This parody of evo devo makes it sound a lot like ID

_{News
December 19, 2017

Cell biology, Evolution, Evolutionary biology

1}_{Categories
Cell biology
Evolution
Evolutionary biology}

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“This is how we go from single cells to people.” Hmmm.

See also: From Biology Direct: Darwinism, now thoroughly detached from its historical roots as a falsifiable theory, “must be abandoned”

Comments

evo devo despacito? :) https://uncommondescent.com/intelligent-design/how-embryonic-development-bears-on-evolution/ https://uncommondescent.com/intelligent-design/allmon-and-ross-demolish-evolution/Dionisio_{January 20, 2018
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evo devo despacito? :) In neo-Darwinian theory, adaptation results from a response to selection on relatively slowly accumulating genetic variation. However, more rapid adaptive responses are possible if selectable or plastic phenotypic variation is produced by epigenetic differences in gene expression. This rapid path to adaptation may prove particularly important when genetic variation is lacking, such as in small, bottlenecked, or asexual populations. To examine the potential for an epigenetic contribution to adaptive variation, we examined morphological divergence and epigenetic variation in genetically impoverished asexual populations of a freshwater snail, Potamopyrgus antipodarum, from distinct habitats (two lakes versus two rivers). These populations exhibit habitat specific differences in shell shape, and these differences are consistent with adaptation to water current speed. Between these same habitats, we also found significant genome wide DNA methylation differences. The differences between habitats were an order of magnitude greater than the differences between replicate sites of the same habitat. These observations suggest one possible mechanism for the expression of adaptive shell shape differences between habitats involves environmentally induced epigenetic differences. This provides a potential explanation for the capacity of this asexual snail to spread by adaptive evolution or plasticity to different environments. L.M. Thorson, Jennifer & Smithson, Mark & Beck, Daniel & Sadler-Riggleman, Ingrid & Nilsson, Eric & Dybdahl, Mark & K. Skinner, Michael. (2017). Epigenetics and adaptive phenotypic variation between habitats in an asexual snail. Scientific Reports. 7. . 10.1038/s41598-017-14673-6. https://www.researchgate.net/publication/320630309_Epigenetics_and_adaptive_phenotypic_variation_between_habitats_in_an_asexual_snail/fulltext/59f37f580f7e9b553eba71a0/320630309_Epigenetics_and_adaptive_phenotypic_variation_between_habitats_in_an_asexual_snail.pdfDionisio_{January 20, 2018
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evo devo despacito? :) In the last 15 years considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of "big" biological questions. Genome mining is expected to reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction, moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory, biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigenetic investigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation, tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish is further suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance of epigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies, environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratory lineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically edited strains. Vogt, Günter. (2017). Investigating the genetic and epigenetic basis of big biological questions with the new crayfish model Procambarus virginalis. .Dionisio_{January 20, 2018
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evo devo despacito? :) There is increasing evidence, particularly from plants, that epigenetic mechanisms can contribute to environmental adaptation and evolution. The present article provides an overview on this topic for animals and highlights the special suitability of clonal, invasive, hybrid, polyploid, and domesticated species for environmental and evolutionary epigenetics. Laboratory and field studies with asexually reproducing animals have shown that epigenetically diverse phenotypes can be produced from the same genome either by developmental stochasticity or environmental induction. The analysis of invasions revealed that epigenetic phenotype variation may help to overcome genetic barriers typically associated with invasions such as bottlenecks and inbreeding. Research with hybrids and polyploids established that epigenetic mechanisms are involved in consolidation of speciation by contributing to reproductive isolation and restructuring of the genome in the neo-species. Epigenetic mechanisms may even have the potential to trigger speciation but evidence is still meager. The comparison of domesticated animals and their wild ancestors demonstrated heritability and selectability of phenotype modulating DNA methylation patterns. Hypotheses, model predictions, and empirical results are presented to explain how epigenetic phenotype variation could facilitate adaptation and speciation. Clonal laboratory lineages, monoclonal invaders, and adaptive radiations of different evolutionary age seem particularly suitable to empirically test the proposed ideas. A respective research agenda is presented. Vogt, Günter. (2017). Facilitation of environmental adaptation and evolution by epigenetic phenotype variation: insights from clonal, invasive, polyploid, and domesticated animals. Environmental Epigenetics. 3. . 10.1093/eep/dvx002. http://academic.oup.com/eep/article-pdf/3/1/dvx002/11124301/dvx002.pdfDionisio_{January 20, 2018
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evo devo despacito? :) What role does non-genetic inheritance play in evolution? In recent work we have independently and collectively argued that the existence and scope of non-genetic inheritance systems, including epigenetic inheritance, niche construction/ecological inheritance, and cultural inheritance—alongside certain other theory revi-sions—necessitates an extension to the neo-Darwinian Modern Synthesis (MS) in the form of an Extended Evo-lutionary Synthesis (EES). However, this argument has been challenged on the grounds that non-genetic inheri-tance systems are exclusively proximate mechanisms that serve the ultimate function of calibrating organisms to stochastic environments. In this paper we defend our claims, pointing out that critics of the EES (1) conflate non-genetic inheritance with early 20th-century notions of soft inheritance; (2) misunderstand the nature of the EES in relation to the MS; (3) confuse individual phenotypic plasticity with trans-generational non-genetic inheritance; (4) fail to address the extensive theoretical and empirical literature which shows that non-genetic inheritance can generate novel targets for selection, create new genetic equilibria that would not exist in the absence of non-genetic inheritance, and generate phenotypic variation that is independent of genetic variation; (5) artificially limit ultimate explanations for traits to gene-based selection, which is unsatisfactory for phenotypic traits that originate and spread via non-genetic inheritance systems; and (6) fail to provide an explanation for biological organization. Mesoudi, Alex & Blanchet, Simon & Charmantier, Anne & Danchin, Etienne & Fogarty, Laurel & Jablonka, Eva & Laland, Kevin & Morgan, Thomas & Müller, Gerd & Odling-Smee, John & Pujol, Benoit. (2013). Is Non-genetic Inheritance Just a Proximate Mechanism? A Corroboration of the Extended Evolutionary Synthesis. Biological Theory. . . 10.1007/s13752-013-0091-5. https://www.researchgate.net/profile/Anne_Charmantier/publication/236873985_Is_Non-genetic_Inheritance_Just_a_Proximate_Mechanism_A_Corroboration_of_the_Extended_Evolutionary_Synthesis/links/59c20c23a6fdcc69b92fb603/Is-Non-genetic-Inheritance-Just-a-Proximate-Mechanism-A-Corroboration-of-the-Extended-Evolutionary-Synthesis.pdfDionisio_{January 20, 2018
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evo devo despacito? :) A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume numerous neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in a changing environment. Finally, we argue that molecular ‘springboards’ such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths. The evolution of complex adaptations poses conceptual challenges. Here, the authors discuss adaptive and non-adaptive scenarios in the evolution of complex adaptations and propose molecular mechanisms that provide access to new adaptive paths. Pál, Csaba & Papp, Balázs. (2017). Evolution of complex adaptations in molecular systems. Nature Ecology & Evolution. 1. 1084-1092. 10.1038/s41559-017-0228-1.Dionisio_{January 20, 2018
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evo devo despacito? :) Darwinism is one of several research traditions in evolutionary biology. I identify it, both before and after its unification with genetics, with Darwin’s theory of descent by natural selection from a common ancestor. Other traditions include saltationism/mutationism, Lamarckism, and evolutionary developmentalism (“evo-devo”). I argue that Darwinism’s continued dominance in evolutionary science reflects its proven ability to interact productively with these other traditions, an ability impressed on it by its founder’s example. Evolution by sudden leaps (saltations) is alien to the spirit of Darwinism, but Darwinism advanced its own agenda by incorporating and subverting saltationist themes. Similarly, Lamarckism’s belief in the heritability of acquired characteristics has been discredited, but some of the facts to which it seems congenial reappear in genetic Darwinism as phenotypic plasticity and niche construction. These examples help assess challenges to Darwinism’s hegemony currently arising from the role of regulatory genes and epigenetic factors in development. Rather than executing already entrenched genetic programs and relying on chance mutation to initiate evolutionary change, the developmental process appears to generate heritable variations that ab initio respond to environmental factors in an adaptive way. Depew, David. (2017). Darwinism in the Twentieth Century: Productive Encounters with Saltation, Acquired Characteristics, and Development. 61-88. 10.1007/978-3-319-69123-7_4.Dionisio_{January 20, 2018
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evo devo despacito? :) Project Genes, Environments, and the Creativity of Natural Selection in the Modern Evolutionary Synthesis and Beyond It (In Preparation) Bruce Weber Goal: (rest of title) Evolutionary Synthesis -- and Beyond David Depew and Bruce Weber (in press)Dionisio_{January 20, 2018
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evo devo despacito? :) The neo-Darwinian paradigm, focusing on natural selection of genes responsible for differential adaption, provides the foundation for explaining evolutionary processes. The modern synthesis is broader, however, focusing on organisms rather than on gene transmissions per se. Yet, strands of current biology argue for further supplementation of Darwinian theory, pointing to nonbiotic drivers of evolutionary development, for example, self-organization of physical structures, and the interaction between individual organisms, groups of organisms, and their nonbiotic environments. According to niche construction theory, when organisms and groups develop, they not only adapt to their environments but modify their environments, creating new habitats for later generations. Insofar as ecological niches persist beyond the lifecycle of individual organisms, an ecological inheritance system exists alongside genetic inheritance. Such ecological structures may even facilitate the development of a cultural inheritance system, as we see in humans. The article discusses theological perspectives of such new developments within holistic biology. Henrik Gregersen, Niels. (2017). THE EXPLORATION OF ECOSPACE: EXTENDING OR SUPPLEMENTING THE NEO-DARWINIAN PARADIGM?: with Fraser Watts and Michael J. Reiss, “Holistic Biology: What It Is and Why It Matters”; Michael Ruse, “The Christian's Dilemma: Organicism or Mecha. Zygon(r). 52. 561-586. 10.1111/zygo.12344.Dionisio_{January 20, 2018
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evo devo despacito? :) Recent developments toward a more holistic biology do not eliminate reductionism and determinism, but they do suggest more complex forms of them, in which there are multiple, interacting influences, as there are in complex or chaotic systems. Though there is a place in biology for both systemic and atomistic modes of explanation, for those with a theological perspective the shift to complex explanations in biology is often welcome. It suggests a more subtle view of divine action in which God's purposes are affected through engagement with the complex systems of creation rather than by discrete interventions. It also invites us to connect the biological interdependence with the interdependence in the nature and purposes of God, and it is consonant with a mystical vision of the unity of all things. Watts, Fraser & Reiss, Michael. (2017). HOLISTIC BIOLOGY: WHAT IT IS AND WHY IT MATTERS. Zygon(r). 52. 419-441. 10.1111/zygo.12339.Dionisio_{January 20, 2018
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evo devo despacito? :) Using the evolution of the stickleback family of subarctic fish as a touchstone, we explore the effect of new discoveries about regulatory genetics, developmental plasticity, and epigenetic inheritance on the conceptual foundations of the Modern Evolutionary Synthesis. Identifying the creativity of natural selection as the hallmark of the Modern Synthesis, we show that since its inception its adherents have pursued a variety of research projects that at first seemed to conflict with its principles, but were accommodated. We situate challenges coming from developmental biology in a dialectic between innovation and tradition, suggesting on the basis of past episodes that even if developmental plasticity and epigenetic inheritance are aligned with its principles the Modern Synthesis (and its image in the public reception of evolution) will be significantly affected. Depew, David & Weber, Bruce. (2017). DEVELOPMENTAL BIOLOGY, NATURAL SELECTION, AND THE CONCEPTUAL BOUNDARIES OF THE MODERN EVOLUTIONARY SYNTHESIS: with Fraser Watts and Michael J. Reiss, “Holistic Biology: What It Is and Why It Matters”; Michael Ruse, “The Christian's Dilemma: Organicism or Mecha. Zygon(r). 52. 468-490. 10.1111/zygo.12332.Dionisio_{January 20, 2018
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evo devo despacito? :) Smulders, Tom. (2017). Evolution Driven by Organismal Behaviour – a Unifying View of Life, Function, Form, Mismatches, and Trends By Rui Diogo, 252 pages. Springer International Publishing AG, Cham, Switzerland, 2017. ISBN: 978?3?319?47580?6.. Journal of Anatomy. . 10.1111/joa.12750.Dionisio_{January 20, 2018
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evo devo despacito? :) Bateson, Patrick & Cartwright, Nancy & Dupré, John & Laland, Kevin & Noble, Denis. (2017). New trends in evolutionary biology: Biological, philosophical and social science perspectives. Interface Focus. 7. 20170051. 10.1098/rsfs.2017.0051. https://www.researchgate.net/profile/John_Dupre/publication/319191327_New_trends_in_evolutionary_biology_Biological_philosophical_and_social_science_perspectives/links/599fee394585151e3c73d877/New-trends-in-evolutionary-biology-Biological-philosophical-and-social-science-perspectives.pdfDionisio_{January 20, 2018
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Since nobody answered the quiz, let's try to encourage more enthusiastic participation in next quiz. Maybe we could offer a nice prize to the winner of the quiz? What could we offer? Here's an idea: A dinner for two at the best restaurant by the littoral in Palermo. This was originally the prize for whoever could explain evolution, but since we have realized that it won't happen, then the funds can be used for the evo devo despacito quiz prize. Would that motivate more enthusiastic participation in the evo devo despacito quiz next time? :)Dionisio_{January 19, 2018
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evo devo despacito quiz: What does MESS stand for? Modern Evolutionary Shaky Synthesis which is based on Messy Evolutionary Shaky Standards IOW, MESS on top of MESS :)Dionisio_{January 19, 2018
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gpuccio @123:
all this stuff about biased mutations being an important factor in explaining biological function is completely unwarranted. Biological variation is both random and unrelated to function. It can explain nothing.
Clear point. Thanks.Dionisio_{January 19, 2018
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gpuccio @123:
the “bias” towards certain mutations cannot in any way explain how the code for a complex functional protein arises.
That's clear. Thanks.Dionisio_{January 19, 2018
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gpuccio @123:
the laws that determine the different probabilities of outcomes of random variation (for example, the different probabilities of specific nucleotide mutations) have no connection at all with the laws that determine the meaning of nucleotide sequences (as coded by the genetic code) and the biochemical functions of protein sequences (which depend on extremely complex biochemical laws, including those which cause folding).
Very valid point. Thanks.Dionisio_{January 19, 2018
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gpuccio @122, That's a valid point. Thanks. Is the author of the paper you referenced @122 another example of someone trying to butter their bread on both sides? :)Dionisio_{January 19, 2018
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Dionisio: d) But there is another important sense in which biological variation can be considered "random", even if random is not the correct word here. Let's say that biological variation, if unguided, is unrelated to function. IOWs, there is no reason why we should expect any statistically significant relationship between random (in the sense discussed at points b) and c) ) biological variation and biological function. Why? Because the laws that determine the different probabilities of outcomes of random variation (for example, the different probabilities of specific nucleotide mutations) have no connection at all with the laws that determine the meaning of nucleotide sequences (as coded by the genetic code) and the biochemical functions of protein sequences (which depend on extremely complex biochemical laws, including those which cause folding). IOWs, the "bias" towards certain mutations cannot in any way explain how the code for a complex functional protein arises. So, all this stuff about biased mutations being an important factor in explaining biological function is completely unwarranted. Biological variation is both random and unrelated to function. It can explain nothing. We can easily see the difference with the concept of NS. NS, even with all its extreme limitations, which I have discussed here: https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/ is, at least, related in some way to function. That's why the traditional algorithm of RV + NS remains the only weapon for neo-darwinism and, in general, for all non design "explanations". We know how weak that weapon is, but it's all they have... :)gpuccio_{January 19, 2018
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Dionisio: Having partially read some of the references you give, I would like to offer a couple of thought about the random nature of biological variation: a) If we exclude the scenario of design, and therefore of guided variation, we can certainly say that biological variation is random, in two important senses that I will try to clarify. b) The first sens is that biological variation is random because we cannot predict it according to necessity laws. In that sense, it is as random as tossing a coin. Both biological variation and coin tossing are completely deterministic (driven by the laws of physics and chemistry), but both systems cannot be described by a necessity system and are better described by a probabilistic system. c) It is absolutely true that biological variation is not an example of uniform distribution of probability. For example, nucleotide mutations are certainly not uniformly distributed, as we can see in this interesting paper by one of the authors you quote: https://academic.oup.com/jhered/article/100/5/637/782212 But I believe that the author is wrong in saying that this means that those mutations are "non random". They are random, because they can be described only by a probabilistic system, but of course the probabilities of the different events are different. That happens in most random systems, For example, in rolling two dice, the probability of the outcomes are very different. So, biological variation is truly random, but certainly different outcomes have different probabilities. More in next post.gpuccio_{January 19, 2018
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Whoever reads the posted paper references in this thread should figure out how to respond the easy evo devo despacito quiz.Dionisio_{January 19, 2018
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Ok, here's the answer to the evo devo despacito quiz: MESS is the acronym for...Dionisio_{January 19, 2018
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Hey, no one dares to respond the evo devo despacito quiz yet?Dionisio_{January 19, 2018
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evo devo despacito quiz: What does MESS stand for?Dionisio_{January 19, 2018
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evo devo despacito? Laland, Kevin & Uller, Tobias & Feldman, Marcus & Sterelny, Kim & Müller, Gerd & Moczek, Armin & Jablonka, Eva & Odling-Smee, John. (2014). Does evolutionary theory need a rethink? - POINT Yes, urgently. Nature. 514. 161-164. https://www.researchgate.net/profile/Gerd_Mueller/publication/278258986_Does_evolutionary_theory_need_a_rethink_-_POINT_Yes_urgently/links/55cd2f8708aebd6b88e05e5f/Does-evolutionary-theory-need-a-rethink-POINT-Yes-urgently.pdfDionisio_{January 18, 2018
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evo devo despacito? :) Many readers of this journal have been schooled in both Darwinian evolution and Skinnerian psychology, which have in common the vision of powerful control of their subjects by their sequalae. Individuals of species that generate more successful offspring come to dominate their habitat; responses of those individuals that generate more reinforcers come to dominate the repertoire of the individual in that context. This is unarguable. What is questionable is how large a role these forces of selection play in the larger landscape of existing organisms and the repertoires of their individuals. Here it is argued that non-Darwinian and non-Skinnerian selection play much larger roles in both than the reader may appreciate. The argument is based on the history of, and recent advances in, microbiology. Lessons from that history re-illuminate the three putative domains of selection by consequences: The evolution of species, response repertoires, and cultures. It is argued that before, beneath, and after the cosmically brief but crucial epoch of Darwinian evolution that shaped creatures such as ourselves, non-Darwinian forces pervade all three domains. Killeen, Peter. (2017). The non-Darwinian evolution of behavers and behaviors. Behavioural Processes. . 10.1016/j.beproc.2017.12.024. https://www.researchgate.net/profile/Peter_Killeen2/publication/322143232_The_non-Darwinian_evolution_of_behavers_and_behaviors/links/5a5eeb54a6fdcc68fa993749/The-non-Darwinian-evolution-of-behavers-and-behaviors.pdfDionisio_{January 18, 2018
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evo devo despacito? :) Noble, Denis & Jablonka, Eva & J. Joyner, Michael & Müller, Gerd & W. Omholt, Stig. (2014). Evolution evolves: Physiology returns to centre stage. The Journal of Physiology. 592. . 10.1113/jphysiol.2014.273151.Dionisio_{January 18, 2018
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evo devo despacito? :) Project Mutation, Randomness and Evolution (book) Arlin Stoltzfus Goal: The randomness doctrine appears to refer to a property of mutation, but when examined more closely, it emerges as one facet of a broad and deep commitment to the unequal marriage of variation and selection proposed by Darwin, in which selection is a governing principle, while variation is relegated to the provision of raw material--- clay to be shaped by the potter---, supplying substance only, not initiative, direction, or creativity. This book uses a dissection of the randomness doctrine to re-think the role of variation in evolution, providing (1) a fresh and useful explanation of how mutation works, and why it is not "random" in any precise sense, (2) how there are different domains of population genetics, only some of which correspond to the neo-Darwinian verbal theories of causation used by nearly all evolutionary biologists, (3) how a commitment to the Darwinian view of roles continues to shape evolutionary thinking, and (4) new analyses showing how mutation operates importantly as a source of initiative and direction, violating the role assigned to it in neo-Darwinism.Dionisio_{January 18, 2018
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evo devo despacito? :) The Functional Constructivism (FC) paradigm is an alternative to behaviorism and considers behavior as being generated every time anew, based on an individual's capacities, environmental resources and demands. Walter Freeman's work provided us with evidence supporting the FC principles. In this paper we make parallels between gradual construction processes leading to the formation of individual behavior and habits, and evolutionary processes leading to the establishment of biological systems. Referencing evolutionary theory, several formal descriptors of such processes are proposed. These FC descriptors refer to the most universal aspects for constructing consistent structures: expansion of degrees of freedom, integration processes based on internal and external compatibility between systems and maintenance processes, all given in four different classes of systems: (a) Zone of Proximate Development (poorly defined) systems; (b) peer systems with emerging reproduction of multiple siblings; (c) systems with internalized integration of behavioral elements ("cruise controls"); and (d) systems capable of handling low-probability, not yet present events. The recursive dynamics within this set of descriptors acting on (traditional) downward, upward and horizontal directions of evolution, is conceptualized as diagonal evolution, or di-evolution. Two examples applying these FC descriptors to taxonomy are given: classification of the functionality of neuro-transmitters and temperament traits; classification of mental disorders. The paper is an early step towards finding a formal language describing universal tendencies in highly diverse, complex and multi-level transient systems known in ecology and biology as "contingency cycles". Trofimova, Irina. (2017). Functional constructivism: In search of formal descriptors. Nonlinear Dynamics, Psychology, and Life Sciences. 21. 441-474. https://www.researchgate.net/profile/Irina_Trofimova2/publication/320418805_Functional_constructivism_In_search_of_formal_descriptors/links/59f89bd00f7e9b553ec0b8da/Functional-constructivism-In-search-of-formal-descriptors.pdfDionisio_{January 18, 2018
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