How to build an animal
Whereas the focus in Part 1 falls on fossil evidence for an explosion of life in the Early Cambrian, we change gear in Part 2 and examine biological research relevant to the origin of animal phyla.
The starting point is the search for ways of measuring biological information representing different body plans. Shannon's theory of information (when applied to the animal genome) has the merit of mathematical rigour, but Meyer shows that this approach gives insight only into a sequence's capacity to carry information. Whether the sequence is functional is undetermined ? so discussion of biological information must extend far beyond quantitative measures. Meyer discusses the number of cell types as an indicator of complexity of embedded information. With reference to the genome, which uses digital codes, he uses the term "specified information", meaning that a genetic sequence can only be functional if the codons have a specific arrangement. Is the neo-Darwinian mechanism adequate to explain the origins of novel specified information associated with the Cambrian Explosion? Meyer describes this as a challenging question for Darwinists and claims that the necessity of "vast amounts" of specificity makes their explanations implausible.
To show that this argument is real, and not an argument from ignorance, Meyer devotes the next chapter to unpacking the issues surrounding specificity. In the early 1960s, Murray Eden (a professor of engineering and computer science at MIT) realised that there was a problem with neo-Darwinian theory and organised a conference to explore the issues at the Wistar Institute in Philadelphia. The theme was: "Mathematical challenges to the neo-Darwinian interpretation of evolution". The participants came from many disciplines and included Ernst Mayr (one of the architects of neo-Darwinism) and Richard Lewontin (Professor of genetics and evolutionary biology). Chairing the meeting was the Nobel laureate Sir Peter Medawar. The discussion provided by Meyer is extremely helpful in clarifying the nature of the problems and summarising some of the suggestions for resolving the dilemmas. The most favoured possible solution is explained in the quotation below, and is significant for stimulating a design-based research programme discussed in the subsequent chapter.
"The solution was this: even though the size of the combinatorial space that mutations needed to search was enormous, the ratio of functional to non-functional base or amino-acid sequence in their relevant combinatorial spaces might turn out to be much higher than Eden and others had assumed. If that ratio turned out to be high enough, then the mutation and selection mechanism would frequently stumble onto novel genes and proteins and could easily leapfrog from one functional protein island to the next, with natural selection discarding the non-functional outcomes and seizing upon the rare (but not too rare) functional sequences." (page 178)
As a research student in the late 80s, Doug Axe was not persuaded by Dawkins' rhetoric in "The Blind Watchmaker", and wanted to undertake research himself into aspects of genetic information. Reading the proceedings of the Wistar Conference stimulated many ideas for further work. This led Axe to join a protein engineering team at the University of Cambridge. Meyer's discussion of his experiments and results need to be read in full to appreciate the robustness of the empirical work undertaken. However, this is the conclusion of the first phase of Axe's research:
"Overall, therefore, he showed that despite some allowable variability, proteins (and the genes that produce them) are indeed highly specified relative to their biological functions, especially in their crucial exterior portions. Axe showed that whereas proteins will admit some variation at most sites if the rest of the protein is left unchanged, multiple as opposed to single amino-acid substitutions consistently result in rapid loss of protein function." (p.193)
In the next chapter, Meyer himself appears as part of the story-line. The year is 2004, when the Proceedings of the Biological Society of Washington carried Meyer's peer-reviewed article that made reference to Axe's work and the Cambrian Explosion dilemma. He argued that "the theory of intelligent design could help explain the origin of biological information" (p.209). In Meyer's own words, the publication of this paper created "a firestorm of controversy". Up to that time, opponents of intelligent design (ID) claimed that until ID made it into peer-reviewed literature, it could not count as science. Once they realised it had passed through, they left no stone unturned in trying to discredit the paper, the journal's editor and their peer-review process. Many months passed before anything looking like a scientific response appeared, drawing heavily on a 2003 review of thinking about the origin of new genes. Meyer devotes the rest of this chapter to analysing the arguments and showing that the research does not explain the origin of specified information and does not solve the combinatorial inflation problem identified by Murray Eden.
"Overall, what evolutionary biologists have in mind is something like trying to produce a new book by copying the pages of an existing book (gene duplication, lateral gene transfer, and transfer of mobile genetic elements), rearranging blocks of text on each page (exon shuffling, retropositioning, and gene fusion), making random spelling changes to words in each block of text (point mutations), and then randomly rearranging the new pages. Clearly, such random rearrangements and changes will have no realistic chance of generating a literary masterpiece, let alone a coherent read. That is to say, these processes will not likely generate specificity of arrangement and sequence and, therefore, do not solve the combinatorial search problem. In any case, all such scenarios also beg the question. There is a big difference between shuffling and slightly altering pre-existing sequence-specific modules of functional information and explaining how those modules came to possess information-rich sequences in the first place." (p.219)
Neo-Darwinians are remarkably satisfied with natural selection and their hypothetical models of gene evolution, so that platitudes often replace science. Meyer gives an example from an evolutionary text-book: "One need not go into the details of the evolution of the bird's wing, the giraffe's neck, the vertebrate eye, [. . .] Even a slight advantage or disadvantage in a particular genetic change provides a sufficient differential for the operation of natural selection." (quoted on p.234). Anyone who wants to grapple with the details soon meets problems that cast doubt on the adequacy of Darwinian mechanisms. Meyer introduces us to Tom Frazzetta, whose specialism is functional biomechanics. He found great difficulty defending the concept of gradual change because all the intermediate forms he could envisage would not have been viable. The interdependence of biomechanical systems meant that design changes could not be incremental and many would have to occur concurrently. Frazzetta came to the conclusion that "Phenotypic alteration of integrated systems requires an improbable coincidence of genetic (and hence hereditable phenotypic) modifications of a tightly specified kind." (quoted on p.233). This brings us to the work of Michael Behe and David Snoke, and their 2004 paper in Protein Science. They recognised that some inferred evolutionary changes require coordinated mutations, and they used the principles of population genetics to assess the likelihood of such coordinated changes occurring. The calculated probabilities are so low as to cast doubt on this being a widespread phenomenon in the history of life. Behe was to return to this theme later in his book: The Edge of Evolution (2007).
"In a real sense, therefore, the neo-Darwinian math is itself showing that the neo-Darwinian mechanism cannot build complex adaptations - including the new information-rich genes and proteins that would have been necessary to build the Cambrian animals." (p.254)
At this point, the focus of interest shifts from molecules to body plans; from population genetics to developmental biology. Paul Nelson (philosopher of biology) is introduced when commenting on the "great Darwinian paradox". This is the observation that mutations affecting early stage development are not beneficial, yet these are the very mutations needed if there is to be any change in the body plan. In Nelson's words:
"Such early-acting mutations of global effect on animal development, however, are those least likely to be tolerated by the embryo and, in fact, never have been tolerated in any animals that developmental biologists have studied." (p.262).
Early stage development appears to be overseen and coordinated by developmental gene regulatory networks, a concept pioneered by Eric Davidson. It is not a coincidence that developmental biologists like him have been pressing for a new evolutionary synthesis to emerge, because they are acutely aware that neo-Darwinism cannot be the way forward. The tightly integrated gene regulatory networks cannot be mutated incrementally so as to produce new body plans:
"contrary to classical evolution theory, the processes that drive small changes observed as species diverge cannot be taken as models for the evolution of the body plans of animals." (words of Davidson, quoted on p.269).
The challenge to the neo-Darwinian synthesis is even more formidable than this. The mindset of Darwinists is that life is digital. Everything is reduced to bits in the genome sequence. However, what happens to the adequacy of their theory if they are dealing with only part of the information story? What happens is some information is located in the cell independent of the genome? At very least, if this is true, the textbook orthodoxy can only claim to be a partial account of origins. But it also needs to be considered whether neo-Darwinism is a diversion to the real issues affecting life's diversity. These matters are discussed in Meyer's chapter dealing with the epigenetic revolution.
"Many biologists no longer believe that DNA directs virtually everything happening within the cell. Developmental biologists, in particular, are now discovering more and more ways that crucial information for building body plans is imparted by the form and structure of embryonic cells, including information from both the unfertilized and fertilized egg." (p.275)
Much of this chapter draws on the work of Jonathan Wells, whose analysis of the inadequacy of neo-Darwinian theory incorporates the growing evidence that epigenetic influences on development are substantial. (See also here.)
"Yet both-body plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn?t wholly responsible for the way an embryo develops - for body-plan morphogenesis - then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand." (p.281)
A particularly useful aspect of these chapters is that ID-related research is presented in a way that demonstrates the coherence and value of the design paradigm. Researchers operating within a design framework are addressing issues that are of central importance, publishing their work in peer-reviewed papers and other scholarly forums, and engaging in a constructive discourse with scientists working within the naturalistic evolutionary paradigm. Many will be aware of the work of individual scientists mentioned above, but Meyer's account shows how they contribute to the bigger picture and complement one another. This approach to science is exemplary and one hopes it will inspire young scientists to emulate their endeavours.
Where does this lead us? For the answer to that question, we must turn to Part 3 of Meyer's book.
"[T]he Cambrian explosion now looks less like the minor anomaly that Darwin perceived it to be, and more like a profound enigma, one that exemplifies a fundamental and as yet unsolved problem - the origination of animal form." (p.287)
To be continued.
Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design
by Stephen C. Meyer
HarperOne (HarperCollins), New York, 2013. 520 pp. ISBN 9780062071477.
Readers of Uncommon Descent will recall that mid-20th century Christian apologist C.S. Lewis's views on Darwinism and scientism have attracted considerable interest of late. And some misrepresentation as well, as some zealous followers of Darwin have tried to claim him as one of their own.
As reported in ENV...Congratulations to The American Spectator for having such sensible readers. Sometimes it's gratifying to find that the people who should know better actually do.
In January, the conservative magazine featured paired articles by Stephen Meyer and John Derbyshire arguing respectively for and against intelligent design. Derbyshire "argued" only in the limited sense of tossing off snide insults and trying to paint ID absurdly with the brush of "Occasionalism," a medieval theological concept.
Christian Post contributor Anugrah Kumar writes that Casey Luskin, a proponent of Intelligence Design, says that most theistic evolutionists appear to be unfamiliar with what ID theorists say, and they wrongly maintain that it's a "God of the gaps" argument.
The new big debate might be multiverse cosmologist Sean Carroll vs. Christian apologist William Lane Craig (who dismisses multiverses). It is sponsored by Greer Heard Point Counterpoint Forum. February 21-22, live streaming.
University College London wanted to honor the father of evolutionary theory on his 205th birthday, but they couldn't seem to do it without intelligent design.
The goal of REASONS 2014 will be to demonstrate the beautiful compatibility and synergy of the natural sciences and orthodox Christianity.
Speakers at this Houston area event include...
Stephen C. Meyer
William A. Dembski
John G. West
Bruce L. Gordon
Nancy R. Pearcey
And Houston Baptist University Faculty:
Holly E. Ordway
Melissa Cain Travis
An endorsement on ENV of the book, which is a collection of philosophical, historical, mathematical, and scientific essays on design in nature. Many of the chapters are written by scientists from outside the United States, with Spain being especially well represented, who are friendly to intelligent design. However, not all of the chapters defend ID. Some of the authors critique ID, or claim it's impossible to scientifically detect design in nature. But even the criticisms are thoughtful, making this volume a worthy addition to anyone's collection of ID-related books.
A South Dakota senator on Thursday killed his proposal that would have allowed teachers to discuss whether a higher power played a role in creation, saying it was too poorly written to pass.
The Senate Education Committee voted to kill the measure, which sought to ensure teachers could tell students about intelligent design, the belief that a higher power must have had a hand in creation because life is too complex to have developed through evolution alone.
The past 10 years has witnessed the rise of New Atheism, particularly in the US and the UK, with leaders who write best-selling books and attract a vociferous following. No doubt the sociologists of science will come up with some interesting things to say about this movement, but it is highly significant that the New Atheists have created deep divisions within their own intellectual community. The latest salvo expressing discontent has been fired by Massimo Pigliucci, evolutionary biologist, philosopher of science and advocate of atheism. In an academic paper, Pigliucci argues that the term "new" does not have anything to do with the public advocacy of atheism. Nor is there novelty in the arguments they use to advance their atheistic claims. However, Pigliucci is able to identify two distinctive characteristics of the New Atheists:
"[The first] is to be found in the indisputably popular character of the movement. All books produced by the chief New Atheists [. . .] have been worldwide best sellers, in the case of Dawkins's God Delusion, for instance, remaining for a whopping 51 weeks on the New York Times best-seller list. While previous volumes criticizing religion had received wide popular reception (especially the classic critique of Christianity by Bertrand Russell), nothing like that had happened before in the annals of Western literature. [. . .]
[Secondly, W]hat I see as a clear, and truly novel, though not at all positive, "scientistic" turn that it marks for atheism in general. [. . .] [We will] explore some examples of what I term the "scientistic turn" that has characterized some (but not all) New Atheist writers (and most of their supporters, from what one can glean from the relevant social networks)." (p.144)
New atheists say they trust science, but they redefine science so it cannot lead them to recognise design in nature. (Source here)
It is the second of these characteristics that elicits protestation from Pigliucci: the New Atheists are advancing ideas that call for a firm rebuttal. There is a strong tendency for these new leaders to be rather disparaging of philosophical arguments and base their polemics on the claims that science is the exclusive route to knowledge and that the findings of science supports the atheist position. According to Pigliucci, their approach necessitates a re-defining of science, and he argues that the new definition is indistinguishable from scientism.
"The New Atheism approach to criticizing religion relies much more forcefully on science than on philosophy. Indeed, a good number of New Atheists (the notable exception being, of course, Daniel Dennett) is on record explicitly belittling philosophy as a source of knowledge or insight. Dawkins says that the "God hypothesis" should be treated as a falsifiable scientific hypothesis; Stenger explicitly - in the very subtitle of his book - states that "Science shows that God does not exist" (my emphasis); and Harris later on writes a whole book in which he pointedly ignores two and a half millennia of moral philosophy in an attempt to convince his readers that moral questions are best answered by science [. . .]. All of these are, to my way of seeing things, standard examples of scientism. Scientism here is defined as a totalizing attitude that regards science as the ultimate standard and arbiter of all interesting questions; or alternatively that seeks to expand the very definition and scope of science to encompass all aspects of human knowledge and understanding." (p. 144)
The paper discusses a great diversity of issues, but we shall note only comments relating to Richard Dawkins' The God Delusion. Two of the issues identified are: his discussion of morality without gods, and his tackling of "the god hypothesis" to show that science-based evidence allows the hypothesis to be rejected. Regarding morality without gods, Pigliucci is unimpressed. Not only does Dawkins pass over the Greek philosophers, he does not interact with more contemporary secular thinkers who have contributed to this issue. Pigliucci draws attention to the Euthyphro dilemma, which stimulates the question: Is an action moral because the gods decree it, or do the gods decree it because it is moral? Plato and Aristotle came to the view that morality takes precedent over divinity. Atheists make a distinction between religion and morality and argue that morality should not be based in the will of a god.
"When it comes to the issue of why being moral, however, Dawkins shows most clearly his limitations. For instance, he seems to be unaware of what many philosophers consider by far the most powerful argument in favor of the idea that gods and morality are entirely logically independent issues: the so-called Euthyphro dilemma posed by Plato in the homonymous dialogue from 24 centuries ago." (p.150)
What Pigliucci might have noted is that the Dawkins promotes the distinction between religion and morality even though he does not use philosophical arguments to justify it. This is why he (and new atheists generally) make frequent references to Old Testament practices, such as slaying enemies and keeping slaves, to show that our sense of morality is such that we would not want to worship the Old Testament God even if he exists. Pigliucci wants to rest his case on the arguments made by secularist moral philosophers; Dawkins wants to rest his case on a scientific assessment of what is morally right; but neither of them engage with the responses of Christian moral philosophers to the Euthyphro dilemma and the secularists, so resting their case appears somewhat premature. (For a brief response, see here. For some discussion, see here).
Turning to "the god hypothesis", Pigliucci acknowledges that Dawkins uses a scientific approach to "make ideas like a young earth, or the slightly more sophisticated concept of "irreducible complexity" championed by Intelligent Design proponents, clearly untenable". Whilst this smacks of spin to members of those groups, the essential point is that there are aspects of YEC and ID that can be addressed using the tools of science. But is the existence of God amenable to scientific investigation? Can God ever be the subject of a scientific hypothesis? Pigliucci thinks not.
"The real issue is that Dawkins (and most if not all of the New Atheists) does not seem to appreciate the fact that there is no coherent or sensible way in which the idea of god can possibly be considered a "hypothesis" in any sense remotely resembling the scientific sense of the term. The problem is that the supernatural, by its own (human) nature, is simply too swishy to be pinpointed precisely enough." (p.148)
No doubt, this challenge to Dawkins' thinking could be discussed further. It might make the point clearer if it was said that science deals with the behaviour of material things, and God is not material - but the Creator of material things. So science cannot put God under the microscope, nor can experiments be devised to test whether he exists. However, this conflicts with the premise of the new atheists that science is the only route to knowledge. Pigliucci draws together his objections to Dawkins' scientism with these words:
"To recap, then, what is considered to be perhaps the quintessential text of the New Atheism is an odd mishmash of scientific speculation (on the origins of religion), historically badly informed polemic, and rehashing of philosophical arguments. Yet Dawkins and his followers present The God Delusion as a shining example of how science has dealt a fatal blow to the idea of gods." (p.148)
The following quotes summarise the conclusions about scientism. They have already antagonised some of the new atheists and Pigliucci responds to their criticisms here. But more generally, these conclusions are relevant to all who have a stake in the scientific enterprise.
"1. Scientism is philosophically unsound. This is because a scientistic attitude is one of unduly expanding the reach of science into areas where either it does not belong [. . .] or it can only play a supportive role. [. . .] What I do object to is the tendency, found among many New Atheists, to expand the definition of science to pretty much encompassing anything that deals with "facts", loosely conceived. So broadened, the concept of science loses meaning and it becomes indistinguishable from just about any other human activity." (p.151)
"2. Scientism does a disservice to science. Despite representing a strong attempt to expand the intellectual territory, as well as prestige, of science, I think that scientism is detrimental to science in at least two ways: internally to the discipline itself, because it represents a misunderstanding of what science is and how it works, which is unlikely to serve well either practicing scientists or graduate students as scientists-in-training; externally because it has the potential of undermining public understanding and damaging the reputation of science." (p.152)
"3. Scientism does a disservice to atheism. Finally, I maintain that a scientistic turn does not do much good to atheism as a serious philosophical position to begin with, contra the obvious explicit belief of many if not all of the New Atheists." (p.152)
As well as drawing attention to the arguments presented in this paper, there are two issues worthy of highlighting here. The first has reference to the place of philosophy in developing an informed mind and a mature judgment. It is noticeable how the scientistic rejection of philosophy is gaining ground. In 2010, Stephen Hawking, in The Grand Design, announced that philosophy was "dead" because it had "not kept up with modern developments in science, particularly physics". A year ago, Lewis Wolpert took the side of scientism when discussing Hawking's views (video here). It is to science leaders like these that Pigliucci's essay is directly relevant. He boldly charges them with anti-intellectualism, because their ideology has made them closed minded about the work of others ploughing in different fields.
"Moreover, it seems clear to me that most of the New Atheists (except for the professional philosophers among them) pontificate about philosophy very likely without having read a single professional paper in that field. If they had, they would have no trouble recognizing philosophy as a distinct (and, I maintain, useful) academic discipline from science: read side by side, science and philosophy papers have precious little to do with each other, in terms not just of style, but of structure, scope, and range of concerns. I would actually go so far as to charge many of the leaders of the New Atheism movement (and, by implication, a good number of their followers) with anti-intellectualism, one mark of which is a lack of respect for the proper significance, value, and methods of another field of intellectual endeavor." (p.152)
The second issue is one where I consider Pigliucci to have underplayed the influence of Darwinism on the rise of atheism. In presenting a historical perspective on atheism, the intellectual leaders are identified as philosophers. This is indicated in the following sentence:
"Even in the twentieth century, that is, before the early twenty-first century advent of New Atheism, the ball was still firmly in the philosophical park when it came to defense of or apologia for atheism: just consider the writings of A. J. Ayer, John Dewey, and, naturally, Bertrand Russell." (p.146)
The impact of Darwin's theory on the acceptance of atheism needs a more thorough discussion than is provided in the paper. Pigliucci does acknowledge that science is not irrelevant to atheism.
"On the contrary, atheism makes increasingly more sense the more science succeeds in explaining the nature of the world in naturalistic terms. After all, Hume's arguments against intelligent design were devastating, but he lacked an alternative explanation for the appearance of design in nature, and it was Darwin that provided it. Indeed, I think the Hume - Darwin joint dispatching of ID is an excellent example of how naturalism - qua philosophical position - is the result of the inextricable link between sound philosophy and good science." (p.152-3)
This quote refers to naturalism rather than atheism, and this is to be commended. Before Darwin, we had the Enlightenment, whereby naturalism replaced Christian Theism as the philosophical stance of scientists. Naturalism led to a wave of religious scepticism - but this was expressed within a Deistic worldview. Most of the Enlightenment scholars were still impressed by the pervasive evidences of design and they reconciled this with naturalism by allowing a creative act at the beginning. However, Darwinism brought immense changes - not to the naturalistic philosophy of science (which was already widespread), but in sweeping away Deism (which was perceived as a god-of-the-gaps blunder). Darwinism then made it possible to be an intellectually-fulfilled atheist, which is what has set Dawkins on his journey to new atheism.
Pigliucci rightly points out that science cannot be extended to cover all aspects of knowledge. However, in calling for a tighter definition of science, he needs to give greater emphasis to the philosophical underpinnings of science. A science that presumes naturalism MUST necessarily end up as an atheistic science. It fails as science because this approach presumes what it then claims science has confirmed. This means that naturalistic science is not objective and is not able to follow the evidence wherever it leads. For example, this is why the advocates of abiogenesis focus their efforts on chemical evolution, as this is the only avenue that naturalistic science permits researchers to follow. Consequently, the information characteristics of life are underplayed and they hope for information to arise by currently unknown emergent processes. The evidence however, points to complex specified information being fundamental to life, which naturalistic science cannot concede. By contrast, theistic science does not prescribe or predetermine outcomes, but it can handle natural processes as well as recognise intelligent agency. We will make progress when multiple working hypotheses can be tested without prescribing philosophical presuppositions for science. This is where education should be heading, not enforcing naturalism as the essence of science.
New Atheism and the Scientistic Turn in the Atheism Movement
Midwest Studies in Philosophy, 37 (1):142-153 (2013)
Abstract: The so-called "New Atheism" is a relatively well-defined, very recent, still unfolding cultural phenomenon with import for public understanding of both science and philosophy. Arguably, the opening salvo of the New Atheists was The End of Faith by Sam Harris, published in 2004, followed in rapid succession by a number of other titles penned by Harris himself, Richard Dawkins, Daniel Dennett, Victor Stenger, and Christopher Hitchens.
Pigliucci, P. On Coyne, Harris, and PZ (with thanks to Dennett), Rationally Speaking (5 February 2014)
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