Science Literature

According to James Pusey, writing in Nature, "Charles Darwin's banner was first unfurled in China during the Reform Movement of 1895-98, in response to China's defeat in the Sino-Japanese War." There were two groups seeking change: the reformers, who were loyal to the Manchu Qing Dynasty, and the revolutionaries, who wanted a clean break with the past.

"The watchword of the reform movement was 'bianfa', meaning 'change our institutions'. But the very word 'change' was anathema to the conservative officialdom of China. So reformers turned to Darwin as a foreign authority on change, presenting him not first and foremost as a natural scientist who had discovered an amazing fact of life, but as a political scientist who had discovered a cosmic imperative for change."

Some today see Darwin as inspiring revolution (Source here)

This led to a change in the way intellectuals approached ethics: reform meant that traditional codes of conduct were fast losing their appeal.

"Meanwhile, the Europeans waved Darwin's banner to justify imperialism. Dubbing themselves 'the fit', they declared their right to rule the 'unfit'. And some Chinese accepted this argument. Liang Qichao, one of the leading reformers, said in 1898: "If a country can strengthen itself and make itself one of the fittest, then, even if it annihilates the unfit and the weak, it can still not be said to be immoral. Why? Because it is a law of evolution.""

The reformers were very interested in democracy, but realized the people were totally unprepared to handle it. Their solution was to emphasise the step-by-step gradualism of Darwinism with direction and stability provided by an appeal to natural law. The revolutionaries also embraced Darwin, drawing inspiration from the thought that the "superior survive and the inferior are defeated". "The man who introduced Darwinian evolution to the reformers of 1895 was Yan Fu."

"Yan wanted democracy for China - even anarchic democracy, without presidential rule. In Whence Strength? his call for reform was revolutionary: "Establish a parliament at the capital and let each province and county elect its own officials." But 'Darwin' held him back from real revolution. Yan believed that step-by-step progress was a fixed natural law, so stages had to be taken in order. America had skipped constitutional monarchy and gone straight to democracy, but a resulting class war, he felt, would be their undoing. "Should we, then, now throw away all loyalty to our ruler?" he asked in his essay. "We most certainly should not! Because the time has not arrived. ... Our people are not yet ready to rule themselves.""

The reformers and the revolutionaries debated vigorously "with both sides wildly waving Darwin's banner" The leaders of these movements imbibed the message of scientific racism coming from America and Europe and presented themselves as 'fit' to rule.

"Sadly, both camps also accepted the pervasive Western view that Darwin had proven races unequal - that one race was 'fitter' and therefore better than another. The reformers had originally done so to disassociate themselves from those who had fallen prey to the imperialists, such as the Africans and Indians. But in their exile in Japan, reformers and revolutionaries alike turned angrily on the Manchus as scapegoats, labelling them evolutionary low life, whose 'unnatural' conquest of the Han Chinese was responsible for China's peril."

The tensions after the end of World War I were extreme. The traditional pacifist Chinese philosophies were perceived as weak and this led to a philosophical and political vacuum. In their place came Marxism: this "seemed to them the fittest faith on Earth to help China to survive".

"This was not, of course, all Darwin's doing, but Darwin was involved in it all. To believe in Marxism, one had to believe in inexorable forces pushing mankind, or at least the elect, to inevitable progress, through set stages (which could, however, be skipped). One had to believe that history was a violent, hereditary class struggle (almost a 'racial' struggle); that the individual must be severely subordinated to the group; that an enlightened group must lead the people for their own good; that the people must not be humane to their enemies; that the forces of history assured victory to those who were right and who struggled.
Who taught Chinese these things? Marx? Mao? No. Darwin."

Ideas have legs and ideas walk. These developments are possible because Darwinism is more than a scientific theory: it is fundamentally a philosophical stance about the nature of reality. The materialism that underpins the Darwinian worldview has spawned scientific racism + eugenics in the West, and revolutionary fervor in the East. We should help the next generation understand and recognize the significance of such matters, and encourage them to ask questions about the philosophical roots of science.

Global Darwin: Revolutionary road
James Pusey
Nature 462, 162-163 (12 November 2009) | doi:10.1038/462162a (Restricted access link)

In China, under the threat of Western imperialism, interpretations of Darwin's ideas paved the way for Marx, Lenin and Mao, argues James Pusey in the third in our series on reactions to evolutionary theory.

Earlier this year, Eugene Koonin published a masterly analysis of the impact of genomics on evolutionary thinking. This proved to be too meaty a study for a concise blog, and my initial draft was abandoned. Happily, a shorter overview has now been published, and this abstracts salient points from the research paper. Koonin notes that the 1959 Origin centennial was "marked by the consolidation of the modern synthesis" but subsequent years have witnessed great changes which have undermined its credibility.

"The edifice of the modern synthesis has crumbled, apparently, beyond repair."

It is time for a paradigm change - but neoDarwinists are stuck because they have so much philosophical baggage holding them down (Image credit: Shaun Curry/AFP/Getty Images, Source here)

Koonin uses the metaphor of "the landscape of evolutionary biology". There are three distinct revolutions have occurred over the past half-century: the molecular, the microbiological and the genomic revolutions.

"[T]his year is the perfect time to ask some crucial questions: how has evolutionary biology changed in the 50 years since the hardening of the modern synthesis? Is it still a viable conceptual framework for evolutionary thinking and research?"

The molecular revolution culminated, says Koonin, in the neutral theory, which means that purifying selection is more common than positive selection. The microbiological revolution brought the world of prokaryotes into the domain of evolutionary biology, but it then became apparent that the concepts of Darwinism and the modern synthesis "applied only to multicellular organisms". The genomic revolution revealed that the living world was "a far cry from the orderly, rather simple picture envisioned by Darwin and the creators of the modern synthesis". In particular, it is now interpreted as an "extremely dynamic world where horizontal gene transfer (HGT) is not a rarity but the regular way of existence, and mobile genetic elements that are vehicles of HGT are ubiquitous".

"The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the tree of life as we knew it but also another central tenet of the modern synthesis inherited from Darwin, namely gradualism. In a world dominated by HGT, gene duplication, gene loss and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable."

Koonin is serious in saying that all the concepts of the modern synthesis are in need of a fundamental overhaul.

"Moreover, with pan-adaptationism gone forever, so is the notion of evolutionary progress that is undoubtedly central to traditional evolutionary thinking, even if this is not always made explicit.
The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking. In the postgenomic era, all major tenets of the modern synthesis have been, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the modern synthesis is gone."

Koonin tentatively identifies two candidates to fill the vacuum left by the discarded modern synthesis. The first of these appears to emphasis the role of chance; the second appears to emphasise law.

"The first is the population-genetic theory of the evolution of genomic architecture, according to which evolving complexity is a side product of non-adaptive evolutionary processes occurring in small populations where the constraints of purifying selection are weak. The second area with a potential for major unification could be the study of universal patterns of evolution such as the distribution of evolutionary rates of orthologous genes, which is nearly the same in organisms from bacteria to mammals or the equally universal anticorrelation between the rate of evolution and the expression level of a gene. The existence of these universals suggests that simple theory of the kind used in statistical physics might explain some crucial aspects of evolution."

It is not difficult to predict that Koonin's analysis will not be received quietly by the very vocal leaders of evolutionary biology. They are still entrenched in neoDarwinism and show no signs of conceding any ground to anyone. From a design perspective, Koonin's analysis of the changing landscape of evolutionary biology is spot on. His two candidates for moving forward the theoretical framework are interesting - but lack any recognition of purposeful design in nature. Dembski's design filter concept is relevant here: there are features in the biological world that are best understood in terms of stochastic processes; there are other features that are best understood in terms of natural law; but there are also features that require a design perspective in order to understand them. It is the latter element, prominent in the thinking of design-orientated scientists, which needs to be part of any discussion of where evolutionary biology is heading.

The Origin at 150: is a new evolutionary synthesis in sight?
Eugene V. Koonin
Trends in Genetics, 25(11), November 2009, 473-475.

Abstract: The 200th anniversary of Charles Darwin and the 150th jubilee of the On the Origin of Species could prompt a new look at evolutionary biology. The 1959 Origin centennial was marked by the consolidation of the modern synthesis. The edifice of the modern synthesis has crumbled, apparently, beyond repair. The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution.

Darwinian evolution in the light of genomics
Eugene V. Koonin
Nucleic Acids Research, 2009, 37(4), 1011-1034 | doi:10.1093/nar/gkp089

ABSTRACT: Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

Darwin was a great composer of metaphors, of which "natural selection" is the best known. Today, few are aware of negative responses from scientists uncomfortable with Darwin's imagery. One of these was Alfred Russel Wallace, the co-originator of evolution by natural selection.

"Wallace remarked, in his article Mr Darwin's Metaphors Liable to Misconception (1868), that the Malthusian progressions and struggle for existence were self-evident "facts". Yet because natural selection seemed to personify a perceptive and forward-thinking selector, or god, he urged Darwin to replace the term with "survival of the fittest". [See also here]
Darwin, however, had brushed him off. "Everyone knows what is meant and is implied by such metaphorical expressions," he had demurred. "And they are almost necessary for brevity"."

Does "natural selection" have the dominant role in unravelling Darwin's entangled bank? (source here)

In a perceptive essay, Daniel Todes focuses attention on the reactions of Russian biologists to Darwin's writings. Many of these naturalists "were evolutionists before 1859", so they did not dissent from common ancestry. However, their experiences of the living world were quite different from Darwin and Wallace, who drew their inspiration from densely populated tropical forests and related habitats. They witnessed a struggle for existence that matched the description Thomas Malthus had given of human communities. Using the same logic, Darwin and Wallace were stimulated to think about winners and losers in populations of animals and plants. The Russian scientists lived in a different world.

[They] "investigated a vast under-populated continental plain. For them, nature was not an "entangled bank" - the image Darwin took from the Brazilian jungle. It was a largely empty Siberian expanse in which overpopulation was rare and only the struggle of organisms against a harsh environment was dramatic."

The Russian response to living in a harsh environment was to develop "the language of communalism - stressing not individual initiative and struggle, but the importance of cooperation within social groups and the virtues of social harmony." The analysis of Malthus did not match the biological communities in their part of the world, so Darwin's metaphor of the "struggle for existence" was not, in their view, well grounded.

"Russian political commentators of the left, right and centre reviled Malthus as an apologist for predatory capitalism and soulless individualism." [. . .]
"[F]ew Russians shared Darwin and Wallace's respect for Malthus, and [. . .] many saw the struggle for existence as an infusion of the British enthusiasm for individualistic competition into natural science. Darwin's theory, as Danilevskii put it, was a "purely English doctrine"."

Dissent did not apply just to the "struggle for existence" metaphor. Natural selection was equally controversial. The Russians wanted to give more emphasis to concepts like the "harmony of nature" and "cooperation". Many of them advocated "the theory of mutual aid". Indeed, Todes says that it became a "staple of Russian evolutionary thought".

"Darwin too had called attention to such cooperation, but the theory of mutual aid went further. It held that the central aspect of the struggle for existence is an organism's struggle with abiotic conditions, that organisms join forces in this struggle, that such mutual aid is favoured by natural selection, and that cooperation so vitiated intraspecific competition as to render it unimportant in the origin of new species."

This essay highlights issues which have been discussed often by design-orientated scientists. These are identified below.

1. Scientific criticism of natural selection as an evolutionary mechanism. It will come as a surprise to many that dissent about the role of natural selection comes from within science. Such dissent was present in Darwin's day and it is still significant. This blog has drawn attention to relevant papers here and here. Those who portray requests for a 'critical evaluation of the role of natural selection' as religiously motivated are living in denial of history and are undermining the integrity of science.

2. Scientific analysis of harmony within the natural world. Due to the dominance of Darwinism, ecological studies have been imbalanced. Evidences of populations regulating their own numbers and of cooperative behaviour have been underplayed or reinterpreted in terms of a "struggle for survival".

3. Science is not a culture-free discipline. Objectivity is a worthy aspiration but it cannot be fully realised because scientists are unaware of most of the cultural norms they bring to their work. Since many aspects of culture are linked to religious/secular convictions, it is absurd when individuals and organisations try to set up demarcation arguments to separate science from ideology (whether religious or atheistic).

"Researchers bring their life experiences and culture with them into the field and laboratory, and in the course of their investigations actively originate, interpret, develop and reject metaphorical pathways. As is shown by the reception of Darwin's theory in Russia, the deployment and criticism of metaphors are part of the ineffably human process by which scientists mobilise their experiences and values to explore the infinite complexity of nature."

Global Darwin: Contempt for competition
Daniel Todes
Nature 462, 36-37 (5 November 2009) | doi:10.1038/462036a (restricted access here)

Darwin's idea of the 'struggle for existence' struck a chord with his fellow countrymen. But Russians rejected the alien metaphor, says Daniel Todes, in the second of four weekly pieces on reactions to evolutionary theory.

See also:

Todes, D.P. Darwin's Malthusian Metaphor and Russian Evolutionary Thought, 1859-1917, Isis, 78(4), December 1987, 537-551

This topic forces us to assess the relationship between science and spirituality: is the invisible spiritual realm generated from the material or should it be considered as having a separate existence? Is religion a phenomenon that can ultimately be explained by science in naturalistic ways, or does religion represent a dimension of reality that cannot be directly probed by the methodologies of science? In an essay in Science, Elizabeth Culotta writes:

"[I]n the past 15 years, a growing number of researchers have followed Darwin's lead and explored the hypothesis that religion springs naturally from the normal workings of the human mind. This new field, the cognitive science of religion, draws on psychology, anthropology, and neuroscience to understand the mental building blocks of religious thought."

Neanderthal burial, considered to be 60,000 years old (Kabara, Israel). Material culture analysis can stimulate hypotheses but the interpretations can easily be dominated by researcher presuppositions. (Source here)

Darwin approached the topic from the perspective of his thesis on the origin of species. He looked for evidence that religion itself could be explained by small incremental steps in human cognition and social structure. He started his "story" with the idea that primitive people had no belief system in an all-powerful God. He wrote: "There is no evidence that man was aboriginally endowed with the ennobling belief in the existence of an Omnipotent God. On the contrary there is ample evidence, derived not from hasty travellers, but from men who have long resided with savages, that numerous races have existed and still exist, who have no idea of one or more gods, and who have no words in their languages to express such an idea." But if the enquiry starts at a much more rudimentary level of spirituality, the emerging picture is different:

"If, however, we include under the term "religion" the belief in unseen or spiritual agencies, the case is wholly different; for this belief seems to be almost universal with the less civilised races. Nor is it difficult to comprehend how it arose. As soon as the important faculties of the imagination, wonder, and curiosity, together with some power of reasoning, had become partially developed, man would naturally have craved to understand what was passing around him, and have vaguely speculated on his own existence." (Source here)

Culotta quotes the above passage to illustrate the thought that "to Charles Darwin, the origin of religious belief was no mystery". Yet those following in Darwin's footsteps have been puzzled, because humans put extraordinary resources into "elaborate religious buildings and rituals, with no obvious boost to survival and reproduction". Her article suggests that while there is no consensus yet among scientists, "potential answers are emerging from both the archaeological record and studies of the mind itself".

Archaeology certainly offers some data that is potentially relevant: geometric designs interpreted as an indication of symbolic behaviour; deliberate burials of the dead pointing to "the birth of metaphysical anguish", and carved figurines suggestive of shamanism. The problem with all these is that the metaphysical messages are read in different ways by scholars: these artefacts may stimulate thoughts about belief systems, but they are not hard evidence that reveals the minds of our ancestors.

Cognitive psychologists often start with children, who are said to reflect innate, rather than cultural, biases. It is not difficult to show that "young children prefer "teleological" or purpose-driven, explanations rather than mechanical ones for natural phenomenon". This leads them to perceive nature as purposefully designed by a designer. For children older than age 5, the researchers refer to the "theory of mind" which is our understanding that other humans have intentions, desires and beliefs like us.

"If you suspect that an agent was responsible for some mysterious event, it's a short step to thinking that the agent has a mind like your own. "Higher order theory of mind enables you to represent mental states of beings not immediately or visibly present, and who could have a very different perspective than your own," says Barrett. "That's what you need to have a rich representation of what it might be like to be a god." (It's also what is needed to have a functional religion, because people need to know that others share their beliefs.) As Darwin put it, humans developing religion "would naturally attribute to spirits the same passions, the same love of vengeance, or simplest form of justice, and the same affections which they themselves feel.""

Although these cognitive models are regarded as building on Darwinian foundations, there is a recognition that they have not provided satisfactory answers. One researcher is quoted as saying: "Deriving belief from the architecture of the mind is necessary but not sufficient". What drives all this? What gives religion the fitness to survive? The adaptationist approach of Darwinism comes to the rescue:

[Religion] "promotes cooperative behavior among strangers and so creates stable groups. Other researchers hypothesize that religion is actually adaptive: By encouraging helpful behavior, religious groups boost the biological survival and reproduction of their members. Adhering to strict behavioral rules may signal that a religion's members are strongly committed to the group and so will not seek a free ride, a perennial problem in cooperative groups."
[. . .]
But others [. . .] counter that this adaptationist explanation is itself light on data. "It is often said that religion encourages or prescribes solidarity within the group, but we need evidence that people actually follow [their religion's] recommendations," says Boyer. "The case is still open."

So the "potential answers" Culotta mentions at the outset have the word potential in bold and the rest is in the imagination. What is strikingly lacking in these studies is any questioning of the materialist mindset of the researchers. The most significant way they follow Darwin is in excluding any thought that intelligent design issues need to be addressed before we can properly understand humanity. Indeed, the researchers set up a culture that portrays teleology as anti-science. Culotta reports on the findings of cognitive psychologists working with some undergraduate students:

"When the undergrads had to respond under time pressure, they were likely to agree with nonscientific statements such as "The sun radiates heat because warmth nurtures life." "It's hard work to overcome these teleological explanations," says Kelemen, who adds that the data also suggest an uphill battle for scientific literacy. "When you speed people up, their hard work goes by the wayside." She's now investigating how professional scientists perform on her tests. Such purpose-driven beliefs are a step on the way to religion, she says. "Things exist for purposes, things are intentionally caused, things are intentionally caused for a purpose by some agent. ... You begin to see that a god is a likely thing for a human mind to construct.""

These attitudes are deeply worrying, because the researchers have started with the premise of philosophical naturalism. If a teleological perspective is correct, these researchers have no way of discovering the truth. When we look at the radiation that life needs to be sustained, and then look at the radiation emitted by the sun, the match is superb. It is perfectly reasonable to make design inferences and to test teleological hypotheses.

The real problems are with researchers who say that the material processes that create the physical bodies of animals and plants are no different in essence from the material processes that create religion and morality. We can make a prediction that these researchers will continue to grope around in the dark, looking for a answers but never finding them. In the end, they will conclude that religion, morality and consciousness are spandrels.

On the Origin of Religion
Elizabeth Culotta
Science, 6 November 2009, 326, 784 - 787 | DOI: 10.1126/science.326_784

How and when did religion arise? In the 11th essay in Science's series in honor of the Year of Darwin, Elizabeth Culotta explores the human propensity to believe in unseen deities. No consensus yet exists among scientists, but potential answers are emerging from both the archaeological record and studies of the mind itself. Some researchers, exploring religion's effects in society, suggest that it may boost fitness by promoting cooperative behavior. And in the past 15 years, a growing number of researchers have followed Darwin's lead and explored the hypothesis that religion springs naturally from the normal workings of the human mind. This new field, the cognitive science of religion, draws on psychology, anthropology, and neuroscience to understand the mental building blocks of religious thought.

Sooner or later, students of abiogenesis will encounter Darwin's 1871 letter to Joseph Hooker with his speculations on the spontaneous generation of life. He was returning some pamphlets which triggered the reaction: "I am always delighted to see a word in favour of Pangenesis, which some day, I believe, will have a resurrection." The next paragraph has his "big if" dream:

"It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, - light, heat, electricity &c. present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed."

Bon appetit Mr Darwin! (Source here)

When taken alongside other comments Darwin made on this theme, it is clear that his public stance was to be cautious. The science of his day was unable to say anything positive about spontaneous generation. He felt the power of Pasteur's experiments which brought to an end all the earlier speculations about life emerging from non-life. The authors of a paper reviewing Darwin's thinking summarises the "big if" in this way:

"In the absence of any real corroborative evidence, it is impossible to guess what Darwin thought about the nature of the first living beings. In any case, Darwin's remarks should not be read to imply that he was thinking in terms of prebiotic chemistry, but rather that he recognized that the chemical gap separating organisms from the non-living was not insurmountable."

Also to be considered is the reference to a "Creator" in the last sentence of all the editions of his magnum opus bar the first:

"There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." (Source on page 490 here)

Does this mean that Darwin was a Deist, invoking the Creator to explain the first cells that can be called living? What is this "breathing" he refers to? Is it a link with the biblical account of origins? Why was the "Creator" absent from the 1st edition but present thereafter? The authors draw attention to Darwin's own explanation, contained in an 1863 letter to Hooker and shortly afterwards another to the Athenaeum, based on the profound ignorance within science of any route for life to have emerged from non-life:

"[to Hooker] But I have long regretted that I truckled to public opinion & used Pentateuchal term of creation, by which I really meant "appeared" by some wholly unknown process. - It is mere rubbish thinking, at present, of origin of life; one might as well think of origin of matter."
[to the Athenaeum] "Now is there a fact, or a shadow of a fact, supporting the belief that these elements, without the presence of any organic compounds, and acted on only by known forces, could produce a living creature? At present it is to us a result absolutely inconceivable. Your reviewer sneers with justice at my use of the "Pentateuchal terms", "of one primordial form into which life was first breathed": in a purely scientific work I ought perhaps not to have used such terms; but they well serve to confess that our ignorance is as profound on the origin of life as on the origin of force or matter."

In the light of these comments, it is curious that Darwin did not drop the word "Creator" in subsequent editions. Whatever regrets he expressed in 1863, they were not deep enough to excise the injudicious word. The authors note the consistency in Darwin's view that science did not have any insights into spontaneous generation. They show from his comments to Haeckel, from the apochryphal account of Darwin's encounter with fossils in a meteorite, and from several other comments made in letters, that Darwin was publicly silent because he could find no basis in science for making any positive statements.

"As for myself I cannot believe in spontaneous generation & though I expect that at some future time the principle of life will be rendered intelligible, at present it seems to me beyond the confines of science." (Letter 5282, 1866)
"I have met with no evidence that seems in the least trustworthy, in favour of the so-called Spontaneous generation. I believe that I have somewhere said (but cannot find the passage) that the principle of continuity renders it probable that the principle of life will hereafter be shown to be a part, or consequence of some general law; but this is only conjecture and not science." (Letter to Wallich, 1882)

This being said, the authors are also at pains to point out that Darwin was consistently predisposed to the origin of life being a wholly natural phenomenon. "Although he insisted over and over again that there was no evidence of how the first organisms may have first appeared, he was firmly convinced it was the outcome of a natural process that had to be approached from a secular framework."

"The intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable." (2nd Notebook, 1837)
"Though no evidence worth anything has as yet, in my opinion, been advanced in favour of a living being, being developed from inorganic matter, yet I cannot avoid believing the possibility of this will be proved some day in accordance with the law of continuity. [. . .] If it is ever found that life can originate on this world, the vital phenomena will come under some general law of nature." (Letter 13711, 1882)

The "secular framework" of Darwin resulted from his adoption of philosophical materialism. He was a child of Enlightenment rationalism, along with Lyell, Huxley and Hooker. He knew that some others wanted to put his ideas into a theistic or a deistic framework, but Darwin always resisted this. His explanation of using the word "Creator" ("I truckled to public opinion") simply reinforces the conclusion that Darwin's science was wholly secularised. It is surprising, therefore, to read this comment of the authors about people who misread Darwin:

"Indeed, a careful examination and critical reading of his public and private writings shows that what appear to be contradictory opinions on the problem of the emergence of life are the result of texts read out of context, sometimes maliciously, as shown by some publications of creationist groups and advocates of the so-called intelligent design."

It is remarkable how often such comments appear in scholarly work, nearly always unsupported by references or quotes. On this occasion, as is generally the case, the charge is erroneous and entirely misplaced. By and large, creationist and ID scholars have exactly the same understanding of Darwin's secular framework as the authors of this paper. Where they differ is in thinking that this secular framework is profoundly wrong and is an inappropriate foundation for science. Here is an example of an ID advocate who gives the same interpretation of events as the authors:

"Nor should we be misled by a sop Darwin attached to later editions of his Origin of Species. The first edition ended with the famous flourish: "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one [. . .]" To smooth ruffled feathers, later editions read: "There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one [. . .]" Some are fooled by this sop even to this day. But what did Darwin himself say about this little addition? "I have long regretted that I truckled to public opinion & used [a] Pentateuchal term of creation, by which I really meant 'appeared' by some wholly unknown process."" (Wiker, B. 2009)

Those who should be accused of taking Darwin out of context are the Theistic Evolutionists, who do not want to acknowledge Darwin's philosophical materialism. They generally refer positively to Darwin's reference to a Creator and try to suggest that Darwinism can be harmonised with Theism. Examples include Richard Aulie, Darwin and spontaneous generation, Journal of the American Scientific Affiliation, 22, 1970, 31-33 (cited by the authors!), William Phipps, Darwin, the Scientific Creationist, Christian Century, 1983, 809-811, Denis Alexander, Creation or Evolution - do we have to choose? Monarch Books 2008, and Nick Spencer, Darwin and God, SPCK 2009. The latter two names are associated with the "Rescuing Darwin" project, funded by The Templeton Foundation, which seeks to find a harmony between Darwinism and God's creative process. For some Christian comment on the project, go here.

As a final thought, Darwin was intellectually honest enough to see the difference between his philosophical materialism (which demanded some form of spontaneous generation) and empirical science (which gave no support for it). My question is: when does it become reasonable to use the findings of abiogenesis research as evidence against spontaneous generation? We have a large body of evidence today and it is telling us something! Some of us have concluded that the materialist paradigm cannot succeed because it fails to recognise the importance of biological information. The question (When does it become reasonable?) is never asked by philosophical materialists because they cannot entertain the notion that causation may be intelligent.

Charles Darwin and the Origin of Life
Juli Pereto, Jeffrey L. Bada and Antonio Lazcano
Origins of Life and Evolution of Biospheres, 39(5), October, 2009, 395-406 | doi 10.1007/s11084-009-9172-7

Abstract: When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that "the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable". Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organic compounds could lead to the appearance of organisms. Although he favored the possibility that life could appear by natural processes from simple inorganic compounds, his reluctance to discuss the issue resulted from his recognition that at the time it was [not] possible to undertake the experimental study of the emergence of life.

See also:

Dawkins, R. There is Grandeur in this View of Life, The Edge (30 September 2009)

Wiker, B., What were Darwin's Religious Views? Discovery Institute (1 May 2009)

Alongside all the public interest in sporting prowess, recent research has added significantly to our knowledge of how the human body actually works. Many characteristics we take for granted now appear to be critical success factors. Take, for example, our toes. We do not need long toes, like monkeys and apes, because our toes are not used for grasping branches. But are they vestigial - withered remnants of once-grand appendages? The answer is: most definitely not! Whilst it is possible to walk comfortably with longer toes, running is different. Increase toe length by just 20% and there is a doubling of the peak digital flexor impulses and the mechanical work required.

An image like this shows just how different the human foot is from the apes (Source here)

It emerges that the human body has numerous traits that all support the ability to run. In an informative piece in the New York Times, author Parker-Pope refers to the research into short toes saying that it:

"showed that the short toes of the human foot allowed for more efficient running, compared with longer-toed animals. Increasing toe length as little as 20 percent doubles the mechanical work of the foot. Even the fact that the big toe is straight, rather than to the side, suggests that our feet evolved for running. "The big toe is lined up with the rest, not divergent, the way you see with apes and our closest non-running relatives," Dr. Bramble said. "It's the main push-off in running: the last thing to leave the ground is that big toe." Spring-like ligaments and tendons in the feet and legs are crucial for running. (Our close relatives the chimpanzee and the ape don't have them.) A narrow waist and a midsection that can turn allow us to swing our arms and prevent us from zigzagging on the trail. Humans also have a far more developed sense of balance, an advantage that keeps the head stable as we run. And most humans can store about 20 miles' worth of glycogen in their muscles."

A few years ago, one of the authors, Daniel Lieberman, was involved in a related study. This was concerned with the gluteus maximus, said to be the the largest muscle in the human body. Parker-Pope also reports on this work, which found that the gluteus maximus is primarily engaged during running.

"Your butt is a running muscle; you barely use it when you walk," Dr. Lieberman said. "There are so many features in our bodies from our heads to our toes that make us good at running."

There would appear to be potential for clarifying the use of this muscle. It is important for posture, and another has made the comment: "As all weightlifters know, the primary purpose of the gluteus maximus is to raise the body from a deep squat." There is more to be said on these matters.

A noticeable element of this research is that the data are consistently interpreted in terms of natural selection pressures acting on natural variation. This is nothing unusual, because most biologists working in this field have come to accept Darwinism as their interpretative paradigm. Richard Dawkins speaks for many when he wrote in The Blind Watchmaker (Chapter 3) that "We have seen that living things are too improbable and beautifully designed to have come into existence by chance." Natural selection is perceived as giving direction to hereditable variation and results in incremental adaptation. This is how Lieberman and his colleagues approach the 'evolution' of short toes:

"The data suggest that having longer pedal phalanges, in the hallux and to some extent in the lateral toes, increases digital flexor force and work and might contribute to an increased risk of overuse injury during running. Although these effects presumably have negligible fitness consequences for habitually shod recent-modern humans who do not run long distances daily, they might have been significant enough to impose the kind of selective pressures that led to the observed changes in phalangeal size and shape during human evolution. For example, partial foot remains recovered at Hadar, Ethiopia, suggest that, by 3.6 million years ago, the lateral phalanges of A. afarensis were shorter than in the African great apes, but approximately 40% longer and more curved than in modern humans. This intermediate phalangeal morphology is thought to reflect a mixed behavioral repertoire comprising substantial arboreality and facultative terrestrial bipedalism."

What makes this a matter for concern is that no one appears to be talking about testing alternative hypotheses. It is as though the Darwinian explanation wins by default, and this does not make for healthy science. In particular, one hypothesis that is held by a great many people but is not admitted to academic debate, is that the human body is a product of intelligent design. The strength of this approach rests (a) in the holistic character of the alleged design; (b) the exquisite nature of the various characteristics; and (c) the claim that some of these features are irreducibly complex. (as in chapter 2 of Stuart Burgess' book The Origin of Man.

There are ways to test the Darwinian hypothesis. The presumed ancestor had elongated foot bones, illustrated here. To transform this stage to a short-toed human foot by natural selection demands gradual change and this is how the hypothesis can be tested. Where is the evolutionary pathway? Incidentally, the australopithecine feet should not be compared with the African great apes (as Lieberman) but with other ancestral apes contemporary with Australopithecus afarensis. This same line of reasoning about hypothesis testing means that design-based predictions of abrupt appearance can also be evaluated. Are evolutionists willing to allow this testing process to occur? Is this a debate that can be permitted in academic literature and in educational contexts?

Almost invariably, in the past, the idea that ID leads to testable hypotheses is blocked by the philosophical principle that all causes in science must be natural (law or chance). Despite repeated efforts to point out this is a metaphysical block, not one required by science, few take the time to address the point. However, it is encouraging to find some shifts in opinion from time to time. An example, surprising to most of us, is the concession Richard Dawkins gave to John Lennox in a debate last year.

"The deist god would be one that I think it would be [pause] one could make a reasonably respectable case for that. Not a case that I would accept, but I think it is a serious discussion that we could have." (The audio of this exchange can be accessed via http://www.fixed-point.org)

This is a welcome acknowledgement. For those wanting more input on this, the day after the debate, Melanie Phillips had an article in Spectator Magazine drawing attention to the significance of Dawkins' admission. The offer of a serious discussion is welcome. ID scientists do not ask for anything more than the freedom to present a respectable case. What is needed is for academics to abandon their doctrinaire attachment to methodological materialism in science.

Another perspective on this issue is to consider what needs to be done to build a robot that walks and runs. This task certainly focuses the mind and clarifies the issues. For an insight into the state-of-the-art, go here. PETMAN is wearing normal athletic shoes and exhibits a normal heel-to-toe gait. This robot is the product of intelligent design: many man-hours of effort by highly skilled scientists and engineers. Those who think natural selection acting on natural variations would do well to consider the immensity of the task they are expecting Darwin's mechanisms to accomplish.

Walking, running and the evolution of short toes in humans
Campbell Rolian, Daniel E. Lieberman, Joseph Hamill, John W. Scott and William Werbel
Journal of Experimental Biology 212, 713-721 (2009) | doi: 10.1242/jeb.019885

Abstract: The phalangeal portion of the forefoot is extremely short relative to body mass in humans. This derived pedal proportion is thought to have evolved in the context of committed bipedalism, but the benefits of shorter toes for walking and/or running have not been tested previously. Here, we propose a biomechanical model of toe function in bipedal locomotion that suggests that shorter pedal phalanges improve locomotor performance by decreasing digital flexor force production and mechanical work, which might ultimately reduce the metabolic cost of flexor force production during bipedal locomotion. We tested this model using kinematic, force and plantar pressure data collected from a human sample representing normal variation in toe length (N=25). The effect of toe length on peak digital flexor forces, impulses and work outputs was evaluated during barefoot walking and running using partial correlations and multiple regression analysis, controlling for the effects of body mass, whole-foot and phalangeal contact times and toe-out angle. Our results suggest that there is no significant increase in digital flexor output associated with longer toes in walking. In running, however, multiple regression analyses based on the sample suggest that increasing average relative toe length by as little as 20% doubles peak digital flexor impulses and mechanical work, probably also increasing the metabolic cost of generating these forces. The increased mechanical cost associated with long toes in running suggests that modern human forefoot proportions might have been selected for in the context of the evolution of endurance running.

See also:

Lieberman, D.E., Raichlen, D.A., Pontzer, H., Bramble D.M. and Cutright-Smith, E., The human gluteus maximus and its role in running, Journal of Experimental Biology 209, 2143-2155 (2006) | doi: 10.1242/jeb.02255

Parker-Pope, T., The Human Body Is Built for Distance, New York Times (October 26, 2009)

Darwinius masillae is the magnificently preserved Ida, the "eighth wonder of the world" unveiled earlier this year: "our Mona Lisa" and an evolutionary "Rosetta Stone". Afradapis is a newly discovered adapoid from Egypt, known from fossilised jaws and teeth. The controversies surrounding Ida have been the subject of comment here and here. A newly published cladistic analysis of 360 morphological features found in 117 living and extinct primates comes down on the side of Ida being more closely related to lemurs and lorises rather than ancestral to anthropoids.

Darwinius was proposed to be on the right branch - an ancestor of apes and humans - but the new study puts it as a dead end on the left branch (Source here)

One of the criticisms of the original report of Darwinius is that the authors did not provide a comprehensive cladistic analysis, but only referred to anthropoid-like characters. That analysis is still not forthcoming, but a new paper by Seiffert and colleagues considers dentition and jaw morphological features for a comprehensive set of primates, including Darwinius. The claim for anthropoid-like characters is put in a new light, because so many adapiform animals (ancestors of lemurs and lorises) have them.

"It has long been known that some adapiform lineages evolved derived morphological features that are also seen in living and extinct anthropoids (for example, fused mandibular symphyses, upper canines with mesial grooves, enlarged and spatulate upper and lower incisors, short and tall rostra). The phylogenetic significance of these features has been a source of ongoing debate for decades."

Their significant finding is that Afradapis (their newly reported fossil species - an undisputed adapiform) has numerous anthropoid-like characters. This leads the authors to conclude that evolutionary convergences are in plentiful supply.

"Of all known fossil prosimians (including Darwinius), Afradapis provides perhaps the most detailed examples of derived anthropoidlike adaptations in its dental and mandibular morphology. As is the case for many of the morphological features that some have argued link adapiforms to anthropoids, however, the anthropoid-like features of Afradapis (fused mandibular symphysis with transverse torus, deep mandibular corpus, deep masseteric fossa, large upper molar hypocones, absence of P2/2 and presence of an enlarged P3 with a honing facet for the upper canine) are not present in the most primitive undoubted fossil anthropoids, such as Biretia and Proteopithecus, indicating that the features are likely to have been acquired through convergent evolution."

The implication, then is that the Darwinius team have been misled by characters that have turned out not to be diagnostic of anthropoid affinities. This conclusion has been picked up and discussed by many commentators, such as Gibbons:

"When they scored Ida and Afradapis against those other primates, Seiffert and colleagues found that adapids do share some traits with anthropoids, such as the loss of a third upper and lower premolar. But these traits evolved more than once among primates, the team reports tomorrow in Nature. They are the result of convergent evolution, which is the acquisition of the same biological trait in unrelated lineages - and, thus, do not indicate inheritance of the trait from a shared ancestor."

Several significant consequences follow from this research. Not least is the reminder that tracking human ancestors by identifying missing links is an exercise fraught with methodological difficulties. As has been previously noted, human evolution data can be likened to a pointillist painting. Like a pointillist painting, evolution is only apparent from a distant vantage point. Close up, we see masses of data, but no coherent picture.

Another issue to address concerns convergent evolution and the problems this phenomenon creates for cladistic analyses. How do we know what characters are primitive and what are derived? Here is an opportunity for human interpretation to be concealed behind a scientific analysis. The extent to which convergences can be invoked raises suspicion in the minds of some:

"One of the researchers who studied Ida, however, responds that Ida and Afradapis look more like the group that gave rise to anthropoids than the group that gave rise to lemurs and lorises - and that there are too many traits to dismiss as convergent evolution. "The complete convergence postulated for Afradapis seems implausible to me," says paleontologist Philip Gingerich of the University of Michigan, Ann Arbor."

The best outcome of all this is for scientists to demonstrate more humility in handling data. So many seem to grasp at some data and brandish 'evidence' as though it provides a definitive answer to controversy. But this is not how data should be handled in research. Data needs to be interpreted and history shows that there is always more than one way of interpreting it. If we can all adopt a 'multiple working hypotheses' approach when using the scientific method, it will be progress indeed.

Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates
Erik R. Seiffert, Jonathan M. G. Perry, Elwyn L. Simons & Doug M. Boyer
Nature 461, 1118-1121 (22 October 2009) | doi:10.1038/nature08429

Adapiform or 'adapoid' primates first appear in the fossil record in the earliest Eocene epoch (~55 million years (Myr) ago), and were common components of Palaeogene primate communities in Europe, Asia and North America1. Adapiforms are commonly referred to as the 'lemur-like' primates of the Eocene epoch, and recent phylogenetic analyses have placed adapiforms as stem members of Strepsirrhini, a primate suborder whose crown clade includes lemurs, lorises and galagos. An alternative view is that adapiforms are stem anthropoids. This debate has recently been rekindled by the description of a largely complete skeleton of the adapiform Darwinius, from the middle Eocene of Europe, which has been widely publicised as an important 'link' in the early evolution of Anthropoidea. Here we describe the complete dentition and jaw of a large-bodied adapiform (Afradapis gen. nov.) from the earliest late Eocene of Egypt (~37 Myr ago) that exhibits a striking series of derived dental and gnathic features that also occur in younger anthropoid primates [. . .] The specialized morphological features that these adapiforms share with anthropoids are therefore most parsimoniously interpreted as evolutionary convergences. [. . .]

See also:

Gibbons, A., New Primate Fossil Poses Further Challenge to Ida, ScienceNOW Daily News (21 October 2009)

Dalton, R., Fossil primate challenges Ida's place, (21 October 2009), 461, 1040 | doi:10.1038/4611040a

Shallow water light ranges from the ultraviolet to red (wavelengths 360 nm - 650 nm). Going deeper, the extremes disappear and the spectrum narrows to a blue (approx 480 nm). Of the fish species whose colour vision has been tested to date, all except one can see in the ultraviolet (UV). The exception is the scabbardfish, which is the subject of a new research paper. The authors find that the fish that are sensitive to UV have a pigment that absorbs UV light, but the scabbardfish lacks this pigment and has, instead, a pigment that is violet-sensitive.

The scabbardfish (Lepidopus fitchi) is now the only fish known to have switched from ultraviolet to violet vision, or the ability to see blue light. (Credit: Carol Clark, Emory University) (Source ScienceDaily)

The researchers have looked at the molecular structure of the relevant pigments and their absorption spectra.

"[T]hey used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.
"Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted," Yokoyama says."

The hypothesis is that the shift from UV to violet vision was adaptive. Since the lampfish is also a benthopelagic marine fish, the adaptation explanation must also address why the lampfish has retained UV vision.

"Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light."

The researchers found several other amino acid sequence variants that could not be linked to any change in function. This stimulated some salutary comments from the authors:

"It is very common that evolutionary biologists infer the possibility of adaptive evolution of various genes by using computer programs, which compare the nonsynonymous and synonymous nucleotide substitutions per site. However, these analyses not only predict a significant number of false-positives but also fail to predict many positively selected sites; consequently, the positively selected amino acid changes inferred by the statistical methods must be tested by using experimental methods."

In the Press Release, Yokoyama is quoted as saying: "Evolutionary biology is filled with arguments that are misleading, at best". The research team is to be commended for connecting changes in amino acid sequences with changes in phenotypes and then relating all to the living environments. This is good science and a big contrast from the story-telling approach. Adaptation can be studied in a rigorous way, and analyses like this are a demonstration of what is possible.

The words "evolutionary" and "evolution" are used by the authors in their paper. It is strange that evolutionary biology has a fixation of the e-word when there are so many different meanings given to it. In this case, we have a study of adaptive change involving the change of a single amino acid in the opsin protein. This can be understood as a means of the organism becoming fine-tuned to its environment. Darwinian mechanisms appear to be adequate for understanding the data. It should not be necessary to point out that 'fine-tuning' is qualitatively different from 'constructing' the visual apparatus of the organism. Fine-tuning is only possible when the eye is functioning. This point can be better appreciated when the change involves the deletion of existing biological information - as it is in this case. Adaptation is not the route to create biological novelties: microevolution is not macroevolution.

There is a design-orientated way of approaching these data. What if organisms are designed to vary so that they can adapt to changes in their environment? In such cases, mechanisms for fine-tuning can be understood as designed mechanisms, thereby shifting the focus away from the biological world being the product of chance + necessity and towards a world resulting from purposeful intelligent agency.

Evolutionary replacement of UV vision by violet vision in fish
Takashi Tada, Ahmet Altun and Shozo Yokoyama
Proceedings of the National Academy of Sciences, October 13, 2009, 106(41), 17457-17462 | DOI: 10.1073/pnas.0903839106

Abstract: The vertebrate ancestor possessed ultraviolet (UV) vision and many species have retained it during evolution. Many other species switched to violet vision and, then again, some avian species switched back to UV vision. These UV and violet vision are mediated by short wavelength-sensitive (SWS1) pigments that absorb light maximally ([lamda]max) at approximately 360 and 390-440 nm, respectively. It is not well understood why and how these functional changes have occurred. Here, we cloned the pigment of scabbardfish (Lepidopus fitchi) with a [lamda]max of 423 nm, an example of violet-sensitive SWS1 pigment in fish. Mutagenesis experiments and quantum mechanical/molecular mechanical (QM/MM) computations show that the violet-sensitivity was achieved by the deletion of Phe-86 that converted the unprotonated Schiff base-linked 11-cis-retinal to a protonated form. The finding of a violet-sensitive SWS1 pigment in scabbardfish suggests that many other fish also have orthologous violet pigments. The isolation and comparison of such violet and UV pigments in fish living in different ecological habitats will open an unprecedented opportunity to elucidate not only the molecular basis of phenotypic adaptations, but also the genetics of UV and violet vision.

See also:

Seeing Blue: Fish Vision Discovery Makes Waves In Evolutionary Biology, ScienceDaily (17 October 2009)

Tyler, D. Adaptations affecting dim-light vision in vertebrates, ARN Literature blog (10 September 2008)

When I took a course leading to the Certificate of Higher Education, we had some lecture inputs on psychology. The rationale was to show how educational strategies can be informed by the findings of psychologists. My abiding memory of these lectures concern the way the thinking of Sigmund Freud was presented: I was astounded that the lecturer was so uncritical of Freundianism. It was as though the great man was an oracle and we were expected to absorb his words rather than appraise them. At the time of taking the course, I was aware that Freud was no scientist. He did not test out his ideas using an experimental approach. Rather, he used his ideology-based theory as a filter through which to interpret the data. It was a useful experience for me - reinforcing the distinction between ideology and empirically based science.

In view of this, I welcomed reading the concerns expressed in an editorial in the current Nature. The opening paragraph reads:

"Anyone reading Sigmund Freud's original works might well be seduced by the beauty of his prose, the elegance of his arguments and the acuity of his intuition. But those with a grounding in science will also be shocked by the abandon with which he elaborated his theories on the basis of essentially no empirical evidence. This is one of the main reasons why Freudian-style psychoanalysis has long since fallen out of fashion: its huge expense - treatment can stretch over years - is not balanced by evidence of efficacy."

Disillusionment with Freud has not led to a better understanding of humanity (source here)

The stimulus for the editorial was a report issued by a report into the current status and future prospects of clinical psychology in the US. This found that a very high proportion of practitioners put more emphasis on their personal experience than on scientific evidence. This leads to a situation where craft practices prevail and interest in science is low. The US is not alone with these problems: go here and here.

"[M]any psychologists continue to use unproven therapies that have no clear outcome measures - including, in extreme cases, such highly suspect regimens as 'dolphin-assisted therapy'."

Questions are raised in the Editorial about the educational programmes leading to professional qualifications. The American Psychological Association is the accrediting body for the United States and Canada. However:

"The APA requires that such courses have a scientific component, but it does not require that science be as central as some members would like. In frustration, representatives of some two-dozen top research-focused graduate-training programmes grouped together in 1994 to form the Academy of Psychological Clinical Science (APCS), with a mission to promote scientific psychology."

The Editorial points out the scientific advances that could support clinical psychology: neuroimaging, molecular and behavioural genetics, and cognitive neuroscience. However, the link between the science and clinical practice is not explained, and it is worth asking whether the lukewarmness of practitioners towards science is because they have not been able to translate the science into therapeutic interventions. These practitioners are pragmatists: they are looking for therapies that they can use. They will not need to be brow-beaten into using scientific psychology if the findings are relevant to their profession.

Without wishing to denigrate in any way the empirical work being done in science laboratories, there is a problem with the theoretical framework adopted by most researchers. Here is one psychologist writing about free-will and his perception of science:

"[T]here can be no such thing as free will for the committed scientist, in his or her professional life. Thus, science itself presupposes that every phenomenon has a cause. We may speak of "spontaneous combustion" or a "spontaneous abortion" or even "spontaneous applause", but in each of these cases, some cause is more than likely . . . it is essential to a sober, naturalistic worldview." (Source here)

In this quote, the writer says that "science itself presupposes that every phenomenon has a cause", but he means that every phenomenon has a natural cause. He refers to a naturalistic worldview. Now this is a real problem. Instead of science being a search for truth, the writer is using science to pre-empt discussion about causation. But what if there are intelligent causes as well as natural ones? How would naturalistic science ever know? The author quotes Daniel Dennett approvingly:

"By trying to answer the questions, by sketching out the non-miraculous paths that can take us all the way from senseless atoms to freely chosen actions, we open up handholds for the imagination. The compatibility of free will and science . . . is not as inconceivable as it once seemed."

The issue is not one of introducing the miraculous to science (which is an impossible scenario) but insisting that there is continuity from senseless atoms to conscious humanity. By excluding intelligent causation, naturalistic science is making a statement about the nature of reality. The assertion does not emerge by the use of the scientific method, but is a dogmatic imposition. Unfortunately, this materialistic mindset is widespread among behavioural geneticists and neuroscientists. If their philosophical stance is wrong, and there are no checks and balances in their science, then they will never understand the human condition. This does not give confidence that their work will lead to therapeutic interventions that will help patients.

This is not to defend "unproven therapies" but to flag up a problem not mentioned in the Editorial. Freud imposed theory onto data, but so also does naturalistic science. We need to be encouraging a science that is free to explore the evidence wherever it leads and which builds into its methodologies the means to challenge its most cherished presuppositions.

Current Status and Future Prospects of Clinical Psychology
Timothy B. Baker, Richard M. McFall, and Varda Shoham.
Psychological Science in the Public Interest, 9(2), November 2008, 67-103.

Excerpt from Summary: Clinical psychologists' failure to achieve a more significant impact on clinical and public health may be traced to their deep ambivalence about the role of science and their lack of adequate science training, which leads them to value personal clinical experience over research evidence, use assessment practices that have dubious psychometric support, and not use the interventions for which there is the strongest evidence of efficacy. Clinical psychology resembles medicine at a point in its history when practitioners were operating in a largely prescientific manner.

Psychology: a reality check
Editorial
Nature 461, 847 (15 October 2009) | doi:10.1038/461847a

Abstract: If clinical psychology in the United States wants to remain viable and relevant in today's health systems, it needs to publicly embrace science.

For more blogs on the nature of humanity, go here, here and here.

Evolutionary theory does not boast of many laws, and those that do are not universal by any means. One of these is Dollo's law, which is said to date back to about 1890. It is really a hypothesis about the non-reversibility of evolutionary pathways. The authors of new research considered the relevance of the law to the molecular evolution of a protein structure and reported a significant constraint preventing reversibility.

"The extent to which our observations concerning the evolutionary reversibility of glucocorticoid receptors can be generalized to other proteins requires further research. We predict that future investigations, like ours, will support a molecular version of Dollo's law: as evolution proceeds, shifts in protein structure-function relations become increasingly difficult to reverse whenever those shifts have complex architectures [. . .]"

A few restrictive mutations meant the key would not turn (Source here)

A description of the work is provided by Carl Zimmer in The New York Times:

"Dr. Thornton and his colleagues [. . .] studied a protein called a glucocorticoid receptor that helps humans and most other vertebrates cope with stress by grabbing a hormone called cortisol and then switching on stress-defense genes. By comparing the receptor to related proteins, the scientists reconstructed its history. Some 450 million years ago, it started out with a different shape that allowed it to grab tightly to other hormones, but only weakly to cortisol. Over the next 40 million years, the receptor changed shape, so that it became very sensitive to cortisol but could no longer grab other hormones. During those 40 million years, Dr. Thornton found, the receptor changed in 37 spots, only 2 of which made the receptor sensitive to cortisol. Another 5 prevented it from grabbing other hormones. When he made these 7 changes to the ancestral receptor, it behaved just like a new glucocorticoid receptor.
Dr. Thornton reasoned that if he carried out the reverse operation, he could turn a new glucocorticoid receptor into an ancestral one. So he and his colleagues reversed these key mutations to their old form. To Dr. Thornton's surprise, the experiment failed. "All we got was a completely dead receptor," he said."

To find out why the receptor was inactive, the researchers looked for other mutations - and found 5. These were described as "restrictive" because when attempts were made to return the receptor to its supposed ancestral form, the additional mutations acted as blocks.

"Dr. Thornton argues that once the restrictive mutations evolved, they made it practically impossible for the receptor to evolve back to its original form. The five key mutations could not be reversed first, because the receptor would be rendered useless. Nor could the seven restrictive mutations be reversed first. Those mutations had little effect on how the receptor grabbed hormones. So there was no way that natural selection could favor individuals with reversed mutations."

Some significant comments on this research have been made by Michael Behe here and here. These comments are highly relevant to discussions of mechanisms of evolutionary transformation. At the outset, Behe said that the work was interesting and the conclusion was reasonable -

"but the result was exceedingly modest and well within the boundaries that an intelligent design proponent like myself would ascribe to Darwinian processes. After all, the starting point was a protein which binds several steroid hormones, and the ending point was a slightly different protein that binds the same steroid hormones with slightly different strengths. How hard could that be?"

Behe's central point is that the evolutionary pathway was relatively easily disrupted by a few other mutations, so it is not satisfactory to think that Darwinian processes can find a way over every hurdle. The conclusions of his first post are as follows:

* The central point of The Edge of Evolution was that if several amino acids of a protein must be changed before a certain selective effect is available, then that is effectively beyond the reach of Darwinian processes. Bridgham et al (2009) confirm that conclusion. [. . .]
* There is no reason to think the protein studied by Bridgham et al (2009) is unusual in its difficulty of developing a binding site for even a relatively closely-related substance. In fact, in the absence of strong opposing data, that should be the default, reasonable assumption.
* That same reasonable assumption counts strongly against any two unrelated proteins easily developing a binding site for each other.
* That reasonable assumption therefore negates all woolly Darwinian evolutionary scenarios where critical protein binding sites are assumed without justification to pop up when needed (such as, say, in the building of multiprotein structures like the cilium or flagellum).
* Thus the work strongly supports the conclusion of Edge that Darwinian processes are highly unlikely to have built the complex molecular machinery of the cell.

The conclusion of the second post is this:

"The bottom line is that, for a given evolutionary task, at best only a handful of proteins will likely be helpful to evolve, at worst none may help. To calculate the probability of, say, a helpful protein-protein interaction developing in response to any particular selective pressure, it's mistaken to gratuitously multiply odds by the total number of proteins in a cell. Combined with the point made by Bridgham et al (2009), that even tiny structural/functional changes may not be achievable by random mutation/selection, these considerations pretty much squelch the likelihood of Darwinian processes doing much of significance during evolution."

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
Jamie T. Bridgham, Eric A. Ortlund & Joseph W. Thornton
Nature 461, 515-519 (24 September 2009) | doi:10.1038/nature08249

The extent to which evolution is reversible has long fascinated biologists. Most previous work on the reversibility of morphological and life-history evolution has been indecisive, because of uncertainty and bias in the methods used to infer ancestral states for such characters. Further, despite theoretical work on the factors that could contribute to irreversibility, there is little empirical evidence on its causes, because sufficient understanding of the mechanistic basis for the evolution of new or ancestral phenotypes is seldom available. By studying the reversibility of evolutionary changes in protein structure and function, these limitations can be overcome. Here we show, using the evolution of hormone specificity in the vertebrate glucocorticoid receptor as a case-study, that the evolutionary path by which this protein acquired its new function soon became inaccessible to reverse exploration. Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent 'restrictive' mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

See also:

Behe, M. Nature Publishes Paper on the Edge of Evolution, Evolution News & Views, 30 September 2009

Behe, M. Nature Paper Reaches "Edge of Evolution" and Finds Darwinian Processes Lacking, Evolution News & Views, 7 October 2009

Dolgin, E. Protein burns its evolutionary bridges, Nature News, 23 September 2009 | doi:10.1038/news.2009.940