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.
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)
Redundancy in the genetic code has long been recognised. Most amino acids can be specified in multiple ways (2-6 synonymous codons). More recently, it has also become known that synonymous codons are non-random, stimulating thought as to why this should be (see here). Since codon usage biases characterise both prokaryotic and eukaryotic genomes, is it possible that they are accidents of evolutionary history? This seems to be ruled out by pervasive evidences of conservation. Since the biases are not removed by mutations, it is inferred that "observed codon preferences in mammalian genomes [. . .] appear to be under selection" (p.1367.) Such a conclusion is reached by deduction from evolutionary theory. If specific (synonymous) codons do not matter when manufacturing proteins, is it possible they are relevant to the regulation of genetic processes? Since there is a presumption favouring simplicity in the minds of most geneticists, this research question has only recently been taken up. There are many synonymous codons when coding for proteins, but are they synonymous if they are also coding regulatory instructions?
"Genomes also contain a parallel regulatory code specifying recognition sequences for transcription factors (TFs), and the genetic and regulatory codes have been assumed to operate independently of one another and to be segregated physically into the coding and noncoding genomic compartments. However, the potential for some coding exons to accommodate transcriptional enhancers or splicing signals has long been recognized." (p.1367)
The challenge of the Human Genome Project has given way to searching for an understanding of multiple overlapping genetic codes. (source here)
With the availability of large amounts of genome data, it is possible to test many hypotheses relevant to the functionality of DNA sequences. The data set used is impressive:
"To define intersections between the regulatory and genetic codes, we generated nucleotideresolution maps of TF occupancy in 81 diverse human cell types using genomic deoxyribonuclease I (DNaseI) footprinting. Collectively, we defined 11,598,043 distinct 6- to 40-base pair (bp) footprints genome-wide (~1,018,514 per cell type), 216,304 of which localized completely within protein-coding exons (~24,842 per cell type). Approximately 14% of all human coding bases contact a TF in at least one cell type (average 1.1% per cell type), and 86.9% of genes contained coding TF footprints (average 33% per cell type)." (p.1367)
A summary of the main findings of the research team is provided in a Perspectives essay by Weatheritt and Babu. The hypothesis of two co-existing codes is fully justified by the evidence. According to the press release: "scientists were stunned to discover that genomes use the genetic code to write two separate languages."
"How widespread is the phenomenon of "regulatory" codes that overlap the genetic code, and how do they constrain the evolution of protein sequences? Stergachis et al. address these questions for the transcription factor-binding regulatory code. They use deoxyribonuclease I (DNase I) footprinting to map transcription factor occupancy (a protein bound to DNA can protect that region from enzymatic cleavage) at nucleotide resolution across the human genome in 81 diverse cell types. The authors determined that ~14% of the codons within 86.9% of human genes are occupied by transcription factors. Such regions, called "duons", therefore encode two types of information: one that is interpreted by the genetic code to make proteins and the other, by the transcription factor-binding regulatory code to influence gene expression. This requirement for transcription factors to bind within protein-coding regions of the genome has led to a considerable bias in codon usage and choice of amino acids, in a manner that is constrained by the binding motif of each transcription factor." (p.1325)
Weatheritt and Babu go further. They suggest a general principle: that redundancy in the genetic code opens the door for, not one, but many regulatory codes that can operate within protein-coding regions of the genome. One research question of the future is: how many overlapping codes can be tolerated by the genetic code?
"This "binding" code joins other "regulatory" codes that govern chromatin organization, enhancers, mRNA structure, mRNA splicing, microRNA target sites, translational efficiency, and cotranslational folding, all of which have been proposed to constrain codon choice, and thus protein evolution." (p.1325)
It should be noted that these research findings do not tell us what binding a transcription factor actually achieves. The field of gene regulation is in its infancy. The research team notes that TF binding "may serve multiple functional roles" but that their analysis is "agnostic" to this functionality. Weatheritt and Babu conclude:
"The investigation of overlapping codes opens new vistas on the functional interpretation of variation in coding regions and makes it clear that the story of the genetic code has not yet run its course." (p.1326)
This discussion of genetic codes is only meaningful if it is recognised that the genome is a carrier of complex specified information. The essence of life is not to be found in chemistry, but in the information carried within the cell. Chemicals are used to carry biological information, but the chemicals are not themselves information. The research team recognises this when they say:
"Our results indicate that simultaneous encoding of amino acid and regulatory information within exons is a major functional feature of complex genomes. The information architecture of the received genetic code is optimized for superimposition of additional information and this intrinsic flexibility has been extensively exploited by natural selection." (p.1371-2)
There is a problem with the last few words of the above quotation. The flexible information architecture is said to be exploited "by natural selection", yet this claim has not emerged from a study of evidences. Rather, the theoretical framework of neo-Darwinism provides the context for interpreting the evidences, so that all signs of complexity and functionality are automatically associated with the operation of natural selection. Yet, we have no evidence to show that natural selection can either produce or refine complex specified biological information.
There is a perfectly viable alternative hypothesis to consider: that biological information is evidence for intelligent agency. The evidence we have already about the genetic code is sufficient to make the point, but new evidences of overlapping codes add weight to the hypothesis. The genetic code with redundancy overlaps with other regulatory codes in ways that test the ability of molecular biologists (intelligent agents) to understand what's happening, let alone write overlapping codes of their own as a biomimetic exercise. From time to time, leading biologists get the message, but seem at a loss to drive it forward.
"Any living being possesses an enormous amount of "intelligence", very much more than is necessary to build the most magnificent of cathedrals. Today, this "intelligence" is called "information", but it is still the same thing. It is not programmed as in a computer, but rather it is condensed on a molecular scale in the chromosomal DNA or in that of any other organelle in each cell. This "intelligence" is the sine qua non of life. If absent, no living being is imaginable. Where does it come from? This is a problem which concerns both biologists and philosophers and, at present, science seems incapable of solving it." Pierre Grasse, Evolution of Living Organisms: Evidence for a New Theory of Transformation, (New York: Academic Press, 1977, 2).
The decision to endorse a naturalistic explanation rather than advance agnosticism about the origins of hidden overlapping codes is a pointer to hidden ideologies in origins-science. It seems that as long as materialism/naturalism is presumed, then a great number of unwarranted assertions (usually linked to Darwinism or abiogenesis) go unchallenged in academic papers. As soon as it is pointed out that only intelligent agents write codes, there is an outcry that science is being subverted by religious fundamentalists. However, the converse is true: intelligent design theory is based on the evidence of complex specified information. The evidences for naturalistic alternatives all evaporate under close scrutiny.
Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
Andrew B. Stergachis, Eric Haugen, Anthony Shafer, Wenqing Fu, Benjamin Vernot, Alex Reynolds, Anthony Raubitschek, Steven Ziegler, Emily M. LeProust, Joshua M. Akey and John A. Stamatoyannopoulos.
Science, 13 December 2013, 342, 1367-1372 | DOI:10.1126/science.1243490 [pdf here]
Abstract: Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons ("duons") that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.
Weatheritt, R.J. and Babu, M, M. The Hidden Codes That Shape Protein Evolution,
Science, 13 December 2013, 342, 1325-1326 | DOI: 10.1126/science.1248425
Klinghoffer, D. Genome Uses Two Languages Simultaneously; Try That Yourself Sometime, Why Don't You, Evolution News & Views (December 13, 2013)
Luskin, C. Codes Within Codes: How Dual-Use Codons Challenge Statistical Methods for Inferring Natural Selection, Evolution News & Views (December 20, 2013)
Quantum phenomena in biology are receiving the attention of more and more researchers, with photosynthesis being the process getting the most attention. Back in 2007, it was apparent that quantum effects were effective for "explaining the extreme efficiency of photosynthesis". Then, in 2010, the photosynthetic apparatus of cryptophyte algae was the focus of research, because its pigments are farther apart than was expected for efficient functioning. In a News & Views article in Nature, van Grondelle & Novoderezhkin discussed evidence suggesting that a process known as quantum coherence is part of the explanation. They added: "This is the first time that this phenomenon has been observed in photosynthetic proteins at room temperature, rather than at much lower temperatures, bolstering the idea that quantum coherence influences light harvesting in vivo." The most recent study has provided a theoretical argument that quantum effects must be present and that classical physics does not provide an explanation. It is claimed to be "the first unambiguous theoretical evidence of quantum effects in photosynthesis". The Press Release describes the work in this way:
"Often, to observe or exploit quantum mechanical phenomena, systems need to be cooled to very low temperatures. This however does not seem to be the case in some biological systems, which display quantum properties even at ambient temperatures. Now, a team at UCL have attempted to identify features in these biological systems which can only be predicted by quantum physics, and for which no classical analogues exist. "Energy transfer in light-harvesting macromolecules is assisted by specific vibrational motions of the chromophores," said Alexandra Olaya-Castro (UCL Physics & Astronomy), supervisor and co-author of the research. "We found that the properties of some of the chromophore vibrations that assist energy transfer during photosynthesis can never be described with classical laws, and moreover, this non-classical behaviour enhances the efficiency of the energy transfer."" (Source here)
New frontiers for understanding the natural world (image source here)
Most light-gathering macromolecules are composed of chromophores (the light-absorbing pigments) attached to proteins. These are responsible for the first step of photosynthesis, which is to capture light and transfer its energy to another system that can store it. Earlier work showed that energy is transferred in a wave-like manner (the quantum coherence model). However, theoreticians were of the opinion that classical physics could still find a way of explaining the observations.
"Molecular vibrations are periodic motions of the atoms in a molecule, like the motion of a mass attached to a spring. When the energy of a collective vibration of two chromophores matches the energy difference between the electronic transitions of these chromophores a resonance occurs and efficient energy exchange between electronic and vibrational degrees of freedom takes place. Providing that the energy associated to the vibration is higher than the temperature scale, only a discrete unit or quantum of energy is exchanged. Consequently, as energy is transferred from one chromophore to the other, the collective vibration displays properties that have no classical counterpart. The UCL team found the unambiguous signature of non-classicality is given by a negative joint probability of finding the chromophores with certain relative positions and momenta. In classical physics, probability distributions are always positive." (Source here)
Bear in mind that considerable resources have already been spent on trying to develop a biomimetic system that captures solar energy like plants - only to find that photosynthesis is extraordinarily complex and the research has not yet delivered any commercial outputs. It is a reminder that the Darwinian vision of ultimate simplicity has been repeatedly falsified. Photosynthesising microorganisms are among the earliest to appear in the Precambrian fossil record - and yet these organisms have chemical and physical pathways that are only beginning to be understood within the research community. What is emerging are processes and structures that carry the hallmarks of design, with complex specified information at every level of analysis. We are at the beginning of a journey into quantum effects in biology. It is the design paradigm that is best equipped to guide our thoughts and keep us on the right path.
"Other biomolecular processes such as the transfer of electrons within macromolecules (like in reaction centres in photosynthetic systems), the structural change of a chromophore upon absorption of photons (like in vision processes) or the recognition of a molecule by another (as in olfaction processes), are influenced by specific vibrational motions. The results of this research therefore suggest that a closer examination of the vibrational dynamics involved in these processes could provide other biological prototypes exploiting truly non-classical phenomena." (Source here)
Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature
Edward J. O'Reilly & Alexandra Olaya-Castro
Nature Communications, 9 January 2014, 5, Article number:3012 | doi:10.1038/ncomms4012
Abstract: Advancing the debate on quantum effects in light-initiated reactions in biology requires clear identification of non-classical features that these processes can exhibit and utilize. Here we show that in prototype dimers present in a variety of photosynthetic antennae, efficient vibration-assisted energy transfer in the sub-picosecond timescale and at room temperature can manifest and benefit from non-classical fluctuations of collective pigment motions. Non-classicality of initially thermalized vibrations is induced via coherent exciton-vibration interactions and is unambiguously indicated by negativities in the phase-space quasi-probability distribution of the effective collective mode coupled to the electronic dynamics. These quantum effects can be prompted upon incoherent input of excitation. Our results therefore suggest that investigation of the non-classical properties of vibrational motions assisting excitation and charge transport, photoreception and chemical sensing processes could be a touchstone for revealing a role for non-trivial quantum phenomena in biology.
Cartwright, J. Quantized vibrations are essential to photosynthesis, say physicists, physicsworld.com (22 January 2014)
Tyler, D. Explaining the extreme efficiency of photosynthesis. ARN Literature Blog (16 April 2007)
Tyler, D. The latest thinking on how photosynthesis evolved. ARN Literature Blog (11 February 2007)
There are two competing paradigms about Neanderthal capabilities and culture. The first considers Neanderthals to be cognitively inflexible, with a limited use of technologies that was unresponsive to environmental change. The second recognises a much wider range of behaviours and technologies, with adaptation to specific local conditions. The paper considered in this blog belongs to the second of these perspectives: the reported work considers artefacts from a cave that was occupied by Neanderthals and dated about 90,000 years ago.
"Here, we present evidence for behavioral variability and complexity among Neanderthals at the beginning of Marine Isotope Stage 4 (MIS 4) at the Abri du Maras located above the Ardeche River in southern France. Using residue analysis of stone tools with supporting evidence from zooarchaeology, we show that Neanderthals at the Abri du Maras had a detailed knowledge of their surrounding environment, captured fast and agile prey (rabbits, fish and birds), exploited a range of plant species, and used composite technology such as hafted stone points and the manufacture of string and cordage. Overall, we present evidence which demonstrates that Neanderthals at the Abri du Maras were far from inefficient foragers." (p.24)
Not just a pretty face (Image: Nikola Solic/Reuters, source here))
Many flake stone tools have been recovered. Microscopic examination of their surfaces has revealed a remarkable variety of traces providing clues about Neanderthal capabilities and lifestyle. The most noteworthy relates to tiny fragments of twisted plant fibres. This is considered to be evidence for human activity: gathering plant material, retting or shredding to extract fibres, twisting to create threads or string, and cutting a length with the stone tools.
"These fibers are not twisted in their natural state which suggests that they were twisted by the inhabitants of the Abri du Maras and may therefore provide evidence of the manufacture of string or cordage. In previous woodworking experiments involving incising, planning, whittling, scraping, and boring, no twisted fibers were observed. Unpublished experiments conducted by BH involving the scraping, cutting, and slicing of a variety of nonwoody plants (roots, tubers, reeds, etc.) also produced no twisted fibers such as those observed here. While not definitive, the lack of twisted fibers in these experiments lends some credence to the hypothesis that these derive from cordage. Future experiments involving cordage and plant processing will help clarify the potential sources of twisted fiber." (p.27,29)
Circumstantial evidence is provided by observations of micro-wear of flake tools that show indications of being hafted to produce stone-tipped javelins. Other uses for string can be inferred because there is evidence at this site that Neanderthals went fishing and at other sites that they crossed open water in boats.
"Since macroscopic remains have not been found prior to 19 ka, it is important to examine other less direct forms of evidence where fiber or string production may leave traces on a microscopic level which may be visible through use-wear and residue analyses. For most of the Paleolithic, the best potential source of evidence for cordage is stone tools. Hurcombe (1998) describes several different points in the chaine operatoire of fiber production where stone tools are likely to be used, including plant harvesting, processing of fibers, and cutting loose ends from cordage.
The production of string along with simple knowledge of knotting, weaving, and looping, make possible a wide range of products including "nets, containers, packaging, baskets, carrying devices, ties, straps, harness, clothes, shoes, beds, bedding, mats, flooring, roofing and walling". In addition, string facilitates the construction of complex, multi-component technologies such as hafts or snares. Finally, string would have been essential for seafaring, maritime technologies used for the colonization of islands, and for many types of fishing." (p.34)
We cannot consider all the evidences discussed by the authors. However, they make an interesting comment on how expectations (influenced by presuppositions) affect research programmes.
"Paleolithic archaeologists have a tendency to focus heavily on reconstructing subsistence activities. Within subsistence, the focus is primarily on animals with even more narrow focus on large animals, partly because their remains preserve better. This focus is justified to some extent as archeologists can only work with the evidence they find. However, this means we are missing a huge component of everyday life. The preservation bias of the archaeological record limits the avenues being investigated. The fiber evidence presented here is a reminder that if we don?t look for it, we won?t find it." (p.35)
We shall pass over much interesting discussion of evidences and reach their conclusion. The authors have used their detective skills to reconstruct a community of Neanderthals that appears to be indistinguishable from modern humans.
"The Abri du Maras overlooks the Ardeche River in south-eastern France. The combination of analyses presented here (mainly residue analysis) has provided a more detailed view into Neanderthal lives than is generally possible. Neanderthals at the Abri du Maras caught and consumed a wide variety of foods, from large herbivores to rabbits, fish, plants, and possibly birds. The occupants of the Abri du Maras may have also been engaged in a variety of other activities: gathering mushrooms, gathering raw materials and manufacturing string, woodworking, constructing composite technologies such as complex projectiles and possibly nets or traps. Given the wide variety of resources exploited at the Abri du Maras, we should heed Hockett's recent caution that we may have "under-appreciated the amount of non-mammal foods eaten by Neanderthals". We would add that the high diversity of resources used by Neanderthals has been generally under-appreciated for decades." (p.38)
This fascinating insight into community life is worthy of our attention because the group members were Neanderthals. For too long, they have been portrayed as pre-human and have been used to buttress evolutionary stories about the origins of mankind. However, archaeological evidence discussed here (and here) suggests that these stories are embellished with evolutionary spin. The evidence shows that Neanderthals are human cousins and deserve quite a different place in history. Unfortunately, this truth about Neanderthals has been missed in the past because the presumption of evolutionary transformation has constrained the minds of researchers. They illustrate the maxim: "if we don't look for it, we won't find it."
Another recent finding that is related to this theme is that a Neanderthal community in Italy organised their cave in a way that is recognisably human. The punchline is the same: here are "close cousins" that do not deserve to be called pre-human.
"Scientists have found that Neanderthals organized their living spaces in ways that would be familiar to modern humans, a discovery that once again shows similarities between these two close cousins. The findings, published in the latest edition of the Canadian Journal of Archaeology, indicate that Neanderthals butchered animals, made tools and gathered round the fire in different parts of their shelters. "There has been this idea that Neanderthals did not have an organized use of space, something that has always been attributed to humans," said Julien Riel-Salvatore, assistant professor of anthropology at the University of Colorado Denver and lead author of the study. "But we found that Neanderthals did not just throw their stuff everywhere but in fact were organized and purposeful when it came to domestic space." [snip] "This is still more evidence that they were more sophisticated than many have given them credit for. If we are going to identify modern human behavior on the basis of organized spatial patterns, then you have to extend it to Neanderthals as well." (source here).
Impossible Neanderthals? Making string, throwing projectiles and catching small game during Marine Isotope Stage 4 (Abri du Maras, France)
Bruce L. Hardy, Marie-Helene Moncel, Camille Daujeard, Paul Fernandes, Philippe Bearez, Emmanuel Desclaux, Maria Gema Chacon Navarro, Simon Puaud, Rosalia Gallotti
Quaternary Science Reviews, Volume 82, 15 December 2013, Pages 23?40
Abstract: Neanderthal behavior is often described in one of two contradictory ways: 1) Neanderthals were behaviorally inflexible and specialized in large game hunting or 2) Neanderthals exhibited a wide range of behaviors and exploited a wide range of resources including plants and small, fast game. Using stone tool residue analysis with supporting information from zooarchaeology, we provide evidence that at the Abri du Maras, Ardeche, France, Neanderthals were behaviorally flexible at the beginning of MIS 4. Here, Neanderthals exploited a wide range of resources including large mammals, fish, ducks, raptors, rabbits, mushrooms, plants, and wood. Twisted fibers on stone tools provide evidence of making string or cordage. Using a variety of lines of evidence, we show the presence of stone projectile tips, possibly used in complex projectile technology. This evidence shows a level of behavioral variability that is often denied to Neanderthals. Furthermore, it sheds light on perishable materials and resources that are not often recovered which should be considered more fully in reconstructions of Neanderthal behavior.
A Spatial Analysis of the Late Mousterian Levels of Riparo Bombrini (Balzi Rossi, Italy)
Julien Riel-Salvatore, Ingrid C. Ludeke, Fabio Negrino, and Brigitte M. Holt
Canadian Journal of Archaeology, 37(1), 70-92 (2013)
Abstract: We present a preliminary analysis of the spatial distribution of various artifact classes in the Late Mousterian levels of Riparo Bombrini (northwest Italy). This work shows the presence of a consistent gap in artifacts across all levels, which is interpreted as reflecting the position of the dripline prior to the shelter's collapse. Hearths are identified in levels M1-3, M4 and M5, and their position at the back of the shelter is similar to that of "sleeping hearths" identified at other Mousterian sites. Lastly, the distribution of artifacts is shown to co-vary with the nature of the prevalent mobility strategies in use at different times over the site's occupational history. Notably, use of the site as a logistical base camp is correlated with the presence of hearths and the accumulation of noisome debris beyond the dripline and outside of the shelter. Other uses of the site seem to have favored the discard of some classes of artifacts within the shelter itself. This shows that Neanderthals were indeed able to organize their use of space in patterned and somewhat predictable manners, and that the length and nature of their occupation of the rockshelter need to be taken into account in such analyses.
Earlier this year, in March, Nature reported that soft-bodied worms from the Burgess Shale fossil beds in Canada, given the name Spartobranchus tenuis, have been identified as ancient examples of acorn worms. They were hailed as a "missing link" in the vertebrate family tree: "a crucial evolutionary link between two distinct living groups of animals: enteropneusts and pterobranchs." The evidence supporting this was said to be the tubes constructed by Spartobranchus tenuis. Living enteropneusts (acorn worms) do not have tubes, whereas living pterobranchs (minute colonial organisms) do. Professor Simon Conway Morris affirmed the significance of the newly discovered fossil tubes with these words: "By finding enteropneusts in tubes we begin to bridge this evolutionary gap." At the time, these issues were discussed in a blog here, and questions were raised about the evolutionary narrative. More now needs to be said, as a recent paper in Nature Communications has documented modern tube-forming acorn worms found in Antarctic benthic communities.
Figure 1b: Large purple morphotype in secreted tube with proboscis expanded. (Source here)
Recent work surveying life in ocean basins has identified a new family of deep-sea enteropneusts, the Torquaratoridae. During oceanographic cruises in the Antarctic, between 2008 and 2013, two new enteropneusts were discovered at depths ranging from 531 to 1,111m. These species secrete translucent tubes in which they live, although they have also been observed abandoning their tubes. The authors recognize that their discovery is directly relevant to the interpretation of the Burgess Shale worm tubes. This is their discussion:
"Foremost, our discovery provides context for the recently re-described Middle Cambrian fossils, S. tenuis from the Burgess Shale Formation. These acorn worm fossils look remarkably like present-day enteropneusts, except many are observed to be within a 'fiberous' tube. The persistence of tubes in Antarctic worms suggests that the tubes contain proteinaceous components functioning as binding agents. Some tubes were lightly covered with sediment giving them a 'ribbed' appearance, similar to those reported for S. tenuis. [. . .] Our observations of Antarctic tubicolous worms and faecal casings imply that the worms often turn and zigzag during movement or may even double back on themselves as reported elsewhere. If buried quickly in a single obtrusion event, as suspected for each of the mudstone beds of the Greater Phyllopod Bed (that is, Walcott's quarry), such tubes could appear helical or even circular as reported for S. tenuis [. . .]. The fossil tubes were interpreted as 'fiberous' based on apparent tearing of the tubes, but a similar phenomenon occurs with the present-day tubes. Given the similarity in tube design between S. tenuis and the Antarctic torquaratorids, similar behavioural repertoires (for example, tube building, vacating tubes and meandering epibenthic movements) appear to have been conserved ~500 million years."
So, the discovery of modern tube-forming acorn worms has assisted the interpretation of the fossil tubes: the fibrous texture is an artifact of preservation and not part of the constructed tube, and the doughnut shapes are likely to be formed by a rapid depositional process and is not representative of the original structure in life. The evidence we have is of stasis in behavioral repertoires as well as in morphology.
This leads to a rather different conclusion about the implications for evolutionary theory. The idea that S. tenuis is a link between the enteropneusts and the pterobranchs lacks credibility. The argument is explained very clearly in the research paper:
"Fossil evidence reveals that graptolites, and even rhabopleurids and cephalodiscids (modern pterobranch lineages), were present in the Middle Cambrian, making S. tenuis contemporary with established pterobranch (including graptolite) lineages. As the split between enteropneust and pterobranch lineages would have been before the Middle Cambrian, the tube of S. tenuis was not a precursor to the pterobranch coenecium. Lack of synapticulae and hepatic sacs were also argued to ally S. tenuis with harrimaniid enteropneusts. However, torquaratorid enteropneusts, like harrimaniids, lack synapticles, and assessing the presence of hepatic sacs often requires microscopy in modern species, much less in fossilized ones. Given the position of torquaratorids and pterobranchs in hemichordate phylogeny, the last common hemichordate ancestor may have been able to build tubes, raising the question whether this ability was present in the last common deuterostome ancestor."
The implication is that the last common hemichordate ancestor lived before the Middle Cambrian and should be located before the Cambrian Explosion. The problem for this hypothesis is that there is a paucity of fossil data: we do not have anything other than speculation for hypothetical ancestors of the animal phyla. Instead of evolutionary theory having anchors in fossil evidence about the past, the Precambrian is effectively a blank sheet where inferences are drawn from selected phylogenetic data and produce conflicting evolutionary trees.
There is a pattern in the way fossil discoveries are reported. If they are deemed to fill in the gaps in a branch of the evolutionary tree, they generally get massive exposure and are hailed as milestones in developing an understanding of life on Earth. However, when new data comes to light that shows the original thinking to be wrong, the exposure is far less and the media show little interest. With acorn worms, we have a case to reflect on worthy of our time. The message we should be taking away is that the fossil record brings us evidence of stasis, not evolutionary transformation. We need a radical rethink of the presuppositions we bring to the story of life on Earth, because the present hegemony of Darwinism has no adequate explanation for the origin of biological information.
Modern Antarctic acorn worms form tubes
Kenneth M. Halanych, Johanna T. Cannon, Andrew R. Mahon, Billie J. Swalla and Craig R. Smith
Nature Communications, 4, No. 2738, 07 November 2013 | doi: 10.1038/ncomms3738
Abstract: Acorn worms, or enteropneusts, are vermiform hemichordates that occupy an important position in deuterostome phylogeny. Allied to pterobranch hemichordates, small colonial tube dwellers, modern enteropneusts were thought to be tubeless. However, understanding of hemichordate diversity is poor, as evidenced by absence of reports from some oceanic regions and recent descriptions of large epibenthic deep-water enteropneusts, Torquaratoridae. Here we show, based on expeditions to Antarctica, that some acorn worms produce conspicuous tubes that persist for days. Interestingly, recent fossil descriptions show a Middle Cambrian acorn worm lived in tubes, leading to speculation that these fossils may have been pterobranch forbearers. Our discovery provides the alternative interpretation that these fossils are similar to modern-day torquaratorids and that some behaviours have been conserved for over 500 million years. Moreover, the frequency of Antarctic enteropneusts observed attests to our limited knowledge of Antarctic marine ecosystems, and strengthens hypotheses relating more northern deep-sea fauna to Antarctic shelf fauna.
Birchfield, C. Auburn University researchers make deep sea creature discovery and set sail for Antarctica, Auburn University News, 20 November 2013.
Whether you are a diver, a geologist, or simply someone with an interest in natural history, you are likely to have a misconception about the structure of coral reefs. The error is ubiquitous in textbooks and is reinforced by media treatments of the topic. Everyone 'knows' that coral reefs have a central zone of organically bound material (the reef core), a leeward zone of flat lying sediments (the back-reef lagoonal area) and a seaward zone of steeply-dipping rubble (the reef talus). The misconception relates to the reef talus. The source of the erroneous view can be traced to Charles Darwin, who sought to follow his mentor (Charles Lyell) in explaining the past by reference to present-day processes.
"Darwin and his many followers regarded contemporary reefs as having shelf-like forms, with steep slopes facing deep water. This morphology differentiates the familiar zones of backreef, reef-crest and fore-reef. Most accounts emphasize the importance of the reef-crest, comprising the growth framework responsible for generating the reef structure. Material eroded from both the reef-crest and the upper reef-slope has been assumed to accumulate on the fore-reef, and it was argued that this provided the foundations that enabled construction to take place in waters that were otherwise too deep. This pervasive idea can be traced to Darwin (1842) and Dana (1853), although it typically only applies to windward, moderately high hydrodynamic energy, regimes. However, numerous conceptual models illustrate reefs in which the fore-reef is shown as a steep debris slope, on which depositional increments are correlated with contemporary intervals of reef growth." (from the Introduction).
An example of an educational graphic showing the fore-reef talus. (Source here)
This understanding of the fore-reef debris slope as talus is described as a "misconception", an "error", a "misleading description" - yet it has achieved widespread acceptance and is regarded as the "traditional" view and a "cherished model". This should be regarded as another example of 'consensus' thinking that owes more to the naive acceptance of Lyellian uniformitarianism than to science. We have Colin Braithwaite to thank for showing that the research findings over the past 30+ years demonstrate clearly that the textbook interpretations of "reef talus" need to be revised. After reviewing numerous papers, he writes:
"What conclusions, vis a vis Darwin's model and "talus slopes", can be drawn from these observations? Early descriptions of reefs by Darwin and others paved the way for an interpretation linking the morphology of 'the reef' to erosion and the formation of coarse debris, 'reef talus', commonly regarded as integral to conceptual models of ancient reefs. However, research over the past decades has shown that present-day processes, that include storm events at the high end of the energy spectrum, are important contributors to reef debris but do not generate large volumes of coarse debris on fore-reef slopes. Although reef erosion is a reality, transport directions generally preclude its involvement in large-scale talus formation. Neither off-reef flow nor large-scale slope failure generates debris on the reef front in the size ranges typically described as "talus"." (From the Conclusions)
Evidence amassed by Braithwaite explains that "reef talus" is a misnomer. In the main, it is not rubble from the reef core that has moved down the steeply-dipping fore-reef slope. The evidence shows that most of the reef debris caused by hurricanes and storms is moved in the other direction - into the back-reef lagoon. The mechanism is understood in this way:
"Why does such transport occur? It reflects wave set-up and the flow generated by breaking waves. However, in contrast to waves breaking on sand or gravel beaches, other than during relatively fair-weather conditions, backwash is effectively eliminated. Flow is able to continue landwards in waves of translation that decay gradually and, on a wide platform, are ultimately dissipated by surface friction. Thus, their ability to transport material is systematically reduced and is only expressed in a broadly decreasing grain-size of deposits landward of the reef margin." (From Section 3 - fore-reefs and transport)
Braithwaite argues that coral reefs in today's oceans are growing on limestone platforms that predate reef growth. The margins of those platforms are subject to a variety of forces that produce the talus slopes.
"Contemporary reefs are shedding sediment into deeper waters, but there is also evidence of larger-scale margin collapse and gravity-driven slope failure of the platforms beneath them. Blocks of kilometre dimensions have been described on the west Florida margin, the Bahamas, and bounding the Nicaraguan Rise." (From Section 5 - slope deposits and platform shedding)
For those with an interest in the geological issues, Braithwaite's discussion is informative and thought-provoking, but this will not be considered further here. Suffice to say that it incorporates plenty of examples from fossil 'reefs' that confirm the proposed model.
"The premise that "reef talus" is an expression of the erosional history of the underlying platform rather than an integral product of a living reef can be illustrated by examples from rocks of a variety of ages." (From Section 6 - Ancient analogues)
Braithwaite=s paper is suggestive of a distinction that can be made between uniformitarianism and actualism. Darwin illustrates the former - although he claimed to be saying that the present is the key to the past, he invoked only gradualist processes that he thought were operative in the present and failed to test his hypotheses rigorously. Those who have followed him appear to have lacked the will to formulate and test hypotheses and to consider the viability of alternative models. Although there is an appeal to contemporary processes, uniformitarians tend to favour those characterised by small incremental effects. By contrast, Braithwaite illustrates actualism, with an evaluation of a much wider range of processes. He considers hurricane-driven tidal flows, tsunamis, and even waves generated by a meteorite impact capable of lifting blocks weighing 100 tons onto cliffs 33m above present sea level. He cites a case of sediment accumulation over about 500 years but all of it being transported and dispersed by a hurricane-induced current in about 5 hours. He shows how alternative models can be tested and how evidence can be used to falsify hypotheses. This approach to science is much more healthy, for there is a willingness to challenge cherished models and an openness to the operation of different mechanisms.
Why is this worthy of our attention? The principles in evidence here are relevant to a large number of topics that relate to the past. Unfortunately, these origins issues often are characterised by excessive appeals to consensus and cherished models, and not enough attention is given to the weight of evidence. Lyell's and Darwin's uniformitarianism still have an undue influence on our educational system and the media. Attempts to increase the level of critical scrutiny are met with emotive responses rather than reasoned arguments. To help us think through our methodology for dealing with these tensions, Braithwaite's approach to the "reef talus" model may provide a useful case study.
Reef Talus: A popular misconception
Colin J.R. Braithwaite
Earth-Science Reviews, Volume 128, January 2014, pages 169?180.
Abstract: Reef fronts have traditionally been regarded as comprising debris derived by contemporaneous erosion of 'the reef'. However, evidence from wave transport indicates that on present-day reefs the bulk of the debris generated in this way accumulates in the back-reef area, with only finer-grained sediment carried off-reef by retreating flows or by overwash. Nevertheless, in contrast to this observation, 'fore-reef' debris slopes are commonly considered "characteristic" of Phanerozoic reefs. This apparent error reflects the conflation of processes defining contemporary growth and accretion of the reef, and the corresponding long-term accretion of the carbonate platform on which it rests. Present-day reefs are commonly (although not exclusively) additions to long-lived carbonate platforms. Growth of the latter is intermittent and has been moderated by changes in sea-level that, for recent reefs, have been on time scales of less than 100 ka. During low sea-level stands, growth ceases or is translated downslope and earlier deposits are subject to lithification and subaerial erosion. Similar changes are applied on a larger scale to the aggrading growth of carbonate platforms, but the bulk accretion of these includes quite different processes and reflects far longer timescales. During low sea-level stands, the margins of platforms commonly become unstable, with instability reflected in slope failure and in the shedding of blocks, ranging from metres to kilometres in diameter, associated with the generation of debris flows and turbidites. It is argued that these are the materials that are commonly described as 'reef talus' in ancient structures, although their formation is largely independent of any contemporary reef growth. Difficulties arise where 'the reef' and 'the platform' are treated as a single functional entity. It is important to recognize the conceptual distinction between them, 'reef talus' is a misleading description of the debris predominantly generated by platform erosion and slope failure.
Tyler, D. The unscientific hegemony of uniformitarianism, ARN Literature Blog (16 May 2011)
Palaeontologists have been developing some highly sophisticated tools for analysing fossil specimens. Of particular interest are techniques that probe the details of soft tissue preservation. In the research considered here, the 30 mm specimen was found at the Chengjiang lagerstatte locality in southwest China. It had large, claw-like appendages on its head and many jointed legs. It is assigned to the arthropods and thought to be a probable extinct chelicerate. It is referred to as one of the megacherian (meaning "great hand") species with the genus name Alalcomenaeus. To analyse the soft tissues, a 3-D model of the specimen was produced using a CT-scanner and, at the same time, an X-ray microscope documented the distribution of selected chemical elements. In particular, iron has been found to map out the nervous system of the animal. The findings are spectacular.
This close-up of the head region of the Alalcomenaeus fossil specimen includes superimposed colors of a microscopy technique that reveal the distribution of chemical elements in the fossil. Copper shows up as blue, iron as magenta and the CT scans as green. The coincidence of iron and CT denote nervous system. The creature boasted two pairs of eyes (ball-shaped structures at the top). (Image: N. Strausfeld/University of Arizona, source here)
Living arthropods are classified into two major groups: the chelicerata (which include spiders, scorpions, mites and horseshoe crabs), and the mandibulata (which includes insects, crustaceans and millipedes). The new research locates the "great appendage arthropods" unambiguously in the chelicerata.
"We now know that the megacheirans had central nervous systems very similar to today's horseshoe crabs and scorpions," senior author Nicholas Strausfeld, a professor in the department of neuroscience at the University of Arizona in Tucson, said in a statement. (source here)
"The animal's brain consists of three fused ganglia, and blends into more ganglia that extend down the length of the animal's body. It has four eyes, each of which is served by just one optic lobe. That's a chelicerate layout - in mandibulates, the body ganglia would be more distinct and separated by long nerves, and there would be two to four optic lobes per eye." (Ed Yong, source here)
Evolutionary biologists are very fond of the terms "stem" and "crown" to describe where fossils fit into the tree of life. A "stem" fossil is supposed to have more transitional characters and the "crown" specimens are essentially modern. These great appendage arthropods were previously interpreted as "stem group chelicerates" or "stem-group arthropods". However, the neural architecture is essentially modern.
"Professor Strausfeld said: 'Greg plugged these characteristics into a computer-based cladistic analysis to ask, "where does this fossil appear in a relational tree?" 'Our fossil of Alalcomenaeus came out with the modern chelicerates." (source here)
This research is actually the second study of its type. The first was concerned with the neural structure of a mandibulate organism, published last year.
"Xiaoya Ma and Nicholas Strausfeld described the brain of a 520-million-year old animal called Fuxianhuia protensa. It consisted of three clusters of nerves (ganglia) that had fused together. (Source here)
"Nerves from the second ganglion reached into the creature's antennae, while nerves from the third one led into a pair of claws. Each of the animal's eyes was served by three further nerve bundles, known as optic lobes. "In other words, the specimen had a brain like that of a modern crustacean," says Strausfeld. Fuxianhuia was clearly an early relative of modern crabs, lobsters and shrimp - a relationship that was unclear from its body alone. [. . .] Fuxianhuia exemplified the mandibulate pattern." (Source here)
"No one expected such an advanced brain would have evolved so early in the history of multicellular animals," said Strausfeld, a Regents Professor in the UA department of neuroscience. [. . .] "In principle, Fuxianhuia's is a very modern brain in an ancient animal." (Source here)
So we have the interesting situation that both groups of arthropods have neural patterns that are essentially modern. Whereas morphology is used to argue the case for "stem" and "crown" organisms, complex specified information is more readily discerned in soft tissues: genetic systems, developmental gene regulatory networks and neural patterns. Research over the past decade has indicated that numerous core genes are common to a large number of phyla with the implication being that they preceded the Cambrian Explosion of animal phyla (here and here). The same applies to developmental pathways. The research considered in this blog shows that the neural pathways for arthropods must be dated at least to the Early Cambrian. This provides an additional dimension to the Cambrian Explosion phenomenon - in that an extraordinary accumulation of biological information is already in place by the Middle Cambrian.
A final point to note relates to the way iron mineralisation has preserved neural patterns, for reasons that are not altogether clear. It appears that nerve cells are more resistant to decay than other soft tissues:
"Strausfeld says that the nerves of invertebrates are dense and rich in fats, which makes them water-repellent. This, combined with their hard external skeleton, might have slowed the process of decay long enough for them to fossilise. Indeed, in an earlier study, Strausfeld's team buried marine worms in mud and put them under high pressure to simulate the start of fossilisation - and their nerves lasted while their muscles decayed." (source here)
Whilst there is a rationale for nerve tissue surviving longer than other tissues, it remains to be discovered why nerve tissue should take up iron mineralisation. Is there something about the nerve cells that attracts iron? All are agreed that soft tissue preservation requires rapid fossilisation, but we may find that nerve cells have to react with iron in solution very soon after burial if we are to preserve the neural ground pattern. Whatever the answers to such questions, soft tissue preservation is a clear pointer to fossilisation in a geological instant. Geologists (and others) are recognising that the principle of uniformitarianism promoted by Charles Lyell is a poor tool for interpreting the rock record, for many geological processes are abrupt and not gradual. Nevertheless, Lyell's legacy lives on in Darwinian evolution, where gradualism reigns supreme. Most Darwinians continue to stumble over the Cambrian Explosion and continue to predict that an extensive Precambrian fossil record will emerge with continued research. However, the fossil record that we do have, especially probed in detail as outlined in this blog, means that scenarios of "climbing Mount Improbable" savours more of a vivid imagination unconstrained by evidence. To understand why uniformitarianism is inappropriate for grappling with the Cambrian Explosion, go here. For a paradigm-shifting treatment of this whole issue, go here.
Chelicerate neural ground pattern in a Cambrian great appendage arthropod
Gengo Tanaka, Xianguang Hou, Xiaoya Ma, Gregory D. Edgecombe & Nicholas J. Strausfeld
Nature, 502, 364-367 (17 October 2013) | doi:10.1038/nature12520 (pdf here)
Preservation of neural tissue in early Cambrian arthropods has recently been demonstrated, to a degree that segmental structures of the head can be associated with individual brain neuromeres. This association provides novel data for addressing long-standing controversies about the segmental identities of specialized head appendages in fossil taxa. Here we document neuroanatomy in the head and trunk of a "great appendage" arthropod, Alalcomenaeus sp., from the Chengjiang biota, southwest China, providing the most complete neuroanatomical profile known from a Cambrian animal. Micro-computed tomography reveals a configuration of one optic neuropil separate from a protocerebrum contiguous with four head ganglia, succeeded by eight contiguous ganglia in an eleven-segment trunk. Arrangements of optic neuropils, the brain and ganglia correspond most closely to the nervous system of Chelicerata of all extant arthropods, supporting the assignment of "great appendage" arthropods to the chelicerate total group. The position of the deutocerebral neuromere aligns with the insertion of the great appendage, indicating its deutocerebral innervation and corroborating a homology between the "great appendage" and chelicera indicated by morphological similarities. Alalcomenaeus and Fuxianhuia protensa demonstrate that the two main configurations of the brain observed in modern arthropods, those of Chelicerata and Mandibulata, respectively, had evolved by the early Cambrian.
Chow, D. Ancient "Mega-Clawed" Creature Had Brain Like a Spider's, Scientific American (21 October 2013)
The steady flow of publications considering the way scientists interacted with the administration of the Nazi regime in Germany reveals some interesting cross-currents. It is well known that scientists who were out of step with the regime, particularly Jewish scientists, either emigrated (like Einstein) or ended up collaborating. Very few found it possible to operate independently of their political masters. Medical scientists have been previously considered in this blog (2008 - here), anatomists (2010 - here) and physicists have been the subject of a book-length study (2012 - here). For those tracing the ideological roots of the Nazi movement, one essential ingredient appears to be Social Darwinism: the application of Darwinian mechanisms to human society to understand change and to inform policy. However, there are some historians who demur, and say that Hitler was not a Darwinian. Chief among these is Robert Richards, whose new book is about to be published: "Was Hitler a Darwinian?" by University of Chicago Press. This divergence of thinking is actually significant in itself and worthy of our attention, especially as we approach the 70th anniversary of the ending of WWII. It is important to know what motivated the Nazis and it is important to reflect on the way the Nazis used science and politicized education - for they were world leaders in both.
Hitler's evolutionary ethic underlay or influenced almost every major feature of Nazi policy (source here)
The paper that addresses these issues directly is by Richard Weikart. He identifies six points of discussion and develops a multi-faceted argument that we cannot understand Nazi policy without recognizing the backdrop of Social Darwinism.
"While examining these lines of evidence, I will highlight the ways that Nazi racial thought was shaped by Darwinism (defined as biological evolution through the process of natural selection). [snip] These six points - derived from the view that humans and human races evolved and are still evolving through the Darwinian mechanism of natural selection - profoundly impacted Nazi policy. They formed the backdrop for eugenics, killing the disabled, the quest for "living space," and racial extermination." (p.538)
We cannot follow all issues covered in the paper, but will select some key topics that inform the conclusions. It is important to recognise that the Nazis saw themselves as mainstream thinkers - in their own eyes they were not a lunatic fringe! This needs to be understood when their thinking about the superiority of their own race is considered.
"[E]ven today some scholars are still loathe to entertain the idea that key elements of Nazi ideology could have been in harmony with the thinking of leading German scientists. Indeed the Nazi embrace of Darwinism in their racial ideology demonstrates the influence of science on Nazi ideology. Nazi racial ideology was largely consistent with the scholarship on race taught at German universities. This makes even clearer why so many German anthropologists and biologists supported Nazi racism - they were already committed to it before the Nazis came to power." (p.539)
It is also important not to think that this is a single issue discussion, and other factors are not relevant. The Nazi worldview has numerous elements, and we must not make the mistake of setting up a polarised straw-man analysis.
"I need to stress from the outset, however, that Nazi racial ideology was not derived exclusively from Darwinism or evolutionary biology. Gobineau - who wrote before Darwin published Origin of Species - contributed the idea that the Aryan race was superior to all other races. He also claimed that racial mixing produced deleterious effects, leading many racial thinkers, including the Nazis, to oppose miscegenation. Hatred of the Jews had a long history predating Darwin and has nothing to do with Darwinism. Also, Mendelian genetics played a role in debates over racial ideology - especially about policy relating to miscegenation - within the Nazi regime. However, in the decades preceding Hitler?s rise to power, many German racial theorists had synthesized Gobineau, Mendel, and antisemitism with social Darwinism. Nazi racial theory generally embraced this synthesis." (p.540)
In Hitler's writings, he makes it clear that racial mixing is not a good idea, because it violates evolutionary principles. His arguments invoke the concepts of selection, fitness, the struggle for survival which are all drawn from Darwinism.
"In the struggle for daily bread all those who are weak and sickly or less determined succumb, while the struggle of the males for the female grants the right or opportunity to propagate only to the healthiest. And struggle is always a means for improving a species' health and power of resistance and, therefore, a cause of its higher evolution." (p.541)
The Nazi regime sought to influence young people via educational programmes and youth movements. The curriculum made connections between what was taught and its social and political implications. Darwinism was explicit, and the textbooks followed suit.
"In 1938 the Ministry of Education published an official curriculum handbook for the schools. This handbook mandated teaching evolution, including the evolution of human races, which evolved through "selection and elimination." It stipulated, "The student must accept as something self-evident this most essential and most important natural law of elimination [of unfit] together with evolution and reproduction." In the fifth class, teachers were instructed to teach about the "emergence of the primitive human races (in connection with the evolution of animals)." In the eighth class, students were to be taught evolution even more extensively, including lessons on "Lamarckism and Darwinism and their worldview and political implications," as well as the "origin and evolution of humanity and its races," which included segments on "prehistoric humanity and its races" and "contemporary human races in view of evolutionary history." (p.542)
Weikart continues by looking at the Nazi leaders in academia and in political life, and in the racial propaganda literature they produced. One of the training pamphlets he quotes gives a clear overview of the message people were expected to absorb and which was reinforced by all the leading German scientists of the day..
"The opening pages explained that the central concepts underlying racial ideology are hard heredity and racial inequality. Then it claimed that racial inequality has come about because evolution proceeds by struggle. Different races simply do not evolve at the same pace, so they are at different levels. The authors then asserted that the three main human races - European, Mongolian, and Negro - were subspecies that branched off from a common ancestor about 100,000 years ago. They argued that races evolved through selection and elimination, and the Nordic race became superior because it had to struggle in especially harsh conditions. Throughout this pamphlet the terms "higher evolution," "struggle for existence," and selection are core concepts that occur repeatedly." (p.550)
The conclusions appear to be compelling. Those who are seeking to draw a line between Darwinism and the Nazi worldview have a hopeless task. This is how Weikart summarises his findings:
"Nazi racial ideology - and the many policies based on it - were profoundly shaped by a Darwinian understanding of humanity. Certainly many non-Darwinian elements were synthesized with Darwinism: Aryan supremacy, antimiscegenation, antisemitism, and many more. Nonetheless, Nazi racial ideology integrated all these factors into a worldview that stressed the transmutation of species, the evolutionary formation of the human races, the need for advancing human evolution, the inevitability of the human struggle for existence, and the need to gain Lebensraum to succeed in the evolutionary struggle." (p.552)
This is not an issue without relevance for societies today. Germany in the 1930s was no cultural backwater. They were confident they were building a worldview on rigorous science, affirmed by scholars across the world as well as in their own country. However, this worldview shaped the values held by the people: on ethics, on the worth of human life, and on their aspirations. There are people today who are seeking to build a worldview on evolutionary concepts. They are seeking to influence the educational processes in their own countries, and are creating a culture where dissent is treated as a betrayal of science. Their counsel is wide open to disasters similar to those faced by the Third Reich. We all need to review our personal worldview and to have answers for questions like: What is truth? What is ethical? Who is my brother? What is the worth of human life? What is worth struggling for?
The Role of Darwinism in Nazi Racial Thought
German Studies Review, 36(3), (October 2013): 537-556 (pdf here)
Abstract: Historians disagree about whether Nazis embraced Darwinian evolution. By examining Hitler's ideology, the official biology curriculum, the writings of Nazi anthropologists, and Nazi periodicals, we find that Nazi racial theorists did indeed embrace human and racial evolution. They not only taught that humans had evolved from primates, but they believed the Aryan or Nordic race had evolved to a higher level than other races because of the harsh climatic conditions that influenced natural selection. They also claimed that Darwinism underpinned specific elements of Nazi racial ideology, including racial inequality, the necessity of the racial struggle for existence, and collectivism.
Images of Neanderthal Man have changed over the years, but there has been a reluctance to portray them as our near-cousins. Neanderthals have been treated as a separate species within the Homo family, and usually described as slow and clumsy, with a limited capacity for creative thinking. The evolutionary context is typically presented in terms of Modern Man's superiority, so that when Homo sapiens migrated from Africa into Europe, it was the Neanderthal population that died out. However, does the evolutionary approach provide the appropriate framework for understanding these events? Recent discoveries suggest that Neanderthals do not fit the descriptions found in the textbooks and the media, and that the evolutionary agenda is actually a negative influence. The presuppositions and perspectives of the evolutionists are proving to be systematically wrong. This blog draws attention to three research papers that document "surprising" findings - i.e. the conclusions run counter to evolutionary expectations.
A reconstruction of how lissoirs, made of deer ribs, could have been used to prepare hides to make them more supple, lustrous and impermeable. The natural flexibility of ribs helps keep a constant pressure against the hide without tearing it. The bottom half of the figure illustrates how the downward pressure ultimately results in a break that produces small fragments like three of the reported bones. (Image copyright Abri Peyrony & Pech-de-l'Aze, larger image can be sourced here)
Specialised bone tools are documented for African humans prior to their migrations into Europe, but these are limited to pointed bone tools. Then, after entering Europe, the human population started using smooth shaped tools made from deer ribs. The new research reports that these smooth shaped tools were used by Neanderthals prior to the migrations of Homo sapiens.
"[The tools ] are similar to a tool type well known from later modern human sites and still in use today by high-end leather workers. This tool, called a lissoir or smoother, is shaped from deer ribs and has a polished tip that, when pushed against a hide, creates softer, burnished and more water resistant leather. The bone tool is still used today by leather workers some 50 thousand years after the Neandertals and the first anatomically modern humans in Europe." (Source here)
No one has doubted that Neanderthals used animal skins for coverings, belts, footwear and for dwelling utilities. The new research implies that the skins were worked with tools and that artefacts were produced using more significant mental and manual skills. Also, the question arises: who learned from who?
"The bones reported here demonstrate that Middle Paleolithic Neandertals were shaping animal ribs to a desired, utilitarian form and, thus, were intentionally producing standardized (or formal) bone tools using techniques specific to working bone. These bones are the earliest evidence of this behavior associated with Neandertals, and they move the debate over whether Neandertals independently invented aspects of modern human culture to before the time of population replacement." (source here)
Of course, technologies can be invented independently, and that may be relevant in this case. But anthropologists do tend to favour cultural traits being passed from the originators to later practitioners. Neanderthals, having a less rich materials culture, have been presumed to be 'less fit' by Darwinists.
"The idea that technologies or traditions passed from Neanderthals to humans has been raised before, says Chris Stringer at the Natural History Museum in London. "For example, it is not clear which population first started the tradition of burial of the dead." Joao Zilhao at the University of Barcelona in Spain, meanwhile, has argued that the fashion among early humans for wearing pendants of animal bone and teeth originally came from Neanderthals. He says he has no problem, in principle, with humans learning new tool technologies from our extinct cousins. But in general, most researchers - including Stringer and McPherron - think that the bulk of any cultural exchange passed the other way, from humans to Neanderthals." (Source here)
The second research paper has the title: "Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus". We have been brought up to think of Neanderthals as hunter/gatherers, but with an emphasis on hunting. Did Neanderthals do anything more than pick edible berries? The answer appears to be yes. The new research has found dramatic evidence of Neanderthals cooking and eating plant foods for nutrition and also imbibing plants for medicinal use.
"[We have identified] material entrapped in dental calculus from five Neanderthal individuals from the north Spanish site of El Sidron. Our results provide the first molecular evidence for inhalation of wood-fire smoke and bitumen or oil shale and ingestion of a range of cooked plant foods. We also offer the first evidence for the use of medicinal plants by a Neanderthal individual. The varied use of plants that we have identified suggests that the Neanderthal occupants of El Sidron had a sophisticated knowledge of their natural surroundings which included the ability to select and use certain plants." (Source here)
An alternative explanation for this dental calculus data has been proposed by Buck and Stringer (2013). They write: "Here we offer an alternative hypothesis for the occurrence of non-food plants in Neanderthal calculus based on the modern human ethnographic literature: the consumption of herbivore stomach contents." Apparently, several human groups regard eating the stomach contents of animals as a desirable practice. Of course, eating chyme (partly digested plant food) is a likely occurrence for carnivores, but there are some questions about how medicinal plants were present in sufficient quantities to leave a signature in dental calculus.
The third research finding is evidence of a tumor in a rib from a Neanderthal skeleton said to be more than 120,000 years old. The tumour is described as a fibrous dysplastic neoplasm. Fibrous dysplasia is a rare type of benign tumor found in the ribs and other bones of modern humans.
"Human paleontologist Fred Smith of Illinois State University [. . .] says that, while he is not surprised by the existence of a Neanderthal tumor of this sort, the finding "underscores in some ways the fact that these Neanderthals basically [had] the same kind of biology that we have and they [were] subject to the same kind of growth and developmental processes, even abnormal." "It is important to know that the very same kind of change associated with this tumor is something that we share with Neanderthals," agrees Monge. "That has a very, very deep history within the human lineage and very much ties us - in terms of disease pathological processes - to Neanderthals."" (Source here)
These three research findings are just part of an on-going journey of discovery that Neanderthals are our human cousins, and they do not belong in a story of the origins of humanity. Rather, they are a chapter in the history of humanity. Interestingly, one of the co-authors of the fibrous dysplasia paper is David Frayer, who has championed the true humanity of Neanderthals for much of his career.
"If David Frayer has his way, the word "Neanderthal" will one day no longer be an insult. For some 25 years, Frayer has fought against the old view that Neanderthals, the human ancestors who populated Europe and some of the Middle East between 35,000 and 200,000 years ago, were a lesser race that lost the evolutionary war. The Kansas University professor of anthropology has argued that Neanderthals were more closely related to today's humans than people realized." (Source here)
In May of this year, Frayer wrote a challenging article for the New York Times, from which the following excerpt is taken:
"But in the last 10 years there has been a major reassessment of the Neanderthals, and it turns out they share a lot of the behavior and capabilities of people in Europe today. This revolution in the way academics think about Neanderthals arises from discoveries in archaeology, re-evaluations of their anatomy and revelations about their genetic makeup.
The most amazing is the extraction of nuclear DNA sequences from Neanderthal remains, which show that Europeans derive up to 4 percent of their genes uniquely from Neanderthals. Some 80 gene sequences come directly from Neanderthals and include regulators of smell, vision, cell division, sperm integrity and smooth muscle contraction.
One gene we share with Neanderthals is FOXP2, part of the gene complex associated with language production. We know variants of this gene in modern people cause language dysfunction and it was long assumed Neanderthals had a non-modern form. This was partly based on the general assumption that Neanderthals were not like us - and some argued that Neanderthals lacked the ability to produce the essential vowels of language - "a," "e" and "u." New anatomical work refutes this, and the evidence from FOXP2 shows that Neanderthals had the exact genetic sequence found in fully vocal moderns." (Source here)
The "long assumed" perspectives and the "general assumption" about Neanderthals derive from evolutionary theory and the desire for a story of human evolution. Neanderthals have long been part of the story that gets presented to children, students, the public and the intelligentsia. But evolutionary theories about Neanderthals have been tested and found wanting. They are not helpful for structuring thought about human history. What is needed now is an atmosphere of academic freedom to propose alternative hypotheses to explain the data associated with the Homoremains. For too long, Darwinism has had an unhealthy influence in anthropology. For the sake of science in general, this hegemony must be broken.
Neandertals Made the First Specialized Bone Tools in Europe
Marie Soressi, Shannon P. McPherron, Michel Lenoir, Tamara Dogandzic, Paul Goldberg, Zenobia Jacobs, Yolaine Maigrot, Naomi Martisius, Christopher E. Miller, William Rendu, Michael P. Richards, Matthew M. Skinner, Teresa E. Steele, Sahra Talamo, Jean-Pierre Texier
Proceedings of the National Academy of Sciences, August 27, 2013, vol. 110 no. 35, 14186-14190 | doi: 10.1073/pnas.1302730110
Abstract: Modern humans replaced Neandertals ~40,000 y ago. Close to the time of replacement, Neandertals show behaviors similar to those of the modern humans arriving into Europe, including the use of specialized bone tools, body ornaments, and small blades. It is highly debated whether these modern behaviors developed before or as a result of contact with modern humans. Here we report the identification of a type of specialized bone tool,lissoir, previously only associated with modern humans. The microwear preserved on one of these lissoiris consistent with the use of lissoirin modern times to obtain supple, lustrous, and more impermeable hides. These tools are from a Neandertal context proceeding the replacement period and are the oldest specialized bone tools in Europe. As such, they are either a demonstration of independent invention by Neandertals or an indication that modern humans started influencing European Neandertals much earlier than previously believed. Because these finds clearly predate the oldest known age for the use of similar objects in Europe by anatomically modern humans, they could also be evidence for cultural diffusion from Neandertals to modern humans.
Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus
Karen Hardy, Stephen Buckley, Matthew J. Collins, Almudena Estalrrich, Don Brothwell, Les Copeland, Antonio Garcia-Tabernero, Samuel Garcia-Vargas, Marco de la Rasilla, Carles Lalueza-Fox, Rosa Huguet, Markus Bastir, David Santamaria, Marco Madella, Julie Wilson, Angel Fernandez Cortes and Antonio Rosas.
Naturwissenschaften, August 2012, Volume 99, Issue 8, pp 617-626 (pdf here)
Abstract: Neanderthals disappeared sometime between 30,000 and 24,000 years ago. Until recently, Neanderthals were understood to have been predominantly meat-eaters; however, a growing body of evidence suggests their diet also included plants. We present the results of a study, in which sequential thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) and pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) were combined with morphological analysis of plant microfossils, to identify material entrapped in dental calculus from five Neanderthal individuals from the north Spanish site of El Sidron. Our results provide the first molecular evidence for inhalation of wood-fire smoke and bitumen or oil shale and ingestion of a range of cooked plant foods. We also offer the first evidence for the use of medicinal plants by a Neanderthal individual. The varied use of plants that we have identified suggests that the Neanderthal occupants of El Sidron had a sophisticated knowledge of their natural surroundings which included the ability to select and use certain plants.
Fibrous Dysplasia in a 120,000+ Year Old Neandertal from Krapina, Croatia
Janet Monge, Morrie Kricun, Jakov Radovcic, Davorka Radovcic, Alan Mann, David W. Frayer.
PLoS ONE, June 2013, 8(6): e64539 | doi:10.1371/journal.pone.0064539
Abstract: We describe the first definitive case of a fibrous dysplastic neoplasm in a Neandertal rib (120.71) from the site of Krapina in present-day Croatia. The tumor predates other evidence for these kinds of tumor by well over 100,000 years. Tumors of any sort are a rare occurrence in recent archaeological periods or in living primates, but especially in the human fossil record. Several studies have surveyed bone diseases in past human populations and living primates and fibrous dysplasias occur in a low incidence. Within the class of bone tumors of the rib, fibrous dysplasia is present in living humans at a higher frequency than other bone tumors. The bony features leading to our diagnosis are described in detail. In living humans effects of the neoplasm present a broad spectrum of symptoms, from asymptomatic to debilitating. Given the incomplete nature of this rib and the lack of associated skeletal elements, we resist commenting on the health effects the tumor had on the individual. Yet, the occurrence of this neoplasm shows that at least one Neandertal suffered a common bone tumor found in modern humans.
Who're You Calling a Neanderthal?
By David Frayer
New York Times: May 2, 2013
First paragraph: Most Westerners think of Neanderthals as stumbling, bumbling, mumbling fools who aimlessly wandered the landscape eking out a miserable, forlorn existence. Yet Neanderthals lived longer in Europe than modern humans have, by several hundred thousand years, and survived good and bad times.
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