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New take on the Red Queen Biologists have assumed that natural selection shapes larger patterns of evolution through interactions such as competition and predation. These patterns may instead be determined by rare, stochastic speciation. On page 349 of this issue, Venditti and colleagues1 provide a revolutionary perspective on a core conundrum in evolution termed the Red Queen hypothesis. Whereas this hypothesis was traditionally based at the level of species in the environment and their interactions with each other, the new work shifts the emphasis to events that result in speciation. Lipid Rafts As a Membrane-Organizing Principle Cell membranes display a tremendous complexity of lipids and proteins designed to perform the functions cells require. To coordinate these functions, the membrane is able to laterally segregate its constituents. This capability is based on dynamic liquid-liquid immiscibility and underlies the raft concept of membrane subcompartmentalization. Lipid rafts are fluctuating nanoscale assemblies of sphingolipid, cholesterol, and proteins that can be stabilized to coalesce, forming platforms that function in membrane signaling and trafficking. Here we review the evidence for how this principle combines the potential for sphingolipid-cholesterol self-assembly with protein specificity to selectively focus membrane bioactivity. Rotation in Xenopus laevis Embryos after the Appearance of the First Cleavage Furrow Two types of motion are observed during the first cycle of amphibian egg cleavage: a turn of the fertilized egg so that the animal pole faces up (the ovoadaptation reaction, according to Terent’ev [1]) and, somewhat later, a turn of the cortical plasma (the so-called fertilization turn). The latter event determines the dorsoventral axis and the bilateral symmetry of the embryo [2, 3]. When examining time-lapse video recordings of the cleavage of African clawed frog (Xenopus laevis Daudin) eggs, we found that, in some eggs, the first cleavage furrow running through the animal pole simultaneously rotated about the animal–vegetative axis of the egg, thus making the impression that the entire egg rotated. Such a motion in cleaving eggs of amphibians has not been mentioned in available publications on the subject. Here, we describe this phenomenon, which obviously has not been noticed before, and put forward some assumption on its nature. Rotation in Xenopus laevis embryos during the second cell cycle Abstract: Using time-lapse video recording and comparing successive digital images, we found that 38% of Xenopus laevis embryos (n=118) exhibited rotation during the second cell cycle. This rotation, which we term the second rotation, started approximately during the appearance of the first cleavage furrow and proceeded clockwise or counterclockwise around the vertical axis. Rotations lasted for 5-30 minutes, i.e. up to the beginning of the third cell cycle. The mean rotation angle was 36.4˚, with a maximum rotation of 77˚. No mortality was observed among the embryos exhibiting rotation. The second rotation was observed to be similar to the well-known fertilization rotation which takes place during the first cell cycle. The possible nature and significance of the second rotation are discussed. It is well known that during the first cell cycle of amphibian embryos, a prolonged rotation of the peripheral layer of the egg (its cortex) relative to the subcortical cytoplasm core takes place. This rotation, termed the fertilization rotation, appears to be necessary for bilateral symmetry formation in embryos (Clavert, 1962; Vincent et al., 1986; Gilbert, 2000). Here, we report that during the second cell cycle, some Xenopus embryos also exhibit a long-term rotation, which we call the second rotation. To the best our best knowledge, this phenomenon has not yet been described. Therefore the aim of this work was to describe the second rotation for the first time and to offer suggestions about its nature and significance. Balloon Biology This comment, addressed to PZ Myers, was posted on his blogsite, Pharyngula, which ridiculed the torus model as balloon biology. Balloon biology was organized as the Pneu Theory (balloon theory) by Adolph Seilacher. Chapter Five of D'Arcy Thompson's On Growth and Form treats the surfaces of cells as inflatables in one hundred pages of mathematical analysis. 66 Posted by: Stuart Pivar | July 6, 2009 1:04 PM Dear PZ, Don't deprecate balloons, as you yourself are one, as we all are, according to the great embryologist Adolph Seilacher at Yale, who established by tensorial analysis in his Pneu theory in the 1980s that the curvature of the arthropod shell and vertebrate body is consistent with that of an inflated balloon. Every cell is a balloon. The body is an inflatable. This characteristic distinguishes living form from the inorganic. Crystals have flat surfaces and sharp edges. In the 1880's Swiss scientist Wilhelm His, father of human embryology, inventor of the microtome, simulated the steps of embryology and the form of the vertebrate internal organs by the deformation of inflated rubber bladders and tubes. His work was ridiculed by Ernst Haeckel as Gummischlauchwissenschaft, rubber balloon science. It was His who exposed Haeckel's embryo drawings as fraudulent. Haeckel destroyed the Swiss Entwicklungsmechanik school of embryology by preventing its members from publishing and teaching in Germany. Embryogenesis is guided by the fluid dynamics of inflating balloons. Gould recounts all this in Ontogeny and Philogeny, 1977. We are all inflatables, some of us more than others. Stuart Irreducible Complexity and Self-Replication The wondrous complexity of living structures is used by Creationists as an argument against evolution. A favorite example is the device which anchors the flagellum to the cell wall. This structure, the basal body, complex and perfectly designed as it appears, is less wondrous when the origin of its separate parts is understood. An automobile assembly plant may well seem to be irreducibly complex in the absence of any other knowledge. The cell contains self-replicating, ring-shaped structures self-organized out of actin and tubulin which serve as centrioles, the midpiece of the sperm, the transport ports in cell membranes, and as bearings in the basal bodies. Life is a self-replicating system, its defining characteristic. In fact, life is the result of two main, coincident, independent, self-replicating systems: The first is the self-organized lipid bilayer cellular bubble which alternately grows and splits in two. The second is the self-replicating DNA molecule inside which endlessly produces lipids from smaller molecules which infilter from the outside. The new lipids enter the wall causing the cell wall to expand. The cell and its DNA both self-replicate at the same moment. In addition the system is advanced by the invention of self- repilcatiing centrioles, which are interchangeable with flagellum basal bodies and midpieces for sperms. This process continues until the available raw materials are completely consumed, upon which the individuals die. Another system can then originate consisting of mutant individuals which can thrive on the more complex molecular remains of the previous system. The cycle can continue ad infinitum, given an exterior energy source, producing ever more complex structures. Self-organizing systems originate by chance. Once in operation, they do not bear any evidence of how they began. This is why after 2,000 years the mechanism of embryology and evolution are still generally unknown to science. ADAPTING TO A PARADIGM CHALLENGE
Thousands of scientists are engaged in a scientific gold rush. Dozens of private and governmental organizations and university departments world-wide declare their mission to study the origin of life and its evolution. Prominent in the effort is NASA, which funds hundreds of astrobiologists to study the question. The problem arises out of the lack of agreement by biologists as to how evolution works and how the body is formed. For over half a century a committee-invented dogma called the “Modern Synthesis,” or the “Neo-Darwinian Theory,” has ruled biology. It states that the body form is encoded in the DNA and that it evolves by the natural selection of random mutations. Now biologists have concluded that there is no code for form in the genes and that the body is not shaped by natural selection, leaving the science of biology paradigm-challenged. It is difficult to abandon the idea of natural selection as a shaper of form because it underlies the idea of adaptation — that organs have evolved, been perfected, and designed for their use — and that it is then necessary to assign survival advantage to everything biological. But if there is no natural selection then survival advantage has no effect, and adaptation must be an illusion. Still, our eyes and hands could not possibly be better designed for what we do with them. Not so our feet and backs. In Nature you make do with what you get. Fish swim and birds fly with the same organ. We walk upright by the coincidence of the flat underdeveloped feet that brought us down from the trees and the failure of the skull to rotate during embryology, leaving humans looking downwards unless they stand up. Virtually all human characteristics may be accounted for as the result of a single effect — the retardation of embryonic development with respect to growth, leaving the human a juvenalized ape (see Stephen Jay Gould's Ontogeny and Phylogeny, 1977). Birds fly because the massive yolk in the bird egg compresses the embryo to a disc, flattening and stretching the forelimbs and causing the extrusion of feathers. Fish have sleek bodies because they inherited the tadpole form of their barnacle-larva proto-chordate ancestors. Natural selection may well have preserved it in many cases, although not in all. Marine invertebrates are not hydrodynamically designed. Some catch fish. There are millions of species, all variants on one of two body plans — either a segmented tube with paired transverse limbs or a sac. Speciation is profligate rather than conservative. Creatures of every degree of variance in form and behavior manage to survive. Why has not some ideal predator emerged, such as a flying tiger? Why are species with ingenious tricks for predation, camouflage, or sexual attraction — like carnivorous plants and angler fish — so rare? Biodiversity is the gamut of variations in the proportions of the parts of one or two basic body plans in nature. During embryology each organ grows at the same time it develops, genetically controlled, by timed endocrinal events in the process called heterochrony. Timing errors produce aberrations in the relative size of the parts of an otherwise immutable body plan (see Gould, ibid). Fortunately some mutants find a niche where the new feature is tolerated and later pressed into use for something, giving the illusion that it was shaped for this purpose. This is called the teleological fallacy. Nature has no goal or purpose. What can DNA tell us? Place your bets now LEWIS WOLPERT's faith in the predictive power of the genome is misplaced. Genes enable organisms to make proteins, but do not contain programs or blueprints, or explain the development of embryos. Random molecular permutations simply cannot explain how organisms work. Instead, cells, tissues and organs develop in a modular manner, shaped by morphogenetic fields, first recognised by developmental biologists in the 1920s. Visions of Evolution: Self-organization proposes what natural selection disposes 1 – CSIRO Marine and Atmospheric Research, Private Bag 1, Aspendale 3195, Australia
SUMMARY INTRODUCTION
Other biologists share similar concerns. For example, while agreeing that natural selection is fundamentally important, Stuart Kauffman claims that it has not labored alone to craft the architectures of the biosphere, from cell to organism to ecosystem. Instead, self-organization is suggested to be the root source of order in the biological world. This order is not merely tinkered, but arises spontaneously because of the physico-chemical principles of selforganization – dynamical rules of complex processes that we are just beginning to uncover and understand (see Kauffman, 1993 & 1995). Although most biologists are now aware of the existence of self-organization, many have chosen to ignore its potential implications. Yet others have gone so far as to declare selection a mere footnote to the work of self-organization in creating new phenotypic configurations and functions, merely disposing what selforganization has proposed (see Reid, 2007). In their book, Depew and Weber tackled this problem philosophically, by posing a set of logically possible relationships between natural selection and self-organization, then surmising how the Darwinian tradition would be affected in each case. Later, they used this discussion to show why the way they elect to look at this relationship is preferable to others. Without wishing to prejudice the reader for or against any of the seven visions of evolution that they proposed, we repeat them below:
Depew and Weber stress that early explorers of this terrain have occupied one or more of these perspectives, but each view has proved spacious enough to accommodate several, seemingly different, possibly competitive theoretical stances. In the first part of this paper, we review each of the seven visions briefly and dispassionately, identify some advocates, explain the context and discuss some issues associated with it. This leads us to the conclusion that these different perspectives may have suited different aims and approaches. In the second section of the paper, we show that these seven viewpoints can be conveniently collapsed into three seemingly different ones: (1) natural selection drives evolution; (2) selforganization drives evolution; (3) natural selection and self-organization are complementary aspects of the evolutionary process. We then argue that these three approaches are not mutually exclusive, since each may apply for different stages of development of different systems. What emerges from our discussion is a more encompassing view: That self-organization proposes what natural selection disposes. (1) Self-organization results from the fact that natural and material laws, together with genetic information and human legislation, cannot and do not govern details of what occurs in Nature, largely because contingency is rampant in complicated locales. Something unprecedented may emerge anywhere at any moment. Also, a locale itself may have some predispositions (2) Natural selection results from the fact that some types in a population may reproduce more successfully than others, increasing the representation of associated genetic configurations in the population's gene pool. Evolutionary Embryo The Origin of Individuals A central question in biology is how multicellular organisms develop from a single cell and how development is controlled. The standard view is that the process is deterministic, following directives governed by information located in the genome. Molecular biologist Jean-Jacques Kupiec contradicts this picture. In the fascinating The Origin of Individuals he argues that there is no plan, pre-pattern or program encoded in the genome. Instead, cell differentiation and development include a random element. In the standard view, development is controlled by the binding of protein transcription factors to promoters that activate genes in the DNA. These genes in turn generate proteins, including other transcription factors and signalling molecules that activate yet more genes. A cascade of gene activation results, leading to the proliferation and differentiation of cells that ultimately generates the organism. Assuming that molecular interactions and gene activation are predictable, the development process should be deterministic. Kupiec argues that this picture is wrong. Gene activation is inherently stochastic, he says, and, therefore, cell differentiation must also be stochastic. Transcription factors attach with certain probabilities to many binding sites in gene promoters, implying that chance plays a dominant role in gene activation and expression. Similarly, cell signalling pathways, and thereby cell interactions, are stochastic, as proteins may bind promiscuously to many partners with various odds. Many interactions and pathways are possible. As a result of this underlying unpredictability, Kupiec claims, stochastic cellular actions such as cell growth, cell differentiation and cell death must be constrained somehow to ensure that the correct sequence of development occurs. Otherwise, a fertilized egg could grow into any organism. The problem that ordered biological structures are rarer than the many possible random states led the physicist Erwin Schr6dinger in his 1944 book What is Life? to contrast the science of life with physics: in statistical thermodynamics, macroscopic order is generated from disorder, whereas for life to develop, order must be generated from order. Schr6dinger introduced the notion of a code script — analogous to a program — contained in the chromosomes, which acts as both plan and operative factor to prevent disorder by guiding the development process. Kupiec disagrees with the idea of programs. Because of the stochastic nature of protein interaction and gene expression, he says, there can be no Aristotelian form or program to give order to life and ward off entropic chaos and death. New Glimpses of Life’s Puzzling Origins ... Simple fatty acids, of the sort likely to have been around on the primitive Earth, will spontaneously form double-layered spheres, much like the double-layered membrane of today’s living cells. These protocells will incorporate new fatty acids fed into the water, and eventually divide.... The following article offers corroboration to the principle of mechanical induction of Emmanuel Farge, 2003, which demonstrates in Drosophila embryology that mechanical deformation is a necessary and sufficient condition for gene expression and cell division, contrary to the accepted wisdom. Developmental biology: Use it or lose it Embryos need to flex their growing muscles if developing cells are to give rise to joints, says a team led by Elazar Zelzer at the Weizmann Institute of Science in Rehovot, Israel. They found that mutant mouse embryos with defective muscles fail to form various joints, including elbows, shoulders and hips (a normal embryo is pictured above). Without muscle contraction, the cells that generate joint tissues do not activate a key regulatory pathway controlled by the protein β-catenin, and the progenitors switch fate to form cartilage instead. One idea put forward by the authors is that the mechanical stress created by developing muscles might inform the cells of where they are and what cell type they should generate. The study could be relevant to rare human cases in which babies whose movement is restricted in utero develop abnormal joints. Why Darwin? ... Coyne is an evolutionary biologist who, like his former student H. Allen Orr, has been a leader in our understanding of the genetic changes that occur when species are formed. His primary object in writing this book is to present the incontrovertible evidence that evolution is a physical fact of the history of life on earth. In referring to the theory of evolution he makes it clear that we do not mean the weak sense of "theory," an ingenious tentative mental construct that might or might not be objectively true, but the strong sense of a coherent set of true assertions about physical reality. In this he is entirely successful. Where he is less successful, as all other commentators have been, is in his insistence that the evidence for natural selection as the driving force of evolution is of the same inferential strength as the evidence that evolution has occurred. So, for example, he gives the game away by writing that when we examine a sequence of changes in the fossil record, we can
But to say that some example is not falsification of a theory because we can always "find" (invent) a feasible explanation says more about the flexibility of the theory and the ingenuity of its supporters than it says about physical nature. Indeed in his later discussion of theories of behavioral evolution he becomes appropriately skeptical when he writes that
Clarifying Tetrapod Embryogenesis, a physicist's point of view Abstract |