Thinking About Evolution25 Questions Christians Want AnsweredRoberts, Anjeanette, Rana, Fazale, Dykes,Sue and Perez,Markp15Outing Our Bias p17 Introduction p23 Ch 1: Does Evolution Explain Life on Earth? Anjeanette Roberts p33 Ch 2: Is Religious Belief the Only Reason to Question Evolution? Anjeanette Roberts p45 Ch 3: What's Philosophy Got to Do with Evolution? Anjeanette Roberts p55 Ch 4: How Can We Keep Our Thinking Free from Fallacy? Mark Perez p65 Ch 5: Is Evolution Really a Problem for the Christian Faith? Fazale Rana p75 Ch 6: What Is Chemical Evolution? Fazale Rana p85 Ch 7: Is Microevolution a Fact? Anjeanette Roberts p99 Ch 8: Does Microbial Evolution Prove Evolution is True? Anjeanette Roberts p107 Ch 9: Is Natural Selection the Blind Force Driving Evolution? Anjeanette Roberts p108 Quotes Dobzhansky with his famous quote: "Nothing in Biology makes sense except in the light of evolution" (Title of his book). Then proceeds to both agree and disagree with him and with the "Campbell's Biology" textbook (high school and college). p111 Looking for thoughts that characterize AJ's thinking. "Under specific selection pressures, specific traits would emerge from those preexisting in the population. This is the extent and role of natural selection. As far as creativity is concerned, it is fairly anemic, limited to sorting through variations within a population." p111 I still need to pin down "gene flow, drift and mutations" more clearly. p112-113 Mentions constructive neutral evolution theory (CNE) and EES (extended evolutionary synthesis), both of which I need to understand more clearly. Cites Gould and Eldridge and punctuated equilibrium with its sudden jumps in complexity but comments "But working out actual mechanisms coincidental to such leaps has remained, for the most part, unsolved and unarticulated." p112 "Although most agree that natural selection is the only evolutionary mechanism that consistently leads to adaptive evolution, the stepwise changes and gradual accrual of these to account for leaps in complexity have been challenged deeply in the scientific community as understanding has increased." p113 "Comparative genomics across higher taxa demonstrate that rather large genetic changes must occur to get from one type of organism to another." Quotes an EES advocate (Gerd B. Muller) and CNE advocates. p113 "Proponents of extended evolutionary synthesis (EES) and constructive neutral evolution theory (CNE) downplay natural selection primarily because functional adaptations tend toward a necessary gradual, stepwise process called panadaptationalism, where each step must gain a functional advantage to spread through and be fixed in a population." p113 "Evolutionary biologist and EES proponent Gerd B Muller, in a presentation to the Royal Society of London in 2016, stated that the modern synthesis can explain gradual variations, adaptations fo phenotypic characteristics, and some genetic variations in speciation. But, he argued, it is inadequate n explaining higher levels of evolution, including the origin of body plans, complex behaviors, complex physiologies, and developmental differences." p114 "Natural selection can only preserve currently functioning components, not neutrally drifting ones." p115 "In the modern synthesis, natural selection is the only directional force; in EES, cells are the agents of their own change." p115 Cites Perry Marshall and Evolution 2.0 Referring to EES "One feature of this model is that it generates information via the agency of the cell through words that may require few (or many) changes to have new meanings (functions) emerge." p116 Mentions teleology in paragraphs 2 & 3 - it's always hovering in the background. p 116 "EES advocates cite live evolutionary experiments that suggest cells possess powerful evolutionary machinery with some ability to predict future outcomes." p 116 "For 200 years, materialists and reductionists tried to ban teleology from science, but EES advocates say that not only is teleology essential to evolution, but ancient questions about mind vs body and free will vs determinism don't merely apply to humans. They reach all the way down to the cell." p117 "Despite all natural selection's shortcomings, many continue to uncritically accept its ability to drive evolutionary systems forward. One has little choice but to do so in a strictly materialistic universe." p119 Ch 10: Is There a Novelty Problem for Evolution? Anjeanette Roberts p120 Casually uses the word "phenotypically" for which I need to check the definition. p121 Good page of the story of Cit+ p122 Muller is the author of "The Extended Evolutionary Synthesis". Maybe need to go back to note her previous references to Muller. Refers to "evo devo" again so I need to clarify meaning. p123 Important page. Discusses evo-devo. "Evolutionary developmental biology (evo-devo) is the field of study shedding the greatest light on generating large morphological novelties in evolution. The work is fascinating and opens many avenues of fruitful exploration." p124 Refers to Michael Denton and notes that he has a chapter on evo devo in his book "Evolution: Still a Theory in Crisis". p125 Asks question "Can EES get us closer to true novelty?" Refers to Muller again, and refers to Perry Marshall, author of "Evolution 2.0". p125 Refers to James Shapiro and his "theory of natural genetic engineering". Sees cells as employing "genome duplication, as well as HGT and transposition, as biomolecular tools to disrupt their own genomes through major rearrangements and expansive acquisitions of new material (something Shapiro refers to as genetic shock)." p126 AJ's response: "Natural genetic engineering may work well in bacterial populations, archaea, simple eukaryotic organisms, and some plants, but it does not pass muster for driving major biological transitions in birds, mammals, and other higher organisms where it faces genuine, widespread species reproductive barriers." p126 Expressing reservations about this and evo-devo, uses quote "empirical evidence is needed to evaluate enthusiastic speculation." p126-127 Sequencing and comparing entire genomes has led to one of the most surprising findings for evolutionary biology. The surprise is the appearance of many genes with no determinable ancestry, called open reading frame genes ORF -> ORFan -> orphan genes. 9000 orphan genes found in an ash tree. The biggest surprise in 20 years. Orphan genes make up a sizable portion of each new genome sequenced. p130 In "Storytelling in Evolution" - still critical of Campbell's Biology, again cites Denton in "Evolution, Still a Theory in Crisis". p131-132 "Our critiques" "Campbell's Biology .. fails to provide credible pathways for developing new complexity." Compares their critique to that of Denton, EES, and CNE. (I need succinct summaries of EES and CNE) "lack of supporting evidence for the sufficiency of natural selection and panadaptationism to drive major biological transitions or leaps in complexity." p131 Modern Synthesis advocate Douglas Futuyma "empirical evidence is needed to evaluate enthusiastic speculation." (Add Futuyma to references including this source) p131 James Shapiro, EES proponent and originator of the theory of natural genetic engineering: "How natural genetic engineering leads to major new inventions of adaptive use remains a central problem in evolution science. To address this problem experimentally, we need to do more ambitious laboratory evolution research looking for complex coordinated changes in the genome." p132 First paragraph of summary is good - maybe I can make a concept map out of it. p132 "still lack plausible mechanisms to account for discontinuities ... The problem of novelty persists despite the best explanatory efforts." p135 Ch 11: What to Do With Teleology in Evolution Anjeanette Roberts p135 Dobzhansky "There is, of course, nothing conscious or intentional in the action of natural selection. A biological species does not say to itself, "Let me try tomorrow (or one million years from now) to grow in a different soil, or use a different food..." "Natural selection is at one and the same time a blind and creative process." p135 "Evolution does not have any predetermined goal in mind. It is a series of provesses that, all along the way, have no purpose driving it forward. At the heart of it evolution has purposeless processes acting within populations on variations that emerge from random mutations and genome-altering mechanisms." p135 "Evolution is largely dysteleological (purposeless), yet organisms fit together in highly complex, purpose-filled systems. It seems evolution has a problem with teleology." p137 Basically skeptical treatment of genetic algorithms (GAs). Cites Evolution 2.0 p138 "What's driving evolution?" Natural law model similar to anthropic principle for cosmology. Cites Davies and Denton. "innate parameters of nature limit the potential paths and outcomes that govern biochemical systems." p139 On anthropomorphing nature .. cites Francis Crick naturalists "must constantly tell themselves that the apparent design in nature is not real." Cites Marshall in Evolution 2.0 "We don't know how cells make choices." p140 "Despite a necessity for natural selection to work through gradual, stepwise advancements that demonstrate a basic continuum of adaptive survival of the fittest, nature is filled with persistent discontiunuities and leaps of complexity. EES proponents, neutral theorists (including CNE proponents), and structuralists (not mutually exclusive categories) are equally harsh on the failure of natural selection to adequately provide or demonstrate plausible provisions fo major biological transitions." "...they face a real or apparent teleology problem." p140 I am still struggling to get a clearer understanding of EES, CNE and their variations. She refers back to material in Ch 9, particularly pf 112-114. "EES advocates fill the gaps by endowing molecules or cells with volitional agency. Structuralists insist the governing laws of the universe must be 'directing' life's transitions according to set constraints. Others abandon natural selection's panadaptationalism and instead adopt neutral theory, proposed and mathematically modeled by Motoo Kimura in 1968." p140 "In neutral theory, it is primarily neutral mutations, especially large-scale neutral mutations occuring by macromutational mechanisms, accruing within populations over time that drive complexity and evolutionary progression. While neutral theory provides genetic grounds for de nova gene generation, constructive neutral evolution (CNE) in particular provides theoretical paths for apparent leaps in complexity." "These theoretical leaps result from neutral accrual of gradual changes and developmental shifts that result in large-scale, morphological changes. The conceptual pathways that CNE proponents propose lead to greater complexity through chance alone. Any teleology is mere illusion." p140 "CNE proponents herald their theory as a rival for intelligent design, rather than as anything demonstrably verifiable or anything that offers predictive value to research. CNE is steeped in philosophy. It only seems scientific because it restricts itself to naturalistic descriptions." p141 Quote from CNE source that tries to counter irreducible complexity with their proposals. p141-2 Includes the famous Lewontin quote which ends with "we cannot allow a Divine Foot in the door." p142 AJ has a couple of neat paragraphs about the obviousness of design. Both paragraphs worth quoting. Part: "Observation gives rise to inferences. If even casual onlookers see design and purpose in complex, hierarchical, information-bearing systems, then surely the burden of proof is on the one who claims design and purpose are not really there." p142 "in a world rightly understood as the masterpiece of a brilliant creator, volition and intent are not characteristics necessary for molecules, viruses, or cells. The Creator would have engineered and endowed living things with extremenly complex capacities for adaptation. " This gives the flavor of her subsequent paragraphs where she argues against volition at the cellular level. Argues that life is just a well-engineered system. p143 "Which Creation Model Gives Life Meaning? .. the Christian worldview not only endows individual lives with meaning, but also manifests purpose in the divinely engineered design of every cell, creature, and ecosystem. Cells and organisms adapt by design - excellent design, in fact." p143 "The divine Engineer used common designs of body plans, metabolic pathways, and biochemistry to form intricate networks of life, from the smallest cell to the grandest ecosystems. The shared biochemical and metabolic pathways allow experimentation and discovery in model organisms with applications across multiple phyla. Our discoveries in simple organisms have profound applications for human health and thriving and for creation care." p144 "A progressive creation model holds that the ultimate purpose - the teleology - of all life is to show God's power and wisdom, to bless humanity, and in a profound act of love, to allow humanity to see the design and enjoy uncovering its wondrous manifestations in nature. A progressive creation model gives life meaning." p147 Ch 12: Can Evolutionary Processes Generate New Information? Anjeanette Roberts p147 "I think that, in principle, evolutionary mechanisms can create information. At the level of microevolution and microbial evolution, natural process can account for the generation of new information. However, I question if these mechanisms can generate biological information under the conditions of early Earth in support of abiogenesis. I also question if these mechanisms can truly generate biological novelty." p148 In response to the question "What is information?" she refers to "Information and the Origin of Life"(1986) by Bernd-Olaf Kuppers and then discusses Shannon information and affirms that the sequence of nucleotides does represent Shannon information. p149 Discusses semantic and pragmatic information (after Kuppers) and says that "At the cellular level both dimensions are defined by the genetic code and the processes of transcription, translation, and the folding and post-translational modifications of proteins." p157 Ch 13: Does Evolution Explain the Fossil Record? Sue Dykes p167 Ch 14: What About the Genetic Similarity between Humans and Chimps? Sue Dykes p177 Ch 15: Are the Hominid Fossils Evidence for Human Evolution? Sue Dykes p189 Ch 16: Did Humans and Neanderthals Interbreed? Sue Dykes p201 Ch 17: Did Neanderthals Create Art? Sue Dykes p213 Ch 18: Can Evolutionary Processes Explain the Origin of Eukaryotic Cells? Fazale Rana p223 Ch 19: Can Evolution Repeat Outcomes? Fazale Rana p233 Ch 20: Can Evolutionary Co-option Explain the Irreducible Complexity of Biochemical Systems? Fazale Rana p243 Ch 21: Has Evolution Defeated the Watchmaker Argument? Fazale Rana p255 Ch 22: Is the Watchmaker Really Blind? Fazale Rana p267 Ch 23: Is Junk DNA Evidence for Evolution? Fazale Rana p275 Ch 24: Why Are We Progressive Creationists? Anjeanette Roberts p281 Ch 25: What If Big-E Evolution Is True? Anjeanette Roberts Working Explanations of Terms
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