms can create genuine environments for discovery, and this is good. However, the tried-and-tested strategy for countering the paradox is to make students aware of controversies within science. This fans the flames of curiosity and demonstrates that the “end of science” has not been documented in the textbook!
In biological education, there is ample evidence of a “culture of conformity with established knowledge”. This is shown by enormous resistance to any suggestion of critical discussion of Darwinism in the classroom. Teachers who entertain the thought may be considered subversive to science. Addressing this problem requires more than providing an environment for discovery. It requires a commitment to freedom of enquiry within science and following the evidence wherever it leads.

INQUIRY LEARNING: Teaching Scientific Inquiry
David I. Hanauer, Deborah Jacobs-Sera, Marisa L. Pedulla, Steven G. Cresawn, Roger W. Hendrix, and Graham F. Hatfull
Science 314, 22 December 2006: 1880-1881.

Opening two paragraphs:
Science teachers in kindergarten to 12th grade (K-12) classrooms face a curious paradox. On one hand, according to the generally accepted theory, scientific inquiry in the classroom is "at the heart of the science and science learning" (1). In essence, the teaching of science should mirror the processes used by professional scientific researchers. On the other hand, a school classroom is not a research laboratory. Scientific research typically involves complex methods and problem-solving approaches (2), resulting in conclusions that are subjected to worldwide evaluation (3-6). Capturing these characteristics of professional science within the K-12 school classroom is daunting (7).
The goals of scientific research and current pedagogical practice are at odds (8, 9). In our culture, schools are designed to present established understandings, not to promote discovery of new knowledge. The focus on persuading students of the correctness of stated information is intensified by increased reliance on broad-based standardized testing, which--especially in the United States and the United Kingdom--has become a popular mechanism for making schools accountable. The ensuing culture of conformity with established knowledge is the very antithesis of scientific inquiry (8).

The publication of genome sequences in recent years is providing a data-rich platform for research. In the paper cited below, the research team considered 110,000 genes in 9,990 gene families that are shared by humans, common chimpanzees, mice, rats and dogs. Of particular interest were examples of “gene gain” and “gene loss”, because these are regarded as providing “clues to the evolutionary forces that have shaped mammalian genomes”. One of the headline findings is that “humans and chimpanzees differ by at least 6% […] in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences.” The authors quote approvingly the words of King and Wilson in 1975 who said of the 1.5% result that “the genetic distance between humans and the chimpanzee is probably too small to account for their substantial organismal differences”.
What is obvious from the new research is that methodology is a critical factor in making comparisons. Change the criteria and you change the measured difference. In the past, acknowledgement of this simple point would have raised the quality of the debate over these issues.
It is worth noting that the authors adopt an evolutionary perspective in their research. Genes are gained or lost via “evolutionary forces”. This contrasts with a design perspective, where functionality is the key. The genetics of chimps and humans are similar, not because they necessarily share a common ancestor, but because they have similar functional needs. Common ancestry has to be justified by the evidence, not assumed to interpret the evidence. This design perspective offers numerous avenues of research to explore these issues further: looking at the non-coding DNA and considering biological information outside the genome, for example. As noted above, methodology is a critical factor.

The Evolution of Mammalian Gene Families
Jeffery P. Demuth, Tijl De Bie, Jason E. Stajich, Nello Cristianini, Matthew W. Hahn
PLoS ONE 1(1): e85. doi:10.1371/journal.pone.0000085

Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

Moth ears have two or four vibration sensitive cells attached to a small eardrum, and are regarded as among the simplest in the insect world. However, in a recent paper, research findings are said to reveal “unexpected sophistication in one of the simplest ears known”. The complexity comes in the way audio signals are processed so as to enhance the sensitivity of certain frequencies. The language of purpose comes naturally: “the moth cleverly tunes its ear to enhance its detection of bats”. These findings are suggested to impact thinking on the co-evolution of bats and moths, but there is no reason why they should not also impact thinking on design in the natural world. Design-oriented biologists have long abandoned the idea that anything is “primitive”. Wherever we look, the reality is always more than first meets the eye!

Keeping up with Bats: Dynamic Auditory Tuning in a MothJames Frederick Charles Windmill, Joseph Curt Jackson, Elizabeth Jane Tuck, and Daniel Robert
Current Biology, Vol 16, 2418-2423, 19 December 2006

Many night-flying insects evolved ultrasound sensitive ears in response to acoustic predation by echolocating bats [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]. Noctuid moths are most sensitive to frequencies at 20–40 kHz [6], the lower range of bat ultrasound [5, 11, 12, 13]. This may disadvantage the moth because noctuid-hunting bats in particular echolocate at higher frequencies shortly before prey capture [7, 11, 12, 13] and thus improve their echolocation and reduce their acoustic conspicuousness [6, 7, 8, 9, 10, 12, 13, 14, 15, 16]. Yet, moth hearing is not simple; the ear's nonlinear dynamic response shifts its mechanical sensitivity up to high frequencies. Dependent on incident sound intensity, the moth's ear mechanically tunes up and anticipates the high frequencies used by hunting bats. Surprisingly, this tuning is hysteretic, keeping the ear tuned up for the bat's possible return. A mathematical model is constructed for predicting a linear relationship between the ear's mechanical stiffness and sound intensity. This nonlinear mechanical response is a parametric amplitude dependence [17, 18] that may constitute a feature common to other sensory systems. Adding another twist to the coevolutionary arms race between moths and bats, these results reveal unexpected sophistication in one of the simplest ears known and a novel perspective for interpreting bat echolocation calls.

The Census of Marine Life is a global network of researchers in a long-term project to document and analyse the diversity of life in our oceans. In its latest census report is a shrimp that was previously known only from fossils from the Jurassic Period. Like all living fossils, such specimens are a witness to stasis as a real phenomenon in the story of life’s diversification. That this shrimp was apparently immune to the influences of natural selection should be sufficient to make a few Darwinists think about the adequacy of their evolutionary mechanism.

Extreme Life, Marine Style, Highlights 2006 Ocean Census,
Press Release @ http://www.coml.org/, 10 December 2006.

Oldest. Census seamount researchers found a shrimp, believed extinguished 50 million years ago, alive and well on an underwater peak in the Coral Sea. Neoglyphea neocaledonica was nicknamed “Jurassic shrimp” by its discoverers, who say it rivals the find in South Africa and Indonesia of the coelacanth, a prehistoric fish previously known only through fossils.

See also:
Jurassic 'shrimp' alive and well, Alister Doyle
Abcnet.au, 11 December 2006
http://www.abc.net.au/science/news/stories/2006/1808557.htm

Although the popular view of genes is that one gene has one function, this has long been recognised as simplistic and misleading. Genes have multiple functions. And genes interact: they have epistatic effects. The Neodarwinian synthesis invokes genetic mutations as the source of variation on which natural selection acts. The theory allows that the majority of these mutations are deleterious, but selection of the few favourable mutations is all that really matters. In the past this mechanism has been discussed without reference to epistatic effects. What relevance is this for mutations that do not appear to be deleterious?
Bershtein and co-workers have been looking at mutation in E. coli proteins. They were interested in exploring “the common view that the vast majority of protein mutations are tolerated.” They devised ways to purge the proteins of detectable deleterious mutations and monitored the fitness with time. Epistasis was observed: “the combined deleterious effects of mutations were, on average, larger than expected from the multiplication of their individual effects.” Although there appeared to be robustness in the mutated proteins, a threshold was reached leading to chronic failure. “Once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.”
The results are very significant for the evolutionary mechanisms advanced by Neodarwinists. Epistasis effects constrain evolutionary trajectories associated with random mutations. Go past the threshold and the apparently “fit” mutations are revealed as deleterious. For a long time, Darwinists have resisted any critical examination of their mechanism for evolution, but the evidence is getting stronger every year that ‘mutations + natural selection’ will not deliver the transformations required.

Robustness–epistasis link shapes the fitness landscape of a randomly drifting protein
Shimon Bershtein, Michal Segal, Roy Bekerman, Nobuhiko Tokuriki and Dan S. Tawfik
Nature 444, 929-932 (14 December 2006) | doi:10.1038/nature05385

The distribution of fitness effects of protein mutations is still unknown1,2. Of particular interest is whether accumulating deleterious mutations interact, and how the resulting epistatic effects shape the protein's fitness landscape. Here we apply a model system in which bacterial fitness correlates with the enzymatic activity of TEM-1 -lactamase (antibiotic degradation). Subjecting TEM-1 to random mutational drift and purifying selection (to purge deleterious mutations) produced changes in its fitness landscape indicative of negative epistasis; that is, the combined deleterious effects of mutations were, on average, larger than expected from the multiplication of their individual effects. As observed in computational systems3,4,5, negative epistasis was tightly associated with higher tolerance to mutations (robustness). Thus, under a low selection pressure, a large fraction of mutations was initially tolerated (high robustness), but as mutations accumulated, their fitness toll increased, resulting in the observed negative epistasis. These findings, supported by FoldX stability computations of the mutational effects6, prompt a new model in which the mutational robustness (or neutrality) observed in proteins, and other biological systems, is due primarily to a stability margin, or threshold, that buffers the deleterious physico-chemical effects of mutations on fitness. Threshold robustness is inherently epistatic—once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.

There is nothing like amber for its ability to preserve insects, plant material and much more. The remarkable ability of amber to preserve soft tissues makes it a tremendous resource for the palaeontologist. This new report is of Upper Triassic amber, which is considerably lower in the stratigraphic succession than most other ambers. It is so low that it predates most of the dinosaur fossil record, so it offers a window on a world that we know very little about. Looking for signs of past life, the researchers found “bacteria, fungi, algae and protozoans” – which in terms of the basal food webs is not so different from today. Furthermore, these organisms “are assignable to extant genera”. The researchers write: “it seems that the basal levels of food webs of terrestrial communities (biocoenoses) have undergone little or no morphological change from the Triassic to the Recent.”
Stasis, it seems, has characterised these organisms, despite the extraordinary changes in the environment that have been documented for this timespan of Earth history. This suggests that environmental selection forces are nowhere near as significant as the Darwinists claim, and it raises (yet again!) questions about the validity of the Neodarwinian Synthesis.

A microworld in Triassic amber
Amber as old as the first dinosaurs captured the diversity of microbial life 220 million years ago.
Alexander R. Schmidt, Eugenio Ragazzi, Olimpia Coppellotti and Guido Roghi
Nature 444, 835 (14 December 2006) | doi:10.1038/444835a

Amber provides an effective medium for conservation of soft-bodied microorganisms1, 2, 3, 4, 5, 6, but finds older than 135 million years are very rare and have not so far contained any microbial inclusions. Here we describe 220-million-year-old droplets of amber containing bacteria, fungi, algae and protozoans that are assignable to extant genera. These inclusions provide insight into the evolution and palaeoecology of Lower Mesozoic microorganisms: it seems that the basal levels of food webs of terrestrial communities (biocoenoses) have undergone little or no morphological change from the Triassic to the Recent.

Until recently, all we knew about Mesozoic mammals was that they were small, shrew-like animals that waited their time and did not diversify until the dinosaurs became extinct. The past few years has seen this view challenged, with several much larger animals described, all showing signs of specialisation. The latest is a squirrel-sized glider said to be from a new mammalian order. Dated as Early Cretaceous (and it may be Jurassic), this is said to extend the “earliest record of gliding flight for mammals to at least 70 million years earlier in geological history.” The degree of specialisation has not been predicted nor expected by Darwinists, who look for gradual changes over time. Yet, “this was just totally out of nowhere,” said Dr. Meng, the lead academic working on the fossil. Specialised features are not unexpected if a design perspective is adopted. This argument has been well-documented in the context of the Cambrian Explosion animals. Here is a striking example from the mammals.

A Mesozoic gliding mammal from northeastern China
Jin Meng, Yaoming Hu, Yuanqing Wang, Xiaolin Wang and Chuankui Li
Nature 444, 889-893 (14 December 2006) | doi:10.1038/nature05234

Abstract: Gliding flight has independently evolved many times in vertebrates. Direct evidence of gliding is rare in fossil records and is unknown in mammals from the Mesozoic era. Here we report a new Mesozoic mammal from Inner Mongolia, China, that represents a previously unknown group characterized by a highly specialized insectivorous dentition and a sizable patagium (flying membrane) for gliding flight. The patagium is covered with dense hair and supported by an elongated tail and limbs; the latter also bear many features adapted for arboreal life. This discovery extends the earliest record of gliding flight for mammals to at least 70 million years earlier in geological history, and demonstrates that early mammals were diverse in their locomotor strategies and lifestyles; they had experimented with an aerial habit at about the same time as, if not earlier than, when birds endeavoured to exploit the sky.

For further reading: Wilford, J.N., Flying Mammal Found from 125 Million Years Ago, New York Times, December 13, 2006.

There seem to be a lot of people about who seem to know exactly what science is, and they seem to regard it as the only route to truth. Such folk could do worse than read an editorial to a special issue of Sedimentary Geology. This does not speak to the ID issue but it helps us understand how some divergences of opinion originate. The editorial refers to the communication gap between East and West and identifies reasons, on both sides of the gap, for why “the directions of science in East and West diverged”.
We need more analysis like this to understand why intelligent scientists can take opposing positions on the value of the ID approach within science. If we don’t, this warning applies: “Where (and when) a true dialogue between those adhering different views is impossible, science suffers.”

Bridging the gap in Quaternary geology between East and West: The Brodzikowski heritage (Editorial)
Beata Gruszka, A.J. (Tom) van Loon and Tomasz Zieliński
Sedimentary Geology, Volume 193, Issues 1-4 , 1 January 2007, Pages 1-5

1. Introduction
No such thing exists as a ‘scientific truth’. Even nowadays, some hypotheses that are considered by a great majority of scientists as ‘scientific truth’ are considered as fundamentally wrong by others. Where (and when) a true dialogue between those adhering different views is impossible, science suffers. We have witnessed such conditions in the recent past in Eastern European countries, where – in addition – the economic conditions hardly allowed any university to buy scientific literature from the West: the differences in price level were just too great. This does not imply that science in Eastern Europe at the time was of a lower quality than in the West. We are convinced that research in the natural sciences – including the earth sciences – was carried out at many eastern universities at a high level. The results were, obviously, published, but this happened, unfortunately, only rarely in a language that was accessible for scientists from western countries.
Since the scientists in Eastern Europe could not afford to buy western literature (and no such a thing as internet was available at the time!), and since Western scientists were not capable of reading the research results from their colleagues in the East, it was unavoidable that the directions of science in East and West diverged. These different developments were not commonly realised until before the ‘iron curtain’ fell. Only a few earth scientists were aware of it earlier, thanks to personal contacts with colleagues ‘on the other side’. These two-sided earth scientists were not always in the position – or willing – to take advantage of the ‘extra’ information that they had. In general, the earth scientists in the West were too busy applying for research grants and/or surviving the publish-or-perish culture, whereas contacts with Western colleagues were not always appreciated in Eastern Europe.
[snip]

According to the Editors of Science, altruism “remains one of the fundamental challenges of biology”. Nowak explains the problem thus: “Evolution is based on a fierce competition between individuals and should therefore reward only selfish behavior. Every gene, every cell, and every organism should be designed to promote its own evolutionary success at the expense of its competitors.” Yet, cooperative behaviour is not hard to find in the biological world. The Neodarwinian response is to identify mechanisms of cooperation that drive altruistic behaviour. In a major review paper, Nowak discusses “the five main mechanisms of cooperation: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection”.
These approaches do offer mechanistic explanations for cooperative behaviour in insects and in other animal societies. However, the real challenge for this approach is human behaviour. Boyd explains the problem thus:

“In every human society, people cooperate with many unrelated individuals. Division of labor, trade, and large-scale conflict are common. The sick, hungry, and disabled are cared for, and social life is regulated by commonly held moral systems that are enforced, albeit imperfectly, by third-party sanctions. In contrast, in other primate species, cooperation is limited to relatives and small groups of reciprocators. There is little division of labor or trade, and no large-scale conflict. No one cares for the sick, or feeds the hungry or disabled. The strong take from the weak without fear of sanctions by third parties.”

The explanations that appear to work for insects (kin selection, direct reciprocity) do not explain the indiscriminate altruism exhibited by humans. For that, the theoreticians have invoked additional mechanisms based on distinctively human traits. So, for example, indirect reciprocity linked to the human longing for reputation is highlighted as significant.

Indirect reciprocity can only promote cooperation if the probability, q, of knowing someone’s reputation exceeds the cost-to-benefit ratio of the altruistic act: q > c/b

There are additional mechanisms linked to the human tendency to develop networks and social groupings where values are different within the network or group to values outside.
So, next time you give something to help tsunami victims or children in need, just remember that it is all because you have deemed the cost-to-benefit ratio of giving to be worth the reputation it brings you.

Of course, there is another avenue for thinking about altruism: but this means going beyond neodarwinism and entertaining the thought that human beings need to be explained not only in terms of law and chance, but also in terms of design.

Five Rules for the Evolution of Cooperation
Martin A. Nowak
Science 314, 8 December 2006: 1560-1563.

Abstract: Cooperation is needed for evolution to construct new levels of organization. Genomes, cells, multicellular organisms, social insects, and human society are all based on cooperation. Cooperation means that selfish replicators forgo some of their reproductive potential to help one another. But natural selection implies competition and therefore opposes cooperation unless a specific mechanism is at work. Here I discuss five mechanisms for the evolution of cooperation: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. For each mechanism, a simple rule is derived that specifies whether natural selection can lead to cooperation.

See also: Boyd, R., The Puzzle of Human Sociality, Science 314, 8 December 2006: 1555-1556.

The australopithicine "Little Foot," has been dated as 3.3 Ma (based on magnetic stratigraphy) and ~4 Ma (based on cosmogenic dating). However, a new study using the U-Pb system dates the cave deposits as 2.2 million years old. This is said to be “surprisingly recent and contemporaneous with tool-using Homo species”. The significance is that a big time gap has opened up between Australopithecenes in different parts of Africa: “This suggests the earliest hominids arrived in South Africa 2 million to 4 million years after they arose in eastern or central Africa.” Instead of being treated as a source of information on human evolution, the fossil remains must now be located in the sidelines. There is something implicit within Darwinism that predicts a “tree of life” with an evolving lineage – but the fossil record continues to resist shoehorning to fit this prediction. The best researchers appear to be able to do is to hunt for our ancestors as they hide behind a bush!

U-Pb Isotopic Age of the StW 573 Hominid from Sterkfontein, South Africa
Joanne Walker, Robert A. Cliff, and Alfred G. Latham
Science 314, 8 December 2006: 1592-1594.

Sterkfontein cave, South Africa, has yielded an australopith skeleton, StW 573, whose completeness has excited great interest in paleoanthropology. StW 573, or "Little Foot," was found 25 meters below the surface in the Silberberg Grotto. 238U-206Pb measurements on speleothems immediately above and below the fossil remains, corrected for initial 234U disequilibrium, yield ages of 2.17 ± 0.17 million years ago (Ma) and 2.24 (+0.09, -0.07) Ma, respectively, indicating an age for StW 573 of close to 2.2 Ma. This age is in contrast to an age of ~3.3 Ma suggested by magnetochronology and ages of ~4 Ma based on 10Be and 26Al, but it is compatible with a faunal age range of 4 to 2 Ma.

See also: Gibbons, A., Little Foot Not So Ancient, ScienceNOW Daily News, 7 December 2006.

Two papers have appeared documenting an association between the end of the late Proterozoic glacial deposits, a rise in oxygen levels in oceanic waters and the appearance of multicellular animals (the Ediacaran fauna). Associations are undoubtedly interesting and they trigger hypotheses about cause and effect. This is apparent in the various commentaries:

Editor of Nature: “an increase in oxygen in the deep ocean […] appears to have been associated with the evolution of complex animals.”
Fike et al (in Nature): “ […] indicating that this event may have had a key role in the evolution of eukaryotic organisms.”
Kerr (in Science): "A Shot of Oxygen to Unleash the Evolution of Animals"
Canfield et al (in Science): “The first known members of the Ediacara biota are found shortly after the Gaskiers glaciation, suggesting a causal link between their evolution and this oxygenation event.”

There is a tendency to for evolutionists to say that if conditions are right, the evolution of life is inevitable. So, given a prebiotic soup in a reducing chemical environment, single cells will form. (Judging by the latest headlines about water on Mars: given just water, life will form!). Having started with single-celled life in the Precambrian, the suggestion is now being made that as oxygen levels rose, new selection forces were unleashed to evolve multicellular organisms. This hypothesis appears to be thrown out without offering any supporting reasons. This illustrates one of the major problems we have with evolutionary theory: a tendency to talk in terms of physics and chemistry to the neglect of information. Without addressing the origin of complex biological information, a hypothesis like this is an evolutionary veneer on some very interesting observations.

Oxidation of the Ediacaran Ocean
D. A. Fike, J. P. Grotzinger, L. M. Pratt and R. E. Summons
Nature 444, 744-747 (7 December 2006) | doi:10.1038/nature05345

Oxygenation of the Earth's surface is increasingly thought to have occurred in two steps. The first step, which occurred ~2,300 million years (Myr) ago, involved a significant increase in atmospheric oxygen concentrations and oxygenation of the surface ocean1, 2. A further increase in atmospheric oxygen appears to have taken place during the late Neoproterozoic period3, 4 (~800–542 Myr ago). This increase may have stimulated the evolution of macroscopic multicellular animals and the subsequent radiation of calcified invertebrates4, 5, and may have led to oxygenation of the deep ocean6. However, the nature and timing of Neoproterozoic oxidation remain uncertain. Here we present high-resolution carbon isotope and sulphur isotope records from the Huqf Supergroup, Sultanate of Oman, that cover most of the Ediacaran period (~635 to ~548 Myr ago). These records indicate that the ocean became increasingly oxygenated after the end of the Marinoan glaciation, and they allow us to identify three distinct stages of oxidation. When considered in the context of other records from this period7, 8, 9, 10, 11, 12, 13, 14, 15, our data indicate that certain groups of eukaryotic organisms appeared and diversified during the second and third stages of oxygenation. The second stage corresponds with the Shuram excursion in the carbon isotope record16 and seems to have involved the oxidation of a large reservoir of organic carbon suspended in the deep ocean6, indicating that this event may have had a key role in the evolution of eukaryotic organisms. Our data thus provide new insights into the oxygenation of the Ediacaran ocean and the stepwise restructuring of the carbon6, 16, 17 and sulphur cycles3, 18, 19 that occurred during this significant period of Earth's history.

Late-Neoproterozoic Deep-Ocean Oxygenation and the Rise of Animal Life
Don E. Canfield, Simon W. Poulton, and Guy M. Narbonne
Science 315, 5 January 2007: 92-95. doi: 10.1126/science.1135013

Animals have an absolute requirement for oxygen, and an increase in late Neoproterozoic oxygen concentrations has been forwarded as a stimulus for their evolution. The iron content of deep-sea sediments show that the deep ocean was anoxic and ferruginous before and during the Gaskiers glaciation 580 million years ago, becoming oxic afterward. The first known members of the Ediacara biota are found shortly after the Gaskiers glaciation, suggesting a causal link between their evolution and this oxygenation event. A prolonged stable oxic environment may have permitted the emergence of bilateral motile animals some 25 million years later.

See also: Kerr, R.A. A Shot of Oxygen to Unleash the Evolution of Animals, Science 314, 8 December 2006: 1529.

Rokas and Carroll have produced a most interesting paper on the results of genome analyses designed to resolve questions about the tree of life (TOL). They draw attention to a prediction made by Richard Dawkins:

“… there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened. It exists. It is in principle knowable. We don't know it all yet. By 2050 we should – or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.”

However, the signs from the expanding research base suggest that this outcome is not likely to be reached. The analyses are producing bushes, not trees. “The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.”
Examples are given of these bushes. Of great interest to us as humans is the gorilla/chimp/human analysis. Based on 98 genes, the results show that ~55% of genes support a human-chimpanzee clade, 40% are evenly split among the two alternative topologies, eith the remaining genes being uninformative.” The results for this clade and others are not as expectated, and the authers explore different ways of reconciling the data with the TOL model. Homoplasy is identified as a major contributor to this “lack of resolution”. They write: “the observed patterns … give cause for concern that the extent of homoplasy is much greater than expected under widely accepted models of sequence evolution and the attendant consequences for the limits to phylogenetic resolution are not sufficiently appreciated.” They conclude by submitting that Dawkins’ prediction will be fulfilled if we end up with “an arborescent bush of life”.
The situation then becomes remarkably similar to the problems of convergent evolution in palaeontology: how do we know what are primitive and what are derived characters? How do we avoid a situation where the data are interpreted through a TOL filter? As is so often the case in evolutionary theory, the empirical evidence does not confirm the theory, but the theory is used to bring “integration” to the data.
What if there is not a TOL, how could we ever know it using contemporary evolutionary theories? What we need are either theoretical approaches that do not presume the outcomes (i.e. presumption as illustrated by the Dawkins’ quote) or the adoption of multiple hypotheses to allow testing of alternative scenarios. In the interests of healthy science, alternatives to common ancestry should be welcomed by the research community.

Bushes in the tree of life
Rokas, A. and Carroll, S.B.
PLoS Biology, 2006, 4(11): e352, 1899-1904

First para: Genome analyses are delivering unprecedented amounts of data from an abundance of organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection. However, recent analyses of some key clades in life's history have produced bushes and not resolved trees. The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted. Here we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences. Because some histories may not be resolvable by even vast increases in amounts of conventional data, the identification of new molecular characters will be crucial to future progress.

The type III secretion system (T3SS) has risen from comparative obscurity to become the focus of attention for many researchers. This is partly because if its potential for medical applications, and partly because it has the distinction of being constructed from a subset of components found in the bacterial flagellum. Some have advanced the view that the T3SS is a link in the gradualist chain leading to the formation of the bacterial flagellum, thereby disproving the claim by Michael Behe that this structure is irreducibly complex. New research is far from confirming the gradualist hypothesis. The “T3SSs are among the most complex protein secretion systems known in bacteria.” In a recent review of what is known of their structure, the authors write: “We have focused on what we believe are the general principles that govern the function of these biological machines.....” Just as the bacterial flagellum is an exquisite nano-machine, so also is the T3SS a striking example of nanotechnology. Whilst it may be possible to interpret T3SS as derived from the more complex flagellum, the route to gradual construction of these structures is as far off as ever.

Protein delivery into eukaryotic cells by type III secretion machines
Jorge E. Galán and Hans Wolf-Watz
Nature 444, 567-573 (30 November 2006) | doi:10.1038/nature05272

Abstract: Bacteria that have sustained long-standing close associations with eukaryotic hosts have evolved specific adaptations to survive and replicate in this environment. Perhaps one of the most remarkable of those adaptations is the type III secretion system (T3SS)—a bacterial organelle that has specifically evolved to deliver bacterial proteins into eukaryotic cells. Although originally identified in a handful of pathogenic bacteria, T3SSs are encoded by a large number of bacterial species that are symbiotic or pathogenic for humans, other animals including insects or nematodes, and plants. The study of these systems is leading to unique insights into not only organelle assembly and protein secretion but also mechanisms of symbiosis and pathogenesis.

The ID debate requires us to address numerous issues relating to the philosophy of science and the nature of the scientific method. Here is an informative case study showing the way a predominant paradigm (referred to as “deep-seated beliefs”) inhibited progress for 25 years. There were a few mavericks around at the time swimming against the tide, but they were cold-shouldered and ignored. The key point to note concerns “the reluctance of many contemporary scientists to accept contradictory evidence”. This episode in science’s past has many similarities with neo-Darwinism today. Despite the publication of “Icons of Evolution” (documenting how the research findings compare with textbook presentations of evolution), the real evidence against neo-Darwinism is received by its supporters like water on a duck’s back.

Deserts on the sea floor: Edward Forbes and his azoic hypothesis for a lifeless deep ocean
Thomas R. Anderson and Tony Rice
Endeavour, Volume 30, Issue 4 , December 2006, Pages 131-137

Abstract: While dredging in the Ægean Sea during the mid-19th century, Manxman Edward Forbes noticed that plants and animals became progressively more impoverished the greater the depth they were from the surface of the water. By extrapolation Forbes proposed his now infamous azoic hypothesis, namely that life would be extinguished altogether in the murky depths of the deep ocean. The whole idea seemed so entirely logical given the enormous pressure, cold and eternal darkness of this apparently uninhabitable environment. Yet we now know that the sea floor is teeming with life. Curiously, it took 25 years for the azoic hypothesis to fall from grace. This was despite the presence of ample contrary evidence, including starfishes, worms and other organisms that seemingly originated from the deep seabed. This is a tale of scientists ignoring observations that ran counter to their deep-seated, yet entirely erroneous, beliefs.