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.

In a recently-published book, Eric Davidson, “the world's leading expert” in the field of evo-devo, offers his perspective “on the gene regulatory networks that control animal development”. The book is significant because Davidson “proposes a scenario to explain how these distinct types of network subcircuits have emerged in animal evolution.”

The complexity of the gene networks is well known. “These networks consist of huge sets of regulatory genes that control one another's expression as well as the expression of downstream effector genes via so-called cis-regulatory elements (to which the transcription factors bind).” The reviewer comments appreciatively on the way Davidson describes the genetic control of development in living animals: “In essence, through a stepwise process, development subdivides the embryo into territories, subterritories, and "progenitor fields" that make up a given body part of the adult animal. This stepwise subdivision is accomplished by gene regulatory network subroutines called subcircuits that consist of small sets of genes and cis-regulatory elements.” Something of this complexity can be appreciated by reference to the figure that accompanies the review.

“The final chapter, on the evolution of gene regulatory networks, is the most speculative and most stimulating. Here, Davidson outlines a possible evolutionary origin of kernels …”. The reviewer refers to three stages of evolution. “In a third stage … , the animal body parts and, concomitantly, the territorial subdivision of the developing embryo became more and more elaborate until finally the underlying subcircuits were locked down into kernels that could no longer be changed without deleterious consequences. According to Davidson, this "triumph of the bilaterian versions of animal body plans" was in place sometime before the Cambrian and has persisted, constraining metazoan evolution ever since with tremendous success.”

The concept being developed here can be related to irreducible complexity (although Davidson clearly thinks these IC systems can be constructed by evolutionary processes). The “kernel” is a term drawn from information science, referring to the core of an operating system. When these kernels were in place, they could no longer be modified by evolutionary processes, because any change was deleterious and was not preserved.

We thus have the developmental architectures of animals in place sometime before the Cambrian. This is a scenario that is discussed in that much denigrated paper by Steve Meyer (“The Origin of Biological Information and the Higher Taxonomic Categories” Proceedings of the Biological Society of Washington 117(2004):213-239.). Meyer writes: “Can neo-Darwinism explain the discontinuous increase in CSI that appears in the Cambrian explosion--either in the form of new genetic information or in the form of hierarchically organized systems of parts?” Davidson’s book undoubtedly puts more substance into the argument, spelling out some essential elements of the complexity that has to be in place for the Cambrian Explosion.

The reviewer continues: “The proposed link between the evolution of kernels and the evolution of bilaterian body plans is exciting, but it awaits validation through more comparative analyses of gene networks. As Davidson himself concedes, "for the identification of kernels … an overwhelming feature of the evidence thus far is its thinness."” This seems to be a realistic assessment of the state of knowledge. There is also the significant absence of ancestors of the Cambrian animals, despite continuing discoveries about the Ediacaran fauna. But it seems to me that the convergence between the thinking of Davidson and Meyer is such that it gives strength to the argument of Meyer’s 2004 paper. I wonder if others see the situation like this?

A Kernel Bears Fruit
Detlev Arendt
Science 314, 17 November 2006: 1085-1086.

A review of: "The Regulatory Genome. Gene Regulatory Networks in Development and Evolution" by Eric H. Davidson, Academic Press (Elsevier), Burlington, MA, 2006.

This review of Paul Davies’ latest book will raise a few eyebrows. Some will think that Davies has abandoned science. Others will express their puzzlement why Davies cannot make a Design Inference. Earlier this week, I was reading Alvin Plantinga on the twin pillars of Christian Scholarship. He identifies three main contestants in the contemporary intellectual world: Christianity, Perennial Naturalism and Creative Anti-realism. The latter finds expression in Kant, Wittgenstein, existentialism, relativism and post-modernism. The reviewer's description of Davies' "more interesting" idea fits neatly into this approach. How curious to find Davies avoiding ID only to end up in the Creative Anti-realist camp!

Books and Arts: Life in the universal porridge
What were the chances that the conditions in the Universe would be just right for life?
Jim Al-Khalili reviews The Goldilocks Enigma: Why Is the Universe Just Right for Life? by Paul Davies
Nature 444, 423 (23 November 2006) | doi:10.1038/444423a

Selected excerpts:
"Davies’ first suggestion is that the ‘biofriendliness' of the Universe may be due to some as yet undiscovered 'life principle: built into the laws of physics from the very beginning, that has steered and constrained the Universe towards producing life. I find this idea hard to swallow and I don't think Davies dwells on it long enough to really make a convincing case.
"He then invites us to consider a more interesting - I hesitate to endorse it with the term 'appealing' - idea originally expounded by physicist John Wheeler. It takes one of the weirdest features of quantum mechanics and pushes it to its logical conclusion: that conscious observers bring about the universe they find themselves in by the very act of observing it, thereby dragging it out of the quantum superposition of all possible paths it could have followed. Actually, I think this is related to what supporters of the Multiverse version of quantum mechanics would argue -with the difference that, for Davies, our universe is the only one.
"The main options, then, are: first, that the Universe is a fluke; second, that it is one of many and happens to be, much like Goldilocks' porridge, just right for us; and third, that conscious observers bring the universe they inhabit into existence simply by observing it, although their teleological actions would have to reach back into the past, forcing the right conditions to be selected at the Big Bang."

The received wisdom that the “DNA of any two humans is 99.9% similar in content and identity” appears not to be true. "One of the real surprises of these results was just how much of our DNA varies in copy number. We estimate this to be at least 12% of the genome.” "The copy number variation that researchers had seen before was simply the tip of the iceberg, while the bulk lay submerged, undetected. We now appreciate the immense contribution of this phenomenon to genetic differences between individuals."
This raises numerous questions about methodology and those embedded assumptions that are usually completely hidden to those outside the research community. A rethink appears to be needed in two areas:
1. The much heralded claim that human genome is only 3% different from the Chimpanzee. Do we now infer that some of the human population are much closer to Chimps than others? Of course not! Something else of significance is going on here.
2. The concept that the human genome can be documented, with all the variants treated as random mutations. The indication is rather that the genome is much more dynamic than this, and that most of the variations are not random mutations at all. A design perspective has great potential to stimulate new hypotheses.

Global variation in copy number in the human genome
Richard Redon, et al.
Nature 444, 444-454 (23 November 2006) | doi:10.1038/nature05329

Abstract: Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.

See also: Shianna, K.V. and Willard, H.F., Human genomics: In search of normality, Nature 444, 428 (23 November 2006) | doi:10.1038/444428a

The biodiversity of marine species since the Cambrian shows significant differences before and after the Permian extinction event. In his commentary, Kiessling writes: “The big surprise in their analysis is a major difference between Paleozoic … and younger communities. In older assemblages, complex and simple distributions are about equally common, but complexly structured assemblages are substantially more common in more recent times. With so many paleobiologists looking at local, regional, and global diversity patterns through time, how could this striking pattern have escaped our attention for so long?”

Maybe because "evolution" rather than "ecology" has been the guiding word? It is increasingly apparent that environmental factors have been a major driver in understanding the pattern of fossils in different strata. The focus needs to shift from viewing the past through “evolutionary” spectacles.

Discussion within the ID community has drawn a parallel between the Cambrian explosion and the post-Permian radiations. In the latter, huge opportunities were present for the evolution of new phyla/body plans, yet what we see are not new phyla but radiations and complex ecosystems. Why the difference with the Cambrian Explosion? Is this yet another case of Darwinism failing to correlate well with the evidence?

Abundance Distributions Imply Elevated Complexity of Post-Paleozoic Marine Ecosystems
Peter J. Wagner, Matthew A. Kosnik, and Scott Lidgard
Science 314, 24 November 2006: 1289-1292.

Abstract: Likelihood analyses of 1176 fossil assemblages of marine organisms from Phanerozoic (i.e., Cambrian to Recent) assemblages indicate a shift in typical relative-abundance distributions after the Paleozoic. Ecological theory associated with these abundance distributions implies that complex ecosystems are far more common among Meso-Cenozoic assemblages than among the Paleozoic assemblages that preceded them. This transition coincides not with any major change in the way fossils are preserved or collected but with a shift from communities dominated by sessile epifaunal suspension feeders to communities with elevated diversities of mobile and infaunal taxa. This suggests that the end-Permian extinction permanently altered prevailing marine ecosystem structure and precipitated high levels of ecological complexity and alpha diversity in the Meso-Cenozoic.

See also: Kiessling, K. Life's Complexity Cast in Stone, Science 314, 24 November 2006: 1254-1255.

The thoracic musculature of insects that enables very high wing beat frequencies is described as “striking”. At a molecular level, a series of interrelated characteristics are required, including: “the highest measured detachment rate of myosin from actin”, “an exceptionally weak affinity of MgATP for myosin” and “a unique rate-limiting step in the cross-bridge cycle at the point of inorganic phosphate release.” Although this paper is written from an evolutionary perspective, the authors are continually flagging up design issues at the molecular level. The properties of the materials used to power flight are remarkable.

An exceptionally fast actomyosin reaction powers insect flight muscle
Douglas M. Swank, Vivek K. Vishnudas and David W. Maughan
Proc. Natl. Acad. Sci. USA. November 14, 2006, vol. 103, no. 46, 17543-17547 | doi:10.1073/pnas.0604972103.

Insects, as a group, have been remarkably successful in adapting to a great range of physical and biological environments, in large part because of their ability to fly. The evolution of flight in small insects was accompanied by striking adaptations of the thoracic musculature that enabled very high wing beat frequencies. At the cellular and protein filament level, a stretch activation mechanism evolved that allowed high-oscillatory work to be achieved at very high frequencies as contraction and nerve stimulus became asynchronous. At the molecular level, critical adaptations occurred within the motor protein myosin II, because its elementary interactions with actin set the speed of sarcomere contraction. Here, we show that the key myosin enzymatic adaptations required for powering the very fast flight muscles in the fruit fly Drosophila melanogaster include the highest measured detachment rate of myosin from actin (forward rate constant, 3,698 s-1), an exceptionally weak affinity of MgATP for myosin (association constant, 0.2 mM-1), and a unique rate-limiting step in the cross-bridge cycle at the point of inorganic phosphate release. The latter adaptations are constraints imposed by the overriding requirement for exceptionally fast release of the hydrolytic product MgADP. Otherwise, as in Drosophila embryonic muscle and other slow muscle types, a step associated with MgADP release limits muscle contraction speed by delaying the detachment of myosin from actin.

For further reading: Myosin's need for speed, JCB, 2006. 175(4), 519. | doi:10.1083/jcb.1754rr3
http://www.jcb.org/cgi/content/full/175/4/519b

Research into taste has not been as extensive as that for sight and hearing. This ‘state of the art’ paper provides a fascinating read, and the “emerging picture of taste coding at the periphery is one of elegant simplicity”. There are unique receptors tuned to detect each of the five basic tastes. These are linked in with other inputs to taste and fed to the brain for neural activity to provide the final orchestration of “positive hedonic value and behavioural acceptance”. All this, according to the authors, is an accommodation to an “evolutionary need.” The paper gives no evidence that this is actually the case. Unspecified hypothetial evolutionary needs are invoked as ‘context’ for the research, but ‘design’ can also provide ‘context’. What is lacking in this paper is a discussion as to why “evolutionary need” should be preferred over “design”.

The receptors and cells for mammalian taste
Jayaram Chandrashekar, Mark A. Hoon, Nicholas J. P. Ryba and Charles S. Zuker
Nature 444, 288-294 (16 November 2006) | doi:10.1038/nature05401

Abstract: The emerging picture of taste coding at the periphery is one of elegant simplicity. Contrary to what was generally believed, it is now clear that distinct cell types expressing unique receptors are tuned to detect each of the five basic tastes: sweet, sour, bitter, salty and umami. Importantly, receptor cells for each taste quality function as dedicated sensors wired to elicit stereotypic responses.

For further reading: Bradbury J (2004) Taste Perception: Cracking the Code. PLoS Biol 2(3): e64
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020064

Non-biting midges reveal not only insects that are similar to those today, but also ecosystem stability in the Caribbean from the Miocene until today. These new results are part of a less-appreciated characteristic of the fossil record: that stasis is widespread and deserves a much higher profile in our scientific thinking.

Chironomidae (Diptera) in Dominican amber as indicators for ecosystem stability in the Caribbean
Martin Grund
Palaeogeography, Palaeoclimatology, Palaeoecology, 241(3-4), 14 November 2006, 410-416.

Abstract: A first overview on fossil chironomids in Dominican amber is given. This fossil assemblage seems to represent an insular fauna, very similar to its living relatives. Stenochironomus sp. and especially the true xylophagous, neotropical/southern North American Xestochironomus spp. prove the persistence of submerged dead wood in nutrient poor mountain streams in the Greater Antilles from the Miocene until today. Their abundance indicates that the special ecological conditions in extant Caribbean tropical mountain streams already ruled the ancient ecosystem. The results arising from the fossils of these freshwater organisms do not coincide with the faunal changes shown by other groups of insects. General systematic descriptions of new fossil representatives of Xestochironomus and Stenochironomus are given.

Genetic information: Codes and enigmas
There's more than one way to read a stretch of DNA, finds Helen Pearson — and we need to understand them all.
Nature 444, 259-261 (16 November 2006) | doi:10.1038/444259a

Computer buffs interested in cracking codes have developed software routines to prise out hidden information. “We are treating DNA as we used to treat problems in intelligence” [Shepherd] says. “We want to break the code at the most fundamental level.”

This is the first point where an ID perspective will help research. “Breaking the code” cannot be reduced to an exercise in computer science. We need to recognise the biological context for the DNA operation and to treat the whole cell as a complex system. This will lead to a systems engineering methodology for analysis.

A highly significant paragraph is as follows:
“DNA seems well adapted for supporting a number of codes. For a start, only 1-2% of the human genome is occupied with protein-coding sequences, which leaves plenty of intervening DNA to hold other information. But many stretches of DNA in humans and other organisms manage to multitask: a sequence can code for a protein and still manage to guide the position of a nucleosome. This is possible because the triplet code is ‘degenerate’. Several slightly different triplets can code for the same amino acid, and many positions in a protein can be filled by different amino acids – so different sequences can effectively mean the same thing. This allows other signals to be imprinted on top of the first – especially when those other signals are themselves encoded with some slack.”

Multitasking is something we typically associate with intelligence. Getting a code to convey one message is a challenge in itself, but getting the same code to carry several messages is evidence of higher level intelligent agency. ID helps here, allowing the premise that the ‘degenerate’ aspects of the triplet code are actually designed to permit sophisticated encoding.

The writer, however, goes on to make an extraordinary comment on this. “This elegance is surely the handiwork of evolution – and if the way in which that hand had worked to solve these problems were clearer, the simultaneous decoding of all the messages involved might become easier.”

It is extraordinary because of the word “surely”. Why “surely”? Not because of the sophisticated design features! Not because the whole thing is “elegant”! I can only think that the word “surely” is deductive: because “we know” that Darwinism is true. The same rationale is behind this comment that appears earlier in the article: “Biology has probably figured out a way to squeeze every bit of information from that molecule it can”.

There is no empirical base for suggesting that these design features can emerge from evolutionary processes. Our recognition of them as a phenomenon comes only because we have met them before in intelligently designed digital information.

That sentence should read: “This elegance is surely the handiwork of an Intelligent Designer – and if the way in which His hand had worked to solve these problems were clearer, the simultaneous decoding of all the messages involved might become easier.”

One further point on the use of anthropomorphic language. Examples already cited are:
“Biology has probably figured out a way to squeeze every bit of information from that molecule it can”.
“This elegance is surely the handiwork of evolution”
“the way in which that hand had worked to solve these problems”

In each case, we have intelligent agency attributed to the mechanistic processes of evolution. As Dembski’s design filter shows, these mechanisms give us law-like and chance-like characteristics, but these are distinct from design-like characteristics. Although the evolutionary paradigm dies not permit intelligent agency, those within its mould have to resort to anthropomorphisms to develop their ideas. Sad. That's perhaps the biggest "enigma" in this essay.

Nature 444, 243-244 (16 November 2006) | doi:10.1038/444243b; Published online 15 November 2006

Order for microbes
Abstract

Burgeoning microbial gene data require coherent efforts to make them readily usable.

Microbes don't subscribe to the single life. They are coupled with complex ecosystems of diverse, mutually dependent species. This complexity and the vast numbers of microbes in the ocean, the soil, in our gut and almost everywhere else pose a challenge to those seeking to understand microbial ecology.

In the 1980s, surveying the microbial world by sequencing the collective ribosomal RNA opened up new avenues. For the first time it was possible to get a glimpse of the make-up of complex microbial systems. It's a reasonable assumption that the more similar these sequences are, the more closely related the microbes are, and the more closely related their lifestyles must be - hence the pursuit of insights into what microbes might be doing in their environments.

But this assumption turned out to be fragile, as it emerged that microbes frequently shuffle around their genes both within and between species. A similarity in one gene does not necessarily correlate with the absence or presence of other genes in the genome.

Fortunately, the continuous decrease in sequencing costs allows today's microbiologists to sequence not only a single gene from each of the most abundant species in a microbial ecosystem, but also, at least in theory, all the genes present. These composite genomes, or 'metagenomes', provide a wealth of information that could only be dreamt of even a couple of years ago. With sequencing facilities continuing to increase their capacities by applying new technologies, and funding agencies supplying the necessary resources, sequencing the ocean or the contents of the human gut has become relatively easy. But how to extract meaningful information from a metagenome, and to gain insight into both the individual species' impact on the microbial community and the impact of this community on the ecosystem?

We can hope to unravel the function of every gene when individual species can be cultivated and genetically manipulated in the laboratory, but this is impossible when dealing with a complex community containing hundreds or thousands of species. Functional assignment of genes needs to be performed, even when the only information available is a string of nucleotide bases.

There are numerous databases and websites, public and not-so-public, some adhering to an easily understandable framework of standards and regulation, and some not so transparent. Five years ago it was a big disappointment to compare one's chosen sequence with the GenBank database and not find a 'hit'. Today there is a feeling of sheer inadequacy in the face of vast quantities of sequence and annotation information - and an acute need for a degree in bioinformatics.

Publication in most cases (including the Nature journals) requires the deposition of sequence data into the GenBank or EMBL databases. Much less effort is spent depositing unpublished data or updating information that is already published. In all probability, in the not too distant future, metagenomic studies will be done not only by the big sequencing centres, but by anybody with a reasonable research budget and university support. To make all the data more easily accessible, it would be desirable to have a collaborative effort of genome centres and funding agencies to build a universal microbial-sequence database, with a readily comprehensible framework for sequencing and annotation standards and regulations.

Microbiology has come a long way from investigating the easily cultured individual microbe from a rich microbial community and describing what is out there, and is now starting to get a grip on what they actually do. With the intrinsic difficulties of dealing with complex systems, it is good to see a field galvanized by new technologies and scientific daring. But more infrastructural order is required, to prevent the discipline getting ahead of itself.

The Archean-Paleoproterozoic transition (dated ca. 2500-2000 Ma) is commonly associated with the establishment of an oxygen-rich atmosphere and the emergence of an aerobic biosphere. The paper below considers rocks at the very beginning of this period and finds in oil-bearing fluid inclusions abundant evidence for photosynthesising eukaryotes. Some have claimed evidences back to 3700 Ma, but this represents the minority. However, this paper will make it easier to defend the claim that photosynthesis is found early in the Archaean. The gradualistic evolutionary story does not fit these data.

Biomarkers from Huronian oil-bearing fluid inclusions: An uncontaminated record of life before the Great Oxidation Event.
Adriana Dutkiewicz, Herbert Volk, Simon C. George, John Ridley and Roger Buick
Geology: 2006, Vol. 34, No. 6, pp. 437-440.

ABSTRACT: We report detailed molecular geochemistry of oil-bearing fluid inclusions from a ca. 2.45 Ga fluvial metaconglomerate of the Matinenda Formation at Elliot Lake, Canada. The oil, most likely derived from the conformably overlying McKim Formation, was trapped in quartz and feldspar during diagenesis and early metamorphism of the host rock, probably before ca. 2.2 Ga. The presence of abundant biomarkers for cyanobacteria and eukaryotes derived from and trapped in rocks deposited before the Great Oxidation Event is consistent with an earlier evolution of oxygenic photosynthesis than previously thought and suggests that some aquatic settings had become sufficiently oxygenated for sterol biosynthesis by this time. It also implies that eukaryotes survived several extreme climatic events, including the Paleoproterozoic "snowball Earth" glaciations. The extraction of biomarker molecules from Paleoproterozoic oil-bearing fluid inclusions thus establishes a new method, using low detection limits and system blank levels, to trace evolution of life through Earth's early history that avoids the potential contamination problems affecting shale-hosted hydrocarbons.

C. G. Kurland and colleagues sever the link between eukaryotes and prokaryotes in this recent article in Science. Their title refers to the "Irreducible Nature of Eukaryote Cells". The logic of their argument confirms this: the structures and the genetics of eukaryotes mean that an evolutionary pathway from prokaryotes must be rejected. However, they do not again use the word "irreducible" in their paper. What is clear is that the "simple" pathway that the textbooks have proclaimed for years must now be abandoned.

Genomics and the Irreducible Nature of Eukaryote Cells
C. G. Kurland, L. J. Collins, and D. Penny Science 312, 19 May 2006: 1011-1014.

Abstract: Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular evolution. The evolutionary trajectory of modern eukaryotes is distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Comparative genomics shows that, under certain ecological settings, sequence loss and cellular simplification are common modes of evolution. Subcellular architecture of eukaryote cells is in part a physical-chemical consequence of molecular crowding; subcellular compartmentation with specialized proteomes is required for the efficient functioning of proteins.

Comparative genomics and proteomics have strengthened the view that modern eukaryote and prokaryote cells have long followed separate evolutionary trajectories. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes (1*4). Nevertheless, comparative genomics has confirmed a lesson from paleontology: Evolution does not proceed monotonically from the simpler to the more complex (5*9). Here, we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage.

Mitochondria, mitosomes, and hydrogenosomes are a related family of organelles that distinguish eukaryotes from all prokaryotes (10). Recent analyses also suggest that early eukaryotes had many introns (11, 12), and RNAs and proteins found in modern spliceosomes (13). Indeed, it seems that life-history parameters affect intron numbers (14, 15). In addition, "molecular crowding" is now recognized as an important physical-chemical factor contributing to the compartmentation of even the earliest eukaryote cells (16, 17).

Nuclei, nucleoli, Golgi apparatus, centrioles, and endoplasmic reticulum are examples of cellular signature structures (CSSs) that distinguish eukaryote cells from archaea and bacteria. Comparative genomics, aided by proteomics of CSSs such as the mitochondria (18, 19), nucleoli (20, 21), and spliceosomes (13, 22), reveals hundreds of proteins with no orthologs evident in the genomes of prokaryotes; these are the eukaryotic signature proteins (ESPs) (23, 24). The many ESPs within the subcellular structures of eukaryote cells provide landmarks to track the trajectory of eukaryote genomes from their origins. In contrast, hypotheses that attribute eukaryote origins to genome fusion between archaea and bacteria (25*30) are surprisingly uninformative about the emergence of the cellular and genomic signatures of eukaryotes (CSSs and ESPs). The failure of genome fusion to directly explain any characteristic feature of the eukaryote cell is a critical starting point for studying eukaryote origins.

Jonathan Wells explains how intelligent design theory may lead to new approaches to cancer research in this article from Rivista di Biologia / Biology Forum 98 (2005), pp. 71-96.

Abstract. A microtubule-dependent polar ejection force that pushes chromosomes away from spindle poles during prometaphase is observed in animal cells but not in the cells of higher plants. Elongating microtubules and kinesin-like motor molecules have been proposed as possible causes, but neither accounts for all the data. In the hypothesis proposed here a polar ejection force is generated by centrioles, which are found in animals but not in higher plants. Centrioles consist of nine microtubule triplets arranged like
the blades of a tiny turbine. Instead of viewing centrioles through the spectacles of molecular reductionism and neo-Darwinism, this hypothesis assumes that they are holistically designed to be turbines. Orthogonally oriented centriolar turbines could generate oscillations in spindle microtubules that resemble the motion produced by a laboratory vortexer. The result would be a microtubule-mediated ejection force tending to move chromosomes away from the spindle axis and the poles. A rise in intracellular calcium at the
onset of anaphase could regulate the polar ejection force by shutting down the centriolar turbines, but defective regulation could result in an excessive force that contributes to the chromosomal instability characteristic of most cancer cells.

Keywords. Centriole; Centrosome; Polar ejection force; Chromosomal instability;
Cancer.

Reviewed by Dennis Wagner

You would be violating the law to require students to read Vij Sodera?s One Small Speck to Man in the Dover County Schools, PA. Not because it is religious (Sodera never mentions God or the Bible), and not because it promotes creation-science or intelligent design (you won?t find those words anywhere in the book), but because this surgeon from the UK, with a special interest in animal biology, provides a detailed and devastating critique of evolution theory. And in Dover, PA the Federal judge ruled that the school district cannot require students to read anything that denigrates the theory of evolution.

In this encyclopedic book, Dr. Sodera explores the living world from coelacanths to embryology; from dinosaurs to muscle contraction; from whales to human fossils; and shows conclusively that the ?one small speck to man? theory of evolution is more imagination than reality. With 464 pages and over 800 color images, this truly outstanding work deals purely with the scientific evidence and provides a highly detailed reference.

Some readers may already be familiar with many of the critiques of Darwin?s theory presented in this book. However, to have them nicely organized in one volume, with outstanding photos and graphics to illustrate the points, makes this a wonderful high school or college level text, as well as a prized coffee table book that is fun to browse. Like most full-color coffee-table books, this volume will cost you a chunk of change. But we think you will find it a worthwhile investment, especially if you are a homeschool teacher looking for a life-sciences textbook that does not assume that Darwinian evolution is the only way to look at the evidence. The topics covered in individual chapters include animal fossils, time, mass extinctions, variation, DNA and proteins, molecular machines, whales, birds, the eye, human fossils, bipedalism, chromosomes, and intelligence.

The chapter on Human Fossils was particularly interesting as Dr. Sodera pictorially and analytically compares human-like fossils with modern man. His conclusion: ?So the human-like fossil evidence actually paints a completely different picture from that which is commonly portrayed. Instead of man evolving from apes via crude-looking ancestors, the evidence points to populations of ancient human beings having passed through some morphological changes (whether from inbreeding and/or disease) before these groups gained the modern human form.?

This is the third major book critiquing evolution to come out of the UK in recent years joining Dawkin?s God: Genes, Memes and the Meaning of Life by Alister McGrath, and Evolution Under the Microscope: A Scientific Critique of the Theory of Evolution by David Swift. Perhaps there is a movement brewing in the UK similar to the ID movement in the US.

Order your copy of One Small Speck to Man: the evolution myth.