Science Literature

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

The Toco Toucan(Source and video here)

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

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

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

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

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

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

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

The findings were spectacular:

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

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

Streptochilus globigerus (credit: Kate Darling, source here)

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

The late Precambrian greening of the Earth
L. Paul Knauth & Martin J. Kennedy
Nature, 460, 728-732 (6 August 2009) | doi:10.1038/nature08213 (pdf here)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

Humans and Orangutan, Buffalo Museum of Science web resource.