Science Literature

Nobel laureate Paul Nurse writes: "Biology stands at an interesting juncture". The many remarkable advances in our understanding of living organisms are mostly built on molecular biology. However, these are mainly at the building block level. And because we have clarified our thinking about these, we have deceived ourselves into thinking that we understand the bigger picture. "Our past successes have led us to underestimate the complexity of living organisms".

"But comprehensive understanding of many higher-level biological phenomena remains elusive. Even at the level of the cell, phenomena such as general cellular homeostasis and the maintenance of cell integrity, the generation of spatial and temporal order, inter- and intracellular signalling, cell 'memory' and reproduction are not fully understood."

Until we understand their information systems, our knowledge of organisms is of a preliminary nature (image source here)

So, where do we go from here? How should these conceptual weaknesses be addressed? The answer is that we need a much greater understanding of information flows in cells, tissues, the whole organisms and also ecosystems.
"We need to focus more on how information is managed in living systems and how this brings about higher-level biological phenomena. There should be a concerted programme to investigate this, which will require both the development of the appropriate languages to describe information processing in biological systems and the generation of more effective methods to translate biochemical descriptions into the functioning of the logic circuits that underpin biological phenomena."

To give an idea of what this means in practice, Nurse refers to the work of describing and cataloguing the logic circuits that are found in nature:

"I shall call these segments 'logic modules'. One example of such a module is the negative feedback loop, which often operates in a homeostatic manner. Another example is the positive feedback loop, which can generate irreversible switch behaviour from one state to another. Combinations of modules will produce more sophisticated outcomes: for example, reversible toggle switches, timers and oscillators."
[snip]
"The next steps will be to use the databases described above to determine the probability that specific components of the chemical tool-kit are associated with a particular logic module. Finally, the modules will be linked together into a complete circuit, allowing outputs to be predicted so that the functioning of the circuit can be translated into a narrative of information flow to describe how the cellular phenomenon works."

There is a welcome emphasis in this essay. However, it is hard to read it without thinking that the author is underplaying the significance of other initiatives to study the role of information in biological systems. Recognition of logic circuits in cell biology is not novel, and systems biology provides an integrated framework for the study of feedback mechanisms, modular structures, robustness of systems and the phenomenon of redundancy. ID scientists have made numerous contributions in this area, witness this position statement from the Biologic Institute:

"When you realize that living cells store, transmit, and process information, the similarities with human technology are unavoidable. But when you get a glimpse of the remarkable sophistication of the cellular processes - and the almost unbelievably small scale of the molecular systems performing them - you begin to realize that humans are novices when it comes to complex design."

The above comment is significant because Nurse has one very important passage where he explains that biological design differs from human design. Nurse comes from the perspective that there is no intelligence behind biological design:

"We need to take account of the biological origins of the logic circuits and networks that operate in cells. Because natural selection operates on pre-existing living organisms, novelties will initially arise as add-ons to systems already in existence, almost guaranteeing some redundancy. Thus, man-made machines, which are generally intelligently designed, will differ from the logic machines found in life. Living machines are intelligently designed and will often be redundant and overly complex. We should anticipate these differences and be prepared for the additional complexity to be found in the logic circuits that manage information in cells."

In principle, here is a way to test the contrasting perspectives of the Blind Watchmaker hypothesis and the Intelligent Design hypothesis. But Nurse is wrong to think that redundancy is not a feature of intelligently designed systems - a chat with a human system designers will quickly reveal many examples! But there are differences: blind evolutionary mechanisms will display the phenomenon of tinkering, with many dead ends and useless pseudosystems. By contrast, intelligent design will evidence exquisite structures with back-up systems that come into operation if the main system fails. If evolutionists will allow their approach to be tested in this way, it could open the door to some really interesting discussions!

One final point: Nurse knows that his proposed project requires a multidisciplinary input. This is absolutely right. Roll on the day when research groups like this consider themselves seriously deficient if there are not at least two members that are open to the possibility of intelligent design. In view of Nurse's personal journey through life, welcoming ID members to his own team could be a stimulus to see if his "sceptical agnostic" position is robust or worthy of fresh critical scrutiny.

"The groups will need to be multidisciplinary, including information theorists, mathematicians, physicists, chemists and computer scientists working closely with experimental biologists who have good biological intuition and who can communicate with members of the other disciplines. Different workshop groups could interact with each other through digital conversations to share ideas."

Life, logic and information
Paul Nurse
Nature 454, 424-426 (24 July 2008) | doi:10.1038/454424a

Focusing on information flow will help us to understand better how cells and organisms work.

In 2005, Massimo Pigliucci, in a book review for Nature, wrote: "The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention. It has been said that science often makes progress not because people change their minds, but because the old ones die off and the new generation is more open to novel ideas." This clamour has not diminished in succeeding years, and one recent evidence of this was a private meeting in Altenberg, Austria, on 10-13 July 2008. This event was publicised in March by Susan Mazur, and her recent comments on the meeting are linked here.

What lies beyond the Modern Synthesis?

However, this blog is to draw attention to a piece in Science from Elizabeth Pennisi. According to Pigliucci, the attention created by Mazur's write-up "frankly caused me embarrassment". The reasons for this are not altogether clear, because there is no doubt that the Altenberg meeting was designed to address the problems of a failing theory. Scientific advances have revealed blind spots in the neo-darwinian synthesis and it is time for a change.

More than genes pass on information from one generation to the next, for example, and development seems to help shape evolution's course. "Many things need fixing," emphasizes one invited speaker, Eva Jablonka of Tel Aviv University in Israel. "I think that a new evolutionary synthesis is long overdue."

Major advances have been made in developmental biology, but these advances reinforce the idea that "development constrains evolution". Neo-darwinians do not warm to this idea, because they have promoted the concept of the adaptive landscape, where there is innate plasticity and where all barriers to transformation can, in principle, be overcome. Discussions of the limits to variation are alien to their mindset. However, once it is recognised that stasis is as important to consider as variation, and that stasis can be a developmental phenomenon (not just governed by the environment), then there are important scientific issues to consider about the limits of variation. Until now, neo-darwinists have treated such questions as an intrusion of religious ideology into science. The contrasting perspectives are explained by Pennisi thus:

From the modern synthesis perspective, Wagner explains, "the body plan is a historical residue of evolutionary time, the afterglow of the evolutionary process" such that more closely related organisms share more features. The alternative view, he says, is that "body plans have internal inertia," and evolution works around this stability.

Another key area of interest concerns "regulation": this is a new buzzword in biology circles; "yet it's another concept virtually ignored in the modern synthesis". This is important because the mechanisms of neodarwinism have been recognised by the Altenberg group as rather ineffective. This follows from any empirical work on what these mechanisms actually achieve.

Bottom line: "New traits contain very little that is new in the way of functional components, whereas regulatory change is crucial," Kirschner and John Gerhart of the University of California, Berkeley, wrote in a supplement to the 15 May 2007 issue of the Proceedings of the National Academy of Sciences. (For my blog on this paper, go here).

A further gap in neodarwinian thinking is epigenetics. Environmental factors can influence the way genes are turned on and off and this creates a "bewildering increase in the complexity of the entire inheritance system". Although it is not mentioned by Pennissi, epigenetics is of interest to ID scientists because the complexity issues have stimulated design inferences.

Certain environmental conditions, such as diet during gestation, can alter the epigenetic patterns of the resulting offspring, and new traits that result can last for generations, says Jablonka, who has been striving to get recognition for this mode of inheritance for years. [. . .] "It's beginning to be accepted that [epigenetics] may actually have something to contribute to evolution," says Jablonka. She argues that because these chemical modifications change how tightly wound DNA is, they also influence other properties of a genome that are relevant to evolution. The coiling of a DNA strand, she points out, can alter the rate of mutation, the ease by which mobile elements can move around, the duplication of genes, and even how much gene exchange occurs between matching chromosomes.

With all this excitement, it is difficult to avoid being seen as a dull spoil-sport if you are a sceptic. However, Jerry Coyne obliges:

It's a joke, says Jerry Coyne of the University of Chicago in Illinois. "I don't think there's anything that needs fixing."

These discussions are interesting to ID scientists, not just because they are addressing issues that are of direct concern to the development of ID thinking. We do not have to presume common descent, and we may yet find that variation is within limits. We may find that the regulatory aspects of genetics are strong evidences for design. We may find that that epigenetics points to new levels of exquisite complexity that reveal the hallmarks of design. We do not presume the outcomes, so for us it is a genuine exploration. By contrast, the secularised approach to science must trace everything back to a universal common ancestor and must explain design in nature entirely by reference to natural causes.

Modernizing the Modern Synthesis
Elizabeth Pennisi
Science 321, 11 July 2008: 196-197 | DOI: 10.1126/science.321.5886.196

Seventy years ago, evolutionary biologists hammered out the modern synthesis to bring Darwin's ideas in line with current insights into how organisms change through time. Some say it's time for Modern Synthesis 2.0

See also:

Pigliucci1, M. Expanding evolution, Nature 435, 565-566 (2 June 2005)

Mazur, S. Altenberg! The Woodstock of Evolution? (Scoop! 4 March 2008)

Nature carries an editorial today relating to the legacy left by the recently deceased John Templeton. The issue is significant because the Templeton Foundation provides significant grants to a great variety of scientists and awards the largest cash prize annually for research relating to spiritual realities. In a world where many scientists seem to compartmentalise science and spiritual realities in two separate boxes, and where others say that spiritual realities are delusional, the Templeton Prize appears distinctly anomalous. The Editorial says that the journal "shares a degree of suspicion with many in the scientific community at any attempt by religiously driven organizations to fund science. A chief concern is that the influential Templeton Foundation might be seeking to inject religion into the scientific world."

Does Darwin needs rescuing from the atheists?

The editorial is concerned that the funding comes with an agenda: one of advocacy. Instead of being open to the evidence, wherever it leads, there is the suspicion that the researchers may be swayed to deliver results that they know the funding body will welcome. It is recognised that Templeton tried to guard against the dangers. "Templeton himself seemed to have just the opposite in mind. He believed institutional religion to be antiquated, and hoped a dialogue with researchers might bring about advances in theological thinking." However, with his passing, there is a need for vigilance:

"A critical scrutiny of the foundation's scientific influence continues to be warranted, and no scientific organization should accept sums of money so large that its mission could be perceived as being swayed by religious or spiritual considerations."

It would have been better if the editorial had set these thoughts in the context of the general principle: that funding bodies must not be allowed to make their grants conditional on advancing their particular agendas. This principle applies to multi-national corporations, governments and pressure groups. The principle in science is that we follow the evidence wherever it leads. So research should never be to "prove" an outcome that is identified at the outset. There should be sufficient in the research programme to allow favoured options to be falsified. As far as I can see, there is no reason to single out the Templeton Foundation for special treatment because it is not unusual for research funding and advocacy to be linked. This is particularly relevant to origins research which is mostly "normal" science in the Kuhnian sense.

Nevertheless, there are grounds for concern in the UK. Recently, a Templeton funded project called "Rescuing Darwin" was announced. This project sets out to "challenge the belief that respect for Darwin and his theory necessitates atheism". (Source here). The partners in the project are Theos, which describes itself as "The Public Theology Think Tank", and the Faraday Institute at Cambridge University. The project will report next year:

"to coincide with the 200th anniversary of Charles Darwin's birth and the 150th anniversary of the publication of The Origin of Species.
The project will research and analyse the extent and nature of evolutionary and anti-evolutionary opinion in the UK, and its relationship to theism, atheism and agnosticism."

Further information on the project has not been released and there is not enough here yet to know whether research funding is linked to advocacy. However, the provisional title of the project raises concerns: "Rescuing Darwin" is about recovering Darwin from the clutches of atheists and showing that theism and Darwinism can coexist. We can get a fair idea of what this means by looking at a recent popular article written by Denis Alexander, who heads up the Faraday Institute. Alexander says that evolution is established "beyond any reasonable doubt". He claims that evolution, as a biological theory "has no ideological implications". He treats every attempt to apply Darwin's theory outside biology as inappropriate and the domain of sociologists (not scientists):

"From a sociological perspective, the phenomenon looks less mysterious. There is a very familiar process in the history of science whereby interest groups move in to utilise the prestige of scientific theories in support of their particular ideology. Unfortunately the end result is that in the public consciousness the actual meaning of the label given to the theory itself changes, and so 'Theory X' becomes socially transformed into 'Theory Y' with all kinds of philosophical barnacles attached to it. Evolution has suffered particularly badly from this kind of process and has been used in support of virtually every kind of 'ism' imaginable, including socialism, capitalism, racism, eugenics, and atheism. As George Bernard Shaw once remarked, Darwin 'had the luck to please everybody who had an axe to grind'."

It is not my intention to critique this excerpt here, although it certainly can be critiqued. My main concern is to point out the implications for research methodology if this stance is adopted. Anyone familiar with the writings of ID scientists will know that the appeal is to evidence. Design inferences are made on the basis of empirical data. If, however, Darwinism is "beyond any reasonable doubt", then the researcher must interpret opposition to Darwinism as a sociological phenomenon and will never acknowledge that scientific dissent is possible. This, in my opinion, undermines the integrity of the research programme and makes it wide open to the charge of advocacy in the name of science. Alexander and the "Rescuing Darwin" project will have to work very hard to address these concerns if they are to have any credence when they present their findings.

Templeton's legacy
Editorial
Nature 454, 253-254 (17 July 2008) | doi:10.1038/454253b

Abstract: The Templeton Foundation's exploration of science and faith merits tolerance, not outright rejection.

See also:

Alexander, D. Viva la evolution! (Third Way, Vol 31, No 6, 28-31, Summer 2008)

Theos wins major grant to 'rescue' Darwin, (Theos News, 3 June 2008)

Flatfish are unusual vertebrates, in that adults are highly asymmetric. Their young are normal enough, but as they get older, they adopt the behavioural traits of mature organisms and undergo significant developmental changes. In particular, one eye migrates around the skull so that both are located on the upper side of the fish. There has been no evidence for this developmental process in the fossil record - until now. According to the Editor of Nature, "a graphic example of a transitional form [has been] spotted in the fossil record, confirming that the evolution of the specialized flatfish bodyplan was a gradual process."

"The drawings show the most ancient fossil (left) with symmetrical eye sockets. Amphistium and Heteronectes, the reexamined fossil fish, show asymmetrical skulls, but maintain eyes on opposite sides of the head. The other two fish drawings show the asymmetrical eye locations and skull of the most current flatfish species." (Source Science News)

The finds are deemed significant because at least one stage of partially offset eyes has been documented. This is considered to challenge advocates of punctuated equilibrium (who argue for sudden jumps) and also creationists (who are supposed to defend the creation of species in their present form).

Matt Friedman, the author of the research paper, says that the fossils are important because "they help to settle a long-standing evolutionary debate and shed light on the mode and tempo of evolutionary change". Apparently, finding one intermediate stage dated at 47 million years is sufficient to say that the tempo was "gradual" and that it occurred over "over thousands to millions of years". We have no earlier fossils without asymmetry, and fully asymmetric flatfish appear in the fossil record at the same time. At very least, we can say that these data do not justify the word "gradual"!

What about the description of the fossils as "transitional"? Morphologically, there is no questioning their intermediate status. The interesting questions relate to understanding this observation. The morphological changes are developmental: they occur in every flatfish living today. These changes do not involve any genetic change - the genome is the same before and after the development of asymmetry. The important difference is that the new fossils are mature, not young. But surely the first explanatory options to be explored relate to developmental mechanisms. Are there environmental factors leading to the retarded development of these fish? Or are there epigenetic influences which mean that normal development was impaired, and these animals represent stunted growth? Curiously, there is no exploration of these options in the research paper or in the science media.

There are further questions about the proposed genetic interpretation of the fossils as transitional. What was driving change? Janvier recognises the importance of asking this question: "What could have been the selective advantage of this unusual anatomy?" He refers to several possible scenarios that have been proposed. However, a friend commented: "The fact the migration of the eye takes place in living creatures should have alerted people to the fact that there is no (significant) selective disadvantage to having an asymmetrical skull."
Arguments over selection forces by Darwinists will no doubt continue, but the quest is, at best, for a plausible 'just-so' story. The real problem is that empirical work with natural selection does not confirm that it is a strong force capable of doing what Darwinists want it to do. Furthermore, it begs the question whether eye migration is a cause or an effect. In 2006, Schreiber concluded:

"Behavior and skull asymmetries precede metamorphosis, and the development of lateralized behaviors was independent of eye position in larvae treated with thyroid hormone and in symmetrical variants. Therefore, lateralized behavior is not an adaptive response to eye translocation, but rather must result from changing vestibular responses to thyroid hormone."

The most noticeable feature of the research concerns the evolutionary hype that has emerged from the journal Nature and from the science media. We are not witnessing an impartial evaluation of the data, but a construction of an argument to "lay to rest" criticisms of Darwinism and evolutionary transformation. For more on this, see Luskin's comments on the National Geographic coverage of the story.

The evolutionary origin of flatfish asymmetry
Matt Friedman
Nature 454, 209-212 (10 July 2008) | doi:10.1038/nature07108

All adult flatfishes (Pleuronectiformes), including the gastronomically familiar plaice, sole, turbot and halibut, have highly asymmetrical skulls, with both eyes placed on one side of the head. This arrangement, one of the most extraordinary anatomical specializations among vertebrates, arises through migration of one eye during late larval development. Although the transformation of symmetrical larvae into asymmetrical juveniles is well documented, the evolutionary origins of flatfish asymmetry are uncertain because there are no transitional forms linking flatfishes with their symmetrical relatives. The supposed inviability of such intermediates gave pleuronectiforms a prominent role in evolutionary debates, leading to attacks on natural selection and arguments for saltatory change. Here I show that Amphistium and the new genus Heteronectes, both extinct spiny-finned fishes from the Eocene epoch of Europe, are the most primitive pleuronectiforms known. The orbital region of the skull in both taxa is strongly asymmetrical, as in living flatfishes, but these genera retain many primitive characters unknown in extant forms. Most remarkably, orbital migration was incomplete in Amphistium and Heteronectes, with eyes remaining on opposite sides of the head in post-metamorphic individuals. This condition is intermediate between that in living pleuronectiforms and the arrangement found in other fishes. Amphistium and Heteronectes indicate that the evolution of the profound cranial asymmetry of extant flatfishes was gradual in nature.

See also:

Cressey, D. The eyes have it, news@nature.com, 9 July 2008 | doi:10.1038/news.2008.946

Janvier, P., Squint of the fossil flatfish, Nature 454, 169-170 (10 July 2008) | doi:10.1038/454169a

Luskin, C. National Geographic Finds Opportunity to Conflate Intelligent Design with Creationism while Misreporting Fish Fossil (Evolution News & Views, July 10, 2008)

Schreiber, A.M. Asymmetric craniofacial remodeling and lateralized behavior in larval flatfish, Journal of Experimental Biology 209, 610-621, 2006.

Ever since its discovery, the platypus has been known as "one of nature's oddest creatures, seemingly assembled from the spare parts of other animals". It was hoped that the genome sequence would cast light on its evolutionary history, but now that it has been published (in May 2008), the picture is no clearer. The mosaic of reptilian, avian and mammalian features apparent at the macro-level is replicated in its genetic code.

"There is nothing quite as enigmatic as a platypus," says Richard Gibbs, who directs the Human Genome Sequencing Center at Baylor College of Medicine in Houston, Texas. "You have got these reptilian repeat patterns and these more recently evolved milk genes and independent evolution of the venom. It all points to how idiosyncratic evolution is."

This graphic in National Geographic "illustrates the traits that the platypus shares with reptiles, birds, and mammals"

"Idiosyncratic" means 'peculiar to the individual', 'eccentric'. Whilst this is a fair summary of the quirky, unpredictable way evolutionary transformation is supposed to occur, the principles underlying the analysis of genomes is that the past course of evolution can be tracked. Cladistic techniques are supposed to offer the possibility of redrawing the Tree of Life. In this case, the real problem is not "idiosyncratic evolution" but the discovery of an idiosyncratic platypus genome!

There are several highlighted genetic features in the Nature News report.

• The platypus has "genes for the family of milk proteins called caseins, which map together in a cluster that matches that of humans."
• "The platypus shares with other mammals four genes associated with the zona pellucida, a gel-like coating that facilitates fertilization of the egg."
• It "has two matches for ZPAX genes that had previously been found only in birds, amphibians and fish. And it shares with the chicken a gene for a type of egg-yolk protein called a vitellogenin."
• "Male platypuses have spurs on their hind legs that are loaded with a venom so potent it can kill a dog. Like the venom of reptiles, the poison is a cocktail of variations on at least three kinds of peptide."
• "[N]one of the platypus X chromosomes resembles the human, dog or mouse X. [. . .] Instead, the platypus Xs better match the avian Z sex chromosome."
• "microRNAs, which regulate gene expression, [revealed] a mix of reptile and mammal examples. "We have microRNAs that are shared with chickens and not mammals as well as ones that are shared with mammals, but not chickens," Hannon says."

Despite the claims that the new data provides more "evidence for its place in the ancestral line of animal evolution", the evolutionary story is distinctly fuzzy. Identifying a reasonable lineage was deemed impossible in the case of the reptilian venom: this is regarded by the researchers as having an independent origin. "The similarity in venom is an example of convergent evolution between the two tetrapods."

These traits, and others, are considered in an article on the Truth in Science website here. The various evidences are weighed and it is concluded that evolutionary theory does not deliver a coherent story. Indeed, it is far worse than this: the platypus genome is truly idiosyncratic! The essay concludes:

"Thus the platypus will remain a significant misfit in any Darwinian scheme. Is it from a sauropsid lineage which includes reptiles and birds? Is it from a synapsid lineage which supposedly led to the emergence of the mammals? Or is it derived independently from some unknown ancestral amniote? Or could it be that the Darwinian hypothesis, cladistic analysis or any other classification system for that matter is just far too restrictive? Without doubt, there are mammal-like reptiles as there are reptile-like mammals. The platypus is a Darwinian cautionary tale. Is it a bird or is it a plain . . . old platypus?"

Genome analysis of the platypus reveals unique signatures of evolution
Wesley C. Warren, et al.
Nature 453, 175-183 (8 May 2008) | doi:10.1038/nature06936

Abstract: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

See also:

Brown, S. Top billing for platypus at end of evolution tree, Nature, 453, 7 May 2008, 138-9 | doi:10.1038/453138a

A draft sequence of the platypus genome reveals reptilian and mammalian elements and provides more evidence for its place in the ancestral line of animal evolution. The platypus (Ornithorhynchus anatinus) is endemic to Australia and one of nature's oddest creatures, seemingly assembled from the spare parts of other animals. The semi-aquatic monotreme is a venomous, duck-billed mammal that lays eggs, nurses its young and occupies a lonely twig at the end of a sparse branch of the vertebrate evolutionary tree. Now, the structure of its genome has revealed new clues to how mammals evolved. [snip]

Platypus: a Darwinian Cautionary Tale (Truth in Science, 7 July 2008)

Contemporary presentations of evolutionary theory seem always to incorporate cladograms, sometimes at the species level and sometimes relating groups of organisms. Cladistics is being used to chart the course of evolutionary history. Yet, since it was first developed as a methodology for phylogenetics, it has routinely attracted the critical attention of philosophers of science. Some years ago, Colin Patterson brought these debates to a head when he championed transformed cladism to free cladistics from the charge of circular reasoning. One of the famous controversies about this is discussed here. However, although the unransformed version of cladistics continues to be widely used, the problems remain.

"All life on Earth is united by evolutionary history; we are all evolutionary cousins - twigs on the tree of life. Phylogenetic systematics is the formal name for the field within biology that reconstructs evolutionary history and studies the patterns of relationships among organisms." (source here)

Lars Vogt has contributed a thoughtful analysis of contemporary thinking in a paper entitled: "The unfalsifiability of cladograms and its consequences". Crucial background theory comes from the philosopher Karl Popper:

"As Popperian falsificationism takes in such a central role within the respective theoretical discussions I will take in the Popperian point of view throughout this paper. [. . .] I will infer and discuss the consequences of consistently applying falsificationism to phylogenetics. Therefore, this paper represents a thought-experiment: let's assume Popperian falsificationism is really the only reasonable and justifiable way to do empirical research - What would this imply for phylogenetics?"

The paper is technically demanding and there's not a lot to be gained by trying to digest it to a paragraph or two here. But we do need to note the conclusion:

"Consequently, sensu Popper's demarcation criterion of falsifiability, seeking phylogenetic trees does not represent a scientific endeavour and cladograms represent no scientific but metaphysical hypotheses."

Putting this in more popular language, cladists have adopted a variety of rationales to justify giving weight and credence to their evolutionary trees, but these rationales do not survive critical scrutiny if the test is Popper's demarcation criterion for science.

This disquieting outcome leads Vogt to point to a resolution that makes a distinction between empirical and historical science and limits Popper's criterion to the former:

"All the conclusions presented here rest on the premise that Popperian falsificationism is the only valid scientific theoretical approach. This is highly questionable and might turn out to be wrong, especially with respect to historical sciences - and phylogenetics represents a historical science. The reason for my doubts refers to the fact that it is in principle impossible to predict future observations to test historical hypotheses, which represents the initial idea of Popper's hypothetico-deductive setting - to test necessary predictions against future observations. This rationale is obviously designed for sciences that use experiments in which they control a set of critical conditions in order to generate the deductively predicted necessary effect in order to test a universal causal hypothesis. Perhaps it is time that phylogeneticists develop their own philosophy, a philosophy of phylogenetics that meets the specific requirements of our scientific field, instead of trying to apply a philosophy like Popper's falsificationism that has been developed for experimental sciences such as physics, which is seeking universal laws and regularities instead of the reconstruction of particular historical events."

Crucial to Vogt's point is the distinction between "experimental science" and "historical science". Many scholars involved in the Origins debate have been arguing for some time that there are significant methodological differences between physics and chemistry (empirical sciences) and historical geology and evolutionary biology (historical sciences). It has been noted on numerous occasions that many evolutionists like to champion empirical science and then claim, using Popper's criterion) that the thinking of their opponents is unjustifiable. Consequently, Vogt's contribution makes a really interesting contribution to debate, because he demonstrates in a compelling way that evolutionary biologists face the same charge of adopting unfalsifiable methodologies. He shows that the cladistic approach rests on metaphysical foundations and the outputs of the method are heavily dependent on the assumptions input by the researchers.

Anyone familiar with origins debates will realise that cladistics is a special case of a general principle. So-called proofs of evolutionary transformation are only convincing to those who presuppose common ancestry. The debates within evolutionary circles are always about specifics: the broader issues are not debated because they have an axiomatic status. So, evolutionary theorists do not have the mental tools that would allow them to disprove common ancestry, or whether design inferences are warranted. Consequently, it is not unreasonable to conclude, from the perspective of empirical science, that proposed evolutionary scenarios represent not "scientific but metaphysical hypotheses".

The unfalsifiability of cladograms and its consequences
L. Vogt
Cladistics, 24(1), February 2008, 62-73 | doi 10.1111/j.1096-0031.2007.00169.x

Abstract: Popper's falsificationism provides the normative reference system in recent discussions regarding theory and methodology of systematics. According to Popper, the falsifiability of a hypothesis represents a necessary precondition for its corroborability. It is shown that cladograms, independent of "strict", "methodological" or "sophisticated" falsification, are not falsifiable in principle. No present observation is prohibited by any tree hypothesis and, thus, no Popperian test of cladograms exists. It is shown that the congruence test, which is commonly said to represent a Popperian test of cladograms, instead tests sets of apomorphy hypotheses. Three different strategies that have been proposed to circumvent this problem are discussed and refuted: (1) referring to Popper's convention to renounce ad hoc maneuvers; (2) referring to Popper's treatment of probability hypotheses; and (3) decoupling corroboration from falsification. As a consequence, within a Popperian framework the unfalsifiability of cladograms implies that cladograms cannot explain any present day observation and, thus, represent metaphysical hypotheses.
However, Popper's falsificationism has been criticized and questioned by many philosophers before and it seems to be about time that phylogeneticists develop their own philosophy of phylogenetics that meets their specific requirements of a historical science that is not seeking for universal laws and regularities, but instead reconstructing particular historical events.

Discussions of ID and related topics are often characterised by the word 'polarised'. Stereotyped thinking is widespread and there is often a lack of any real engagement with the issues. It is a pleasure, therefore, to find a thoughtful contribution that stands back from the confrontational stance.

"As a philosopher of science, I am mainly interested in the arguments. At the end of the day, do we need an explanation for the fine-tuning of the cosmos? If so, what is the best explanation? Likewise for the origin of life on Earth and its evolution over time; what are the competing explanations and how do we assess them? These are questions that can be discussed at a scholarly level. The purpose of this essay is to push that discussion along just a bit."

"Surrounded by sophists, we are left without a Socrates" - Jeffrey Koperski

Koperski considers four arguments against ID, two of which are flawed and deserve to be refuted. The other two have some value for meaningful discourse. These arguments are highlighted below, together with Koperski's evaluation of them. The additional thoughts are mine.

The first flawed argument concerns the way ID is regarded as a Trojan horse, "sneaking good old-fashioned creation science past the censors". This is the message conveyed by the label "Intelligent Design Creationism". Koperski's evaluation is clear enough:

"In my view, labeling those who doubt the efficacy of genetic mutation and natural selection "creationists" is a rhetorical strategy, what some logic texts call "stereotyping". Cable television provides ready exemplars for both the creationist stereotype and its cousin, the fundamentalist. Critics try to shape the debate by connecting ID to these templates. If successful, little work needs to be done. The labels tell us who represents the side of rationality over and against the side of ignorance. Having sorted us and them, what they actually say matters little, whoever they happen to be. We must recognize that although this is a common argumentative strategy in talk radio and presidential politics, it is not itself a logical critique. Placing the black hat on one's opponent is no substitute for an argument."

The second flawed argument is that "ID posits a nonphysical intelligence, it violates MN [methodological naturalism] and is therefore not science". This argument essentially defines the problem away. It is as though ID can be dismissed on philosophical grounds without considering any other arguments. Here is Koperski again:

"The bottom line is this: The future use or suspension of MN depends on what is discovered. If the best explanation for some new phenomenon is design, even supernatural design, it would still count as a scientific explanation. It borders on academic incompetence to pretend that science has strict boundaries and then gerrymander those boundaries to keep out the riffraff. Philosophers of science in particular should know better."

In this section, Koperski deals with the charge that ID is a science-stopper:

"Let us consider an objection. Some argue that design explanations would hamper the progress of science. Because "God did it" is potentially an answer to any Why question, allowing design back into biology is a science stopper. If divine fiat is an acceptable explanation, why push on with difficult and expensive research? [. . .] I think this is a plausible objection. If one already has an answer to a question, why search for another? The only thing I ask is that we hold this claim up against the history of science in order to test it. [. . .] As far as I can tell, "God did it" is simply not an answer that theists reach for whenever research bogs down."

Significantly, both of these flawed arguments played a significant role in the Kitzmiller v. Dover 2005 trial. Judge Jones would do well to read what Koperski has to say about this. His words are sufficient to show that the legal judgment was flawed.

"We have examined two bad arguments used against ID. Both are rhetorically effective, persuading teachers and judges alike, and I fully expect to see them in the future. My appeal to those in the academy is this: Let us not use bad arguments as a means to an end."

So, we move on to consider two grounds for properly criticising ID. Allowing that it can contribute to science, is ID demonstrating good science? Some ID science focuses on the problems for evolutionary theory, and neo-Darwinism in particular. These contributions point out examples of irreducible complexity and complex specified information. Without going into details, Koperski considers the responses that have been made to these arguments sufficient to show that neo-Darwinism is still alive and well. "In other words, there are many soft anomalies in the literature but no hard ones."

"The second kind of ID science includes research that fits nicely within a design framework, even though the researchers themselves do not support ID. For example, ID proponents often speak favorably of research showing that so-called junk DNA actually is functional. The idea is that one should expect more purpose in biological structures than would be expected from a Darwinian point of view. The nanotechnology approach to microscopic systems is also considered very ID-friendly. The reason scientists find such utility in thinking of biological systems as machines is because, in some sense, that is what they are. The conceptual link with human artifacts is not merely a metaphor. These kinds of ID-related science are well and good, as far as they go. What critics rightly clamor for, however, is peer-reviewed research in which design has more than a mere heuristic role."

Certainly, both these aspects of ID science feature in this blog and many other ID writings. Basically, we are ready to accept Koperski's challenge and engage further on these matters - but we do ask that this be conducted within the science community. The evidence to date is that science journals and science conferences are willing to discuss these issues as long as ID advocates are excluded from having a voice. This is not an acceptable way to conduct this debate. Furthermore, Koperski is too willing to accept the peer-review argument. All the evidence to date is that editors publishing an overt ID paper are deemed to have failed in their duty to the science community and are therefore incompetent. Koperski writes: "Some think of ID primarily as a weapon in the culture wars. Anti-design bias in the academy is part of the backlash. Had ID consistently emphasized research over public exposure, the atmosphere of the debate would be different today." But this argument presupposes that the culture war is an ID invention! If there really is a culture war, no amount of ID research will satisfy the critics! For more on this, go here.

The second "good" argument against ID is that it is more radical than necessary. Koperski refers to the conservatism of science and the preference for incremental change.

"Even if orthodox neo-Darwinism collapses, design obviously is not the only alternative. More important, the rivals are more conservative vis a vis the reigning theory. They do not challenge MN. In fact, very little would have to be added to textbook evolutionary theory if one or more of these is accepted. If any one of them is capable of resolving the problems posed by complex structures and macroevolution, ID is a more radical solution than is needed. In short, if scientific conservatism is a defensible, normative principle of theory change, it undermines the acceptability of ID."

The problem with this analysis is that it has no sense of history. The pioneers of science were ID advocates. Science was born and nurtured with the legitimacy of making design inferences. The trends over the centuries have been towards secularisation and achieving this in biology was Darwin's achievement. This is why the secularists are so keen to make Darwin's bicentennial a success. The issue is not conservatism, but metaphysics. For some of us, the issue is one of science reconnecting with its roots.

Two Bad Ways to Attack Intelligent Design and Two Good Ones
Jeffrey Koperski
Zygon, 43 (2), June 2008, pages 433-449

Abstract: Four arguments are examined in order to assess the state of the Intelligent Design debate. First, critics continually cite the fact that ID proponents have religious motivations. When used as criticism of ID arguments, this is an obvious ad hominem. Nonetheless, philosophers and scientists alike continue to wield such arguments for their rhetorical value. Second, in his expert testimony in the Dover trial, philosopher Robert Pennock used repudiated claims in order to brand ID as a kind of pseudoscience. His arguments hinge on the nature of methodological naturalism as a metatheoretic shaping principle. We examine the use of such principles in science and the history of science. Special attention is given to the demarcation problem. Third, the scientific merits of ID are examined. Critics rightly demand more than promissory notes for ID to move beyond the fringe. Fourth, although methodological naturalism gets a lot of attention, there is another shaping principle to contend with, namely, conservatism. Science, like most disciplines, tends to change in an incremental rather than revolutionary manner. When ID is compared to other non- or quasi-Darwinian proposals, it appears to be a more radical solution than is needed in the face of the anomalies.