Why Darwins theory of evolution does not explain biodiversity
https://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity
Claim: Natural Selection, Genetic Drift, and Gene Flow explain the origin of organismal complexity, and form.
https://www.nature.com/scitable/knowledge/library/natural-selection-genetic-drift-and-gene-flow-15186648/#:~:text=Natural%20selection%2C%20genetic%20drift%2C%20and%20gene%20flow%20are%20the%20mechanisms,Weinberg%20assumptions%2C%20and%20evolution%20occurs.
Reply: The assertion that biodiversity is due to evolution is held on faith by its supporters since the crucial evidence to back up the claim is lacking.
Natural selection is not powerful enough to cause huge change—it is not powerful enough to generate large sections of brand new genetic code (which would be necessary to generate entirely new taxonomic families)
Gerd B. Müller: Why an extended evolutionary synthesis is necessary 18 August 2017
These examples of conceptual change in various domains of evolutionary biology represent only a condensed segment of the advances made since the inception of the MS theory some 80 years ago. Relatively minor attention has been paid to the fact that many of these concepts, which are in full use today, sometimes contradict or expand central tenets of the MS theory. Given proper attention, these conceptual expansions force us to consider what they mean for our present understanding of evolution. Obviously, several of the cornerstones of the traditional evolutionary framework need to be revised and new components incorporated into a common theoretical structure.
Although today's organismal systems biology is mostly rooted in biophysics and biological function, its endeavors are profoundly integrative, aiming at multiscale and multilevel explanations of organismal properties and their evolution. Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction.
https://royalsocietypublishing.org/doi/10.1098/rsfs.2017.0015
Brian R. Johnson (2010): The nature of pattern-formation processes within the cell challenges the traditional view of genetic circuit boards (Kurakin 2005, 2007). According to that view, gene products—structural or enzymatic—do the work within the cell. When thinking about what sorts of genes should evolve and why, one naturally considers genes as acting either independently or in concert with one another. If, however, gene products guide processes already in motion, then the emphasis changes to selection for genes that manipulate and control pattern-formation mechanisms that have their own complex properties. This constrains (at the molecular level) what sort of evolutionary change is possible and also leads to a vision of evolution in which saltatory changes are more important than traditionally thought, as self-organizing mechanisms do not seem to be the products of slow, incremental change.
Brian R. Johnson: Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software December 2010
Marta Linde‑Medina On the problem of biological form 5 May 2020
At present, the problem of biological form remains unsolved. Another relevant finding has been the high degree of conservation of developmental genes across taxa. Developmental genes include those encoding transcription factors as well as genes encoding signalling molecules, both of which are involved in gene regulation during embryogenesis. Gene regulation provided an answer to some puzzling results, for example, why species as morphologically diferent as humans and mice nonetheless share 99% of their protein-coding sequences.
https://sci-hub.ren/10.1007/s12064-020-00317-3
What you believe to be true about evolution, is it true? Or do you just believe that it is true, because you were taught that it is true, but you never looked any further?
NEVER, in over 150 years, since Darwin's book " On the origin of species " was published, has even ONE, amongst hundreds or thousands, if not millions of science papers, provided ONE DEMONSTRATION, and empirical verifiable replicable evidence, that any of the evolutionary mechanisms proposed, could produce a primary macroevolutionary transition zone of speciation and population differentiation.
Simon Conway Morris: Evolutionary Paleobiology at Cambridge, (Runes of Evolution, 38)
argues that adaptation is not an undirected, random walk through all possibilities. For example, when muscle tissue develops into organs that produce electricity, the process requires very precise amino acid replacements at specific sites, together with accelerated evolution of the new function, and Conway Morris concludes that:
“there is little doubt that these changes are very far from random”
He, therefore, argues that while the underlying principles of Darwinian evolution are correct, they do not provide a complete explanation of development, and a more comprehensive theory of evolution is required.
R. DeSalle: Molecular Systematics and Evolution: Theory and Practice 2002
It remains a mystery how the undirected process of mutation, combined with natural selection, has resulted in the creation of thousands of new proteins with extraordinarily diverse and well-optimized functions. This problem is particularly acute for tightly integrated molecular systems that consist of many interacting parts . . . It is not clear how a new function for any protein might be selected for unless the other members of the complex are already present, creating a molecular version of the ancient evolutionary riddle of the chicken and the egg
https://3lib.net/book/2142545/34d7a6
Premise 1: In biosynthesis pathways, proteins are interdependent, meaning they rely on each other for the proper functioning of the pathway.
Premise 2: Interdependence among proteins in biosynthesis pathways indicates a purposeful arrangement to achieve a specific outcome.
Premise 3: A stepwise, evolutionary process would involve the gradual development of biosynthesis pathways, which could require the formation of intermediate protein components.
Premise 4: Many intermediates in an evolutionary process may not have full functionality or may even be nonfunctional.
Conclusion: Therefore, the interdependence of proteins in biosynthesis pathways, along with the presence of potentially nonfunctional intermediates, suggests that a stepwise, evolutionary process is not possible to explain the complex and interdependent nature of these pathways. An intelligent and intentional design is a more plausible explanation for the intricate and functional arrangement observed in biosynthesis pathways.
James A. Shapiro: Evolution: A View from the 21st Century May 18, 2011
It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant non-random patterns of change, and genome sequence studies confirm distinct biases in location of different mobile genetic elements’
https://3lib.net/book/1234158/b6c101
J Baguna: Evo-Devo: the Long and Winding Road 2003
Even to the most unbounded optimist, we are still far from understanding morphological diversity.
Eugene V. Koonin: The Origin at 150: is a new evolutionary synthesis in sight? 2010 Nov 1.
The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone. The idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784144/
Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Eugene V. Koonin*
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440604/
Is complexification the prevailing modality of evolution?
Phylogenomic reconstruction, at least for bacteria and Archaea, suggests otherwise. It is not surprising that differential gene loss dominates the evolution of commensal bacteria, such as Lactobacilli, from a complex free-living ancestor. A qualitatively similar pattern was detected in evolutionary reconstructions for all bacteria and archaea. Strikingly, more recent reconstructions that were performed using larger genome sets and more sophisticated computational methods confidently indicate that the genome of the last common ancestor of all extant archaea apparently was at least as large and complex as that of typical modern organisms in this domain of cellular life. Fully compatible reconstruction results have been reported for the expanded set of cyanobacterial genomes. Thus, counter-intuitively, at least in prokaryotes, genome shrinkage that is sometimes called streamlining and is attributed to increasing selective pressure in successful, large populations , appears to be is no less and probably more common than genome growth and complexification.
Sweeping gene survey reveals new facets of evolution MAY 28, 2018
The most extensive genetics study ever completed the Journal of Human Evolution May, 2018, revealed NO genetic evidence for Evolution. The author, an avid proponent of evolution, was reduced to the following conclusions:
And yet—another unexpected finding from the study—species have very clear genetic boundaries, and there's nothing much in between. "If individuals are stars, then species are galaxies," said Thaler. "They are compact clusters in the vastness of empty sequence space." The absence of "in-between" species is something that also perplexed Darwin, he said.
Perplexed and unexpected? Yes because they so desire proof, yet they can find none. Repeating a lie often may make the lie sound convincing to some, but it does not make it true.
https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html
Evolution physical intelligent guiding principle
Numerous scientists have questioned the efficacy of selection and random mutational changes as a mechanism for generating the bio-information necessary for morphological novelty (Eden 1966; Wadington 1968a, b, c; Gould 1982; Yockey 1992, Thomson 1992; Kauffman 1995; Perez 2010; Jorgensen 2007, 2012; Elsheikh 2010, 2014). Eden who was especially concerned about the elements of randomness contended “No currently existing language can tolerate random changes in the symbol sequences which express its sentences. Meaning is almost invariably destroyed. Any changes must be syntactically lawful ones.”
What, if Anything, Is an Evolutionary Novelty? Massimo Pigliucci
The modern synthesis ( of evolution ) provides us with explanatory tools to understand adaptations (natural selection) but falls short when it comes to the question of novelties
http://philpapers.org/archive/PIGWIA/
The origin of the vertebrate skeleton 16 August 2010
No coherent causative model of morphogenesis has ever been presented.
http://journals.cambridge.org/action/displayAbstract;jsessionid=79710AE9A71071921BD4A3CAC34D5C80.journals?aid=7928966&fileId=S147355041000025X
“Scaling expectations for the time to establishment of complex adaptations”, September 7, 2010,
“Although the vast majority of research in evolutionary biology is focused on adaption, a general theory for the population-genetic mechanisms by which complex adaptations are acquired remains to be developed.”
http://www.pnas.org/content/early/2010/08/30/1010836107.abstract
“Foundational Concepts: Evolution”
“Scientists are still uncovering the specifics of how, when, and why evolution produced the life we see on Earth today.”
http://www.nmnh.si.edu/paleo/geotime/main/foundation_life3.html
Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution May 3, 2018
A major goal of biology is to identify the genetic causes of organismal diversity.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007375
Evolution of Homeobox Gene Clusters in Animals: The Giga-Cluster and Primary vs. Secondary Clustering14 April 2016
There is uncertainty in our understanding of homeobox gene cluster evolution at present. This relates to our still rudimentary understanding of the dynamics of genome rearrangements and evolution over the evolutionary timescales being considered when we compare lineages from across the animal kingdom.
https://www.frontiersin.org/articles/10.3389/fevo.2016.00036/full
My comment: OH NO !!! I can't believe it !! They have no clue? Right. Pro scientists working on the field which try to find out how the instructions of gene expression and repression emerged, admit, they have no idea !!
What’s wrong with evolutionary biology? 20 December 2016
There have been periodic claims that evolutionary biology needs urgent reform. Irrespective of the content of the individual critiques, the sheer volume and persistence of the discontent must be telling us something important about evolutionary biology. Broadly speaking, there are two possibilities, both dispiriting. Either (1) the field is seriously deficient, but it shows a peculiar conservatism and failure to embrace ideas that are new, true and very important; or (2) something about evolutionary biology makes it prone to the championing of ideas that are new but false or unimportant, or true and important, but already well studied under a different branding.
It has been argued here that the discontent is better understood as stemming from a few inescapable properties of living things, which lead to disappointment with evolutionary biology, and a nagging feeling that reform must be overdue. Evolutionary biology, like history, but unlike other natural sciences, raises issues of purpose and agency, alongside those of complexity and generality.
https://link.springer.com/article/10.1007/s10539-016-9557-8?fbclid=IwAR37cKt9BHLC8m4W2YCxYLR9ywLp9Z3-WxSVKm0lPmkEguDYm6MAZvYvTFw
The fundamental theorem of natural selection with mutations 07 November 2017
...THE VAST MAJORITY OF MUTATIONS ARE DELETERIOUS. THIS IS ONE OF THE MOST WELL-ESTABLISHED PRINCIPLES OF EVOLUTIONARY GENETICS, SUPPORTED BY BOTH MOLECULAR AND QUANTITATIVE-GENETIC DATA."
"...a great deal of evidence from several sources strongly suggests that the overall effects of mutations are to REDUCE FITNESS."
Genome-wide analysis of a long-term evolution experiment with Drosophila.
2010 Sep 15
Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. 6
Evolution by epigenesis: farewell to Darwinism, neo- and otherwise
2004 May-Aug
In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. 7
https://www.ncbi.nlm.nih.gov/pubmed/15612191
Dissecting Darwinism
2012 Jan; 25
regarding the origin of the species and life (DNA), even Darwin commented, “If it could be shown that complex systems could not arise by small sequential steps, then my theory would completely break down.” Irreducibly complex systems involving thousands of interrelated specifically coded enzymes do exist in every organ of the human body. At an absolute minimum, the inconceivable self-formation of DNA and the inability to explain the incredible information contained in DNA represent fatal defects in the concept of mutation and natural selection to account for the origin of life and the origin of DNA. As new theories emerge that explain the origin of life, the inevitable emotional accusations of heresy and ignorance are not surprising in a period of scientific revolution. It is therefore time to sharpen the minds of students, biologists, and physicians for the possibility of a new paradigm. 8
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246854/
Werner Arber Nobel Prize in 1978, Physiology or Medicine (sharing the honor with Daniel Nathans and Hamilton O. Smith) for the discovery of restriction enzymes and their application to molecular genetics.
The deeper we penetrate in the studies of genetic exchange the more we discover a multitude of mechanisms" involved in human genetics that falsify the mutation plus natural selection core of macroevolution.
Arber, W, D. Nathans, and H. O. Smith. 1992. 1978 Physiology or Medicine, Nobel Lectures: Physiology or Medicine 1971-1980, 469-492.
James Shapiro Microbiologistof the University of Chicago :
There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations” (Shapiro 1996).
Lynn Margulis:
Although random mutations influenced the course of evolution, their influence was mainly by loss, alteration, and refinement... Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear. Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.
The accumulation of genetic mutations were touted to be enough to change one species to another….No. It wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.
I was taught over and over again that the accumulation of random mutations led to evolutionary change - led to new species. I believed it until I looked for evidence.
biology is opening the black box, and demonstrating how organisms develop. We are slowly getting out of a state of ignorance in regard of what mechanisms determines cell shape, assignment of their planes of division, tendencies to move, directions and rates of movement, modes of differentiation into particular cell types, and cell death (apoptosis).
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. The discovery and description of the spatial– temporal distribution of the gene expression pattern during morphogenesis, together with its key regulators, is one of the main recent achievements in developmental biology. Nevertheless, gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. 1
Kevin N. Laland: Animal learning as a source of developmental bias 26 August 2019
Learning can influence evolutionary processes in at least two separate ways: either through generating some phenotypic forms more readily than others (a variational bias) or through generating some environmental states more readily than others (a selective bias, a.k.a. “niche construction”).
https://onlinelibrary.wiley.com/doi/abs/10.1111/ede.12311
Based on evidence seen in biochemistry on a molecular level, we can now say affirmatively and conclusively, that Darwin's theory of evolution by natural selection in regards of primary speciation & macroevolutionary level has been falsified.
The selection of random changes of nucleotides being the source of all biological engineering: that claim is nonsense.
Genetic and epigenetic programmed instructional complex codified information and signaling through various signaling pathways on an integrated structural systems-level replace a Darwinian gene-centric view and its various subsequent adaptations, extensions, and new proposals like the modern extended synthesis or the so-called " third way ". The true mechanism is " Biochemical systems programming and signaling", and special creation of species and/or kinds by an intelligent powerful creator. Long periods of time and gradual, evolutionary development is not possible, face the fact that cells and organisms work like gigantic interlocked machines and factory complexes, wherein any case, if one tiny part is missing, nothing goes. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. No glycine amino acids, no pyrimidines, no DNA - no life. No Watson Crick base pair fine-tuning, no DNA - no life. No ribosomal mechanism for amino acid amide bondage, no proteins, no life. No nitrogenase enzymes to fix nitrogen in an energy-demanding, triple bond-breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life. No chlorophylls, no absorption of light to start photosynthesis, no starch and glucose - cells will have no food supply to sustain complex organisms - no advanced life on earth. No rubisco, no fix of CO2, no hydrocarbons - no advanced life. No counterion in retinal, and rhodopsin could not receive visible light - and there would be no vision on earth by any organism.
A framework for parsing heritable information 22 April 2020
A new framework recasts heredity as a complex, networked information system in which all the regulatory molecules that help the cell to function can constitute a store of hereditary information. Instructions not coded in the DNA are contained in the arrangement of the molecules within cells and their interactions with one another. This arrangement of molecules is preserved and passed down from one generation to the next. framework recasts inheritance as the combined effects of three components: entities, sensors and properties. Sensors are specific entities that interact with and respond to other entities or to their environment. Sensors respond to certain properties, such as the arrangement of a molecule, its concentration in the cell or its proximity to another molecule. Together, entities, sensors and properties enable a living organism to sense or 'know' things about itself and its environment. Some of this knowledge is used along with the genome in every generation to build an organism. Scientists don't currently have methods to measure some of these things, so this work points to potentially important new avenues for research. 3
http://spaceref.com/news/viewpr.html?pid=55614
Epigenetic Principles of Evolution, 2011, page 19:
The basic tenet of the neo-Darwinian paradigm that changes in genes are responsible for morphological evolution, on which this edifice rises, is not substantiated, hence the empirical foundation of the structure is questionable at best.
If I had to mention ONE word which refutes evolution by mutations and natural selection to explain biological development, body architecture, biodiversity, adaptation, regulation, governing, controlling, recruiting, interpretation, recognition, orchestrating, elaborating strategies, guiding, it would be: SIGNALING. Furthermore the transmission of codified genetic and epigenetic information for development, and adaptation to external cues like food resources and availability, and environmental conditions.
Natural selection cannot induce a design to appear.
And yet, an Aristotelian mythology has been erected, imagining that natural selection creates things. This brings us back to this weekend’s debate, in which evolutionists Lawrence Krauss and Denis Lamoureux propagated and insisted upon this myth, and Stephen Meyer was presented with an enormous unpacking job. How does one disabuse two interlocutors whose perceived success depends on them not understanding the basic facts—in 30 seconds or less? 7
The Biological Big Bang model for the major transitions in evolution
Eugene V Koonin 20 August 2007
Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.
A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs.
EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY
Eric H. Davidson 2011 Feb 12
The neo-Darwinism ‘erroneously assumes that change in protein coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual.’ 1
James Shapiro: Microbiologistof the University of Chicago :
There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations” (Shapiro 1996).
Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words : Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system ?
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional. Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.
Claim: Evolution is a scientific theory with emphasis on the word “scientific”. It is observable, based on PHYSICAL evidence.
Answer: Evolution by natural selection ( as the mechanism of the origin of species ) is the most successful and widely believed and accepted fairy-tale story ever invented and told, which keeps surviving despite 160 years of scientific advance and discoveries which have falsified the claim. It is able to survive by hiding and disguising behind names as " science', " peer reviewed", " fact", " consensus", and " rational", and because sold and indoctrinated in schools at science classes as credible serious science, endorsed and defended by most specialists like chemists and biologists, and at most universities in the world. Since 90% of the population is gullible and prefer simply to believe others say, they buy the lie, endorse and defend it. Most do not know that there is no consensus about common ancestry. There are critical differences in DNA replication, and the cell membrane, between eukaryotes, and prokaryotes. And mutations in DNA are not determinant of many determinants of body form, shape, and cell differentiation. Epigenetic factors are probably even more relevant than genetic variation to define body form and development. And with that baggage in their mind, they make the leap of faith and believe, that their "knowledge" makes God superfluous. And so, they can live their lives as pleases, leaving God out of their lives.
The implicit connotation is that when a claim is scientific, it is most probably true since it went through an exhaustive process of peer review and empirical tests. Since evolution as scientific theory stood the test of time, it merits credibility. Science equals to the truth. Since evolution is scientific, it's trustworthy. If the claim is not scientific, it is most probably based on blind faith, and not worth to be taken seriously. For this reason, Darwinists try to discredit Intelligent Design as not being science, but religion. Once they achieve that goal, a further investigation of the scientific facts becomes superfluous.
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Darwins Theory of Natural selection has been falsified
https://reasonandscience.catsboard.com/t2484-darwins-theory-of-natural-selection-has-been-falsified
Op-Ed: Genetic mutations challenges Darwin’s evolution theory
DEC 28, 2012
The death of Darwin's evolution theory continues due to the evidence found in genome deterioration, sickle cell anemia mortality, beneficial mutations elusiveness, disease proliferation, and recent genetic mutations. Analysis of DNA/RNA mutations reveals that these genetic transformations cannot offer meaningful new information in significant quantities. Rather, these mutations will generate information degradation in the genome. 1
Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
PEER-REVIEWED September 26, 2008
We allowed mutation rates to evolve, and we evaluated the proximity to the optimum. Although we chose conditions favorable for mutation rate optimization, the evolved rates were invariably far below the optimum across a wide range of experimental parameter settings. We hypothesized that the reason that mutation rates evolved to be suboptimal was the ruggedness of fitness landscapes. We conclude that rugged fitness landscapes can prevent the evolution of mutation rates that are optimal for long-term adaptation. This finding has important implications for applied evolutionary research in both biological and computational realms. 2
Random mutations deteriorate the genome
In a new paper in Science, 3Khan et al, working with Richard Lenski [Michigan State], leader of the longest-running experiment on the evolution of E. coli, found a law of diminishing returns with beneficial mutations due to negative epistasis. The abstract said:
Epistatic interactions between mutations play a prominent role in evolutionary theories. Many studies have found that epistasis is widespread, but they have rarely considered beneficial mutations. We analyzed the effects of epistasis on fitness for the first five mutations to fix in an experimental population of Escherichia coli. Epistasis depended on the effects of the combined mutations—the larger the expected benefit, the more negative the epistatic effect. Epistasis thus tended to produce diminishing returns with genotype fitness, although interactions involving one particular mutation had the opposite effect. These data support models in which negative epistasis contributes to declining rates of adaptation over time. 3
Non-random mutations: How life changes itself: the Read-Write (RW) genome
And all available scientific evidence also indicates that evolution is an engineered process. In engineering and computer science, evolution never happens by accident. It’s always the result of a deliberate act. A program that can self-evolve is always considered an engineering marvel. 4
Scientists engineer animals with ancient genes to test causes of evolution
January 13, 2017
“For the first test case, we chose a classic example of adaptation-how fruit flies evolved the ability to survive the high alcohol concentrations found in rotting fruit. We found that the accepted wisdom about the molecular causes of the flies’ evolution is simply wrong. 5 Siddiq and Thornton realized that this hypothesis could be tested directly using the new technologies. Siddiq first inferred the sequences of ancient Adh genes from just before and just after D. melanogaster evolved its ethanol tolerance, some two to four million years ago. He synthesized these genes biochemically, expressed them, and used biochemical methods to measure their ability to break down alcohol in a test tube. The results were surprising: the genetic changes that occurred during the evolution of D. melanogaster had no detectable effect on the protein’s function.[/size]
What’s that you say? No detectable effect?
One supposes that the gene selected is one, among very many, that can be best ‘reverse-engineered’ to give a facsimile of the ‘ancient’ form. Yet, when tested in vivo, there is no difference found between the supposed ‘slow’ ancestral gene, and the ‘fast’ extant form. This is not how neo-Darwinism is supposed to work. Something is seriously wrong, no? It might be that the techniques employed to identify the ‘ancestral’ form are bad. Maybe that’s it, and it alone. But, OTOH, maybe something is seriously wrong with current neo-Darwinian theory. Some notions concerning adaptation will, therefore, remain difficult to study rigorously. Nevertheless, because of technical and conceptual advances, it should now be possible to experimentally assess the causal predictions of many previously untested or weakly tested hypotheses of historical molecular adaptation, allowing them to be corroborated or, like the classic hypothesis of ADH divergence in D.melanogaster, decisively refuted. One wonders what’s really left of natural selection. Between Behe’s Edge of Evolution, Shapiro’s “Natural Genetic Engineering,” the whole field of epigenetics, the disappearing of “Junk-DNA”, and now the disappearance of a ‘fitness’ change in a “classic case” of molecular adaptation, can anyone seriously believe that Darwinism has much to say about how life evolves? Remarkably, already in 2010, following paper reported that the claim of NS was not observed in Drosophila.
Genome-wide analysis of a long-term evolution experiment with Drosophila.
2010 Sep 15
"Genomic changes caused by epigenetic mechanisms tend to fail to fixate in the population, which reverts back to its initial pattern." That's not all that doesn't fixate. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. 6
Evolution by epigenesis: farewell to Darwinism, neo- and otherwise
2004 May-Aug
In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. 7
https://www.ncbi.nlm.nih.gov/pubmed/15612191
Dissecting Darwinism
2012 Jan; 25
regarding the origin of the species and life (DNA), even Darwin commented, “If it could be shown that complex systems could not arise by small sequential steps, then my theory would completely break down.” Irreducibly complex systems involving thousands of interrelated specifically coded enzymes do exist in every organ of the human body. At an absolute minimum, the inconceivable self-formation of DNA and the inability to explain the incredible information contained in DNA represent fatal defects in the concept of mutation and natural selection to account for the origin of life and the origin of DNA. As new theories emerge that explain the origin of life, the inevitable emotional accusations of heresy and ignorance are not surprising in a period of scientific revolution. It is therefore time to sharpen the minds of students, biologists, and physicians for the possibility of a new paradigm. 8
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246854/
Werner Arber Nobel Prize in 1978, Physiology or Medicine (sharing the honor with Daniel Nathans and Hamilton O. Smith) for the discovery of restriction enzymes and their application to molecular genetics.
The deeper we penetrate in the studies of genetic exchange the more we discover a multitude of mechanisms" involved in human genetics that falsify the mutation plus natural selection core of macroevolution.
Arber, W, D. Nathans, and H. O. Smith. 1992. 1978 Physiology or Medicine, Nobel Lectures: Physiology or Medicine 1971-1980, 469-492.
James Shapiro Microbiologistof the University of Chicago :
There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations” (Shapiro 1996).
Lynn Margulis:
Although random mutations influenced the course of evolution, their influence was mainly by loss, alteration, and refinement... Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear. Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.
The accumulation of genetic mutations were touted to be enough to change one species to another….No. It wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.
I was taught over and over again that the accumulation of random mutations led to evolutionary change - led to new species. I believed it until I looked for evidence.
biology is opening the black box, and demonstrating how organisms develop. We are slowly getting out of a state of ignorance in regard of what mechanisms determines cell shape, assignment of their planes of division, tendencies to move, directions and rates of movement, modes of differentiation into particular cell types, and cell death (apoptosis).
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. The discovery and description of the spatial– temporal distribution of the gene expression pattern during morphogenesis, together with its key regulators, is one of the main recent achievements in developmental biology. Nevertheless, gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. 1
Steve Meyer: Darwins Doubt, page 136
Randomly cutting and pasting larger blocks of text, as evolutionary biologists often envision, would not make any appreciable difference to the efficacy of a random search of sequence space. Imagine a computer “mutating” at random the text of the play Hamlet either by individual-letter substitutions or by duplicating, swapping, inverting, or recombining whole sections of Shakespeare’s text. Would such a computer simulation have a realistic
chance of generating a completely different and equally informative text such as, say, The Blind Watchmaker by Richard Dawkins, even granting multiple millions of undirected mutational iterations?
===============================================================================================================================================
1. The term 'evolution' is an equivocation fallacy that attempts to define two different proposed processes under the same definition. It is a violation of the logical reasoning process to conclude that the genetic variation we can observe within and around species explains the creation of complex body plans, organs, and other complex systems. Darwin's theory is illogical, serendipitous, and unproven.
2. Complex life by complete accident over billions and trillions of successive serendipitous accidents is an incredulous claim without evidence.
3. Calculations of the time necessary to evolve from goo-to-you reveal such a low probability of macro-evolution happening that the odds are beyond the threshold of 'impossible'. Hitchen's was correct - "What can be asserted without evidence can be dismissed without evidence"...
1. Neo-Darwinism and the Modern Synthesis propose a gene-centric view, a scientific metabiological proposal going back to Darwin's landmark book " On the origin of species " in 1859, where first natural selection was proposed as the mechanism of biodiversity, and later, gene variation defining how bodies are built and organized.
2. Science researchers have discovered, that robust networks of interactions and biological function, major morphological innovation, development and body form are based on integrative mechanisms, the interplay of genes with the gene regulatory network, Transposons and Retrotransposons, so-called Junk DNA, splicing, and over a dozen epigenetic codes, Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, Ion channels, Sugar molecules on the exterior of cells (the sugar code), that are not specified by nuclear DNA - that is, inheritance is not defined through DNA sequences alone.
3. Science is coming to recognize, that none of the recently proposed alternatives, like the third way, Saltationism, Saltatory ontogeny, mutationism, Genetic drift, or combined theories, do full justice by taking into account all organizational biophysiological hierarchy and complexity which empirical science has come to discover. As such, only a holistic view, namely structuralism, takes into consideration all influences that form cell form and size, body development and growth, doing justice to the scientific evidence.
4. Scrutinizing which causes ultimately respond for the complexity discovered in life is only satisfying, once the epistemologically flawed foundation of methodological naturalism is taken out of the box, and replaced by a new paradigm, where all possible mechanisms and causal influences are permitted to be scrutinized, investigated, and scientifically tested, including the interaction and creative force of an external intelligent, mental agency outside the known physical world, which through its transcendent power creates, forms and builds all physiobiological lifeforms in all its astounding diversity.
1. Evolution depends on huge ages, billion of years. Radiometric dating is not reliable.
2. The millions or billions of transitional fossils are missing
3. There is no empirical data of an unorganized undirected unguided Neo-Darwinian accidental random macro-evolutionary event of a change/transition, where one "kind" did evolve into another beyond the species level (i.e. speciation) , like an organism randomly changing/transition into a whole entirely different, new fully functioning biological organism, the emergence of new complex functions, a new genus or higher rank in taxonomy, with the rise of new body plans
4. Species appear and disappear abruptly in the fossil record.
5. Homo erectus, the precursor of homo sapiens, supposedly populated the earth for 1,5 million years. Where are the millions of fossils that should be buried and be found? They are missing.
6. Most species never changed. We have many animals, like Crocodiles, fish, crabs, insects, that can be found in the fossil record. unchanged.
7. Many fossils have been found with soft tissue, collagen, and proteins, which could not have remained preserved for millions of years.
8. DNA contains a blueprint, an instruction manual to make you, for example. Books, Blueprints, Instruction manuals, information retrieval, transmission, and translation systems do not emerge randomly. They have always an author and can be traced back to an intelligent source.
9. Machines, assembly lines, computers, recycle systems, error check and repair systems are always invented by intelligence. Biological cells host all this.
10. The information in the genome does not increase but deteriorate.
11. The human brain is 4 times the size and weight of a Chimp. It is supposed that a common ancestor of Apes and Humans lived 4 million years ago, and from there on, speciation into humans and apes began. The human brain has about 100 billion neurons. That means, there would have had to be the evolution from about 25billion of the common ancestor to 100billion of humans today, or an increase of 75 billion neurons in 4 million years. Or 25 thousand new neurons per year. Each Neuron has 10 thousand synapses, which connect to other neurons. Synapses function like a microprocessor and these over ten thousand per neuron would have had to find out how to connect correctly to other neighboring neurons. That is, 25 thousand new neurons, each with 10 thousand synapses, interconnecting correctly, per year !!
12. You cannot change just one body part. In order for evolution to account for the transition of land-living animals, to birds, for example, the whole body plan has to change, and not just single point mutations.
13. Natural selection has been shown to be able to account maximum for two mutations ( malaria ), but for new complex traits to emerge, at least six mutations are required, and it would take too much time to fix them into the population. ( Behe )
14. It has commonly been claimed that the question of how the eye evolved, has been answered. But scientists know this is not true. Rhodopsin is the key enzyme of sight. It is composed of two interdependent parts. Opsin, and retinal. One has no function without the other. And both are finely tuned to interact together. How can evolution explain its origin, if one has no function alone?
An article in Nature magazine confirms :
even as far back as the prokaryotes, the complex seven transmembrane domain arrangement of opsin molecules seems to prevail without simpler photoreceptors existing concurrently. Darwin’s original puzzle over ocular evolution seems still to be with us but now at a molecular level.
15. All complex life forms require interdependent parts. The human eye consists of over two million working parts making it second only to the brain in complexity. The human visual system depends on eye muscles, lubrification, a reliable communications channel (the optic nerve), the data to the central processing unit (the brain) via the visual cortex. If one of these components is missing, no deal. They had to evolve together, but during the evolution process, the single components would confer no survival advantage. What good would an optic nerve be for, without the eye, and the brain?
If someone approaches you, and asks, why is evolution not true, how could we answer in simple terms, without being too technical? I would first outline, that there must be made a differentiation. Darwin's theory has to be subdivided into three main aspects of the theory. 1. Adaptation, the tree of life, where it is claimed, that all life and biodiversity originated from one single ancestor, and macroevolution, and biodiversity which is claimed to be due to macroevolution. The dispute is about common ancestry and macroevolution. Bacteria do not share the same replication process, nor the same cell membrane as animals ( eukaryotes ). Even peer-reviewed science papers admit that, and so, common ancestry of all domains of life is a refuted claim. Most phyla ( animal forms ) appear suddenly in the geological strata, and not gradually, so the fossil record does not support evolution. Macro-evolution has also never been observed in the laboratory. Bacterias can adapt to antibiotics, but will never become something else, then bacteria. A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional. Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution. Furthermore, organisms on a molecular level are full of molecular machines, Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. 1. Complex machines and factories are intelligently designed 2. Biological cells are factories full of complex machines 3. Biological cells are intelligently designed. It has been claimed that so called Junk DNA is evidence of remnants of evolution, and is junk - or, has no function. The design prediction that Junk DNA HAS function is being unraveled, and more and more it is clear, that Junk DNA fullfills life essential functions, like gene regulation ( that is, when a gene is expressed ). Body plan building, and consequently, its supposed evolution, does not depend uniquely on information contained in the genetic code, but beyond ( epigenetics ). That is, what causes body form, and cell size and shape, depends on Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, cell membrane Ion channels and their location, and sugar molecules on the exterior of cells (the sugar code), Gene regulatory networks, Transposons and Retrotransposons, and at least on a dozen epigenetic informational codes.
Many individuals who believe in evolution are convinced that there exists an abundance of transitional forms to support evolution. However, what they regard as "transitional" are simply biological similarities between various species or groups, and are not true or actual transitions in Nature. Creationists believe that the biological similarities between various species are due to a common Designer who designed similar functions for similar purposes in all of the various forms of life, from the simplest to the most complex. Evolutionists believe that the biological similarities between species are evidence of common ancestry between all forms of life. Neither position can be scientifically proved.
https://english.pravda.ru/science/106586-evolution_theory/
T.Yonezawa (2012): Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth
It seems likely that a huge amount of trials and errors of different forms occurred during the emergence of life and that UCA if existed was just one of them. The probability of survival of life is low unless there are multiple origins.
https://www.hindawi.com/journals/tswj/2012/479824/
Evolution: Charles Darwin was wrong about the tree of life
Genetic tests on bacteria, plants and animals increasingly reveal that different species crossbreed more than originally thought, meaning that instead of genes simply being passed down individual branches of the tree of life, they are also transferred between species on different evolutionary paths. The result is a messier and more tangled "web of life". The findings mean that to link species by Darwin's evolutionary branches is an oversimplification. "The tree of life is being politely buried," said Michael Rose, an evolutionary biologist at the University of California, Irvine. "What's less accepted is that our whole fundamental view of biology needs to change."
https://www.theguardian.com/science/2009/jan/21/charles-darwin-evolution-species-tree-life
Frank Zindler, President of American Atheists, in 1996
The most devastating thing though that biology did to Christianity was the discovery of biological evolution. Now that we know that Adam and Eve never were real people the central myth of Christianity is destroyed. If there never was an Adam and Eve there never was an original sin. If there never was an original sin there is no need of salvation. If there is no need of salvation there is no need of a Savior. And I submit that puts Jesus, historical or otherwise, into the ranks of the unemployed. I think that evolution is absolutely the death knell of Christianity.
Reply: The two basic tenets upon which the theory of evolution rests, are the claim of universal common ancestry, and the tree of life. The two claims have been refuted on many grounds. When we talking about the tree of life, we cannot overlook the origin of viruses. Eugene V. Koonin admitted openly in 2020: In the genetic space of viruses and MGEs, no genes are universal or even conserved in the majority of viruses. Viruses have several distinct points of origin, so there has never been a last common ancestor of all viruses. The universal common ancestry of life is also disputed. For example Eric Bapteste, evolutionary biologist: "We have no evidence at all that the tree of life is a reality." DAVID M. RAUP, paleontologist: Multiple origins of life in the early Precambrian is a reasonable possibility. And C.P. Kempes in the peer-reviewed article: The Multiple Paths to Multiple Life (2021): We argue for multiple forms of life realized through multiple different historical pathways. In regard to the origin of humans: All human beings are 99.9 percent identical in their genetic makeup. Harmful protein-coding mutations in people arose largely in the past 5,000 to 10,000 years. Evidence for a Human Y Chromosome Molecular Clock: Pedigree-Based Mutation Rates Suggest a 4,500-Year History for Human Paternal Inheritance. By comparing the mitochondrial DNA of 147 people from five different ethnic groups, the researchers found that all the individuals analyzed were descendants of the same female lineage, that is, they all had the same original "mother" at the beginning of everything. Thus, they confirmed that all humanity descends from the same woman, who would have been the first Homo sapiens. And they called her "Mitochondrial Eve". These few quotes demonstrate that the major evolutionary tenets are far from being a scientific fact, or consensus among specialists in the field. Adding the complete failure of abiogenesis research permits the inference from eliminative induction:
The most devastating thing though that biology has done to naturalism is the failed claim of chemical and biological evolution. Now that we know that Adam and Eve were real people the central creation narrative of Christianity is confirmed. If there was an Adam and Eve there was an original sin. If there was an original sin there is need of salvation. If there is need of salvation there is need of a Savior. And I submit that puts Jesus, historical or otherwise, into the ranks of the necessary. I think that the failure of abiogenesis and evolution is absolutely the death knell of naturalism.
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/
https://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity
Claim: Natural Selection, Genetic Drift, and Gene Flow explain the origin of organismal complexity, and form.
https://www.nature.com/scitable/knowledge/library/natural-selection-genetic-drift-and-gene-flow-15186648/#:~:text=Natural%20selection%2C%20genetic%20drift%2C%20and%20gene%20flow%20are%20the%20mechanisms,Weinberg%20assumptions%2C%20and%20evolution%20occurs.
Reply: The assertion that biodiversity is due to evolution is held on faith by its supporters since the crucial evidence to back up the claim is lacking.
Natural selection is not powerful enough to cause huge change—it is not powerful enough to generate large sections of brand new genetic code (which would be necessary to generate entirely new taxonomic families)
Gerd B. Müller: Why an extended evolutionary synthesis is necessary 18 August 2017
These examples of conceptual change in various domains of evolutionary biology represent only a condensed segment of the advances made since the inception of the MS theory some 80 years ago. Relatively minor attention has been paid to the fact that many of these concepts, which are in full use today, sometimes contradict or expand central tenets of the MS theory. Given proper attention, these conceptual expansions force us to consider what they mean for our present understanding of evolution. Obviously, several of the cornerstones of the traditional evolutionary framework need to be revised and new components incorporated into a common theoretical structure.
Although today's organismal systems biology is mostly rooted in biophysics and biological function, its endeavors are profoundly integrative, aiming at multiscale and multilevel explanations of organismal properties and their evolution. Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction.
https://royalsocietypublishing.org/doi/10.1098/rsfs.2017.0015
Brian R. Johnson (2010): The nature of pattern-formation processes within the cell challenges the traditional view of genetic circuit boards (Kurakin 2005, 2007). According to that view, gene products—structural or enzymatic—do the work within the cell. When thinking about what sorts of genes should evolve and why, one naturally considers genes as acting either independently or in concert with one another. If, however, gene products guide processes already in motion, then the emphasis changes to selection for genes that manipulate and control pattern-formation mechanisms that have their own complex properties. This constrains (at the molecular level) what sort of evolutionary change is possible and also leads to a vision of evolution in which saltatory changes are more important than traditionally thought, as self-organizing mechanisms do not seem to be the products of slow, incremental change.
Brian R. Johnson: Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software December 2010
Marta Linde‑Medina On the problem of biological form 5 May 2020
At present, the problem of biological form remains unsolved. Another relevant finding has been the high degree of conservation of developmental genes across taxa. Developmental genes include those encoding transcription factors as well as genes encoding signalling molecules, both of which are involved in gene regulation during embryogenesis. Gene regulation provided an answer to some puzzling results, for example, why species as morphologically diferent as humans and mice nonetheless share 99% of their protein-coding sequences.
https://sci-hub.ren/10.1007/s12064-020-00317-3
What you believe to be true about evolution, is it true? Or do you just believe that it is true, because you were taught that it is true, but you never looked any further?
NEVER, in over 150 years, since Darwin's book " On the origin of species " was published, has even ONE, amongst hundreds or thousands, if not millions of science papers, provided ONE DEMONSTRATION, and empirical verifiable replicable evidence, that any of the evolutionary mechanisms proposed, could produce a primary macroevolutionary transition zone of speciation and population differentiation.
Simon Conway Morris: Evolutionary Paleobiology at Cambridge, (Runes of Evolution, 38)
argues that adaptation is not an undirected, random walk through all possibilities. For example, when muscle tissue develops into organs that produce electricity, the process requires very precise amino acid replacements at specific sites, together with accelerated evolution of the new function, and Conway Morris concludes that:
“there is little doubt that these changes are very far from random”
He, therefore, argues that while the underlying principles of Darwinian evolution are correct, they do not provide a complete explanation of development, and a more comprehensive theory of evolution is required.
R. DeSalle: Molecular Systematics and Evolution: Theory and Practice 2002
It remains a mystery how the undirected process of mutation, combined with natural selection, has resulted in the creation of thousands of new proteins with extraordinarily diverse and well-optimized functions. This problem is particularly acute for tightly integrated molecular systems that consist of many interacting parts . . . It is not clear how a new function for any protein might be selected for unless the other members of the complex are already present, creating a molecular version of the ancient evolutionary riddle of the chicken and the egg
https://3lib.net/book/2142545/34d7a6
Premise 1: In biosynthesis pathways, proteins are interdependent, meaning they rely on each other for the proper functioning of the pathway.
Premise 2: Interdependence among proteins in biosynthesis pathways indicates a purposeful arrangement to achieve a specific outcome.
Premise 3: A stepwise, evolutionary process would involve the gradual development of biosynthesis pathways, which could require the formation of intermediate protein components.
Premise 4: Many intermediates in an evolutionary process may not have full functionality or may even be nonfunctional.
Conclusion: Therefore, the interdependence of proteins in biosynthesis pathways, along with the presence of potentially nonfunctional intermediates, suggests that a stepwise, evolutionary process is not possible to explain the complex and interdependent nature of these pathways. An intelligent and intentional design is a more plausible explanation for the intricate and functional arrangement observed in biosynthesis pathways.
James A. Shapiro: Evolution: A View from the 21st Century May 18, 2011
It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant non-random patterns of change, and genome sequence studies confirm distinct biases in location of different mobile genetic elements’
https://3lib.net/book/1234158/b6c101
J Baguna: Evo-Devo: the Long and Winding Road 2003
Even to the most unbounded optimist, we are still far from understanding morphological diversity.
Eugene V. Koonin: The Origin at 150: is a new evolutionary synthesis in sight? 2010 Nov 1.
The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone. The idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784144/
Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Eugene V. Koonin*
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440604/
Is complexification the prevailing modality of evolution?
Phylogenomic reconstruction, at least for bacteria and Archaea, suggests otherwise. It is not surprising that differential gene loss dominates the evolution of commensal bacteria, such as Lactobacilli, from a complex free-living ancestor. A qualitatively similar pattern was detected in evolutionary reconstructions for all bacteria and archaea. Strikingly, more recent reconstructions that were performed using larger genome sets and more sophisticated computational methods confidently indicate that the genome of the last common ancestor of all extant archaea apparently was at least as large and complex as that of typical modern organisms in this domain of cellular life. Fully compatible reconstruction results have been reported for the expanded set of cyanobacterial genomes. Thus, counter-intuitively, at least in prokaryotes, genome shrinkage that is sometimes called streamlining and is attributed to increasing selective pressure in successful, large populations , appears to be is no less and probably more common than genome growth and complexification.
Sweeping gene survey reveals new facets of evolution MAY 28, 2018
The most extensive genetics study ever completed the Journal of Human Evolution May, 2018, revealed NO genetic evidence for Evolution. The author, an avid proponent of evolution, was reduced to the following conclusions:
And yet—another unexpected finding from the study—species have very clear genetic boundaries, and there's nothing much in between. "If individuals are stars, then species are galaxies," said Thaler. "They are compact clusters in the vastness of empty sequence space." The absence of "in-between" species is something that also perplexed Darwin, he said.
Perplexed and unexpected? Yes because they so desire proof, yet they can find none. Repeating a lie often may make the lie sound convincing to some, but it does not make it true.
https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html
Evolution physical intelligent guiding principle
Numerous scientists have questioned the efficacy of selection and random mutational changes as a mechanism for generating the bio-information necessary for morphological novelty (Eden 1966; Wadington 1968a, b, c; Gould 1982; Yockey 1992, Thomson 1992; Kauffman 1995; Perez 2010; Jorgensen 2007, 2012; Elsheikh 2010, 2014). Eden who was especially concerned about the elements of randomness contended “No currently existing language can tolerate random changes in the symbol sequences which express its sentences. Meaning is almost invariably destroyed. Any changes must be syntactically lawful ones.”
What, if Anything, Is an Evolutionary Novelty? Massimo Pigliucci
The modern synthesis ( of evolution ) provides us with explanatory tools to understand adaptations (natural selection) but falls short when it comes to the question of novelties
http://philpapers.org/archive/PIGWIA/
The origin of the vertebrate skeleton 16 August 2010
No coherent causative model of morphogenesis has ever been presented.
http://journals.cambridge.org/action/displayAbstract;jsessionid=79710AE9A71071921BD4A3CAC34D5C80.journals?aid=7928966&fileId=S147355041000025X
“Scaling expectations for the time to establishment of complex adaptations”, September 7, 2010,
“Although the vast majority of research in evolutionary biology is focused on adaption, a general theory for the population-genetic mechanisms by which complex adaptations are acquired remains to be developed.”
http://www.pnas.org/content/early/2010/08/30/1010836107.abstract
“Foundational Concepts: Evolution”
“Scientists are still uncovering the specifics of how, when, and why evolution produced the life we see on Earth today.”
http://www.nmnh.si.edu/paleo/geotime/main/foundation_life3.html
Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution May 3, 2018
A major goal of biology is to identify the genetic causes of organismal diversity.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007375
Evolution of Homeobox Gene Clusters in Animals: The Giga-Cluster and Primary vs. Secondary Clustering14 April 2016
There is uncertainty in our understanding of homeobox gene cluster evolution at present. This relates to our still rudimentary understanding of the dynamics of genome rearrangements and evolution over the evolutionary timescales being considered when we compare lineages from across the animal kingdom.
https://www.frontiersin.org/articles/10.3389/fevo.2016.00036/full
My comment: OH NO !!! I can't believe it !! They have no clue? Right. Pro scientists working on the field which try to find out how the instructions of gene expression and repression emerged, admit, they have no idea !!
What’s wrong with evolutionary biology? 20 December 2016
There have been periodic claims that evolutionary biology needs urgent reform. Irrespective of the content of the individual critiques, the sheer volume and persistence of the discontent must be telling us something important about evolutionary biology. Broadly speaking, there are two possibilities, both dispiriting. Either (1) the field is seriously deficient, but it shows a peculiar conservatism and failure to embrace ideas that are new, true and very important; or (2) something about evolutionary biology makes it prone to the championing of ideas that are new but false or unimportant, or true and important, but already well studied under a different branding.
It has been argued here that the discontent is better understood as stemming from a few inescapable properties of living things, which lead to disappointment with evolutionary biology, and a nagging feeling that reform must be overdue. Evolutionary biology, like history, but unlike other natural sciences, raises issues of purpose and agency, alongside those of complexity and generality.
https://link.springer.com/article/10.1007/s10539-016-9557-8?fbclid=IwAR37cKt9BHLC8m4W2YCxYLR9ywLp9Z3-WxSVKm0lPmkEguDYm6MAZvYvTFw
The fundamental theorem of natural selection with mutations 07 November 2017
...THE VAST MAJORITY OF MUTATIONS ARE DELETERIOUS. THIS IS ONE OF THE MOST WELL-ESTABLISHED PRINCIPLES OF EVOLUTIONARY GENETICS, SUPPORTED BY BOTH MOLECULAR AND QUANTITATIVE-GENETIC DATA."
"...a great deal of evidence from several sources strongly suggests that the overall effects of mutations are to REDUCE FITNESS."
Genome-wide analysis of a long-term evolution experiment with Drosophila.
2010 Sep 15
Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. 6
Evolution by epigenesis: farewell to Darwinism, neo- and otherwise
2004 May-Aug
In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. 7
https://www.ncbi.nlm.nih.gov/pubmed/15612191
Dissecting Darwinism
2012 Jan; 25
regarding the origin of the species and life (DNA), even Darwin commented, “If it could be shown that complex systems could not arise by small sequential steps, then my theory would completely break down.” Irreducibly complex systems involving thousands of interrelated specifically coded enzymes do exist in every organ of the human body. At an absolute minimum, the inconceivable self-formation of DNA and the inability to explain the incredible information contained in DNA represent fatal defects in the concept of mutation and natural selection to account for the origin of life and the origin of DNA. As new theories emerge that explain the origin of life, the inevitable emotional accusations of heresy and ignorance are not surprising in a period of scientific revolution. It is therefore time to sharpen the minds of students, biologists, and physicians for the possibility of a new paradigm. 8
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246854/
Werner Arber Nobel Prize in 1978, Physiology or Medicine (sharing the honor with Daniel Nathans and Hamilton O. Smith) for the discovery of restriction enzymes and their application to molecular genetics.
The deeper we penetrate in the studies of genetic exchange the more we discover a multitude of mechanisms" involved in human genetics that falsify the mutation plus natural selection core of macroevolution.
Arber, W, D. Nathans, and H. O. Smith. 1992. 1978 Physiology or Medicine, Nobel Lectures: Physiology or Medicine 1971-1980, 469-492.
James Shapiro Microbiologistof the University of Chicago :
There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations” (Shapiro 1996).
Lynn Margulis:
Although random mutations influenced the course of evolution, their influence was mainly by loss, alteration, and refinement... Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear. Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.
The accumulation of genetic mutations were touted to be enough to change one species to another….No. It wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.
I was taught over and over again that the accumulation of random mutations led to evolutionary change - led to new species. I believed it until I looked for evidence.
biology is opening the black box, and demonstrating how organisms develop. We are slowly getting out of a state of ignorance in regard of what mechanisms determines cell shape, assignment of their planes of division, tendencies to move, directions and rates of movement, modes of differentiation into particular cell types, and cell death (apoptosis).
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. The discovery and description of the spatial– temporal distribution of the gene expression pattern during morphogenesis, together with its key regulators, is one of the main recent achievements in developmental biology. Nevertheless, gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. 1
Kevin N. Laland: Animal learning as a source of developmental bias 26 August 2019
Learning can influence evolutionary processes in at least two separate ways: either through generating some phenotypic forms more readily than others (a variational bias) or through generating some environmental states more readily than others (a selective bias, a.k.a. “niche construction”).
https://onlinelibrary.wiley.com/doi/abs/10.1111/ede.12311
Based on evidence seen in biochemistry on a molecular level, we can now say affirmatively and conclusively, that Darwin's theory of evolution by natural selection in regards of primary speciation & macroevolutionary level has been falsified.
The selection of random changes of nucleotides being the source of all biological engineering: that claim is nonsense.
Genetic and epigenetic programmed instructional complex codified information and signaling through various signaling pathways on an integrated structural systems-level replace a Darwinian gene-centric view and its various subsequent adaptations, extensions, and new proposals like the modern extended synthesis or the so-called " third way ". The true mechanism is " Biochemical systems programming and signaling", and special creation of species and/or kinds by an intelligent powerful creator. Long periods of time and gradual, evolutionary development is not possible, face the fact that cells and organisms work like gigantic interlocked machines and factory complexes, wherein any case, if one tiny part is missing, nothing goes. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. No glycine amino acids, no pyrimidines, no DNA - no life. No Watson Crick base pair fine-tuning, no DNA - no life. No ribosomal mechanism for amino acid amide bondage, no proteins, no life. No nitrogenase enzymes to fix nitrogen in an energy-demanding, triple bond-breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life. No chlorophylls, no absorption of light to start photosynthesis, no starch and glucose - cells will have no food supply to sustain complex organisms - no advanced life on earth. No rubisco, no fix of CO2, no hydrocarbons - no advanced life. No counterion in retinal, and rhodopsin could not receive visible light - and there would be no vision on earth by any organism.
A framework for parsing heritable information 22 April 2020
A new framework recasts heredity as a complex, networked information system in which all the regulatory molecules that help the cell to function can constitute a store of hereditary information. Instructions not coded in the DNA are contained in the arrangement of the molecules within cells and their interactions with one another. This arrangement of molecules is preserved and passed down from one generation to the next. framework recasts inheritance as the combined effects of three components: entities, sensors and properties. Sensors are specific entities that interact with and respond to other entities or to their environment. Sensors respond to certain properties, such as the arrangement of a molecule, its concentration in the cell or its proximity to another molecule. Together, entities, sensors and properties enable a living organism to sense or 'know' things about itself and its environment. Some of this knowledge is used along with the genome in every generation to build an organism. Scientists don't currently have methods to measure some of these things, so this work points to potentially important new avenues for research. 3
http://spaceref.com/news/viewpr.html?pid=55614
Epigenetic Principles of Evolution, 2011, page 19:
The basic tenet of the neo-Darwinian paradigm that changes in genes are responsible for morphological evolution, on which this edifice rises, is not substantiated, hence the empirical foundation of the structure is questionable at best.
If I had to mention ONE word which refutes evolution by mutations and natural selection to explain biological development, body architecture, biodiversity, adaptation, regulation, governing, controlling, recruiting, interpretation, recognition, orchestrating, elaborating strategies, guiding, it would be: SIGNALING. Furthermore the transmission of codified genetic and epigenetic information for development, and adaptation to external cues like food resources and availability, and environmental conditions.
Natural selection cannot induce a design to appear.
And yet, an Aristotelian mythology has been erected, imagining that natural selection creates things. This brings us back to this weekend’s debate, in which evolutionists Lawrence Krauss and Denis Lamoureux propagated and insisted upon this myth, and Stephen Meyer was presented with an enormous unpacking job. How does one disabuse two interlocutors whose perceived success depends on them not understanding the basic facts—in 30 seconds or less? 7
The Biological Big Bang model for the major transitions in evolution
Eugene V Koonin 20 August 2007
Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.
A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs.
EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY
Eric H. Davidson 2011 Feb 12
The neo-Darwinism ‘erroneously assumes that change in protein coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual.’ 1
James Shapiro: Microbiologistof the University of Chicago :
There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations” (Shapiro 1996).
Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words : Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system ?
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional. Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.
Claim: Evolution is a scientific theory with emphasis on the word “scientific”. It is observable, based on PHYSICAL evidence.
Answer: Evolution by natural selection ( as the mechanism of the origin of species ) is the most successful and widely believed and accepted fairy-tale story ever invented and told, which keeps surviving despite 160 years of scientific advance and discoveries which have falsified the claim. It is able to survive by hiding and disguising behind names as " science', " peer reviewed", " fact", " consensus", and " rational", and because sold and indoctrinated in schools at science classes as credible serious science, endorsed and defended by most specialists like chemists and biologists, and at most universities in the world. Since 90% of the population is gullible and prefer simply to believe others say, they buy the lie, endorse and defend it. Most do not know that there is no consensus about common ancestry. There are critical differences in DNA replication, and the cell membrane, between eukaryotes, and prokaryotes. And mutations in DNA are not determinant of many determinants of body form, shape, and cell differentiation. Epigenetic factors are probably even more relevant than genetic variation to define body form and development. And with that baggage in their mind, they make the leap of faith and believe, that their "knowledge" makes God superfluous. And so, they can live their lives as pleases, leaving God out of their lives.
The implicit connotation is that when a claim is scientific, it is most probably true since it went through an exhaustive process of peer review and empirical tests. Since evolution as scientific theory stood the test of time, it merits credibility. Science equals to the truth. Since evolution is scientific, it's trustworthy. If the claim is not scientific, it is most probably based on blind faith, and not worth to be taken seriously. For this reason, Darwinists try to discredit Intelligent Design as not being science, but religion. Once they achieve that goal, a further investigation of the scientific facts becomes superfluous.
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Darwins Theory of Natural selection has been falsified
https://reasonandscience.catsboard.com/t2484-darwins-theory-of-natural-selection-has-been-falsified
Op-Ed: Genetic mutations challenges Darwin’s evolution theory
DEC 28, 2012
The death of Darwin's evolution theory continues due to the evidence found in genome deterioration, sickle cell anemia mortality, beneficial mutations elusiveness, disease proliferation, and recent genetic mutations. Analysis of DNA/RNA mutations reveals that these genetic transformations cannot offer meaningful new information in significant quantities. Rather, these mutations will generate information degradation in the genome. 1
Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
PEER-REVIEWED September 26, 2008
We allowed mutation rates to evolve, and we evaluated the proximity to the optimum. Although we chose conditions favorable for mutation rate optimization, the evolved rates were invariably far below the optimum across a wide range of experimental parameter settings. We hypothesized that the reason that mutation rates evolved to be suboptimal was the ruggedness of fitness landscapes. We conclude that rugged fitness landscapes can prevent the evolution of mutation rates that are optimal for long-term adaptation. This finding has important implications for applied evolutionary research in both biological and computational realms. 2
Random mutations deteriorate the genome
In a new paper in Science, 3Khan et al, working with Richard Lenski [Michigan State], leader of the longest-running experiment on the evolution of E. coli, found a law of diminishing returns with beneficial mutations due to negative epistasis. The abstract said:
Epistatic interactions between mutations play a prominent role in evolutionary theories. Many studies have found that epistasis is widespread, but they have rarely considered beneficial mutations. We analyzed the effects of epistasis on fitness for the first five mutations to fix in an experimental population of Escherichia coli. Epistasis depended on the effects of the combined mutations—the larger the expected benefit, the more negative the epistatic effect. Epistasis thus tended to produce diminishing returns with genotype fitness, although interactions involving one particular mutation had the opposite effect. These data support models in which negative epistasis contributes to declining rates of adaptation over time. 3
Non-random mutations: How life changes itself: the Read-Write (RW) genome
And all available scientific evidence also indicates that evolution is an engineered process. In engineering and computer science, evolution never happens by accident. It’s always the result of a deliberate act. A program that can self-evolve is always considered an engineering marvel. 4
Scientists engineer animals with ancient genes to test causes of evolution
January 13, 2017
“For the first test case, we chose a classic example of adaptation-how fruit flies evolved the ability to survive the high alcohol concentrations found in rotting fruit. We found that the accepted wisdom about the molecular causes of the flies’ evolution is simply wrong. 5 Siddiq and Thornton realized that this hypothesis could be tested directly using the new technologies. Siddiq first inferred the sequences of ancient Adh genes from just before and just after D. melanogaster evolved its ethanol tolerance, some two to four million years ago. He synthesized these genes biochemically, expressed them, and used biochemical methods to measure their ability to break down alcohol in a test tube. The results were surprising: the genetic changes that occurred during the evolution of D. melanogaster had no detectable effect on the protein’s function.[/size]
What’s that you say? No detectable effect?
One supposes that the gene selected is one, among very many, that can be best ‘reverse-engineered’ to give a facsimile of the ‘ancient’ form. Yet, when tested in vivo, there is no difference found between the supposed ‘slow’ ancestral gene, and the ‘fast’ extant form. This is not how neo-Darwinism is supposed to work. Something is seriously wrong, no? It might be that the techniques employed to identify the ‘ancestral’ form are bad. Maybe that’s it, and it alone. But, OTOH, maybe something is seriously wrong with current neo-Darwinian theory. Some notions concerning adaptation will, therefore, remain difficult to study rigorously. Nevertheless, because of technical and conceptual advances, it should now be possible to experimentally assess the causal predictions of many previously untested or weakly tested hypotheses of historical molecular adaptation, allowing them to be corroborated or, like the classic hypothesis of ADH divergence in D.melanogaster, decisively refuted. One wonders what’s really left of natural selection. Between Behe’s Edge of Evolution, Shapiro’s “Natural Genetic Engineering,” the whole field of epigenetics, the disappearing of “Junk-DNA”, and now the disappearance of a ‘fitness’ change in a “classic case” of molecular adaptation, can anyone seriously believe that Darwinism has much to say about how life evolves? Remarkably, already in 2010, following paper reported that the claim of NS was not observed in Drosophila.
Genome-wide analysis of a long-term evolution experiment with Drosophila.
2010 Sep 15
"Genomic changes caused by epigenetic mechanisms tend to fail to fixate in the population, which reverts back to its initial pattern." That's not all that doesn't fixate. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. 6
Evolution by epigenesis: farewell to Darwinism, neo- and otherwise
2004 May-Aug
In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. 7
https://www.ncbi.nlm.nih.gov/pubmed/15612191
Dissecting Darwinism
2012 Jan; 25
regarding the origin of the species and life (DNA), even Darwin commented, “If it could be shown that complex systems could not arise by small sequential steps, then my theory would completely break down.” Irreducibly complex systems involving thousands of interrelated specifically coded enzymes do exist in every organ of the human body. At an absolute minimum, the inconceivable self-formation of DNA and the inability to explain the incredible information contained in DNA represent fatal defects in the concept of mutation and natural selection to account for the origin of life and the origin of DNA. As new theories emerge that explain the origin of life, the inevitable emotional accusations of heresy and ignorance are not surprising in a period of scientific revolution. It is therefore time to sharpen the minds of students, biologists, and physicians for the possibility of a new paradigm. 8
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246854/
Werner Arber Nobel Prize in 1978, Physiology or Medicine (sharing the honor with Daniel Nathans and Hamilton O. Smith) for the discovery of restriction enzymes and their application to molecular genetics.
The deeper we penetrate in the studies of genetic exchange the more we discover a multitude of mechanisms" involved in human genetics that falsify the mutation plus natural selection core of macroevolution.
Arber, W, D. Nathans, and H. O. Smith. 1992. 1978 Physiology or Medicine, Nobel Lectures: Physiology or Medicine 1971-1980, 469-492.
James Shapiro Microbiologistof the University of Chicago :
There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations” (Shapiro 1996).
Lynn Margulis:
Although random mutations influenced the course of evolution, their influence was mainly by loss, alteration, and refinement... Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear. Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.
The accumulation of genetic mutations were touted to be enough to change one species to another….No. It wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.
I was taught over and over again that the accumulation of random mutations led to evolutionary change - led to new species. I believed it until I looked for evidence.
biology is opening the black box, and demonstrating how organisms develop. We are slowly getting out of a state of ignorance in regard of what mechanisms determines cell shape, assignment of their planes of division, tendencies to move, directions and rates of movement, modes of differentiation into particular cell types, and cell death (apoptosis).
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. The discovery and description of the spatial– temporal distribution of the gene expression pattern during morphogenesis, together with its key regulators, is one of the main recent achievements in developmental biology. Nevertheless, gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. 1
Steve Meyer: Darwins Doubt, page 136
Randomly cutting and pasting larger blocks of text, as evolutionary biologists often envision, would not make any appreciable difference to the efficacy of a random search of sequence space. Imagine a computer “mutating” at random the text of the play Hamlet either by individual-letter substitutions or by duplicating, swapping, inverting, or recombining whole sections of Shakespeare’s text. Would such a computer simulation have a realistic
chance of generating a completely different and equally informative text such as, say, The Blind Watchmaker by Richard Dawkins, even granting multiple millions of undirected mutational iterations?
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1. The term 'evolution' is an equivocation fallacy that attempts to define two different proposed processes under the same definition. It is a violation of the logical reasoning process to conclude that the genetic variation we can observe within and around species explains the creation of complex body plans, organs, and other complex systems. Darwin's theory is illogical, serendipitous, and unproven.
2. Complex life by complete accident over billions and trillions of successive serendipitous accidents is an incredulous claim without evidence.
3. Calculations of the time necessary to evolve from goo-to-you reveal such a low probability of macro-evolution happening that the odds are beyond the threshold of 'impossible'. Hitchen's was correct - "What can be asserted without evidence can be dismissed without evidence"...
1. Neo-Darwinism and the Modern Synthesis propose a gene-centric view, a scientific metabiological proposal going back to Darwin's landmark book " On the origin of species " in 1859, where first natural selection was proposed as the mechanism of biodiversity, and later, gene variation defining how bodies are built and organized.
2. Science researchers have discovered, that robust networks of interactions and biological function, major morphological innovation, development and body form are based on integrative mechanisms, the interplay of genes with the gene regulatory network, Transposons and Retrotransposons, so-called Junk DNA, splicing, and over a dozen epigenetic codes, Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, Ion channels, Sugar molecules on the exterior of cells (the sugar code), that are not specified by nuclear DNA - that is, inheritance is not defined through DNA sequences alone.
3. Science is coming to recognize, that none of the recently proposed alternatives, like the third way, Saltationism, Saltatory ontogeny, mutationism, Genetic drift, or combined theories, do full justice by taking into account all organizational biophysiological hierarchy and complexity which empirical science has come to discover. As such, only a holistic view, namely structuralism, takes into consideration all influences that form cell form and size, body development and growth, doing justice to the scientific evidence.
4. Scrutinizing which causes ultimately respond for the complexity discovered in life is only satisfying, once the epistemologically flawed foundation of methodological naturalism is taken out of the box, and replaced by a new paradigm, where all possible mechanisms and causal influences are permitted to be scrutinized, investigated, and scientifically tested, including the interaction and creative force of an external intelligent, mental agency outside the known physical world, which through its transcendent power creates, forms and builds all physiobiological lifeforms in all its astounding diversity.
1. Evolution depends on huge ages, billion of years. Radiometric dating is not reliable.
2. The millions or billions of transitional fossils are missing
3. There is no empirical data of an unorganized undirected unguided Neo-Darwinian accidental random macro-evolutionary event of a change/transition, where one "kind" did evolve into another beyond the species level (i.e. speciation) , like an organism randomly changing/transition into a whole entirely different, new fully functioning biological organism, the emergence of new complex functions, a new genus or higher rank in taxonomy, with the rise of new body plans
4. Species appear and disappear abruptly in the fossil record.
5. Homo erectus, the precursor of homo sapiens, supposedly populated the earth for 1,5 million years. Where are the millions of fossils that should be buried and be found? They are missing.
6. Most species never changed. We have many animals, like Crocodiles, fish, crabs, insects, that can be found in the fossil record. unchanged.
7. Many fossils have been found with soft tissue, collagen, and proteins, which could not have remained preserved for millions of years.
8. DNA contains a blueprint, an instruction manual to make you, for example. Books, Blueprints, Instruction manuals, information retrieval, transmission, and translation systems do not emerge randomly. They have always an author and can be traced back to an intelligent source.
9. Machines, assembly lines, computers, recycle systems, error check and repair systems are always invented by intelligence. Biological cells host all this.
10. The information in the genome does not increase but deteriorate.
11. The human brain is 4 times the size and weight of a Chimp. It is supposed that a common ancestor of Apes and Humans lived 4 million years ago, and from there on, speciation into humans and apes began. The human brain has about 100 billion neurons. That means, there would have had to be the evolution from about 25billion of the common ancestor to 100billion of humans today, or an increase of 75 billion neurons in 4 million years. Or 25 thousand new neurons per year. Each Neuron has 10 thousand synapses, which connect to other neurons. Synapses function like a microprocessor and these over ten thousand per neuron would have had to find out how to connect correctly to other neighboring neurons. That is, 25 thousand new neurons, each with 10 thousand synapses, interconnecting correctly, per year !!
12. You cannot change just one body part. In order for evolution to account for the transition of land-living animals, to birds, for example, the whole body plan has to change, and not just single point mutations.
13. Natural selection has been shown to be able to account maximum for two mutations ( malaria ), but for new complex traits to emerge, at least six mutations are required, and it would take too much time to fix them into the population. ( Behe )
14. It has commonly been claimed that the question of how the eye evolved, has been answered. But scientists know this is not true. Rhodopsin is the key enzyme of sight. It is composed of two interdependent parts. Opsin, and retinal. One has no function without the other. And both are finely tuned to interact together. How can evolution explain its origin, if one has no function alone?
An article in Nature magazine confirms :
even as far back as the prokaryotes, the complex seven transmembrane domain arrangement of opsin molecules seems to prevail without simpler photoreceptors existing concurrently. Darwin’s original puzzle over ocular evolution seems still to be with us but now at a molecular level.
15. All complex life forms require interdependent parts. The human eye consists of over two million working parts making it second only to the brain in complexity. The human visual system depends on eye muscles, lubrification, a reliable communications channel (the optic nerve), the data to the central processing unit (the brain) via the visual cortex. If one of these components is missing, no deal. They had to evolve together, but during the evolution process, the single components would confer no survival advantage. What good would an optic nerve be for, without the eye, and the brain?
If someone approaches you, and asks, why is evolution not true, how could we answer in simple terms, without being too technical? I would first outline, that there must be made a differentiation. Darwin's theory has to be subdivided into three main aspects of the theory. 1. Adaptation, the tree of life, where it is claimed, that all life and biodiversity originated from one single ancestor, and macroevolution, and biodiversity which is claimed to be due to macroevolution. The dispute is about common ancestry and macroevolution. Bacteria do not share the same replication process, nor the same cell membrane as animals ( eukaryotes ). Even peer-reviewed science papers admit that, and so, common ancestry of all domains of life is a refuted claim. Most phyla ( animal forms ) appear suddenly in the geological strata, and not gradually, so the fossil record does not support evolution. Macro-evolution has also never been observed in the laboratory. Bacterias can adapt to antibiotics, but will never become something else, then bacteria. A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional. Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution. Furthermore, organisms on a molecular level are full of molecular machines, Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. 1. Complex machines and factories are intelligently designed 2. Biological cells are factories full of complex machines 3. Biological cells are intelligently designed. It has been claimed that so called Junk DNA is evidence of remnants of evolution, and is junk - or, has no function. The design prediction that Junk DNA HAS function is being unraveled, and more and more it is clear, that Junk DNA fullfills life essential functions, like gene regulation ( that is, when a gene is expressed ). Body plan building, and consequently, its supposed evolution, does not depend uniquely on information contained in the genetic code, but beyond ( epigenetics ). That is, what causes body form, and cell size and shape, depends on Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, cell membrane Ion channels and their location, and sugar molecules on the exterior of cells (the sugar code), Gene regulatory networks, Transposons and Retrotransposons, and at least on a dozen epigenetic informational codes.
Many individuals who believe in evolution are convinced that there exists an abundance of transitional forms to support evolution. However, what they regard as "transitional" are simply biological similarities between various species or groups, and are not true or actual transitions in Nature. Creationists believe that the biological similarities between various species are due to a common Designer who designed similar functions for similar purposes in all of the various forms of life, from the simplest to the most complex. Evolutionists believe that the biological similarities between species are evidence of common ancestry between all forms of life. Neither position can be scientifically proved.
https://english.pravda.ru/science/106586-evolution_theory/
T.Yonezawa (2012): Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth
It seems likely that a huge amount of trials and errors of different forms occurred during the emergence of life and that UCA if existed was just one of them. The probability of survival of life is low unless there are multiple origins.
https://www.hindawi.com/journals/tswj/2012/479824/
Evolution: Charles Darwin was wrong about the tree of life
Genetic tests on bacteria, plants and animals increasingly reveal that different species crossbreed more than originally thought, meaning that instead of genes simply being passed down individual branches of the tree of life, they are also transferred between species on different evolutionary paths. The result is a messier and more tangled "web of life". The findings mean that to link species by Darwin's evolutionary branches is an oversimplification. "The tree of life is being politely buried," said Michael Rose, an evolutionary biologist at the University of California, Irvine. "What's less accepted is that our whole fundamental view of biology needs to change."
https://www.theguardian.com/science/2009/jan/21/charles-darwin-evolution-species-tree-life
Frank Zindler, President of American Atheists, in 1996
The most devastating thing though that biology did to Christianity was the discovery of biological evolution. Now that we know that Adam and Eve never were real people the central myth of Christianity is destroyed. If there never was an Adam and Eve there never was an original sin. If there never was an original sin there is no need of salvation. If there is no need of salvation there is no need of a Savior. And I submit that puts Jesus, historical or otherwise, into the ranks of the unemployed. I think that evolution is absolutely the death knell of Christianity.
Reply: The two basic tenets upon which the theory of evolution rests, are the claim of universal common ancestry, and the tree of life. The two claims have been refuted on many grounds. When we talking about the tree of life, we cannot overlook the origin of viruses. Eugene V. Koonin admitted openly in 2020: In the genetic space of viruses and MGEs, no genes are universal or even conserved in the majority of viruses. Viruses have several distinct points of origin, so there has never been a last common ancestor of all viruses. The universal common ancestry of life is also disputed. For example Eric Bapteste, evolutionary biologist: "We have no evidence at all that the tree of life is a reality." DAVID M. RAUP, paleontologist: Multiple origins of life in the early Precambrian is a reasonable possibility. And C.P. Kempes in the peer-reviewed article: The Multiple Paths to Multiple Life (2021): We argue for multiple forms of life realized through multiple different historical pathways. In regard to the origin of humans: All human beings are 99.9 percent identical in their genetic makeup. Harmful protein-coding mutations in people arose largely in the past 5,000 to 10,000 years. Evidence for a Human Y Chromosome Molecular Clock: Pedigree-Based Mutation Rates Suggest a 4,500-Year History for Human Paternal Inheritance. By comparing the mitochondrial DNA of 147 people from five different ethnic groups, the researchers found that all the individuals analyzed were descendants of the same female lineage, that is, they all had the same original "mother" at the beginning of everything. Thus, they confirmed that all humanity descends from the same woman, who would have been the first Homo sapiens. And they called her "Mitochondrial Eve". These few quotes demonstrate that the major evolutionary tenets are far from being a scientific fact, or consensus among specialists in the field. Adding the complete failure of abiogenesis research permits the inference from eliminative induction:
The most devastating thing though that biology has done to naturalism is the failed claim of chemical and biological evolution. Now that we know that Adam and Eve were real people the central creation narrative of Christianity is confirmed. If there was an Adam and Eve there was an original sin. If there was an original sin there is need of salvation. If there is need of salvation there is need of a Savior. And I submit that puts Jesus, historical or otherwise, into the ranks of the necessary. I think that the failure of abiogenesis and evolution is absolutely the death knell of naturalism.
1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/
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