Science Literature

Although "less than 2% of the human genome is translated into protein, yet more than 40% of the genome is thought to be transcribed into RNA." This non-coding RNA has some "truly remarkable" characteristics: "microRNAs, short interfering (si)RNAs, repeat-associated RNAs and germline-specific RNAs) and of new members of existing classes (for example, small nucleolar (sno)RNAs)".

A recent review paper is concerned with the "biogenesis, trafficking and mechanisms of action of small nuclear and small nucleolar ribonucleoproteins (RNPs)." The authors refer to the "remarkable complexity" of these RNP complexes, pointers to which are as follows:
"ncRNAs have emerged as key trans-acting regulators of diverse cellular activities in all three domains of life."
"Ongoing studies of snRNPs and snoRNPs have revealed unexpectedly elaborate biogenesis pathways."
"ncRNAs often require partner proteins that provide various essential functions in addition to the obvious associated enzymatic activities."
"A common principle in the biogenesis of both snRNPs and snoRNPs is the assembly of stable, but inactive, pre-RNPs that require maturation at locations distinct from the functional sites."

It used to be said that DNA coding for protein was the only thing that mattered in the genome, and all else was lumped under the descriptor "Junk DNA". But not now! Is the term "Junk DNA" best understood as an outdated concept emerging from a very inadequate view of the genome? But even more important, with all this complexity emerging from DNA that does not code for protein, what does this imply for our understanding of living things? A friend writes: "Probability decreases EXPONENTIALLY as complexity increases. When do we reach an increase that makes the Darwinian hypothesis completely incredible? Seems like we must be there now."

Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs
A. Gregory Matera, Rebecca M. Terns and Michael P. Terns
Nature Reviews Molecular Cell Biology, 8, 209-220 (March 2007) | doi:10.1038/nrm2124

Abstract: Recent advances have fuelled rapid growth in our appreciation of the tremendous number, diversity and biological importance of non-coding (nc)RNAs. Because ncRNAs typically function as ribonucleoprotein (RNP) complexes and not as naked RNAs, understanding their biogenesis is crucial to comprehending their regulation and function. The small nuclear and small nucleolar RNPs are two well studied classes of ncRNPs with elaborate assembly and trafficking pathways that provide paradigms for understanding the biogenesis of other ncRNPs.

Summary of paper here.

Alex Rosenberg is a hardened reductionist who has written a book to persuade biologists that "interactions of macromolecules" are sufficient to explain all biological data. "The only serious challenge that he sees to reductionism comes from the principle of natural selection (PNS), which he believes has a central role in the subject." Rosenberg then attempts to present PNS as a biological law, but "he cannot find an acceptable definition, which is unsurprising given that many others before him have also tried and failed." The reviewer adds: "My own view is that PNS is a tautology, not a law."
Rosenberg writes: "Darwinism includes the claim that natural selection is at least the most significant causal mechanism of evolutionary change instantiated by lineages on Earth's tree of life." In which case, PNS is just declared to have the role that Darwinism assigns to it. It is not something that emerges from empirical science. The reviewer adds: "Darwinism as so defined is not a tautology, but it is more a theory or a paradigm than a law."
So Rosenberg's reductionist crusade founders on not being able to integrate PNS into his philosophical framework. Saunders is not too impressed with the way he handles genetic reductionism either. "Rosenberg has made a serious attempt at an impossible goal. I would like to think that his failure will help convince Darwinians that they should show the same degree of reticence in biology that some are already demonstrating in the study of human behaviour."
This is an interesting review, covering several issues much discussed by scholars associated with the ID Movement. It is encouraging to find common ground with many of the points made by Saunders.

Reductio ad absurdum
Peter T. Saunders
Trends in Ecology & Evolution , Volume 22, Issue 3 , March 2007, Pages 118-119

Book Review: Darwinian Reductionism: Or How to Stop Worrying and Love Molecular Biology, by Alex Rosenberg. University of Chicago Press, 2006.

Most contemporary biologists believe that biological processes are essentially physical. Despite this, most of us do not accept that explanations in biology can be truly satisfactory only if they can be formulated in terms of the laws of physics. In Darwinian Reductionism, Alex Rosenberg dismisses this as illogical. He insists 'that there is a full and complete explanation of every biological fact, state, event, process, trend or generalization, and that this explanation will cite only interactions of macromolecules to provide this explanation.' If this were merely a statement of what is possible in principle, there would be no real disagreement with the majority view. For Rosenberg, however, reductionism is not only a metaphysical thesis, but is also a claim about explanations and a research programme. His aim in Darwinian Reductionism is 'to convince the reader that heaven belongs to the molecular biologist, and to convince non-molecular biologists that there is room for them in the molecular biologist's heaven.'
[snip]

Ever since the first exoplanet was discovered, there has been an insatiable appetite for news of places with environments suitable for life. With over 200 exoplanets documented, none have yet satisfied this hunger. The next phase of research has now commenced, with two reports of planetary atmospheres.
The first is HD 209458b, at a distance of 150 light years from Earth. This gave a flat spectrum "showing nothing apart from a peak (Richardson] attributes to silicates, and possibly a molecule containing carbon-carbon bonds such as those seen in benzene." There was no trace of water, carbon dioxide or methane. The second report concerns HD 189733b, 60 light years from Earth. This also documents "a flat spectrum, with no water, methane or carbon dioxide" and no silicates either.
Richardson et al. comment: "All hot Jupiter spectra are expected to be shaped by water absorption because water is an abundant gas at the high temperatures of hot Jupiters (1,000 - 2,000 K)." Consequently, it is a real puzzle not to detect water in the spectra of these two planets. If water is present, it must be hidden by some means: "Unanticipated sources of opacity may be required to produce a temperature inversion at these altitudes, and thereby mask the effect of water opacity."
Theories of how planetary atmospheres formed will need to be reappraised. The findings create yet more problems for OOL research. In other contexts, finding water outside the Earth has been used to raise expectations of finding life, but at least that does not arise here. However, it is worth contrasting this point with some of the more sensational media reports: "Giant step in search for alien life" and "Nasa closer to discovering life on other planets". Beware of spin!

[Please note: this blog entry is written in the knowledge that some scientists think the earth's water came from comets, and recognises that their hypothesis is unaffected by the new finds. Also, the comments above do not imply that exoplanets containing water will not be found, nor that earth-size planets will not be discovered in the liquid water zone.]

A spectrum of an extrasolar planet
L. Jeremy Richardson, Drake Deming, Karen Horning, Sara Seager and Joseph Harrington
Nature 445, 892-895 (22 February 2007) | doi:10.1038/nature05636

Of the over 200 known extrasolar planets, 14 exhibit transits in front of their parent stars as seen from Earth. Spectroscopic observations of the transiting planets can probe the physical conditions of their atmospheres1, 2. One such technique3, 4 can be used to derive the planetary spectrum by subtracting the stellar spectrum measured during eclipse (planet hidden behind star) from the combined-light spectrum measured outside eclipse (star + planet). Although several attempts have been made from Earth-based observatories, no spectrum has yet been measured for any of the established extrasolar planets. Here we report a measurement of the infrared spectrum (7.5-13.2 [micro]m) of the transiting extrasolar planet HD 209458b. Our observations reveal a hot thermal continuum for the planetary spectrum, with an approximately constant ratio to the stellar flux over this wavelength range. Superposed on this continuum is a broad emission peak centred near 9.65 [micro]m that we attribute to emission by silicate clouds. We also find a narrow, unidentified emission feature at 7.78 m. Models of these 'hot Jupiter'5 planets predict a flux peak6, 7, 8, 9 near 10 m, where thermal emission from the deep atmosphere emerges relatively unimpeded by water absorption, but models dominated by water fit the observed spectrum poorly.

See also:

Sanderson, K. Direct view of a dark and distant world, Nature 445, 803 (22 February 2007)

Minkel, J.R., Water Mysteriously Absent from Extrasolar Planets' Atmospheres, Scientific American News, February 21, 2007
Contrary to predictions, two planets orbiting distant stars show no signs of water and other simple compounds; dark clouds or haze may hide them

Humans are used to the idea that we extract information from our environment, process it and determine an appropriate response. This is OK for those of us with brains that are large enough to do this, but these mental gymnastics are not going to suit creatures of small brain, like insects. Nevertheless, flying insects do not seem phased by this neural problem and they travel with ease over different terrains - rugged or smooth - with headwinds of varying intensities. It has been proposed that, instead of extracting information, insects utilise a visual-feedback loop linking flight with visual cues. "When insects are flying forward, the image of the ground sweeps backward across their ventral viewfield and forms an "optic flow", which depends on both the groundspeed and the groundheight." If a regulation system exists to stabilise the optic flow as perceived by the insect, it provides a means of controlling takeoff and landing, flight against wind, and flight over irregular terrains.
To test this idea, the researchers constructed a micro-helicopter equipped with an optic-flow regulator. The flying robot performed in ways that mirrored the distinctives of insect flight, and the authors, quite rightly, claim that it "sheds light on insect piloting abilities". They also claim numerous advantages for flying robot design, reducing the need for sensors and signal processing.
The authors add that the optic-flow system is "quite simple in terms of its neural implementation". Also that "its neural implementation is not very demanding". These comments do not seem to do justice to the need in flying insects for low weight with corresponding limited neuronal capabilities. Furthermore, the authors have only started to explore the control issues and the underlying neural circuits. They acknowledge themselves that there is some evidence for a second optic-flow regulator that "may be in charge of adjusting the groundspeed by regulating the lateral OF". In a commentary article, Webb identifies another factor: "Ventral optic flow can be easily detected if the animal is flying straight ahead and the sensor is pointing straight down. But if the insect pitches, rolls or rotates, ventral optic flow will be distorted. Can the animal measure and discount these movements, or are other sensorimotor loops, such as the optomotor reflex, deployed simultaneously to minimise them?"
What we have here is an interesting exercise in product development. A design brief could be written for a control system that enables lightweight flyers "to deal single handedly with all maneuvers, such as taking off, flying at a level height, landing, and responding appropriately to wind, without being informed about groundheight, groundspeed, airspeed, windspeed, or ascent or descent speed, and hence without any need for the metric sensors with which conventional aircraft are equipped." To achieve this, we would expect a substantial investment in intelligent design engineering. We recognise that the problem has many complex issues to resolve. Delivering a product that meets the design brief allows us to make inferences about intelligent agency.

A Bio-Inspired Flying Robot Sheds Light on Insect Piloting Abilities
Nicolas Franceschini, Franck Ruffier and Julien Serres
Current Biology, Vol 17, 329-335, 20 February 2007

Summary: When insects are flying forward, the image of the ground sweeps backward across their ventral viewfield and forms an "optic flow", which depends on both the groundspeed and the groundheight. To explain how these animals manage to avoid the ground by using this visual motion cue, we suggest that insect navigation hinges on a visual-feedback loop we have called the optic-flow regulator, which controls the vertical lift. To test this idea, we built a micro-helicopter equipped with an optic-flow regulator and a bio-inspired optic-flow sensor. This fly-by-sight micro-robot can perform exacting tasks such as take-off, level flight, and landing. Our control scheme accounts for many hitherto unexplained findings published during the last 70 years on insects' visually guided performances; for example, it accounts for the fact that honeybees descend in a headwind [1], land with a constant slope [2], and drown when travelling over mirror-smooth water [3]. Our control scheme explains how insects manage to fly safely without any of the instruments used onboard aircraft to measure the groundheight, groundspeed, and descent speed. An optic-flow regulator is quite simple in terms of its neural implementation and just as appropriate for insects as it would be for aircraft [4].

See also:
Insect Behaviour: Controlling Flight Altitude with Optic Flow
Barbara Webb
Current Biology, Vol 17, R124-R125, 20 February 2007

Summary: Insects can smoothly control their height while flying by adjusting lift to maintain a set-point in the ventral optic flow. The efficacy of this simple flight-control mechanism has been demonstrated using a robot helicopter.

The ability of chimpanzees to construct tools has long been an interest of anthropological researchers. The first and only data regarding past tool-making activity has just appeared in the PNAS. The Panin sites from West Africa are the only known prehistoric chimpanzee settlements, and these have "yielded behaviorally modified stones, dated by chronometric means to 4,300 years of age".
The press release explains the rationale for the researchers' conclusion: "The stones they excavated show the hallmarks of use as tools for smashing nuts when compared to ancient human or modern chimpanzee stone tools." In other words, the researchers have made a design inference, based on the data they have gathered. The stones bear the characteristic marks of being used as tools, and starch grains were found on the stones (an indication that the chimps were cracking nuts). It is a good example of a design inference in science, in this case involving non-human subjects. It is a much needed reminder that science should never be defined so as to exclude intelligent causation.
Some analysis of the significance of the finding has been made. The researchers say their work "suggests that percussive material culture could have been inherited from an common human-chimpanzee clade, rather than invented by hominins, or have arisen by imitation, or resulted from independent technological convergence." This does seem to be premature at best. What the data shows is behavioural stasis: chimps today can use tools to crack nuts; chimps 4300 years ago used tools to crack nuts. The data does not constrain explanations of the origins of this trait. One can interpret this in terms of Kuhnian "normal" science, whereby evidence for stasis is interpreted in terms of the prevailing evolutionary paradigm. Of the various options, the authors favour the idea that humans and chimps shared a common ancestor that possessed tool-making abilities. One suspects this hypothesis will not survive critical appraisal by peers.

4300-year-old chimpanzee sites and the origins of percussive stone technology
Mercader, Julio, Huw Barton, Jason Gillespie, Jack Harris, Steven Kuhn, Robert Tyler, and Christophe Boesch
Proceedings of the National Academy of Sciences, published February 20, 2007, 10.1073/pnas.0607909104

Abstract: Archaeological research in the African rainforest reveals unexpected results in the search for the origins of hominoid technology. The ancient Panin sites from Cote d'Ivoire constitute the only evidence of prehistoric ape behavior known to date anywhere in the world. Recent archaeological work has yielded behaviorally modified stones, dated by chronometric means to 4,300 years of age, lodging starch residue suggestive of prehistoric dietary practices by ancient chimpanzees. The "Chimpanzee Stone Age" pre-dates the advent of settled farming villages in this part of the African rainforest and suggests that percussive material culture could have been inherited from an common human-chimpanzee clade, rather than invented by hominins, or have arisen by imitation, or resulted from independent technological convergence.

See also:

The Chimpanzee Stone Age . West African chimpanzees have been cracking nuts with stone tools for thousands of years
Max Planck Society, 13 February 2007.

Ancient chimps 'used stone tools'
Chimpanzees in West Africa used stone tools to crack nuts 4,300 years ago. BBC News, BBC News, 13 February 2007.

Origin Of Life theories all have to engage with the improbability problem. Researchers have to decide whether the low probabilities are telling them NOT to pursue a particular investigation, or whether there is sufficient to justify persevering. There is no escape from this, because natural selection cannot yet be invoked.

The majority of OOL researchers favour a reductionistic approach, via the Miller-Urey model of synthesis of amino acids in a reducing environment followed by the RNA World. Shapiro hows how improbable this option is and comments:

"A highly implausible start for life, as in the RNA-first scenario, implies a universe in which we are alone. In the words of the late Jacques Monod, "The universe was not pregnant with life nor the biosphere with man. Our number came up in the Monte Carlo game.""

As an alternative paradigm, Shapiro favours the "metabolism first" scenario, where small bounded reaction-chambers reach the stage when significant chemical reactions take place but without replication. "Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them. In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle." In this situation, a variety of events might be possible. "[B]ecause we know that evolution does not anticipate future events, we can presume that nucleotides first appeared in metabolism to serve some other purpose, perhaps as catalysts or as containers for the storage of chemical energy (the nucleotide ATP still serves this function today). Some chance event or circumstance may have led to the connection of nucleotides to form RNA." Perhaps because the experimental work is so limited, Shapiro is willing to entertain the possibility that this route to life is not so improbable, and that what happened on Earth could have happened elsewhere in the Cosmos.

From an Intelligent Design perspective, none of these research paradigms will succeed. This is because none of them address the challenges of biological information. For as long as researchers are content to immerse themselves in the chemistry, they will not progress beyond the empty soup kettle. Is information an accident? Or is information a hallmark of intelligent agency and design? This is why ID needs to be integrated within science and evaluated on its merits (rather than rejected because of the ideology prevailing within the scientific community).

A Simpler Origin for Life
By Robert Shapiro
Scientific American, February 12 2007.

The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. Energy-driven networks of small molecules afford better odds as the initiators of life.

The translation of mRNA into protein "occurs on one of nature's most versatile molecular synthesizers: the ribosome." The analogy for this machine in the human world is the factory: the mass production line from which emerges a stream of products. However, the factory is not like a Fordist assembly line, with lots of workstations, but more like an Advanced Manufacturing Technology cell, where all the instructions are digital and where the machinery translates information into a physical product.
"In the past decade or so, the ribosome has gone from being a biomolecule whose very structure was largely a mystery to one whose architecture is known at an atomic level and whose detailed workings are beginning to be better understood." The fruits of this research are to be found in a variety of formats, including some remarkable simulations, such as here. The most favoured model for the working of ribosomes involves the "proton-shuttle mechanism".
"Computation and simulation are likely to be extraordinarily useful for further clarifying the ribosome's mechanism", because nothing else approaches being able to capture the molecular-level motions and chemical reactions. One recent study is described as "the largest simulation performed to date in biology."
One researcher has commented: "at this point, in spite of high-resolution crystal structures and decades of biochemical, genetic, and biophysical studies, I don't think we understand the fundamental mechanisms at all." Another says: "Where one person says we have the answers, the next person says we have the questions."

So how should we approach the next phase of research into this "huge complex of protein and RNA with a practical and life-affirming purpose-catalyzing protein synthesis"? Without ribosomes, DNA and mRNA are destined to degradation. Like a human factory, information by itself is necessary by not sufficient. The ribosome is a super-machine, not a basic tool. The bacterium E. coli has a ribosome made-up of 50 proteins, each of which requires manufacturing prior to assembly. This is the old "which came first: the chicken or the egg?" conundrum. It is a major challenge for abiogenesis, which is still dabbling with organic chemistry and is not within sight of a working cell (the only environment that can be deemed stable for any possible precursor molecules).
The day is coming when biologists will look at the animations of the ribosome and say: "Why did we resist considering the design inference for so long?"

Protein Factory Reveals Its Secrets
Stu Borman
Chemical & Engineering News, 19 February 2007

Last year, the Nobel Prize in Chemistry heralded work on DNA transcription, a cornerstone process in molecular biology in which a cell synthesizes a messenger RNA (mRNA) version of genomic DNA. For some time, many research teams have been studying the other side of molecular biology's central dogma - the translation of mRNA into protein. That translation occurs on one of nature's most versatile molecular synthesizers: the ribosome. [snip]

Translation Movie shows the process of mRNA-to-protein translation, including initiation, protein chain elongation, and termination.

Michael Ruse, in the introduction of his latest book, protests that "well-qualified and articulate evolutionary biologists . . . have been showing so visceral a hatred of Darwinian thinking that one suspects that their objections cannot be grounded purely in theory or evidence." Ruse has Stephen Jay Gould in his sights, and thinks that Marxism is part of the explanation. However, one thing that Ruse and Gould could agree on is the NOMA thesis: that science is a domain of human activity that does not overlap with the religious domain of human experience. The essential Darwinism is science, addressing empirical data and thereby integrating all biology via organic descent. Darwinism does not entail any position on "the reality of free will, the existence of purpose and direction in the universe, the origin of life, the foundations of human ethical behavior, and the moral and political implications of human differences." Consequently, not only is the ID Movement wrong, and not only are creationists wrong, but also many Darwinists are wrong to draw inferences about social, moral and cultural implications. Ruse "seeks "to defend Darwinism from false (or misguided) friends," those who bastardize or misapply Darwin's ideas to advance their own cultural agendas."
The problem for those of us who have not joined "the Darwinian Revolution" is that NOMA only works one way. It provides a barrier to stop creationists and ID people encroaching on science, but it completely fails to inhibit Darwinists from encroaching on issues to do with purpose, meaning, morality and human values. Gould, for example, exemplified this repeatedly: he often wrote about the contingencies of life and the purposeless of history.
What is lacking from Ruse's book appears to be any serious engagement with actual arguments of those who claim that Darwinism is inseparable from its "intellectual baggage". There's lots of stuff about science grinding to a halt if design thinking becomes "an acceptable part of scientists' explanatory tool kit." But there's no evidence! There's no acknowledgement that science emerged in a culture where design thinking was part of the explanatory tool kit! There's no acknowledgement that the ID community is pro-science. One wonders who this book is written for.

Defending Darwinism
Richard Bellon
American Scientist, March-April 2007.

Darwinism and Its Discontents. Michael Ruse. x + 316 pp. Cambridge University Press, 2006. $30.

The historian and philosopher Michael Ruse has spent decades explaining the nature of the Darwinian Revolution. The result has been a constant stream of innovative, provocative, informative, witty and entertaining scholarship. No other contemporary writer has Ruse's knack for seamlessly weaving together history, philosophy, theology and science.
In his latest salvo, Darwinism and Its Discontents, Ruse turns his good-natured pugnacity to a robust and comprehensive defense of the theory of evolution by natural selection as elaborated by Charles Darwin in On the Origin of Species (1859). [snip]

The songs of female birds have attracted very little research interest, with males made the focus of attention because of their plumage and their songs. "Males do the singing and females do the listening" is the preconception of most academic studies. The new research tested the hypothesis that female singing is ancestral and that absence (rather than presence) is the derived trait. The authors write: "To summarize (. . .), we demonstrated that song in females could be an ancestral condition, from which sexual selection may drive females of some species to give up singing." This appears to be an interesting example of evolutionary thinking inhibiting thought processes. "Garamszegi blames Charles Darwin for the oversight. 'He emphasised the importance of male sexual display, and this is what everyone has been looking at.'" Female bird song appears to be yet another case of the ancestral condition being anything but simple.

The evolution of song in female birds in Europe
Laszlo Zsolt Garamszegi, Denitza Zaprianova Pavlova, Marcel Eens, and Anders Pape Moller
Behavioral Ecology, 2007, 18: 86-96; doi:10.1093/beheco/arl047

Abstract: Bird song is usually regarded as an attribute of males. However, in some species, females may also produce songs even with comparable complexity to that of males. It has been suggested that female song may evolve due to similar selection pressures acting on males, but no study has yet investigated the evolution of female vocalization in a phylogenetic context, a gap that we intended to fill with this study. Based on standard descriptions in The Birds of Western Palearctic, we classified 233 European passerine species with respect to whether females are known to produce songs or not. We were more likely to find information on female song for species whose song is more studied than for less intensively studied species. When we traced information on female song on a phylogeny, we found that at least in 2 avian families, female song appeared to be the ancestral state, but such an ancestral state may be expected to be even deeper in the phylogenetic tree with increasing information on female song. In fact, we cannot exclude the possibility that the ancestor of European passerines had females capable of singing. In a preliminary comparative study based on the available data, we found some evidence that female song may have evolved under the influence of sexual selection as carotenoid-based dichromatism was positively related to female song among species. Our findings imply that due to publication bias, the evolutionary importance of female song is generally underestimated.

See also:
Are female songbirds evolution's unsung heroines?
New Scientist, 3 February 2007, page 17.

MALES do the singing and females do the listening. This has been the established, even cherished view of courtship in birds, but now some ornithologists are changing tune.
[snip]Females that sing have been overlooked, the team say, because either their songs are quiet, they are mistaken for males from their similar plumage or they live in less well-studied areas such as the tropics (. . .). Garamszegi blames Charles Darwin for the oversight. "He emphasised the importance of male sexual display, and this is what everyone has been looking at."
[snip]

A News & Views essay in Nature addresses a very significant question. The authors write: "Biologists agree that cyanobacteria invented the art of making oxygen, but when and how this came about remain uncertain." The measure of the problem is here: "Oxygenetic photosynthesis involves about 100 proteins that are highly ordered within the photosynthetic membranes of the cell. The main players are two molecular machines, photosystem I and photosystem II, that act as electrochemical solar cells. With the help of chlorophyll (...), they transform sunlight into electrical current."

Did the precursurs specialise in anoxygenic photosynthesis? There are bacteria that do this, but none have the two photosystems: it is a case of either photosystem I or photosystem II. "No tree of bacterial life can readily account for the observed distributions of the two sets of photosystem genes among the species. This has left biologists with little alternative but to suggest that genes encoding the photosystems have moved across species boundaries during evolution, a process called lateral gene transfer."

With the field apparently wide open for hypotheses, the authors comment approvingly on a recent paper by Mulkidjanian and colleagues suggesting that both photosystems arose in "a precursor of cyanobacteria - a 'protocyanobacterium' - later to be exported to other lineages by lateral transfer." The protocyanobacterium is hypothesised to have a regulatory switch, allowing it to go from photosystem I to photosystem II depending on the environment. The model appears to be one of degeneration: the anoxygenic photosynthesisers were derived by genetic system loss from the precursor.

The cyanobacteria also are associated with genetic loss: in their case the switch. "It would have been only a small step away from the cyanobacterial state of oxygenic photosynthesis provided that it underwent the right mutation - disabling the regulatory switch - and provided that this happened in the right environmental setting and at the right time."

The authors say: "The best evidence for this evolutionary scheme would be the discovery of a modern-day protocyanobacterium." The Editor's summary refers to this hypothetical organism as a "missing link".

However, instead of a gradual increase in complexity (which is most people's perception of a "missing link"), the authors favour a scenario that starts with all the complex machinery and changes thereafter either involve genetic loss or some "fine-tuning" of the existing system. This illustrates the problems of evolving irreducible complexity: if you want to produce an IC system like photosynthesis, you must first start with an IC system! Complexity has to be front loaded. Neo-darwinism cannot deliver this. Intelligent design can.

Out of thin air
John F. Allen and William Martin
Nature 445, 610-612 (8 February 2007) | doi:10.1038/445610a

The invention of oxygenic photosynthesis was a small step for a bacterium, but a giant leap for biology and geochemistry. So when and how did cells first learn to split water to make oxygen gas?

Flying insects need to have some feedback mechanisms to aid flight control. Two winged flies have halteres which "detect Coriolis forces and thereby mediate flight stability during maneuvers." Four winged insects do not have halteres but need ways of getting the appropriate sensory inputs. Dragonflies appear to use visual inputs to track their position, but this option is not open to night-flying insects. Until recently, it has been said that the moth's antennae are "primarily known as super-sensitive odor receptors--used to sniff out females and food from miles away--and researchers had hypothesized that they assist in flight only by acting as air flow sensors." But not now! The hawk moth's antennae have been found to perform the same role as the flies' halteres. They also experience Coriolis forces, detect rotational motion and relay this mechanosensory input to neural centers to maintain stability during flight.
As research progresses, the living world appears to be packed with complex specified information. In these cases, it is legitimate to include intelligent design as an option in the causal explanations under consideration. This is because, outside the natural world, complex specified information is always associated with intelligent causation. This point is worth making because the abstract refers to flying insects evolving "sophisticated sensory capabilities", the hind wings having been "modified into club-shaped, mechanosensory halteres" and the editors of Science refer to the halteres as "vestigial". The science of this paper needs to be distinguished from the Darwinian spin.

Antennal Mechanosensors Mediate Flight Control in Moths
Sanjay P. Sane, Alexandre Dieudonne, Mark A. Willis, and Thomas L. Daniel
Science 315, 9 February 2007: 863-866.

Abstract: Flying insects have evolved sophisticated sensory capabilities to achieve rapid course control during aerial maneuvers. Among two-winged insects such as houseflies and their relatives, the hind wings are modified into club-shaped, mechanosensory halteres, which detect Coriolis forces and thereby mediate flight stability during maneuvers. Here, we show that mechanosensory input from the antennae serves a similar role during flight in hawk moths, which are four-winged insects. The antennae of flying moths vibrate and experience Coriolis forces during aerial maneuvers. The antennal vibrations are transduced by individual units of Johnston's organs at the base of their antennae in a frequency range characteristic of the Coriolis input. Reduction of the mechanical input to Johnston's organs by removing the antennal flagellum of these moths severely disrupted their flight stability, but reattachment of the flagellum restored their flight control. The antennae thus play a crucial role in maintaining flight stability of moths.

See also:
Antennae as Gyroscopes by R. McNeill Alexander, Science 315, 9 February 2007: 771-772.

The Moth's Gyroscope by Brendan Borrell, ScienceNOW Daily News, 8 February 2007

Enzymes are really useful organic molecules, speeding up chemical reactions without being consumed. They are essential components of cells, and widely used in industrial processes. Getting the enzyme to work in the precise conditions required by many industrial applications has engaged the attention of many researchers: "there is a strong interest in developing experimental and theoretical methods for changing the pH-dependent characteristics of enzymes."
The authors of the paper abstracted below review these problems and explain that specific mutations in the active site can change the pH-activity profiles, but these mutations are actually very difficult to engineer. "The conclusion from two decade's work is that very specific point mutations in the active sites can change the pH dependence of enzymatic activity, but unless such specific active site point mutations are known (e.g., from comparative studies), there is not much hope of achieving a dramatic pH-activity profile shift with rational engineering methods. This somewhat disheartening conclusion is reached because mutations that give large pH-activity profile shifts normally are close to the active site and therefore likely to give mutant enzymes that are inactive or have dramatically reduced activity."
In ID circles, this would be described as "fine tuning", as a pointer to intelligent design, and an example of why random mutations and natural selection is an inappropriate mechanism to achieve the exquisite properties of the enzymes found in living things.

Redesigning protein pKa values
Barbara Mary Tynan-Connolly and Jens Erik Nielsen
Protein Science (2007), 16:239-249

The ability to re-engineer enzymatic pH-activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re-engineering enzymatic pH-activity profiles by changing active site pKa values using point mutations. We calculate the maximum achievable delta pKa values for 141 target titratable groups in seven enzymes by introducing conservative net-charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10Ã… can change pKa values up to two units, but that the introduction of a requirement to keep other pKa values constant reduces the magnitude of the achievable delta pKa. The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server at http://enzyme.ucd.ie/pKD.

This is from the introduction:
[snip] ... there is a strong interest in developing experimental and theoretical methods for changing the pH-dependent characteristics of enzymes. Advances have been made in the fields of protein engineering and directed evolution, and it is presently possible to routinely optimize the performance of enzymes for a range of conditions using either rational engineering or screening/selection-based approaches (Cherry et al. 1999; Farinas et al. 2001). Unfortunately, not all characteristics of enzymes are equally easy to optimize and successes in rational re-engineering of enzymatic pH-activity profiles remain few despite decades of studies on enzyme structure-function relationships.
[snip]

In this review essay, Ernst Haeckel is presented as the "archetypal German Romantic" who somehow managed to combine his artistic and philosophical interests with his work as Professor of Zoology. His espousal of Darwinism was accompanied by "a search for order, systematization and hierarchy that would reveal far more logic and purpose in life than a mere struggle for survival." His Biogenic Law ("organisms retrace their evolutionary history as they develop from an egg") "was an attempt to extract such a unifying scheme from the natural world." The reviewer finds tensions with science here, for Haeckel had a strong vision of what the world ought to be like. "Haeckel supplies a case study in the collision between Romanticism and science."
The subject of the notorious doctored embryo images is raised. The reviewer says "to my eye the evidence [of doctoring] looks pretty strong". However, the author of the book being reviewed suggests that the illustrations "instructed the reader how to interpret the shapes of nature properly."
Many of us think that generations of students have been cheated by being fed a diet of biogenic law, which is rooted in Haeckel's vision rather than in empirical data. The seriousness of the situation is shown by the way these errors have repeatedly surfaced, even in recent years. It really is time for Haeckel to be reinterpreted as a subversive influence in science. He was a gifted man, but he misused his gifts. He is an example of an ideologically motivated scholar who failed to subject his own ideas to proper critical scrutiny.

Painting the whole picture?
Philip Ball reviews Visions of Nature: The Art and Science of Ernst Haeckel by Olaf Breidbach
Nature 445, 486-487 (1 February 2007) | doi:10.1038/445486a