Science Literature

The fossil record of fish has provided numerous enigmas for those who like to construct evolutionary trees. A major branching point is at the inferred transition from jawless fish to jawed vertebrates (gnathostomes). The next notable inferred branching point relates to the separation of cartilaginous and bony fishes. But somewhere in the picture, a place must be found for the placoderms and the acanthodians, both archaic jawed fish. (For a previous blog on placoderms, go here)

The acanthodians are thought to be close to the branching point, but more than this is unclear. The problem has been one of very limited data - the fossil record of acanthodians is sparse. The best known specimen is Acantholes, a Permian acanthodian (just before the group became extinct). One specimen is comparatively well preserved and this has been used as evidence for bony fish affinities.

Climatius (top left; Lower Devonian), Diplacanthus (top right; Middle Devonian)and Acanthodes (center; Lower Permian) (copyright Dennis C. Murphy, Source: Devonian Times)

New research is based on an Early Devonian fossil with the name Ptomacanthus anglicus. First described about 30 years ago, this fossil comes from the Wayne Herbert Quarry in Herefordshire. The animal's braincase is preserved, and this has proved to be very significant. The research, by palaeontologist Martin Brazeau, has revealed characters similar to sharks and placoderms. This undermines the previous association with the bony fishes. The question for us is: does this new knowledge clarify the "tree of life" story, or does it undermine its foundations?

Cladistic analyses should always make clear the assumptions made by the analyst. (For a discussion of some of the principles of cladistics, go here). Brazeau summarises the previous work in this area with these words;

"Most of the recent hypotheses of acanthodian relationships expressed in cladistic terms have focused on their sister-group relations with chondrichthyans or osteichthyans. All of these studies have presupposed acanthodian monophyly and stereotyped acanthodian endoskeletal morphology on Acanthodes, the latest-occurring, and a highly apomorphic, genus."

The braincases of Acanthodes and Ptomacanthus show significant differences. Characters Acanthodes shared with bony fish led to cladograms where the acanthodians are aligned with the osteichthyans. The newly reported braincase of Ptomacanthus places the acanthodians tentatively with the chondrichthyans.

"A cladistic analysis of 45 ingroup and two outgroup taxa was performed on the basis of 134 characters. Ptomacanthus is placed as a basal stem chondrichthyan, but this result should be viewed with caution. [. . .] Many of the supporting characters are not known or applicable in recognized crown-group chondrichthyans."

These findings have led to big questions being raised about acanthodian monophyly. Do we have two groups here, or even more? This is not a simple case of moving the acanthodians from near the base of the bony fish branch to a similar place in the cartilaginous fish branch. There are too many characters that are distinctive to the early acanthodians, so this means organising the data using the perspective of an evolutionary tree is a challenge that is even more of a challenge than it was. Brazeau puts a brave face on this when he concludes with these words:

"Current conceptions of gnathostome phylogeny depict a rather simplistic arrangement of nominally monophyletic and, apparently, morphologically disparate groups. The emerging picture of acanthodian (and perhaps placoderm) paraphyly does not overturn a general consensus about gnathostome interrelationships. Instead, it populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes."

Whatever this "richer picture" is, we can say with confidence that it is not Darwinian. The fossil record demonstrates that diversity did not emerge gradually, but appears abruptly. Then, the drivers for innovation apparently declined. Those familiar with other animal groups will not be too surprised at these comments: fish are not providing a pattern of diversification that is at all exceptional. A cause for concern, however, is the Darwinian insistence that their theoretical framework brings integration and coherence to biology. The inconvenient data tells us something rather different: the gradualist integration is imposed upon the data and is not required by it. The observed patterns of initial diversity followed by relative stasis fit well into a design paradigm, as has often been pointed out.

Also of concern is the way Darwinians claim ownership of the research findings. They keep presenting each new discovery as another successful step towards reaching their goal:

"Prehistoric Fish Provides New Piece In Evolution's Jigsaw Puzzle." (Science Daily)
"This figures in nicely with the emerging idea that acanthodians don't form a group of fishes that are all closely related to each other. Some of these fossils are primitive sharks while others are primitive bony fishes." (BBC News)
"It's an important piece in the puzzle for trying to understand one of the biggest events not only in our own evolutionary history, but also the vast majority of living animals with backbones." (National Geographic)

Why is this a concern? It is because press releases and media reports are packaging the research into tidy boxes for the masses. No one is thinking outside the box. No one is even questioning whether Darwinism is the appropriate paradigm for analysing the data. Whatever is found, the response is the same: we are putting the jigsaw puzzle together and it will eventually give us the picture we anticipate of the Tree of Life. What we need are methodologies that are open to the possibility that the picture may not be a tree: when the puzzle pieces are allowed to fit together properly, we may be looking at a forest.

The braincase and jaws of a Devonian 'acanthodian' and modern gnathostome origins
Martin D. Brazeau
Nature 457, 305-308 (15 January 2009) | doi:10.1038/nature07436

Modern gnathostomes (jawed vertebrates) emerged in the early Palaeozoic era, but this event remains unclear owing to a scant early fossil record. The exclusively Palaeozoic 'acanthodians' are possibly the earliest gnathostome group and exhibit a mosaic of shark- and bony fish-like characters that has long given them prominence in discussions of early gnathostome evolution1. Their relationships with modern gnathostomes have remained mysterious, partly because their un-mineralized endoskeletons rarely fossilized. Here I present the first-known braincase of an Early Devonian (approximately 418-412 Myr bp) acanthodian, Ptomacanthus anglicus, and re-evaluate the interrelationships of basal gnathostomes. Acanthodian braincases have previously been represented by a single genus, Acanthodes, which occurs more than 100 million years later in the fossil record. The braincase of Ptomacanthus differs radically from the osteichthyan-like braincase of Acanthodes in exhibiting several plesiomorphic features shared with placoderms and some early chondrichthyans. Most striking is its extremely short sphenoid region and its jaw suspension, which displays features intermediate between some Palaeozoic chondrichthyans and osteichthyans. Phylogenetic analysis resolves Ptomacanthus as either the most basal chondrichthyan or as the sister group of all living gnathostomes. These new data alter earlier conceptions of basal gnathostome phylogeny and thus help to provide a more detailed picture of the acquisition of early gnathostome characters.

See also:

Origin of Jawed Vertebrates: Prehistoric Fish Provides New Piece in Evolution's Jigsaw Puzzle, ScienceDaily (Jan. 19, 2009)

Syed, T. Fossil illuminates jaw evolution, BBC News (19 January 2009)

Dell'Amore, C. Oldest Shark Braincase Shakes Up Vertebrate Evolution, National Geographic News (January 14, 2009)

Authors Adrian Desmond and James Moore are very clear in their view that social context is crucial for understanding anyone, whether they lived in generations past, or whether they are alive today. They have applied this thinking to Charles Darwin. They are aware that not all share their approach or enthusiasm:

"Many scientists and philosophers think that explaining genius and its insights as we do saps the power of science and, given the challenge of creationism, is an act of treachery. The reluctance to dig beneath the surface of Darwin's books into the social and cultural resources of his times is as dogged as ever."

These two have been working on a sequel to their 1991 biography of Darwin and their publisher is claiming they have come up with a "revolutionary thesis". The book is said to be "astonishing". They suggest that Darwin's abhorrence of slavery was a major driver for his evolutionary theorising.

"One such resource in Darwin's world was anti-slavery, the greatest moral movement of his age. Our thesis is that the anti-slavery values instilled in him from youth became the moral premise of his work on evolution."
and
"We are not trying to explain away all of Darwin's work as being due to his passion for emancipation, but our argument is that his passion for racial unity is what drove him to touch this untouchable and treacherous subject."

The new book (source here)

Although the book is not yet published, Desmond and Moore did provide an extended abstract of their thinking in the Introduction of a new edition of The Descent of Man, published in 2004. This attracted some critical analysis in the pages of The British Journal for the History of Science. It is worth highlighting some of the points in that review, because it sets an agenda for evaluating the significance of the new book, when it appears. The reviewer, Robert J. Richards, finds the thesis implausible on several counts. First, he finds that their case is built on inference rather than direct evidence:

"This account of Darwin's motivation for his theory of human evolution does suffer the inconvenience of being unsupported by any evidence. Darwin certainly was a foe of slavery. His abolitionist sentiments were nurtured in the enlightened Whig household of his father and voluble sisters, and his hatred of slavery became incandescent as the result of poignant experiences in South America. But there is no indication in the Descent - or elsewhere - that he formulated his conception of human evolution in order to undermine the peculiar institution."

Secondly, Darwin did exhibit a tendency to racialism. Rather than take opportunities to stress the equality of the various human races, he drew attention to their differences and linked this with the demise of some.

"Despite Moore and Desmond's suggestions to the contrary, in his book Darwin described the races as forming an obvious hierarchy of intelligence and moral capacity, from savage to civilized, with the 'intellectual and social faculties' of the lower races comparable to those that must have characterized ancient man (p. 209). Accordingly, he ventured that 'the grade of their civilisation seems to be a most important element in the success of competing nations' (p. 212), which explained for him the extermination of the Tasmanians and the severe decline in population of the Australians, Hawaiians and Maoris. Those groups succumbed in struggle with more advanced peoples (pp. 211-22). In this respect Darwin was no different from Haeckel, whose conception of 'human genealogy' the Englishman emphatically endorsed in the introduction to his book (p. 19)."

The trail divides sharply when these authors consider how sexual selection was addressed by Darwin. First, Desmond and Moore's analysis:

"The pair claim in a new book that Darwin partly chose to highlight the common descent of man from apes to show that all races were equal, as a rebuttal to those who insisted black people were a different, and inferior, species from those with white skin. They say Darwin attempted to show that his theory of sexual selection, where traits seen as desirable but which give no competitive advantage to a species are passed down through generations, was responsible for differences in appearance between races of both animals and humans."

By contrast, this is from Robert Richards:

"In the late 1860s Darwin and Wallace had a protracted disagreement about how sexual selection operated in birds and other organisms - hence Darwin's cascading discussions in the second volume of his book (almost four hundred pages) of sexual selection in beetles, butterflies, birds and bucks. But an even more significant dispute with Wallace arose because of his friend's conversion to spiritualism. Wallace had come to argue that the distinctive features of human beings - naked skin, aesthetic sense, moral character and large intellect - could not be explained by natural selection because such traits conferred little or no survival advantage. Only higher spiritual powers could have produced them. Darwin accepted Wallace's analysis that these traits could not be explained by natural selection, but he did not fall prey to Wallace's new faith. Rather, he proposed other powerful but natural forces to account for the distinctive traits characterizing human societies, namely the forces of sexual selection and group selection - elegant solutions to a vexing conceptual problem."

These issues were highlighted two years ago and the advance blurb of the book does little to raise confidence that they have been addressed. We do not doubt that Darwin was shocked by slavery. We do not doubt that he had relatives and friends who were active abolitionists. The question being raised is: Was Darwin motivated by these convictions in developing his ideas in The Descent of Man? Alternatively, was he motivated by a grand vision of all life as the unfolding of a naturalistic evolutionary process? These issues will no doubt be explored further during this Bicentennial year. But to conclude this blog, here is something on which we agree with Desmond and Morris (and which goes against much of the rhetoric about the "pure" science associated with Darwinism:

Question: What lessons does this book contain for the relationship between religion and science?
"That 'the relationship between religion and science' never existed; that religion in science was the norm in Darwin's day, and he never escaped its aura; that biological theorizing about human nature inevitably poses moral questions, and in so far as these questions have religious answers, to that extent 'religion and science' are inseparable."

Darwin's Sacred Cause: How a Hatred of Slavery Shaped Darwin's Views on Human Evolution
by Adrian Desmond and James Moore
Allen Lane, Publication date: 29 Jan 2009

An astonishing new portrait of a scientific icon. In this remarkable book, Adrian Desmond and James Moore restore the missing moral core of Darwin's evolutionary universe, providing a completely new account of how he came to his shattering theories about human origins. [snip]

Review of new edition of The Descent of Man
Robert J. Richards
The British Journal for the History of Science (December 2006), 39:4:615-617 | doi:10.1017/S0007087406409055

1st para: James Moore and Adrian Desmond have brought out a new paperback edition of Darwin's Descent of Man, and Selection in Relation to Sex. They chose the final printing (1879) of the second edition (1874) as the text, which for scholars will serve as a handy companion to the first edition (1871), readily available from Princeton University Press. For teaching purposes, the Penguin version may even be preferred to the first edition because of the inclusion of a chronology of Darwin's life, an appendix containing thumbnail sketches of individuals named in the text and, most especially, Moore and Desmond's provocative fifty-page introduction - an introduction admirable in its social detail and implausible in its deflationary thesis.

See also:

Gray, R. Charles Darwin's research to prove evolution was motivated by his desire to end slavery, Telegraph Online, 24 Jan 2009.

A Conversation with Adrian Desmond and James Moore.

Flannery, M. Darwin's "Sacred" Cause: How Opposing Slavery Could Still Enslave, Uncommon Descent (16 February 2009)

During this Bicentennial year, we must expect Darwin's intellectual heirs to flex their muscles and bluntly tell those who want to move beyond neodarwinism that they are wasting their time. Such a stance is taken by Jerry Coyne in a critical review of Mark Lumberg's new book about the Freaks of Nature. Coyne claims that the evidence presented "is not strong enough to upset the orthodox view".

Do developmental quirks tell us about evolution? - or about development? (source here)

In the course of the review, Coyne identifies three threads of thought within evolutionary biology that have been perceived as challenging Darwinism. These are structuralism, evo-devo and epigenetics. He interprets Blumberg's book as a synthesis of concepts generally associated with the evo-devo approach, and recognises that it was written with the intention of challenging neodarwinism.

"Blumberg's ambitions transcend storytelling: he aims to show that developmental biology has made real contributions to evolutionary theory. The theory's problem, as Blumberg maintains, is its "gene-centered, population-level thinking", also described as "simplistic single-cause, gene-centered thinking". What paradigms, then, should supplant our misguided embrace of Gregor Mendel?"

The paradigms that he discusses are epigenetics, phenotypic accommodation and genetic assimilation. It is not the purpose of this blog to align itself with any of these positions, but rather to consider the nature of the response Coyne is making. He starts with a discussion that took place in 1980, when Lewis Wolpert responded to the structuralists present by saying that he also had a radical and heretical view: "Genes control development". To make his point, he switched off the lights in the lecture room: a simple switch has the power to make big changes. Apparently, the structuralists were not impressed, but Coyne thought Wolpert had scored a victory.

"Wolpert was puckishly defending what he saw as a perfectly adequate paradigm against those who minimized the importance of genes."

Coyne returns to the importance of genes again and again in his review. Regarding epigenetics:

"Some adaptive 'epigenetic' phenomena, such as parental imprinting of chromosomes, which influences gene expression depending on which parent passed on the gene, are based on instructions in DNA. [. . .] And in nearly all cases, epigenetic effects peter out after a few generations, unable to promote major evolutionary change. Perhaps the most serious criticism of epigenetics is that of the thousands of inherited mutations found in model organisms such as mice and fruit flies, virtually all reside in DNA."

Phynotypic accommodation was supported in the book by the example of a deformed goat. Without forelimbs, it learned to hop around like a kangaroo. Slijper's autopsy showed numerous modifications that facilitated its bipedal hopping. Coyne is unimpressed (but I doubt that he has any evidence to support his comments about natural selection in the quote below):

"The phenotypic changes in Slijper's goat did not result from some inherent self-regulating property of development. Rather, they reflect an evolved phenomenon: natural selection has given bones and muscles the adaptive property of developing in response to the stresses they experience."

Genetic assimilation is despatched as unsupported by evidence. But here again, Coyne leads with neodarwinian theory by invoking "pre-existing genetic variation" as a given:

"As with phenotypic accommodation, here the phenotype changes before the genes. During assimilation, an initial environmental change alters the phenotype of many individuals, exposing previously hidden genetic variation that can then be selected. Eventually, what was an environmental change becomes genetic, mimicking the inheritance of acquired traits. [. . .] But we can also explain such cases by invoking simple selection on pre-existing genetic variation. In the absence of a single credible example of genetic assimilation in nature, it remains an appealing but untested speculation."

The concluding paragraph is a plea for consensus science to prevail. In his view, there are only unconfirmed hypotheses coming from those who want to go beyond "orthodoxy" (i.e. neodarwinism).

"In the end, the problem with these explanations is not so much that they are wrong, or of no potential importance in evolution. Rather, it is that Blumberg gives the impression that they are established truths rather than hypotheses that have remained unconfirmed for three decades. In his anxiety to boost the status of evo-devo in the pantheon of evolutionary subdisciplines, Blumberg has short-changed orthodoxy. Not only does the traditional view of evolution explain far more than he allows, but Blumberg shapes his own vision of development to inflate its challenge to neo-Darwinism. I, for one, am with Wolpert."

For those of us who think that it is neodarwinism that has given us "hypotheses that have remained unconfirmed for three decades", these comments appear hypocritical. By and large, Darwinism is content with minimalistic "proofs" of its dogmas: the creative role of natural selection is not demonstrated, but only its existence in ecosystems; the incremental nature of evolution is still characterised more by gaps than by identifiable trajectories; crucial stages in evolutionary transformations continue to be mysteries. Past blogs have documented many examples of these problems. Go here for a specific example. Furthermore, some recognition needs to be given to those who are prepared to stick their neck above the parapet and say that neodarwinism is bankrupt. All credit to Lynn Margulis (whose model of an "ancestral cell's ingestion of the bacteria that evolved into mitochondria" is accepted by Coyne), who put matters very plainly:

"Having gained acceptance for her work on the origin of eukaryotic cells, she seems willing to take on any sacred cow. Indeed, she is now aiming for the biggest target in evolutionary biology: neo-Darwinism. First named in 1896, neo-Darwinism is the synthesis of Darwinian natural selection and Mendelian-style genetics. Today, it is the reigning paradigm of the discipline, but to Margulis it is little more than a "quaint, but potentially dangerous aberration" that needs to be tossed out in order for science to answer "basic questions" like why stasis is so prevalent in the fossil record, and how one species can evolve from another."

A worthy addition to the web resources on evolutionary theory is Darwin's Predictions by Cornelius G. Hunter. This demonstrates why Coyne's bold claims for the success of neodarwinism should be interpreted as spin.

"Evolution has a long history of false predictions leading to rising complexity. The evolutionist's claim that all of this is a sign of good science, of learning how evolution actually occurred, is not consistent with evolution's many falsified predictions and complex adjustments. This document summarizes a representative set of such falsifications, including the reactions of evolutionists showing how the contradictory findings were accommodated, and concludes with an examination of why evolutionists believe their theory is a fact and what this tells us about the theory."

Evolution's challenge to genetics
Jerry A. Coyne
Nature, 457, 382-383 (22 January 2009) | doi:10.1038/457382a

Abstract: Do conjoined twins and two-legged goats suggest a minor role for genetics in evolution? The evidence is not strong enough to upset the orthodox view, argues Jerry A. Coyne.

BOOK REVIEWED - Freaks of Nature: What Anomalies Tell Us About Development and Evolution, by Mark S. Blumberg, Oxford University Press: 2009. 344 pp.

See also:

Darwin's Predictions by Cornelius G. Hunter.

Mark S. Blumberg's personal home page for the book

Mann, C. Lynn Margulis: Science's Unruly Earth Mother, Science, 252, 19 April 1991: 378-381.

A notable feature of life in the Western World is the large number of people suffering from osteoarthritic pains and bad backs. It is not unusual to find people complaining about "bad design" and suggesting that walking upright is unnatural. People with attitudes like this would do well to read Jacob Klein's Perspective piece in Science. Here's a taster:

"The ultralow friction coefficients between the articulating cartilage surfaces in human hips or knees cannot be duplicated even by the most sophisticated technological means."

Osteoarthritis is a chronic disease of the joint cartilage and bone (source here)

The essential starting point for any analysis of the degeneration of hip or knee joints is an appreciation of the very efficient lubrication system in place. These joints have to withstand pressures of about 5 MPa (equivalent to about 50 times atmospheric pressure) and friction coefficients associated with the joints are about 0.001. These are very low values and are vital for avoiding wear and tear in use. Significantly, friction coefficients for man-made lubricants are far higher than the 0.001 typical of human joints.

The secrets of cartilage lubrication need to be probed at the nano-level of detail. Brush-like molecules and water combine to produce lubricating surface layers.

"Recent efforts to elucidate these molecular origins have focused on nanotribological studies of surface-attached molecules in aqueous media, seeking to emulate those at the cartilage surface. Raviv et al. showed that synthetic polyelectrolyte brushes attached to opposing surfaces can provide remarkable lubrication when mutually compressed to moderate pressures and made to slide past each other, with friction coefficients similar to those in healthy joints. Briscoe et al. found that boundary lubrication under water was far superior to that in air or oil, and mediated by the hydrated surfactant head-groups. These and other studies emphasize the importance of hydration layers surrounding charges in aqueous media as a basic lubrication element."

This lubrication mechanism demonstrates excellent results at low pressures, but it fails to mimic the natural system at pressures of 5 MPa. Clearly, more biomimetic work is needed to reach a better understanding of "the very efficient lubrication in living joints". This opens the door for a variety of repair and replacement measures to treat patients:

"Future materials challenges will be to design scaffolds that provide optimal environments for the progenitor cells that they bring to the damaged tissue, or to stimulate indigenous cells; and to develop bioadhesives that promote tissue integration and prevent scaffold detachment during joint articulation. In replacement strategies, surface treatments that suppress the wear leading to implant failure may allow a closer approach to "lifetime" prostheses for the most widely used polymer-metal implant combinations."

Approaching the problem with the premise of design functionality leads to the identification of numerous avenues worth exploring further. What factors have led to degeneration and how can they be addressed? What can be done to promote self-healing? (Regeneration and repair) What can be synthesised as a substitute for permanently damaged joints? (Replacement) All these leads follow from a design perspective. But what shall we say to those who persist with "bad design" arguments and evolutionary arm-waving? Do these particular emphases result in novel insights? As far as I can see, the 'evolutionary tinkering' perspective plays no part in the contemporary search for solutions.

Repair or Replacement - A Joint Perspective
Jacob Klein
Science, 323, 2 January 2009: 47-48.

Summary: Insights into the molecular origins of cartilage lubrication could lead to more efficient tissue repair and to longer-lasting prostheses for hip and knee joints.

See also:

Tyler, D. The remarkable phenomenon of biological lubrication, ARN literature blog (11 February 2008)

This Bicentennial year will provide numerous opportunities to examine Darwin's life and work. The journal Science has published an interesting review by Peter Bowler with the title "Darwin's Originality". The topics covered are numerous and many of them give useful leads into discussions. For example, David Coppedge builds on what Bowler says about Social Darwinism. He considers how "Darwin's world view in which nature ruthlessly destroys the "unfit" in an unending struggle for existence was used by later political leaders to justify their atrocities as a rational outworking of the laws of nature." However, this blog will limit its scope to Darwin's thinking about the question "What is a species?"

Darwin's first evolutionary tree diagram in Notebook B (Source here)

The concept involved a fluid morphology which exhibited a branching pattern with the passing of time. This was a radical departure from the perception that species had their own essence and were not part of a continuum. Bowler emphasises the significance of animal and plant breeding for Darwin: breeders selected traits they desired and managed their breeding programmes to preserve and enhance those traits. Thus, variations (or breeds) merged into species which (it was argued) merged into genera, families and the higher taxonomic categories.

"Traditionally, species were treated as idealized types with a fixed essence, any variation from the norm being trivial and impermanent. The breeders knew that they could produce huge changes in structure by accumulating normal variations over a number of generations. When Darwin linked this information with his conviction that species could change indefinitely over time, he was driven toward a new form of species concept in which the population becomes paramount. The natural range of variability becomes part of the species' character, not the result of accidental deviations from a fixed norm. This is what Mayr called the transition from typological thinking to population thinking [. . .]"

Bowler finds originality in Darwin's thinking about the analogy between breeding programmes and natural selection. I do not see how this can be described as "truly unique" because in 1831 the plant breeder Patrick Matthew proposed such a link and identified natural selection as the mechanism of evolutionary transformation. Bowler also points out that Wallace did not make a connection between artificial selection and natural selection.

"Darwin's study of breeding in the formulation of his theory is much debated by historians, but there can be little doubt of how important the analogy between artificial and natural selection became in his later thinking. In this case, Darwin was truly unique, because even Wallace did not take this step and dissociated himself from the link with artificial selection expressed in Darwin's later writings."

Whilst it is true that Wallace differed from Darwin in this matter, it can be argued that Wallace was justified in the judgment he made. For those interested in the details of how they saw the issue, Kutschera's comparative analysis of Darwin and Wallace is here. The specific comment on this point is as follows:

"Wallace emphasized the distinction between domestic and natural varieties. In fact, he regarded domestic animals as "abnormal" and pointed out that they cannot be regarded as "model systems" for animals in nature. Darwin, however, stressed the similarities between domestic and natural variants in the construction of his argument." (pages 350-351)

This aspect of Darwin's originality is perceived by Bowler as a major reason why his contemporaries questioned his proposed mechanism:

"One of the most disturbing aspects of Darwin's theory was its appeal to the struggle for existence as the natural process that equates with the breeder's activity as a selecting agent. This very harsh vision of nature certainly threatened the traditional belief in a benevolent Creator. The term "struggle for existence" occurs in Thomas Robert Malthus's An Essay on the Principle of Population, although used in the context of tribal groups competing for limited resources. Darwin saw that population pressure would lead to competition between individuals and was perhaps the first to realize that it might represent a means by which the population could change through time. The process worked by eliminating the least fit variants within the population and allowing the better adapted to survive and breed. This was what the philosopher Herbert Spencer would later refer to as the "survival of the fittest." Strictly speaking, natural selection requires only differential reproduction among variants, but Darwin thought that the pressure of competition was necessary to make it effective. It seems that without the input from Malthus, he would not have come up with the theory."

It was not just that his contemporaries were disturbed by these ideas - they doubted, on scientific grounds, that natural selection was capable of doing the work required of it. They were not disputing the existence of natural selection, but were not convinced that it could be be incorporated into a creative process. Stephen Jay Gould drew attention to this in The Structure of Evolutionary Theory (2002, p. 139):

"Darwin's theory therefore cannot be equated with the simple claim that natural selection operates. Nearly all his colleagues and predecessors accepted this postulate. Darwin, in his characteristic and radical way, grasped that this standard mechanism for preserving the type could be inverted, and then converted into the primary cause of evolutionary change. Natural selection obviously lies at the center of Darwin's theory, but we must recognize, as Darwin's second key postulate, the claim that natural selection acts as the creative force of evolutionary change. The essence of Darwinism cannot reside in the mere observation that natural selection operates - for everyone had long accepted a negative role for natural selection in eliminating the unfit and preserving the type."

There was, and still is, a scientific debate to be made about the efficacy of natural selection as an element of evolutionary theory. Peppered moths, finch beaks and lizard legs certainly give us evidence of selection forces in the natural world, but they do not demonstrate natural selection as a creative process. Students and scholars therefore need the academic freedom to consider the implications - without the threat of being taken to court for bringing religion into science lessons.

There was, and still is, a scientific debate to be made about the natural limits of variation. In Darwin's day, people were aware that artificial selection ran up against natural limits, and this finding has been abundantly confirmed since then. The science of genetics reveals that most of the domestic breeding variations Darwin was considering were because of innate genetic material. To get beyond that reservoir of variation, mutations of various kinds are needed. This area of knowledge was unknown to Darwin, so references today to artificial selection which make no reference to the genetics of variation are likely to be very misleading. Students and scholars therefore need the academic freedom to consider the implications of both variation and stasis - without the threat of being taken to court for bringing religion into science lessons.

Furthermore, anyone reading Bowler's essay would have to be naive to think that there is a rigid divide between science and religion. Darwin's theory replaced thinking based on order and predictability with "a ruthless 'struggle for existence' [that] did not seem the kind of process that would be instituted by a benevolent God". Note also Bowler's closing sentence:

"But if we accept science's power to upset the traditional foundations of how we think about the world, we should also accept its potential to interact with moral values."

Darwin's Originality
Peter J. Bowler
Science, 9 January 2009: 323, 223-226 | DOI: 10.1126/science.1160332

Abstract: Charles Darwin's theory of natural selection has been hailed as one of the most innovative contributions to modern science. When first proposed in 1859, however, it was widely rejected by his contemporaries, even by those who accepted the general idea of evolution. This article identifies those aspects of Darwin's work that led him to develop this revolutionary theory, including his studies of biogeography and animal breeding, and his recognition of the role played by the struggle for existence.

See also:

Coppedge, D.F. Darwinists Cannot Deny "Disturbing" Implications, (Creation-Evolution Headlines, 15 January 2009)

The quest for life on Mars is unabated. There is a hunger for news: even finding water is heralded as a major find - it is a though water is half-way to finding living things! Today, The Sun newspaper published a story with the headline: "Nasa reveals life on Mars" and the tagline: "ALIEN bugs are responsible for strong plumes of methane gas detected on Mars, it was claimed tonight." This story would be big news, if it were true. However, the journalism exhibited here does not convey the research findings at all well.

For several years, it has been known that methane is a component of the Martian atmosphere, and it is also known that this situation is not stable. There are various mechanisms for removing the methane and so there must be a mechanism for renewing the gas. The research paper reports on observed releases of methane, confirming that these occur and also carrying the implication that oxidising agents in the crustal materials is a big factor in methane degradation.

The research does not reveal the source of this methane. The researchers keep the options open: it could be linked to microbial life, but it could be geochemical.

"Thus, the presence of significant methane would require recent release from sub-surface reservoirs; the ultimate origin of this methane is uncertain, but it could be abiotic or biotic."
and:
"Both geochemical and biological origins have been explored, but no consensus has emerged".

The excitement over Mars not being a dead planet can be traced to the Nasa Press Release, which has these words:

Indeed it looks like Mars has been cold and dry for billions of years, with an atmosphere so thin, any liquid water on the surface quickly boils away while the sun's ultraviolet radiation scorches the ground. The situation sounds bleak, but research published today in Science Express reveals new hope for the Red Planet. The first definitive detection of methane in the atmosphere of Mars indicates that Mars is still alive, in either a biologic or geologic sense, according to a team of NASA and university scientists.

This description of Mars as "alive" has stimulated interest worldwide. The Sun story goes on to qualify its eye-catching headline with "NASA scientists say the gas emissions could have either a geological or biological source" but makes it clear that some of the researchers favour the biological explanation:

Scientist Michael Mumma of NASA's Goddard Space Flight Center said: "This raises the probability substantially that life was there or still survives at the present. We think the probability is much higher now based on this evidence."

A more judicious comment comes from Ian Sample at The Guardian Science Blog. His headline is "Has NASA found life on Mars?" and he comments:

"If a newspaper headline ends in a question mark, the answer is almost always "no". And so it is in this case. Later today, NASA scientists will announce they have detected enormous releases of methane from Mars. Could it be evidence of martian life? Undoubtedly yes. Is it proof of life on Mars? Certainly not."

The scoop that was not a scoop (source here)

ID comments on this topic range from Fuz Rana's (2005) emphasis on geochemical sources of methane, to DaveScot's advocacy of directed panspermia at Uncommon Descent, and Denyse O'Leary's observations at Colliding Universes on the need to raise funds for future Nasa missions. At this stage, further comment would be speculative, but ID scientists are looking forward to evaluating further findings as they are published.

Strong Release of Methane on Mars in Northern Summer 2003
Michael J. Mumma, Geronimo L. Villaneuva, Robert E. Novak, Tilak Hewagama, Boncho P. Bonev, Michael A. DiSanti, Avi M. Mandell, and Michael D. Smith
Science Express, Published online January 15 2009; 10.1126/science.1165243

Living systems produce more than 90% of Earth's atmospheric methane; the balance is of geochemical origin. On Mars, methane could be a signature of either origin. Using high-dispersion infrared spectrometers at three ground-based telescopes, we measured methane and water vapor simultaneously on Mars over several longitude intervals in (northern) early- and late-summer 2003 and near vernal equinox 2006. When present, methane occurred in extended plumes and the maxima of latitudinal profiles imply that the methane was released from discrete regions. At northern mid-summer, the principal plume contained ~19,000 metric tons of methane and the estimated source strength (>=0.6 kg s-1) was comparable to that of the massive hydrocarbon seep at Coal Oil Point (Santa Barbara, CA).

See also:

The Red Planet is Not a Dead Planet, NASA Press Release, Jan. 15, 2009:

Nasa reveals life on Mars, The Sun (16 January 2009)

The idea that special potions can be made to enhance or compel love is not new. William Shakespeare wrote it into the words of Oberon in Midsummer Night's Dream:

'Fetch me that flower; the herb I show'd thee once.
The juice of it, on sleeping eyelids laid,
Will make or man or women madly dote
Upon the next live creature that it sees.'

Sadly, in our own day, many rare and exotic animals have been ruthlessly killed so that extracts from their body parts can be processed and sold as an aphrodisiac or something similar. The question is: is there any basis for such potions and even if there is, do they help us to understand and practise love?

According to some, inhaled oxytocin tunes people into the emotions of others (Graphic Source here, The Economist, 12 February 2004)

Larry Young knows it happens with prarie voles: "A female prarie vole rapidly becomes attached to the nearest male if her brain is infused with oxytocin." He finds an "intriguing overlap between the brain areas associated with vole pair bonding and those associated with human love". He writes about it in a "Being Human" essay in Nature. He claims that "reducing love to its component parts helps us to understand human sexuality, and may lead to drugs that enhance or diminish our love for another."

This emphasis on "reducing" emotions, feelings and relationships to biochemistry is very popular within neuroscience today. Many researchers have adopted materialism as their underpinning philosophy. Humans are physical entities, they say, and they can, in principle, be understood completely in terms of physical causes and effects.

"Now researchers are attempting to isolate and identify the neural and genetic components underlying this seemingly uniquely human emotion. Indeed, biologists may soon be able to reduce certain mental states associated with love to a biochemical chain of events. This has implications for the evolution of human sexuality [snip]."

No one saying that biochemistry is not involved in human emotions. The issue is whether materialism is the right conceptual framework for neuroscience. Adopting that philosophy makes researchers blind to non-material factors affecting humanity. This is where there are serious consequences of getting it wrong. For a start, materialism has no basis for morality. Conduct becomes a matter of personal choice and there are no rights and wrongs. Very quickly, we enter the irrational. This is well expressed by the feminist writer, Marilyn French:

"Well, love is insanity. The ancient Greeks knew that. It is the taking over of a rational and lucid mind by delusion and self-destruction. You lose yourself, you have no power over yourself, you can't even think straight."

Shakespeare recognised the problem: Oberon's plan for the "herb" was perverted. Larry Young sees possible dangers ahead but does not think there is a problem:

"recent advances in the biology of pair bonding mean it won't be long before an unscrupulous suitor could slip a pharmaceutical 'love potion' in our drink. And if they did, would we care? After all, love is insanity."

Unfortunately, there is a problem. Love is such a powerful human emotion that people are wide open to exploitation. We should care! Unscrupulous people will turn love into a biochemical experience and play down the importance of relationships. Marilyn French was wrong - love is not insanity. Nor is it irrational. Love is a relationship of trust and commitment. It is not a delusion, nor an existential experience. Those who cannot handle these thoughts would be wise to reconsider their own conceptual framework regarding what it means to be human.

Love: Neuroscience reveals all
Larry J. Young
Nature 457, 148 (8 January 2009) | doi:10.1038/457148a

Poetry it is not. Nor is it particularly romantic. But reducing love to its component parts helps us to understand human sexuality, and may lead to drugs that enhance or diminish our love for another, says Larry J. Young.

See also:

Alleyne, R. Love spray being developed by scientists, The Daily Telegraph, 8 Jan 2009

Every cell has a nucleus equipped with gatekeepers that manage the flow of materials into and out of the nucleus. These gatekeepers are receiving much attention from researchers because of their importance to the cell and because of the perceived value placed on enhanced knowledge.

The nuclear pore is the center of so much attention because everything that goes in and out of the nucleus has to pass through. But apart from a few binding sites, "the structure is essentially a black box," Hoelz says. "And if we don't know how it looks and how it is constructed in atomic detail, then we have no way to figure out how this large transport machine works."

Core pore. A new model for the nuclear pore complex predicts that a membrane "coat" is scaffolded by two alternating pairs of upright proteins (yellow). These "fence posts" are predicted to be linked horizontally by three other yet to be discovered proteins (green). (Credit: The Rockefeller University)

A team from Rockefeller University have developed a structural model of the nuclear pore membrane and are steadily working through issues of testing and validation. In a recent paper, they report some successes:

The model proposes a cylindrical nuclear pore complex comprised of rings of alternating protein structures that zip together, providing the flexibility and space the pore needs to let pass a variety of materials in and out of the cell's nucleus. "We were very excited to find a protein that is so similar in structure to what our model predicts," Hoelz says.

Seven complex proteins are thought to provide a cylindrical coat for the pore membrane. Two pairs of proteins combine to form the rods that cross the nuclear envelope. The other three proteins are thought to join these protein pairs together to form "a picket fence of sorts". Of course, it is much more than a picket fence, because the pore is not just a structural feature, but a gatekeeper managing the flow of materials into and out of the nucleus. This higher-level functionality has yet to be understood. "The nuclear pore complex is one of the most mysterious things in cell biology. It's basically a black box," says Andre Hoelz, a research associate at The Rockefeller University

The Summary of the paper concludes: "Shared architectural and mechanistic principles with the COPII coat indicate a common evolutionary origin and support the notion that the NPC coat represents another class of membrane coats." What is of concern here is the way shared characteristics are regarded as pointers to "a common evolutionary origin". As was pointed out in a related blog a year ago, shared characteristics are also found in designed objects. By excluding the design option, the researchers are closing up possible avenues of research and artificially constraining their thinking.

This is not an abstract point to make. The nuclear pore complex is a fundamental element within all eukaryotes including humans. Malfunctioning structures can have serious consequences.

Given the central role of the nuclear pore complex in the most basic cell processes, defects in its assembly, structure and function can have lethal consequences. Its proteins have been associated with primary biliary cirrhosis, cancer, viral infections and triple A syndrome, says Erik Debler, postdoctoral fellow in the Blobel laboratory and first author of the paper. A better understanding of how the complex works could lead to treatments for these diseases.

The above quote is suggestive of irreducible complexity. If any part of the nuclear pore complex fails, the whole structure may fail to perform. There is only limited information about this at the present time, but a design perspective is open to the concept of IC and the implications if elements of the structure are faulty. If IC proves to be a valid description of any part of the nuclear pore complex, then it is pointless to pursue Darwinian mechanisms for evolving these structures because small incremental changes driven by natural selection has a very poor record for explaining the origin of such complexity.

A Fence-like Coat for the Nuclear Pore Membrane
Erik W. Debler, Yingli Ma, Hyuk-Soo Seo, Kuo-Chiang Hsia, Thomas R. Noriega, Gunter Blobel and Andre Hoelz
Molecular Cell, 26 December 2008, 32(6), 815-826 | doi: 10.1016/j.molcel.2008.12.001

Summary: We recently proposed a cylindrical coat for the nuclear pore membrane in the nuclear pore complex (NPC). This scaffold is generated by multiple copies of seven nucleoporins. Here, we report three crystal structures of the nucleoporin pair Seh1.Nup85, which is part of the coat cylinder. The Seh1.Nup85 assembly bears resemblance in its shape and dimensions to that of another nucleoporin pair, Sec13.Nup145C. Furthermore, the Seh1.Nup85 structures reveal a hinge motion that may facilitate conformational changes in the NPC during import of integral membrane proteins and/or during nucleocytoplasmic transport. We propose that Seh1.Nup85 and Sec13.Nup145C form 16 alternating, vertical rods that are horizontally linked by the three remaining nucleoporins of the coat cylinder. Shared architectural and mechanistic principles with the COPII coat indicate a common evolutionary origin and support the notion that the NPC coat represents another class of membrane coats.

See also:

New model of a nuclear pore complex is based on crystal structure of its key component, The Rockefeller University Newswire (Jan 15 2008)

New Model For Nuclear Pore Complex Backed By Structural Study, ScienceDaily (Jan. 3, 2009)

Gatekeeper for the nucleus, ARN Literature Blog (3 December 2007)