Science Literature

Darwin devoted a large part of his life to understanding heredity. He wrote books on the subject. However, his views fluctuated with time, and historians have spent much time analysing the different ideas he entertained.

"Darwin's conclusion from his studies on inheritance was always the same, that the rules and mechanisms of inheritance were complex and not ready for a definitive analysis."

Darwin's conceptual model of evolution meant his experiments on inheritance were quite different from those of Mendel (source here)

In a helpful analysis of the issues, Jonathan Howard of the University of Cologne suggests that it is legitimate to ask why Darwin did not reach a satisfying conclusion:

"The solution, at least to the inheritance problem, was apparently easily amenable to an experimental approach with materials that were daily to hand. Furthermore the time was ripe in the middle of the 19th century, with many breeders interested in the problem for commercial as well as scientific reasons. And after all, Mendel solved the logic of inheritance in his own backyard in the monastery at Brno with no more technology than Darwin had at his disposal in his garden at Down House. Why couldn't Darwin have done it too?"

Howard looks carefully at Darwin's writings on the subject, and finds he was highly selective in his interests. He sought to document the small variations that he thought could accumulate and lead eventually to speciation. His writings reflect his commitment to this concept: "the selection of infinitesimal varieties", "differences absolutely inappreciable to the naked eye", "the accumulation of infinitesimally small inherited modifications". Howard makes this comment on Darwin's 1876 book The Effects of Cross and Self-Fertilisation in the Vegetable Kingdom:

"His overriding purpose was to establish that progeny produced by self-fertilization are less thrifty than the products of cross-fertilization. He rightly concentrated his analysis not on unit characters, but on the quantitative characters that fitted better with his concept of differential fitness, the attributes that, by their infinitesimal differences, determine life and death in the wild. So Darwin counted seeds, weighed and measured them, planted them and looked for their vitality. He measured growth and general thriftiness in his self-fertilized and cross-fertilized progeny. Everything he measured was a quantitative variable that under these simple experimental conditions could yield no information about inheritance at all. His experiments are overwhelming in scale and scope; they established the point that he wanted to establish beyond all doubt, but they contributed nothing relevant to our understanding of the underlying logic of inheritance."

This distinction between 'quantitative measures of variation' and 'unit characters' provides a clear contrast between the respective methodologies of Darwin and Mendel. Whilst Darwin was trying to put some substance into the word 'fitness' by measuring dimensions and weighing samples (continuous data), Mendel was counting characters (discrete data). Howard points out that, in the course of Darwin's research, he documented findings that we can now understand as Mendelian behaviour. Because he was not looking for it, Darwin did not see it.

"In one especially poignant case, working with the recessive character of radially symmetrical (peloric) flowers of Antirrhinum, Darwin came close to the kind of result that might have ended with a law of segregation. He crossed pure-breeding peloric plants with pure breeding wild types, noting the dominance of the wild type in the F1 progeny. He then established the F2 generation and obtained wild-type and peloric plants in a ratio (88:37) that Mendel (and now we) would effortlessly accept as representing 3:1. However, Darwin had other priorities and was in no way programmed to see the critical meaning in these numbers. He cites them within a sentence and they receive no further comment."

Darwin tried to present his approach to research as Baconian. He is often described as a scientist who gathered data and, by a process of induction, drew out theory that was grounded in evidence. Yet his work on inheritance was not at all like this. He designed his experiments and gathered data about breeding in order to develop and elaborate on his theory of evolution by natural selection. Other data was overlooked or dismissed as not relevant to the problem he was considering.

"The explanation, though, for why Darwin turned away from the inheritance of unit characters as a possible route to resolving the general inheritance problem was simply that he did not believe that such characters had anything to do with the kind of variations that he thought were the raw materials of evolutionary change. Such qualitative and striking variations he characterized as 'sports'. They might be useful for the breeders of fancy plants and animals, but although artificial selection of such anomalous variants could provide an analogy to evolution by natural selection, this was not the real thing. Again and again, when Darwin wrote generally about evolution, he came back to one issue, the infinitely tiny differences between individuals that confer infinitesimal advantages or disadvantages in the interminable struggle for existence. The selection of these variants, continued over hundreds of thousands of generations, was the critical process in evolution. These were the variations, and this was the inheritance, that mattered."

But how did Darwin develop this blindness? Is it a quirk of his personality - or are there influences on his thinking which need to be more clearly recognised. Howard traces this back to the influence Charles Lyell had on Darwin via his books.

"This view of biology was uniquely Darwin's and one he took over wholesale from Charles Lyell's uniformitarian geology during and after the Beagle voyage. Indeed this was by far the strongest, most important, and heuristically most productive of all the influences Darwin was subject to ("I always feel as if my books came half out of Lyell's brain"."

So Darwin was a product of his age. Through Hutton and Lyell, uniformitarianism entered geological science and became dominant for 150 years until people recognised that it was not unscientific to invoke catastrophes and discontinuities. Darwin brought this thinking into biology and the influence of uniformitarianism has had a negative impact on biological science for 150 years also! It delayed the acceptance of Mendelian genetics and steered scientists towards thinking that gradual adaptation was the only issue for understanding the history of life on Earth.

"However, if Darwin failed to discover Mendel's laws, it was not so much because of what he lacked in genius or numeracy or the experimental cast of mind, but rather because of the forceful tendency of what he already possessed. His focus on continuous variation as the source of evolutionary change was not wrong, and coupled with the power he could see in the integration of infinitesimals over time he built his case on the solid foundation of Lyell's uniformitarian thinking. Much of variation and inheritance was simply opaque in those terms, but continuous variation, not unit characters, was, for Darwin, the way forward. Thus Darwin boxed himself in, unable to see the laws of inheritance in continuous variation, unable to see the real importance of discontinuous variation where the laws of inheritance could be discerned."

There are some really important lessons here for science students. Whilst researchers may set out with the best of intentions to implement Baconian induction, they need to realise that they bring mental constructs which govern experimental design and the interpretation of data. Even a genius cannot escape this! Darwin illustrates the negative impacts of uniformitarianism in biological science and provides some timely warnings to those who want to treat all critical evaluation of Darwin's work as subversive to science. In education, we need to encourage the critical appraisal of evolutionary theories, and Darwin's research into inheritance is a good place to start. The health and vigour of science demands it.

Why didn't Darwin discover Mendel's laws?
Jonathan C Howard
Journal of Biology 2009, 8:15, 1-8 | doi:10.1186/jbiol123

Abstract: Darwin's focus on small quantitative variations as the raw material of evolution may have prevented him from discovering the laws of inheritance.

See also:

Janick, J. 1989. Gregor Mendel, In: Classic Papers in Horticultural Science. Prentice Hall, Englewood Cliffs, NJ. p.406-412.

Professor Walter Bock introduces his short essay by referring to the letter Darwin wrote to Asa Gray in 1860: "I am conscious that I am in an utterly hopeless muddle. I cannot think that the world, as we see it, is the result of chance; and yet I cannot look at each separate thing as the result of design". Ernst Mayr took up the challenge and he also found a tension between his understanding of evolutionary theory and the need to use terms like "design" and "purposefulness". Mayr concluded: "Given all this, the conclusion is inevitable: we find in all organisms a fitting together of inborn actions or structures so perfect that one can hardly avoid such terms as "design" or "purposefulness"."

There have now been four international conferences on Comparing Design in Nature with Science and Engineering. Scientists and engineers have no problems using the D-word (Source here)

Bock's discussion seeks to move the thinking of biologists beyond Darwin and Mayr. He points out that "design" is a loaded word. He cannot find a synonym for "design" that does not also incorporate the concept of a designer. Since this implication is not acceptable to Darwinians, Bock wants to remove all references to design from biology:

"the term design carries with it too many undesirable connotations, such as the existence of a creator, and should not be used in evolutionary theory. Design could be replaced with non-accidental or non-stochastic, but these substitute terms are awkward and not really informative. Darwin developed his theory of organic evolution in part as an explanation of the appearance and perfection of adaptations to counter the idea of design as advocated by Paley and accepted then by almost everyone in the western world, including biologists."

In the past, Bock has written on this subject and has proposed the word "paradaptation" to capture the stochastic aspects of mutations affecting the organism's phenotype; also the word "adaptation" to match the action of natural selection on the phenotype. He claims: "These terms may not allow for a catchy slogan or title, but they do not carry any baggage in the form of unwanted connotations, such as a designer or an adapter." This leads to his general conclusion:

"Mayr (1976a: p. 43) concluded that: "In short, the solution of Darwin's paradox is that natural selection itself turns accident into design". A better expression for Mayr's conclusion would be: "In short, the solution of Darwin's paradox is that natural selection itself turns accidental paradaptations into adaptations"."

This communication can be addressed at various levels. Paul Nelson rightly charges Bock with promoting a Darwinian version of Newspeak. George Orwell in 1984 foresaw things far more clearly than others of his generation! But it seems to me that Bock's proposal can be challenged on scientific grounds. He claims that his terminology does not "carry any baggage in the form of unwanted connotations", but they do! Bock's proposal is specifically wedded to the Neo-Darwinist perspective and it is very important for science that theories are evaluated on their merits, not by defining vocabulary that presumes one particular theory over another, nor by making up the rules of engagement.

Neo-Darwinism has two mechanisms: hereditable mutations and natural selection. It is not universally agreed that these mechanisms can achieve the task of large-scale evolutionary transformation. As an example, take a recent interview with Scott Gilbert, Professor of Biology at Swarthmore College in Pennsylvania where he teaches embryology, developmental genetics and the history of biology.

"I think natural selection occurs. And I think natural selection occurs within species. I don't think natural selection alone can explain how butterflies got their wings or how the turtle got its shell. But I think that once you have variation within species, then natural selection can work."

Gilbert is of the view that development plays the major role in all the big changes in evolution. If dissenters like him deserve any credibility, then the adaptationist agenda is an imposition on research. So Bock's terminology can be interpreted as a pre-emptive strike to establish Neo-Darwinism as the voice of academia. This is rhetoric, not science. Bock is free to develop his arguments, but he should not claim that his terminology is free from baggage and he should not dismiss other voices in the biological world by saying that their views are "unusually vague".

Where does this leave us on "Design"? Many years ago, Richard Dawkins suggested that biologists use the term "designoid", but that has not been greeted with enthusiasm. Despite 150 years of trying, the Darwinists have not persuaded the population at large that the living world can be described completely in terms of the action of natural, unguided processes. Bock concludes his paper by saying: "Actually the living world as we see it is the result of chance because all of the attributes of these organisms evolved and the process of evolution is stochastic. To paraphrase a well-known statement by Einstein, God apparently does play with dice." However, the rationale for this position statement is what many of us want to challenge. We do not consider the statement emerges from the science, but from the underlying philosophy of naturalism. As scientists, we seek the liberty to interact with statements like this, showing that they are deductions from premises rather than conclusions emerging from a scientific analysis. We want the rhetoric of hostility to design to be put aside, allowing a mature debate about the evidences for and against intelligent design in the natural world.

Design - an inappropriate concept in evolutionary theory
W. J. Bock
Journal of Zoological Systematics and Evolutionary Research, (February 2009) 47(1), 7-9

Abstract: The concept of accident in evolution refers to causes which are stochastic with respect to selective demands arising from the external environment and acting on the organism, while the concept of design refers to causes which meet the requirement of these selective demands. The condition 'with respect to selective demands' is generally forgotten so that evolutionary changes are described as being design modifications. Design is an invalid synonym for adaptation. Further it implies a designer and has been used by some authors since before Darwin to argue that design in organisms demonstrates the existence of a designer and hence a plan. Yet if evolution depends on two simultaneously acting causes, one of which is accidental, then the process of evolution and all attributes of organisms are accidental. The concept of design is inappropriate in biology and should be eliminated from all biological explanations.

See also:

Nelson, P., Don't use the D word. It's being eliminated. Uncommon Descent (19 February 2009)

Bullock, R. Darwinists on Design: Jumping to Confusions, ARN ID Report, 28 February 2009

All traffic between a cell's nucleus and its cytoplasm has to pass through a nuclear pore complex (NPC) which selects which macromolecules will pass and which will not. Research into the structure of the NPC, previously discussed here and here, is being supplemented by research into the mechanisms that turn a pore into a gateway. A major step forward has been the construction of an artificial nanopore that mimics the action of the NPC.

Artificial transportation. A schematic representation of the genuine (top) and artificial (bottom) nuclear pore complexes. By experimenting with a nuclear pore complex "mimic", researchers have shown how transport factors (red), which help proteins move through the complex, are assisted by proteins called FG-nucleoporins (twisting lines).(Source here)

In the nuclear envelope, the pores are about 30 nm in diameter. Previous work revealed that, "at its simplest, the pore's organization consists of an anemone-like configuration, with folded proteins forming the hole itself and unfolded, tentacle-like proteins called FG-nucleoporins around the opening." This formed the basis of work to mimic the structure.

"[T]he researchers are looking at the functionality of the complex at its most basic configuration: a membrane pockmarked with FG-nucleoporin-coated holes. "We wondered whether we could create a simple artificial mimic, made of just a tiny hole and some of these tentacle proteins," Chait says. "So we built one to see if it really works." To do so, postdoctoral associate Tijana Jovanovic-Talisman started with simple polycarbonate membranes strewn with little holes and coated with a thin layer of gold, and then attached a type of FG-nucleoporin to the membrane."

The nuclear envelope is represented by a polycarbonate sheet perforated with nanopores about 30 nm in diameter. One face of the sheet was coated in gold, to which active FG-nucleoporins were attached, separated by low complexity hydrophilic spacers. The nucleoporins were not synthesised, but obtained from budding yeast. They were arranged in approximately the same density as found in the NPC (about 70 molecules per pore).

"Using confocal microscopy, [Jovanovic-Talisman] tested how efficiently proteins crossed this artificial membrane. Then she added transport factors, which bind to the FG-nucleoporins and selectively ferry cargo across the membrane barrier. The researchers saw that transport factors crossed the artificial membrane much faster than proteins alone, just as occurs in the natural nuclear pore complex. Without the transport factors, that selectivity largely disappeared. The research gave the scientists and their collaborators [. . .] a new perspective on the cell's nuclear transport mechanism. "We're beginning to think of the transport factors in a different way," Jovanovic-Talisman says, "as if they're a mobile part of the nuclear pore complex machine."

This role for the transport factors is a significant addition to knowledge. The artificial nanopore permits experimentation to establish critical factors. For example, as predicted, "the larger the pore size, the weaker the selectivity of the membrane". Other experiments showed the potential for "future carefully tuned alterations in the design of our device could significantly enhance its selectivity".

"The artificial pore could be used to test the importance of pore shape and size. And it has potential biomedical applications, too. Because it can separate particular proteins out of very complex mixtures, the device could have enormous implications for biopharmaceuticals. "It's a device that mimics what nature does and has some beautiful properties, in that it decides what passes through a hole in a very complex mixture," Chait says."

From a design perspective, these findings are tremendously important. Instead of finding simplicity as the black box of the NPC is opened, we discover hidden depths of complexity. There are numerous factors that have to be in place before there is functionality. The characteristics of irreducible complexity are becoming clearer with time. What this means is that incremental development and billions of years cannot be involved in any explanation of the origin of the NPC. It must be formed abruptly if it is to work at all. But note this:

"The team is now working toward making the synthetic pore as selective and efficient as the natural one. "Our machine doesn't work as well as the nuclear pore complex. We've had only three years, while nature's had billions of years to do this," Chait says. "We've got lots of work to do." "

Unfortunately for Chait, geology will not allow him billions of years either. There is evidence for eukaryotes just before the Great Oxidation Event (back to 2.6 Ga) and the distinctive structure of eukaryotes appears to have been very stable since then. Abrupt appearance followed by stasis is the norm in the fossil record, and it does strain gradualist thinking beyond breaking point. It is suggested that a research methodology based on Design will yield productive outcomes quicker than any other approach.

Artificial nanopores that mimic the transport selectivity of the nuclear pore complex
Tijana Jovanovic-Talisman, Jaclyn Tetenbaum-Novatt, Anna Sophia McKenney, Anton Zilman, Reiner Peters, Michael P. Rout & Brian T. Chait
Nature 457, 1023-1027 (19 February 2009) | doi:10.1038/nature07600

Nuclear pore complexes (NPCs) act as effective and robust gateways between the nucleus and the cytoplasm, selecting for the passage of particular macromolecules across the nuclear envelope. NPCs comprise an elaborate scaffold that defines a ~30 nm diameter passageway connecting the nucleus and the cytoplasm. This scaffold anchors proteins termed 'phenylalanine-glycine' (FG)-nucleoporins, the natively disordered domains of which line the passageway and extend into its lumen. [. . .] To test whether a simple passageway and a lining of transport-factor-binding FG-nucleoporins are sufficient for selective transport, we designed a functionalized membrane that incorporates just these two elements. Here we demonstrate that this membrane functions as a nanoselective filter, efficiently passing transport factors and transport-factor-cargo complexes that specifically bind FG-nucleoporins, while significantly inhibiting the passage of proteins that do not. This inhibition is greatly enhanced when transport factor is present. Determinants of selectivity include the passageway diameter, the length of the nanopore region coated with FG-nucleoporins, the binding strength to FG-nucleoporins, and the antagonistic effect of transport factors on the passage of proteins that do not specifically bind FG-nucleoporins. We show that this artificial system faithfully reproduces key features of trafficking through the NPC, including transport-factor-mediated cargo import.

See also:

Researchers construct a device that mimics one of nature's key transport machines, PhysOrg.com, January 6th, 2009

Transparent materials like glass are extremely useful, but the proportion of light reflected from the surface can, in some applications, be a problem. For many years, spectacles have been supplied with antireflection coatings, and there is increasing interest in improving "the light coupling into solar cells, [and enhancing] the extraction of light from light-emitting diodes." The critical parameters are the refractive index of the medium (such as air) and the refractive index of the substrate (such as glass or plastic). The bigger the differences, the more significant are the reflection problems. It has been recognised for some time that a coating with a gradual change in the refractive index will yield substantial benefits. Graded index coatings are designed so that the "refractive index is gradually increased from that of the surrounding material to the refractive index of the substrate, and the reflection is decreased by optical impedance matching at the interfaces." (For more technical details, go here). The main problem is that fabricating these graded index coatings is "very challenging".

Moth eyes have a graded index coating to help them see in the dark. (Credit: Rick Cowen, source here, for larger image, click here)

It was as long ago as 1973 that Clapham and Hutley confirmed that moths had a graded transition of refractive index between their eyes and the air. Since then, several research groups have been active, and commercial products are already in existence. New research by a Dutch group has been reported recently.

"To maximize the amount of light entering their eyes, to help them see at night, the insects' eyes are covered in tapered nanostructures. This creates an "effective medium" where the refractive index gradually increases as light travels from air through to the insects' optical nerve. The resulting effective index is graded from close to one at the top to close to 3.4 at the bottom, which means that very little light is reflected out of the eye. Inspired by these biostructures, Gomez Rivas and colleagues have mimicked the effect by growing nanowires of different lengths - creating a metamaterial with optical properties that change gradually as a function of distance."

This group has experimented with cylindrical and conically-shaped nanorods. "The team used gallium phosphide (GaP) nanorods on top of a GaP substrate, then measured reflection and transmission simultaneously". This allowed them to check whether the observed effects are actually due to the graded refractive index or whether absorption was significant.

"We have shown that the enhanced transmission and corresponding reduced reflection of these layers is related to a graded refractive index in the nanorod layer. The enhanced direct transmission and the total transmission and reflection presented in this work show that scattering and absorption are weak in these layers. The antireflection behavior over a broad wavelength and angular range, and the low amount of light scattered, renders these nanorod antireflection coatings a very promising material for enhancing light coupling in solar cells or for more efficient light extraction from LEDs."

The goal is, of course, to develop commercial products. But more development work is needed to fine-tune the manufacturing process and to determine the optimum conditions to reduce both reflectance and cost.

"Rivas told physicsworld.com that his team's long term goal is to turn this into a product but, for the next few years, they will continue to seek even lower reflection. "In theory we could get 99 per cent transmission; the difficulty is that our nanowires will need to get longer and thicker and then scattering come into play," he said."

In the meantime, spare a thought for the moths, whose eyes have set the standard for antireflection coatings. Clapham and Hutley said that "nature may have anticipated the problems", but what they really meant is that the Blind Watchmaker has been at work: beneficial mutations preserved by the process of natural selection. When we consider that teams of researchers over many years are just beginning to emulate what we find in the natural world, we must conclude either that Darwinian processes are highly effective (and should be easily demonstrated by field observations), or that something other than Darwinian processes must have been involved. Can we allow students the liberty to apply their critical minds to evaluate these options? As a group of senior academics wrote recently to The Daily Telegraph:

"Is it surprising that there is a degree of incredulity that random mutation and natural selection alone can account for the vast complexity of life? A much more open and honest debate is needed. If we lose a spirit of critical inquiry, even about Darwinism, we dishonour the pursuit of science."

Broad-band and Omnidirectional Antireflection Coatings Based on Semiconductor Nanorods
Silke L. Diedenhofen, Gabriele Vecchi, Rienk E. Algra, Alex Hartsuiker, Otto L. Muskens, George Immink, Erik P. A. M. Bakkers, Willem L. Vos, Jaime Gomez Rivas.
Advanced Materials, 2009, 21, 1-6 | doi 10.1002/adma.200802767

Excerpt from 2nd para: The fabrication of graded index coatings is very challenging when the substrate is surrounded by air, as a solid material that matches a refractive index of 1 is needed. Obviously, the refractive index of any dense solid material is too large to match the refractive index of air. To overcome this problem, more effort has been made over the last years to obtain graded index coatings, by applying nanostructuring techniques inspired by biological structures such as moth eyes.

See also:

Clapham, P.B. and Hutley, M.C. Reduction of lens reflexion by the 'Moth Eye' principle, Nature, 244, 281 (1973)

Dacey, J. Moth eyes inspire more efficient solar cell, Physics World (9 February 2009)

Professor Philip Skell is Emeritus Professor of Chemistry from Pennsylvania State University and is also a Member of the National Academy of Sciences (NAS). His review of the NAS booklet Science, Evolution, and Creationism (2008) expresses serious concerns about the warfare thinking expressed in that booklet. At very least, one point can be made clearly: the publication does not communicate the collective view of NAS members.

This influential booklet raises more questions than it answers (source here)

The first point of discussion relates to the conflation of historical science with empirical science. The authors of the booklet pass seamlessly from advances in the study of fossils to advances in understanding of living organisms. This approach is problematical because it opens the door for people with philosophical and ideological agendas to promote their personal views in the name of science.

"This booklet [. . .] conflates the history of living organisms on Earth over the past 3.5 billion years with the advances of the last century made by experimental biologists." [. . .]
"To conflate contemporary scientific studies of existing organisms with those of the paleontologists serves mainly to misguide the public and teachers of the young."

The booklet argues that unless students have a solid grounding in the concepts of organic evolution, they will be ill-equipped to practise science as a profession. Evolutionary theory is regarded as the essential underpinning. Skell reports his own background research on this claim, actively gathering information about the extent to which evolutionary thinking actually influences and guides the research of biologists.

"Examining the major advances in biological knowledge, one fails to find any real connection between biological history and the experimental designs that have produced our cornucopia of knowledge of how the great variety of living organisms perform their functions. It is our knowledge of how organisms actually operate - not speculations about how they may have arisen millions of years ago - that is essential to doctors, veterinarians, farmers, and other practitioners of science today."
[. . .]
"I have queried biologists working in areas where one might have thought the Darwinian paradigm could guide research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I learned that the theory had provided no discernible guidance in choosing the experimental designs but was brought in, after the breakthrough discoveries, as an interesting narrative gloss."

What then is the ideology driving this? What metaphysical agenda does Skell find in the booklet?

"Yet, the Academy's new booklet posits that, without the study of ancient biological history, guided by a reductionist philosophical or theological position that we might call "Scientism", our students will not be prepared to engage in the great variety of modern experimental activities expected of them. The public should view with profound alarm the unnecessary and misguided reintroduction of speculative historical, philosophical, and religious ideas into the realms of experimental science, coming from various sources, including this current publication of the National Academy of Sciences. Are we perhaps setting the stage for a return to that earlier, worldviewbound, pre-modern type of science, only this time with the substitution of Scientism for the earlier worldviews?"

The booklet does attempt to set out evidence to support the claim that without evolutionary theory, nothing makes sense in biology. However, Skell is unimpressed:

"The Academy's new booklet has three inserts, highlighted in yellow, on pages 5, 6, and 9, which are offered as proof of the value of evolutionary theory for medicine, agriculture, and industry, that fail to support the claims: they totally neglect to address the matter of the essential experimental designs scientists require, offering instead vague statements about evolution. The essence of the evolution theory is the hypothesis that historical diversity is the consequence of natural selection acting on variations. Regardless the verity for explaining the biohistory, they provide no guidance to the experimenter, concerned for example, with the goal of finding, or synthesizing, a new antibiotic, or how it functions to disable a disease-producing organism, what dosages are required, and which individuals will not tolerate it. Studying biohistory is, at best, an entertaining distraction from the goals of a working biologist."

More positively, Skell traces out two ways to move beyond the agenda set by Scientism. He provides an overview of what he thinks students should know if they are to be successful participants in biological science. Not "immersion in historical biology", but:

"1. What living organisms inhabit our Earth; 2. How they reproduce their unique characteristics over time and maintain their coherent functions over their lifetimes; and 3. How they interact with one another."

Furthermore, these students need to considerably more savvy about matters of philosophy and worldviews, so that they are better able to recognise and evaluate scientism when it rears its head.

"Outside of biological science, it is certainly true that the education of our young in matters related to development of their worldviews is sadly neglected - to their and society's detriment, since such studies serve to define the matrix, structures, and evolution of our societies and cultures. This neglect speaks urgently for a significant restructuring of educational curricula as a whole to include introductions to philosophy, metaphysics, cosmology, history (including biological history), and comparative theologies. In this way, students could have a deeper understanding of the forces buffeting them and the nature of the damaging pestilential war currently infecting biological science."

It is the view of many of us that the rise of secularism in science, particularly since the Enlightenment, has not been at all healthy for the scientific enterprise. There is an intolerance of different approaches demonstrated by the promotion of consensus science, position statements from science organisations and the erosion of academic freedom. The NAS appears not to be without fault in these matters. It should be noted that The National Academy of Sciences was signed into being by President Abraham Lincoln on March 3, 1863. It is mandated to "investigate, examine, experiment, and report upon any subject of science or art" whenever called upon to do so by any department of the government.

"The misguided emphasis on biological history has produced an unremarked change in the mission of the Academy, which was chartered during President Lincoln's administration to advise on matters of science and technology, and for which, over the years, it has credibly maintained a membership of persons renowned in those fields."

Book Review: National Academy of Sciences, Science, Evolution, and Creationism (Washington, D.C.: NAS Press, 2008).
Philip S. Skell
Politics and the Life Sciences, October 2008, 27(2), 47-49.

First para: Earlier this year, the National Academy of Sciences released the latest version of Science, Evolution, and Creationism. This booklet is no doubt intended to inform the public - and teachers - of developments within biology. Like its earlier versions, however, it conflates the history of living organisms on Earth over the past 3.5 billion years with the advances of the last century made by experimental biologists.

See also:

Skell, P.S., Why do we invoke Darwin? The Scientist, Aug. 29, 2005, 19(16), 10.

Skell, P.S., The Dangers Of Overselling Evolution, Forbes (02/23/2009)

Tyler, D. Spreading the word about evolution, ARN Literature Blog (10 January 2008)

150 years after the publication of On the Origin of Species, it is useful to reflect on how evolutionary theory has changed with time. Which of his contributions have stood the test of time? This was the exercise chosen by Massimo Pigliucci for a piece appearing in Philosophy Now. He refers to the "Darwinian view of the world" and goes on to explain why this can be understood as a paradigm shift in the mindset of scientists and other scholars in the Nineteenth Century.

It is important to analyse the philosophical ideas underpinning Darwinism (Source here)

Pigliucci traces three main stages in Darwinism's evolution. However, even before Darwin, it must be recognised that evolutionary thinking was to be found among the intelligentsia. What was lacking, however, was a theory of transformation. Lamark had proposed some ideas, but "already in Darwin's day there was compelling empirical evidence that Lamarckism didn't work." So, Stage 1 of Pigliucci's story concerns the contribution of Charles Darwin. His approach was to draw on a large body of empirical evidence and interpret it all with the help of two guiding principles.

"Darwin's fundamental insight was grounded on thousands of observations and two principles: common descent and natural selection. Based on his detailed studies of the character and distribution of species across the world, Darwin built a robust inference to the conclusion that all living organisms share common ancestors and are therefore related to each other by a process of 'descent with modification'. But what was doing the modifying? The brilliant answer was: natural selection."

It has to be said that Darwin's approach was more controversial with scientists than most people think. Natural selection was already recognised as a force in nature by many: e.g. Auguste Comte, Comte de Buffon and particularly the research of Edward Blyth. However, these people understood it to be a conserving force in nature rather than a means of transformation. "Few people doubted the idea of common descent, but natural selection was not yet accepted as a sufficient, or even important, mechanism for evolutionary change." Furthermore, Darwin did not have a theory of heredity that worked: his "blending inheritance" did not stand up to critical scrutiny. When Mendel's research was known, it "appeared to deal a fatal blow to Darwinism" because it explained much of the variation observed and discussed by Darwin as innate. Later, with Weissman's work, the situation became even more problematic for Darwin.

"[W]hatever the answer to the question of heredity was going to be, it had to take into account that living organisms completely separate the reproductive cells (the germ line) which convey inheritance from their body cells (the somatic line)."

Stage 2 brings us to the "Modern Synthesis", which Pigliucci describes as "still the standard model in biology". This was the outcome of the collective work of some "theoretical biologists" who employed "statistical analysis" to unify the contributions of Darwin and Mendel. This synthesis is the one that dominates the textbooks and is being hailed as robust by most of the people lauding Darwin's contribution in this Bicentennial year.

"It is founded on Darwin's original principles, with the addition of a mathematical-statistical theory, a theory of heredity, and a much more extensive empirical base than Darwin and his contemporaries had been able to assemble."

However, Pigliucci is not finished. He has more to write! Stage 3 has a question mark after it - but it also has a name: "The Extended Synthesis". Pigliucci is a member of the Altenberg 16, a group that some regard as subversive of the neodarwinian consensus. (For more on this, go here). There are significant sources of dissatisfaction with what Pigliucci calls "the current version of the theory":

"An increasing number of scientists - including yours truly - have grown dissatisfied with the fact that the current version of the theory does not adequately address many important questions. These include the role of developmental processes in evolution, the origin of completely novel traits (such as the turtle's shell, for instance), the increasingly-plausible possibility of so-called 'soft' inheritance (ie, mechanisms of heredity that do not depend on DNA), and even whether and how the propensity to evolve - the so-called 'evolvability' of a lineage - can change during the course of evolution."

These scientists find the Modern Synthesis too restrictive, and they also are taking seriously "the possibility that natural selection may not be the only natural mechanism generating complexity." They are interested in "emergent" properties of complex systems, and are wondering whether additional complexity can be generated "for free". Evo-Devo is said to be a well-established sub-discipline of this new direction of thought. Other avenues of exploration are more speculative, but they are needed in order to "break new theoretical barriers".

Finally, Pigliucci considers whether any of these changes to Darwinian biology constitute a paradigm shift in the sense advanced by Thomas Kuhn. Should any of these developments be regarded as fundamental? Reference is made to 'incommensurable' theories: from the vantage point of one model of reality, there is no way to make sense of a different model. Pigliucci argues that the transitions within Darwinism are gradual, rather than punctuated.

"But when it comes to the evolution of evolutionary theory we see much more continuity than incommensurability. [. . .] In this sense, therefore, I do not think that evolutionary theory has ever undergone a true paradigm shift. With one exception."

It is to that exception we must now turn. Before Darwin, although there had been many significant moves towards the secularisation of science (the so-called Enlightenment), design thinking was still widespread because no one had found a viable mechanism to explain biological complexity. This is what Darwin achieved: an "alternative explanation for the complexity and diversity of life". Darwin brought about a change of worldview - a true paradigm shift in the Kuhnian sense.

"That job was Darwin's chief contribution to humanity - and this alternative explanation truly was a paradigm shift, whose effects still reverberate in the modern creation-evolution 'controversy'. To abandon a supernaturalist view of life on earth in favor of explanations based on natural causes does create an incommensurability - one that finally moved biology from the realm of natural theology and mythology to that of serious science. Charles Darwin will justly be celebrated this year for this momentous achievement in the history of thought."

There you have Pigliucci's analysis. The Darwinian revolution did involve a change of view about the world in which we live. The only explanations deemed to be "scientific" involved natural causes. Pigliucci uses the word "supernaturalist" whereas he should be referring to intelligent causation, but this simply reflects the fact that Pigliucci is a product of the Darwinian worldview and he finds it difficult to appreciate thinking within a different paradigm. In a similar way, he portrays science prior to Darwin as belonging to "the realm of natural theology and mythology" rather than the realm of "serious science". In this he does a grave injustice to the pioneers of science, including biological science, who saw no incompatibility between their research activities and the recognition of intelligent causation. Here again, Pigliucci reveals that he has difficulty understanding what life is like for scholars working within a different paradigm.

The take-home message from Pigliucci is clear: Darwin's major contribution was not in the originality of his thought or the details of his theory (which have evolved and developed with the passing of time) but in championing a science committed to naturalism: i.e. only natural causes are acceptable within science. Once people grasp this, many things become clear.
1. Scientists committed to naturalism find it really difficult to understand Intelligent Design primarily because they are operating within a different paradigm.
2. Those who regard ID as a threat to science and education are actually seeking to promote a version of science and education that is committed to philosophical naturalism.
3. The Bicentennial celebrations for Darwin are more inspired by a commitment to the Darwinian worldview rather than to Darwin's contribution to science.
4. Gould's NOMA thesis and the complementarity approach of theistic evolutionists are way off the mark because they fail to acknowledge the critical role played by naturalistic philosophy in contemporary science.

The Evolution of Evolutionary Theory
Massimo Pigliucci
Philosophy Now, Jan/Feb 2009

First para: Evolution is arguably one of the most profound and controversial ideas ever to hit a human mind. On the Origin of Species flew off the bookshelves when it was published 150 years ago, and it remains one of the most crucial books in the history of science. However, despite the fact that the Darwinian view of the world was swiftly embraced by scientists, as much as half of the population in the United States still today doesn't buy it, because it seems to undermine their view of who we are, where we came from, and what we are here for.

See also:

Tyler, D. How much of evolutionary theory needs fixing? ARN Literature Blog (25 July 2008)

Wells, J. Happy Darwin Day? The Washington Times (February 12, 2009)

Coastal waters provide about 90% of global fish stocks, but significant geographical variations have been noted. For example, the subtropical eastern boundary coastal waters off the Americas are highly productive, but similar coastal waters off Namibia support comparatively meager fish populations.

"This apparent anomaly has been attributed to the episodic occurrence of hydrogen sulphide gas, which is toxic to economically important fish in the southwest African shelf waters. In fact, scientific reports of massive fish mortality in the Namibian coastal waters associated with sulphidic waters date back more than half a century."

A large patch of discoloured surface waters off Namibia attributed to toxic hydrogen sulphide release from the seafloor. (Credit: Image: Jacques Descloitres, MODIS Rapid Response Team, NASA/GS. Source here.)

Despite the potential economic importance, very little was known of these sulphidic events and of any mechanisms of detoxification. This has now changed. During 2004, the RV Alexander von Humboldt monitored a sulphidic event affecting about 7000 square kilometres and took water samples at various locations and depths. They found that microbial life was responsible for detoxifying the waters.

"[T]he detoxification [. . .] was mainly catalysed by two discrete populations of gamma- and epsilon-proteobacteria. Chemolithotrophic bacteria, accounting for ~20 per cent of the bacterioplankton in sulphidic waters, created a buffer zone between the toxic sulphidic subsurface waters and the oxic surface waters, where fish and other nekton live. This is the first time that large-scale detoxification of sulphidic waters by chemolithotrophs has been observed in an open-ocean system."

The key observation was that the sulphidic waters were detoxified without the presence of oxygen. There was no chemical oxidation. The researchers concluded that biological processes must have been involved, and when they looked for microbes, they found them. Known as chemolithotrophs (because they live on inorganic materials), these bacteria had previously been known only near black smokers. Their food comes from the hydrothermal vents, rich in hydrogen sulphide, that emerge from mid-ocean ridges. The researchers carried out lab tests to check that the bacteria could do the work of detoxification:

"Pure cultures of nitrate-reducing, sulphide-oxidizing bacteria have doubling times as short as ~1.5 h, indicating that these chemolithotrophs are capable of creating blooms under the correct conditions. The combined results indicate that the observed bloom of chemolithotrophs was sufficient to create a buffer zone between the oxic environment - where fish and other nekton live - and the toxic sulphidic Namibian shelf waters, by oxidizing sulphide with nitrate."

Looking more generally at ecological systems, it is apparent that there are many, many feedback loops - some positive and some negative - to consider. Simplicity exists only in the textbooks. In this case, there are disastrous emissions of a toxic gas that bring mass mortality to marine animals, but the mechanism is there to restore the system and allow recolonisation of the devastated areas. So effective is this mechanism that many events like this may be undetected by human observers:

"On the basis of our results from Namibia, we postulate that many sulphidic events in coastal waters may go unnoticed because bacteria consume sulphide before it reaches the surface."

The problem we face is that the degree of complexity is never fully appreciated. We are continually learning more about the biosphere and, by now, we should be recognising that we have still much more to learn. It is a human trait that we want to control our environment (rather than consider ourselves a part of it), and we like to think that we have us the tools to achieve our goals. A good example is iron-induced carbon sequestration. Research in this area has been quite extensive, and many are calling for more and more resources to pursue the goal of terraforming our own planet. Happily, new research, reported in the same issue of Nature as the detox research, has questioned the wisdom of taking this forward. One oceanographer is quoted as saying: "Ocean iron fertilization is simply no longer to be taken as a viable option for mitigation of the CO2 problem". (Restricted link here)

Why is this relevant to design in nature? It is because the ability of ecosystems to recover from major perturbations continually challenges the idea that these systems are the product of undirected evolutionary tinkering. The feedback systems are pervasive, and they interact in ways that defy simplistic modeling. Design is suggested here at the level of hypothesis. What if we infer design: will this help or hinder policy? The null hypothesis, that there is no design, is already dominant. However, it is leading to oversimplification and much funding is being spent trying to run before we can walk (e.g. iron-induced carbon sequestration). The design hypothesis suggests we try to work with the natural world, not try to control it.

Another tendency stimulated by the null hypothesis is to regard the Earth's ecosystems as fragile and easily devastated by change. A good example of this is climate modelling, where the world's most powerful computers are harnessed to predict the future. However, the outputs are only as good as the inputs, and our knowledge of climate is small compared with our ignorance. In order to replicate some of the dramatic climate changes that have occurred in times past, the researchers have found it necessary to construct delicately balanced models so that the climate goes into a runaway mode (either to freeze or to roast). A design perspective is sceptical of these finely-tuned models. They are over-sensitive to perturbations, not because of empirical evidence, but because the modellers need to explain hot and cold periods in Earth history. The empirical evidence, as illustrated by the detox research reported above, is that there are robust feedback mechanisms. If the 'robust biosphere' hypothesis is correct, then there must be better ways of spending climate research money.

Detoxification of sulphidic African shelf waters by blooming chemolithotrophs
Gaute Lavik, Torben Stuhrmann, Volker Bruchert, Anja Van der Plas, Volker Mohrholz, Phyllis Lam, Marc Mu mann, Bernhard M. Fuchs, Rudolf Amann, Ulrich Lass & Marcel M. M. Kuypers
Nature 457, 581-584 (29 January 2009) | doi:10.1038/nature07588

Coastal waters support ~90 per cent of global fisheries and are therefore an important food reserve for our planet. Eutrophication of these waters, due to human activity, leads to severe oxygen depletion and the episodic occurrence of hydrogen sulphide - toxic to multi-cellular life - with disastrous consequences for coastal ecosytems. Here we show that an area of ~7,000 km2 of African shelf, covered by sulphidic water, was detoxified by blooming bacteria that oxidized the biologically harmful sulphide to environmentally harmless colloidal sulphur and sulphate. [. . .] This is the first time that large-scale detoxification of sulphidic waters by chemolithotrophs has been observed in an open-ocean system. The data suggest that sulphide can be completely consumed by bacteria in the subsurface waters and, thus, can be overlooked by remote sensing or monitoring of shallow coastal waters. Consequently, sulphidic bottom waters on continental shelves may be more common than previously believed, and could therefore have an important but as yet neglected effect on benthic communities.

See also:

Living dangerously: Implications of hydrogen sulphide for marine life along the Namibian coast (pdf presentation)
B. Currie, K. R. Peard, V. Bruchert, K-C. Emeis,R. Endler, A. Salvanes, A. C. UtnePalm, S. Weeks, A. Bakun,R. Bahlo, A. Goosen.
Namibian Ministry of Fisheries and Marine Resources, Max Planck Institute for Marine Biology.