The Whitewash Continues: Cosmos Conceals the Sources of Scientific Inspiration for Michael Faraday, James Clerk Maxwell
In ENV, Jay Richards opines that "host Neil deGrasse Tyson and the Cosmos producers have enshrouded this basic science with the same materialist narrative we've come to expect. Pre-modern peoples universally see false patterns and portents in the heavens, and invariably see the irregular specter of comets as portents of doom. We get the stereotypical contrast between a "prescientific world ruled by fear" - signaled by a cartoon drawing of a malevolent figure wearing a bishop's miter - and the emergence of modern science, which finally delivered us from such obscurantism."
"This way of framing the history of science, however, requires a great deal of distortion and misrepresentation, especially when it comes to the figure of Isaac Newton. With Newton, the Cosmos writers encountered a dilemma: Either ignore his frankly religious and theistic view of reality, or misrepresent and compartmentalize it. They chose the latter course.
ScienceDaily reports "New findings show that much of the mineral from which bone is made consists of 'goo' trapped between tiny crystals, allowing movement between them. It is this flexibility that stops bones from shattering."
"Latest research shows that the chemical citrate - a by-product of natural cell metabolism - is mixed with water to create a viscous fluid that is trapped between the nano-scale crystals that form our bones. This fluid allows enough movement, or 'slip', between these crystals so that bones are flexible, and don't shatter under pressure. It is the inbuilt shock absorber in bone that, until now, was unknown."
Here is the review of the first episode of Cosmos by Casey Luskin of the Discovery Institute. The next two episodes have not been much better.
"If there was any doubt that the rebooted Cosmos series...would be politically charged and have a materialistic ideological message, consider what viewers saw in its first 60 seconds. The initial opening featured President Obama, with the Presidential Seal in the background, giving a statement endorsing the new series praising "the spirit of discovery that Carl Sagan captured in the original Cosmos." That's not necessarily bad, except for what happened next. Immediately following President Obama's endorsement, the show replayed Carl Sagan's famous materialistic credo from the opening of the original Cosmos series, stating: "The cosmos is all that is, or ever was, or ever will be." Does it violate the separation of church and state for the President of the United States to be portrayed seemingly officially endorsing Sagan's materialistic philosophy? Is this what President Obama intended when he promised in his first inaugural address to "restore science to its rightful place..."
I bought and read "The Explanation for Everything" by Lauren Grodstein a few months ago. I hoped it would be a balanced approach to the debate. I was sorely disappointed.
Now, Kelley J. Unger of Discovery Institute has read the book, and provides a great review: "I've just read a new fiction book that has won praise from critics, Lauren Grodstein's The Explanation for Everything. In the marketing materials provided by Algonquin Books, the author is lauded for not taking sides in the evolution debate. She says herself that she wants to "figure out why people believe what they believe." But as one reads the book it's evident that she is indeed taking sides, doesn't fully develop why her characters believe what they believe, and certainly hasn't fully investigated the theory of intelligent design."
In this post in Uncommon Descent I (Eric Anderson) want to consider a fundamental aspect of intelligent design theory: the concept of "information'.
This is centrally relevant to the intelligent design concept of "complex specified information". Attempts have been made by ID critics to derail ID by critiquing each of these three words: complexity, specification and information. Indeed, it is not uncommon to see long, drawn-out, battles over these terms in an attempt to avoid getting to the central issue of whether design can be detected.
In ENV, Casey Luskin writes that..."Jerry Coyne is playing more games, constantly pretending that we have "admitted" intelligent design is religious when we criticize Ball State University (BSU) for being "anti-religious." In his post, Coyne was responding to a letter I published in the Muncie Star Press explaining the anti-religious nature of the book What's Your Dangerous Idea?."
A branching pattern of variation was central to Darwin's concept of speciation. As one population of organisms follows one trajectory, another population may spin off in a different direction. When they are sufficiently far apart, they are considered to be separate species. The Galapagos finches have been regarded as exemplars of Darwinian transformation, even leading to the claim that one newly developed population is "behaving as a separate species". However, the most recent study, from one of the smaller islands (Floreana), concludes that the most likely cause of the disappearance of one of these species is hybridization.
"The authors suggest that hybridization may have been responsible for the disappearance of the large tree finch from Floreana, and that it may now be causing the remaining two species to fuse into one: speciation in reverse." (p.179)
Small Tree Finch (C. parvulus) from Floreana, about 4 years old. (Credit: Jeremy Robertson, source here)
Until recently, three species of tree finch were known from Floreana Island. Morphological differences noted were limited to body size and beak dimensions. Their names are the small tree finch, the medium tree finch, and the large tree finch. They are found living together in several other Galapagos islands. Now Kleindorfer and colleagues report that the large tree finch has disappeared from Floreana. The remaining two species are affected by hybridization.
"The analyses also revealed that individuals that do not fit into either population show intermediate characteristics, suggesting that they are hybrids. Consistent with the hypothesis of ongoing hybridization on the island, the authors observed females of the morphologically larger group (the medium tree finch) pairing with males of the smaller group, and they identified 15% of yearling males in 2010 as hybrids." (p.170)
Most of the researchers appear to think that their studies are probing the essence of speciation, and are providing the empirical evidence that supports the Darwinist claim that natural selection acting on inheritable variation is the key to understanding the origin of species. Peter and Rosemary Grant say that these studies are "Uniquely valuable in showing how speciation is done" (p.179). Kleindorfer et al. say that research programmes over "the past 2 decades have transformed our understanding of the ecological context of processes that underpin speciation" (p.325). With specific reference to the new findings, they write:
"The results presented here go to the heart of evolutionary biology: by what criteria do we denote species, and by what criteria do new species form or collapse? Here we present evidence that three sympatric species of Darwin's tree finches in the 1900s have collapsed, under conditions of hybridization, into two species by the 2000s. The proportion of yearling hybrid birds increased from 0% in 2005 to 14.6% in 2010, indicating a potential for elevated hybrid fitness in this system. [. . .] There is widespread agreement that the benefits of hybridization include increased genetic variance that facilitates novel evolutionary trajectories in changing environments." (p.334)
Whilst the new research is a useful contribution to knowledge, the results do not go to "the heart of evolutionary biology". The reason is that the important questions to do with diversity in the living world relate to the origin of biological information. What factors and processes are relevant to building novelty and complexity? The finches of Floreana Island are distinguished by very minor morphological differences, and the observed changes tell us nothing about the origin of new biological information.
Please can we have some realism from researchers adhering to the Darwinian paradigm. In the main, their research findings cast light on ecology but they are failing to touch the real challenges facing evolutionary biology. This assessment of their work is now appearing in mainstream peer-reviewed literature and in articles written by influential scientists. Here is a comment from Professor John Dupre, who is Director of the ESRC Center for Genomics in Society, University of Exeter.
"Further destabilizing evolutionary theory is the growing realization that many factors, not just the genome, determine an individual organism's development. Ironically, as the discovery of DNA's structure - initially lauded as the final act in the triumph of the new synthesis - led to a better understanding of genomes' functioning, it ended up weakening belief in their unique role in directing biological development. Those who long deplored the omission of development from evolutionary models - a decades-old critique made under the scientific banner of evolutionary developmental biology ("evo-devo") - together with the insistence that organisms' development draws on a wide variety of resources, have been vindicated.
"Recent developments in molecular biology have put the final nail in the coffin of traditional genetic determinism. For example, epigenetics - the study of heritable modifications of the genome that do not involve alterations to the genetic code - is on the rise. And the many kinds of small RNA molecules are increasingly recognized as forming a regulatory layer above the genome.
"Beyond undermining the gene-centered theories of evolution that have dominated public consciousness for several decades, these developments call for new philosophical frameworks. Traditional reductionist views of science, with their focus on "bottom-up" mechanisms, do not suffice in the quest to understand top-down and circular causality and a world of nested processes." (Source here. Related comments are here)
Of the greatest urgency is attention to educational textbooks. For too long, the Darwinists have maintained a hegemony that resists all critiques of their arguments. Typically, they present any questioning of their interpretation of the evidence as religiously motivated and anti-science. For the good of science, this situation has to change.
Species Collapse via Hybridization in Darwin's Tree Finches
Sonia Kleindorfer, Jody A. O'Connor, Rachael Y. Dudaniec, Steven A. Myers, Jeremy Robertson, and Frank J. Sulloway
The American Naturalist, Vol. 183, No. 3, March 2014, 325-341.
Abstract: Species hybridization can lead to fitness costs, species collapse, and novel evolutionary trajectories in changing environments. Hybridization is predicted to be more common when environmental conditions change rapidly. Here, we test patterns of hybridization in three sympatric tree finch species (small tree finch Camarhynchus parvulus, medium tree finch Camarhynchus pauper, and large tree finch: Camarhynchus psittacula) that are currently recognized on Floreana Island, Galapagos Archipelago. Genetic analysis of microsatellite data from contemporary samples showed two genetic populations and one hybrid cluster in both 2005 and 2010; hybrid individuals were derived from genetic population 1 (small morph) and genetic population 2 (large morph). Females of the large and rare species were more likely to pair with males of the small common species. Finch populations differed in morphology in 1852?1906 compared with 2005/2010. An unsupervised clustering method showed (a) support for three morphological clusters in the historical tree finch sample (1852?1906), which is consistent with current species recognition; (b) support for two or three morphological clusters in 2005 with some (19%) hybridization; and (c) support for just two morphological clusters in 2010 with frequent (41%) hybridization. We discuss these findings in relation to species demarcations of Camarhynchus tree finches on Floreana Island.
Peter R. Grant & B. Rosemary Grant
Nature, 507, 178-179 (13 March 2014) | doi:10.1038/507178b
Hybridization can cause two species to fuse into a single population. New observations suggest that two species of Darwin's finches are hybridizing on a Galapagos island, and that a third one has disappeared through interbreeding.
At ENV, there will be more to say about Seth MacFarlane's revival of the Carl Sagan vehicle for scientific materialism after we've seen it. In the meantime, you may wish to have access to the antidote handy before grappling with the ailment itself.
For that, you couldn't do better than Illustra Media's series of stunning video documentaries on the theme of intelligent design in cosmology and biology. Most of these are actually viewable immediately as Amazon instant videos. The single most relevant film is The Privileged Planet, but don't forget The Case for a Creator, Darwin's Dilemma, Unlocking the Mystery of Life, Flight and Metamorphosis. Find them on the Illustra website or, on Amazon.
In an Evolution News & Views...In case you had any uncertainty about the upcoming 13-part Cosmos series, a revival of the Carl Sagan franchise, executive producer Seth MacFarlane has Darwin skeptics and alternatives to Darwinian evolution very much in his crosshairs. This is a major and costly project, though Fox won't say how costly - so it's flattering in a way. In an interview in the Los Angeles Times, MacFarlane says:
We've had a resurgence of creationism and intelligent design quote-unquote theory. There's been a real vacuum when it comes to science education. The nice thing about this show is that I think that it does what the original "Cosmos" did and presents it in such a flashy, entertaining way that, as Carl Sagan put it in 1980, even people who have no interest in science will watch just because it's a spectacle. People who watched the original "Cosmos" will sit down and watch with their kids.
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.