Arguments based on biocomplexity and biodiversityGod creates using his intelligence and power. We know both are
1. We DO know that intelligent engineers can create complex structures, like scaffolds to construct a factory building, and the building itself.
2. The Intelligent Design hypothesis has a known cause and proponents of natural causes have no clue if nature can instantiate the same since it has never been demonstrated to be possible.
3. This means the logical and scientific conclusion is to assume design until any other evidence comes along to show a natural mechanism.
The Factory maker argument ( Paley's watchmaker 2.0)1. We have empirical experience and background knowledge that intelligent agents can and do create information storage mechanisms ( hardware), codes and languages, and instructional assembly information ( data) using a codified language ( software) information transmission systems ( post-delivery services, worldwide web) translation software, transistors, complex machines, automated robotic production lines, integrated circuit boards, energy turbines, and factories. Intelligence can conceptualize and create and design these things from scratch, select the building materials, create data that directs the making and joining of physical parts together in the right way, ( blueprints to create robots) and fine-tune them, to achieve a functional outcome.
2. We have no theoretical, conceptual, practical, or hypothesized and scientifically tested experimental evidence that unguided, nonintelligent, random causes and mechanisms can create and fabricate these things stochastically, or be instantiated by physical necessity and constraints.
3. All the mentioned things in premise 1 exist analogously to man-made artifacts in nature, not only in an analogous manner but literally so. Cells are in a literal sense chemical factories, driven by molecular machines (proteins), directed by data stored in the genome ( the nucleotide sequence), epigenetic data systems, and driven by energy (ATP).
4. Therefore, it is rational, logical, and plausible, to infer and prefer the conclusion that an intelligent agent with foresight created biological embodied life, rather than random events.
The Classical Teleological Argument1. The essential parts of a living cell cohere only because they have a function such as membrane proteins ( factory portals ), DNA ( hardware ), the genetic code and instructional complex information stored in DNA (software), RNA polymerase ( information retrieval/encoding ) messenger RNA ( transmission ) Ribosome ( translation/decoding ) proteins ( complex machines ) dynein, kinesin ( taxis ) tubulins ( molecular highways ) mitochondria ( power generating plants ) ATP synthase ( power turbines ) the metabolic network ( electric circuits ) and so on, which are found forming an integrated interdependent system because they make it possible together for the cell to self-replicate, adapt, and remain alive.
2. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a junk yard could not assemble a 747.)
3. These chemicals, building blocks, and macromolecules must have a designer who designed them with their function in mind: just as a watch implies a watchmaker, a machine implies a designer of the watch. Living cells were not created by human designers. Therefore, living cells must have had a non-human intelligent designer
Error check and repair mechanisms1 a)The genetic code is at or very close to a global optimum for error minimization. Only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors. That would be expected if the code were the product of intelligent selection.
b)The assignment during translation of 64 codons ( 1 codon = 3 RNA nucleotides, where each can be one of the four used in life) 4x4x4=64 is assigned to only 20 ( in some cases 22) puts in question, why not attempting to accomodate just 2 codons with 4x4=16 possible positions to 16 amino acids. Or 64 codons to 61 amino acids. This “redundancy” was initially interpreted as an inefficient artifact of natural, sometimes messy trial-and-error processes. Since then, however, we have discovered that the redundancy is actually vital. The apparent overkill minimizes reading and transmitting errors so that the same amino acid is transferred to each generation.
c)The genetic information is transmitted by over 25 extremely complex interconnected and interdependent molecular machines. This communication system encodes, sends, and decodes genetic texts, which requires as well error check and repair mechanisms along the way to maintain low genetic mutation rate, and minimizing replication, transcription, and translation errors, and permit organisms to pass accurately genetic information to their offspring, and survive. This system had to be set-up prior to when life began because it depends on it. During replication, nucleotides, which compose DNA, are copied. When
E coli makes a copy of its DNA, it makes approximately one mistake for every billion new nucleotides. It can copy about 2000 letters per second, finishing the entire replication process in less than an hour. Compared to human engineering, this error rate is amazingly low.
E coli makes so few errors because DNA is proofread in multiple ways.
d) Proteins,marvelous pieces of chemical nanoengineering, in order to become functional, must fold from linear, to specific 3-D forms. Properly folded proteins are essential for life because they conduct most of the necessary functions in a cell. If it folds into the wrong shape, a protein is useless. If the first proteins fell into these death valleys, life on Earth would never have appeared. Spontaneous folding is quite rapid (milliseconds to seconds) for many proteins, but many large, critical proteins fail to find by themselves the right shape and, without help, would become only so much molecular waste.So when a protein misfolds, other proteins, named chaperonins, help proteins fold into the right shape. They have been shown to interact with up to 30% of the cell’s proteins, so their importance is real. Now, amazingly, even these very own proteins, named GroEL, which help misfolded proteins to fold properly, can also misfold. And it has been shown that GroES, a co-chaperone assists in folding GroEL. Amazing. Machines, that help other machines to assemble properly, are by themselves subject to errors, and life has inbuilt mechanisms to fix as well these machines that help fixing other machines !!
Regulation is essential in biology1. Regulation is ubiquitous in biology, and a fundamental property of living systems. Keeping a stable internal cellular environment requires constant adjustments as conditions change inside and outside the cell. The adjusting of systems within a cell is called homeostatic regulation. Because the internal and external environments of a cell are constantly changing, adjustments must be made continuously to stay at or near the set point (the normal level or range). Regulation of biological processes occurs when any process is modulated in its frequency, rate or extent. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. While Gene expression in prokaryotes is regulated primarily at the transcriptional level, in eukaryotic cells, it is regulated at many levels (epigenetic, transcriptional, post-transcriptional, translational, and post-translational). Metabolism or intracellular signaling also requires regulation. Gene regulation is a dynamical process composed of a number of steps, for example the binding of Transcription Factors to DNA, recruitment of transcription machinery and the production of the messenger RNA, post-transcriptional regulation, splicing and transport of mRNA, translation, maturation and possible localization of proteins.
2. Regulation requires a distinctive architecture of functional relationships, and specifically the action of a dedicated subsystem whose activity is dynamically decoupled from that of the constitutive regime. Regulate means control or maintain the rate or speed of (a machine or process) so that it operates properly. Regulation is the management of complex systems
according to a set of rules and trends. It is a rule or directive made and maintained by an authority. Regulating is always either a) a preprogrammed action by an intelligent agency, or b) an action where an intelligent agent is directly actively involved.
3. Setting rules, giving directives for specific purposes or functions is always the result of a mental action. It is logical to conclude that biological regulation requires intelligent set up.
Waste management in biology points to design1. Waste management (or waste disposal) includes the activities and actions required to manage waste from its inception to its final disposal. This includes the collection, transport, treatment, and disposal of waste, together with monitoring and regulation of the waste management process, and is always preceded by careful planning and foresight of the entire process by waste management engineers, and implemented virtually simultaneously. 2. Biological cells have cleverly engineered mechanisms that grind molecular protein garbage ( Proteasome Garbage Grinders ), coordinate loading and translocation of the waste products ( by superb Multisubunit peptide-loading complexes (PLC) ) to the waste disposal site, where the waste products are processed and sorted out (Histocompatibility complex class I (MHC-I) with 1,6 million atoms that to work with atomic precision ), and the final products are transported to the surface of the cell through the exquisite secretory pathway. There, T-Cells scan the MHC-I with receptors, and recognize when the cell was infected by foreign invaders, and induce their apoptosis ( cell suicide)At least 9 macromolecular complexes need to work together in a joint venture, which communicates with each other to orchestrate this masterfully information-based process through signaling languages. If one of the complexes in the pathway is missing, no deal, the immune system cannot do its job, and the organism cannot survive and dies. Of course, all this incredible marvel of molecular engineering had to be born fully set up. No stepwise evolutionary process would lead to such a system. 3. Therefore, the intelligent design theorist is justified to posit an unfathomably clever intelligent designer with foresight, who knew how to implement such a masterfully crafted waste management system on a molecular scale. 1. High information content (or specified complexity), irreducible complexity, and the setup of exquisitely integrated circuits, which by significant alterations are inevitably damaged or destroys the function, constitute strong indicators or hallmarks of (past) intelligent design.
2. The high information content and biological irreducible metabolic pathways which also require regulation and structured in a cascade manner, similar to electronic circuit boards, utilizing proteins and enzymes that manifest by themself irreducible complexity, constitute strong indicators or hallmarks of (past) creation through intelligent intervention, and design.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex circuits with little tolerance of change.
4. Therefore, intelligent design constitutes the best explanation for the origin of information and irreducible complexity in metabolic biological circuits.
Within an embryo, several processes play out at the cellular and tissue level to create an organism. These processes include cell proliferation, differentiation, and cellular movement1. Cell fate determination depends on various kinds of codified information, communication and feedback systems, signaling, and bar-code marking. These information systems prescribe, drive, direct, operate, control, and induce reacting to stimuli, provide patterning cues, regulation, determine and permit the making of decisions based on memory, control transcription, remodel chromatin structure and state, control cell-cell interactions, differential gene expression, regulate which genes are transcribed in a cell ( which genes are turned on and off ), influence the arrangement of different cell types during embryological development, give cues to cleavage patterns, create asymmetry from homogeneity, induce concentration gradients, cell positioning, and many more. 2. These are not simply chemical reactions, but actions directed by prescribed, instructional complex information input. This orchestration depends on a network of logic interactions programmed into the DNA sequence, epigenetic information, and signaling networks that amount essentially to a hardwired biological computational device. Animal forms depend on tightly integrated networks of genes, proteins, and other molecules to regulate their development.3. Neither proponents of "evo-devo," nor proponents of other proposed materialistic theories of evolution, have identified a mutational mechanism capable of generating anything even remotely resembling a complex integrated circuit. In our experience, the functional integration of parts in complex systems generally—are known to be produced by intelligent agents—specifically, by engineers. Intelligence is the only known cause of such effects. Developing animals employ a form of integrated circuitry, and certainly one manifesting a tightly and functionally integrated system of parts and subsystems, and intelligence is the only known cause of these features. Once established, the complexity of integrated circuits and signaling networks makes them stubbornly resistant to mutational change. Disarming any one of these hierarchically structured systems produces some abnormality in expression.The cell is a factory - adios materialism.1. Computer hard-drives with high capacity of digital data storage, software programs based on languages using statistics, syntax, semantics, pragmatics, and apobetics, and the elaboration of complex instructional blueprints through those software programs, and data transmission systems (encoding, sending, decoding), all operated through computers and interlinked computer networks, which prescribe, drive, direct, operate and control interlinked compartmentalized factory parks making products for specific purposes, full of autonomous, robotlike high-tech production lines, high-efficiency power plants, complex high-tech robots with autoregulation and feedback loops, producing products with minimal error rates, that are transported through GPS driven transport carriers to their destination, all driven through energy made by high rotative turbines and power plants, are always set up by intelligent agents designing those things for purposeful goals.
2. Science has unraveled, that cells, strikingly, contain, and operate through all those things. Cells are cybernetic, ingeniously crafted cities full of factories. Cells contain information, which is stored in genes (books), and libraries (chromosomes). Cells have superb, fully automated information classification, storage, and retrieval programs ( gene regulatory networks ) that orchestrate strikingly precise and regulated gene expression. Cells also contain hardware - a masterful information-storage molecule ( DNA ) - and software, more efficient than millions of alternatives ( the genetic code ) - ingenious information encoding, transmission, and decoding machinery ( RNA polymerase, mRNA, the Ribosome ) - and highly robust signaling networks ( hormones and signaling pathways ) - awe-inspiring error check and repair systems of data ( for example mind-boggling Endonuclease III which error checks and repairs DNA through electric scanning ). Information systems, which prescribe, drive, direct, operate, and control interlinked compartmentalized self-replicating cell factory parks that perpetuate and thrive life. Large high-tech multimolecular robotlike machines ( proteins ) and factory assembly lines of striking complexity ( fatty acid synthase, non-ribosomal peptide synthase ) are interconnected into functional large metabolic networks. In order to be employed at the right place, once synthesized, each protein is tagged with an amino acid sequence, and clever molecular taxis ( motor proteins dynein, kinesin, transport vesicles ) load and transport them to the right destination on awe-inspiring molecular highways ( tubulins, actin filaments ). All this, of course, requires energy. Responsible for energy generation are high-efficiency power turbines ( ATP synthase )- superb power generating plants ( mitochondria ) and electric circuits ( highly intricate metabolic networks ). When something goes havoc, fantastic repair mechanisms are ready in place. There are protein folding error check and repair machines ( chaperones), and if molecules become non-functional, advanced recycling methods take care ( endocytic recycling ) - waste grinders and management ( Proteasome Garbage Grinders )
3. Chemist Wilhelm Huck, professor at Radboud University, Netherlands: A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity. Cells, containing all those things are irreducibly complex. Without energy, information, or the basic building blocks fully synthesized, there would be no life. All this is best explained as a product of a super-intellect, an agency equipped with unfathomable intelligence - through the direct intervention, creative force, and activity of an intelligent cognitive agency, a powerful creator.
Information directing the make of factories has always mental origin1. Cells are cybernetic, ingeniously crafted cities full of interlinked fully autonomous chemical nano factories. They host large high-tech macromolecular machines, superb power plants, and striking nano-robots. Wonderful arrays of fully automated manufacturing production lines, transport carriers, generate energy through incredibly efficient turbines, neuron transistors, miniaturized Computers. All those things are made based on algorithmic specified instructional complex information, which prescribes how all those things have to be made, controlled, assembled, and work together in an integrated fashion.
2. The emergence of cities full of interlinked factories full of computer directed machines, assembly lines made of a series of robots working in a joint venture, energy turbines, transistors, circuit boards, logic gates for specific purposes,directed by prescribed, instructional complex assembly information have only been observed to come from intelligent minds. Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic codes, and upon it, instructional information, is like suggesting that a rainbow can write poetry... it is never going to happen!
3. Therefore, most probably, cell factories containing all those things are the product of an intelligent designer.
1. A transistor can be considered an artificial Neuron. Every living cell within us is a hybrid analog–digital supercomputer. The brain is like 100 billion computers working together.
2. Biological cells are programmed to be experts at taking inputs, running them through a complicated series of logic gates through circuit-like operations and producing the desired programmed output.
3. The origin of programs, logic gates, and complex circuits to obtain a purposeful specific outcome is always tracked back to intelligent implementation.
1. The more statistically improbable something is, the less it makes sense to believe that it just happened by blind chance.
2. Statistically, it is practically impossible, that the primordial genome, proteome, and metabolome of the first living cell arose by chance.
3. Furthermore, we see in biochemistry purposeful design.
4. Therefore, an intelligent Designer is by far the best explanation for the origin of life.
1. The mechanisms required to build complex organismal form are preprogrammed instructional complex information encoded in various genetic and at least 41 epigenetic codes and languages and communication by various signaling codes through various physicochemical signaling networks.
2. Science has demonstrated, that evolution by mutations and natural selection genetic drift, and gene flow result in entropy, deteriorate the genome, rather than increasing information and organismal complexity.
3. The origin of instructional complex information ( analogous to blueprints ) and signaling networks is always tracked back to intelligence setting them up with specific purposes.
4. Therefore, biodiversity and organismal architecture are better explained by an intelligent creator, rather than mindless evolution.
1. Regulating, governing, controlling, recruiting, interpreting, recognizing, orchestrating, choreographing, elaborating strategies, guiding, instructing, fine-tuning, monitoring, organizing, are all tasks of the gene regulatory network, which are ultrasophisticated communication networks, analogous to electric circuits in man-made devices.
2. In the same sense as copper, plastic, basic electronic parts do not turn into a printed circuit board randomly, molecular regulators, transcription factors, on/off switches, feedback loops do not turn into a gene regulatory network by unguided processes. Communication networks and signal transmission systems, similar as seen in gene regulatory networks, highly flexible, and able to rapidly reconfigure to deliver different outputs can only be implemented and pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was implemented and programmed by an intelligent agency.
1. Regulation, governing, controlling, recruiting, interpretation, recognition, orchestrating, elaborating strategies, guiding, instruct are all tasks of the gene regulatory network.
2. Such activity can only be exercised if no intelligence is present if the correct actions were pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was programmed by an intelligent agency.
1. Complex multicellular lifeforms depend on gene regulatory networks (dGRN's) which are a collection of molecular regulators that interact with each other and with other substances in the cell to orchestrate the expression of DNA.
2. dGRN's operate based on logic gates and their networks process chemical input signals similar to computers. These encoded instructions are based on boolean logic.
3. Logic depends on reason. Reason depends on intelligence. Only an intelligent mind can think rationally, and implement a system based on conceptual laws of logic. Therefore, the best and most reasonable explanation for the existence of complex gene regulatory networks based on boolean logic, essential for the making of complex multicellular organisms, is the creative action of a powerful, transcendent, intelligent Creator.
1. The setup of functional Information retrieval systems, like a library classification system, is always tracked back to intelligence
2. The gene regulatory network is a fully automated, pre-programmed, ultra-complex gene information extraction system
3. Therefore, its origin is best explained through the intelligent setup
1. The genomic program for development operates primarily by the regulated expression of genes encoding transcription factors and components of cell signaling pathways.
2. A program can always be traced back to a programmer.
3. Therefore, the genomic program of development most probably was programmed by a programmer. That programmer is God.
1. A transistor can be considered an artificial Neuron. Every living cell within us is a hybrid analog-digital supercomputer. The brain is like 100 billion computers working together.
2. Biological cells are programmed to be experts at taking inputs, running them through a complicated series of logic gates through circuit-like operations and producing the desired programmed output.
3. The origin of programs, logic gates, and complex circuits to obtain a purposeful specific outcome is always tracked back to intelligent implementation.
The oxygen-evolving complex (OEC) of photosystem II is irreducible complex.
1. One of the most important and fundamental biochemical reactions on which all advanced life-forms depend is performed by the oxygen-evolving complex (OEC) in oxygenic photosynthesis, responsible for catalyzing the light-driven oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. It is also described as "undoubtedly one of the most remarkable inventions in all of biology." OEC is surrounded by 4 core proteins of photosystem II at the membrane-lumen interface. It remains a fundamental mystery of how this complicated, four-electron transfer process originated. Enigmatic is how the precise geometry and unique mechanism of the OEC came about. Key differences exist between oxygenic and anoxygenic photosynthetic machinery with no apparent homologs or transitional forms that would provide clues to their development. Foremost among these differences is the presence and key role of manganese at the site of water oxidation in photosystem II. This is distinct from bacterial anoxygenic reaction centers, which rely on redox-active periplasmic proteins as electron donors.
2. According to peer-reviewed scientific papers, each of the four extrinsic proteins, (PsbO, PsbP, PsbQ, and PsbR) of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster and D1 protein subunit of PSII is also indispensable, and irreducible. Site-directed mutants show severe impairment of the water oxidation cycle and fail to grow photoautotrophically.
3. That means evolutionary intermediates are non-functional. There is a precise fit and size matching of the residues with the individual atoms of the clusters. This is evidence, that this most fundamental biochemical reaction could not have emerged by evolutionary, step-wise mechanisms, and therefore, Darwin's theory has been falsified and refuted. The only plausible alternative to darwinian evolution is intelligent design.
1. The grand overarching scheme of the morpho-genesis and formation of single eukaryotic cell form, shape, architecture, function, structure, following the formation of tissues and higher order of biological structures is that information conveyed through codified signaling directs intracellular molecular actors. It is due to at least 36 different signaling molecules & mechanisms which direct at least 15 force-generating molecules, through least 38 different mechanisms. They are classified into two groups: a) Semantophoretic molecules ( carry genetic and epigenetic information) that provide complex instructional cues of action through signaling which is fundamental to coordinate any common behavior and organize the division of labor. The following activities are performed in an integrated, orchestrated, interdependent manner by at least 36 different signaling molecules & mechanisms in following different ways: 8 molecules signal, 4 orient, 5 activate, 2 direct, 3 promote, 2 regulate, 1 guide, 3 organize, 1 inform, 1 coordinate, 1 specify, 1 modulate, 1 provide position cues, 2 mediate, 1 provoke change.b) At least 15 force-generating actors, molecules that are directed through those signals and instructions, are responsible for cell morpho-genesis,that is: Filaments, microtubules, lamellopodia, crosslinkers, motors, protein complexes, the centrosome, adhesion proteins, force generators, the extracellular matrix, intra-cellular modules, key regulators, protein gradients, the mitotic spindle, mechanical signals which act in at least 38 different ways, to name: activating, binding, breaking, coordinating, conferring positional information, directing, forcing transmission, generating, guiding, helping to organize, inducing, informing, mediating, modulating, organizing, orienting, providing positioning rules, provoking changes, promoting, regulating, signaling, stretching, specifying. 2. The molecules, acting upon the instructional signals received, form patterns, force change, stretch, change and induce cell shape, move positions, orient, provoke ingress, express, align, deform, accumulate molecules, invaginate, extend, form a web, concentrate, hold together, give mechanical support, stiffen, promote stabilization, form geometry, polarity, form division-plane positioning, phosphorylate, dephosphorylate, force transmission, couple molecules physically, form gradients, deform, pull forces, promote cell rounding, transduce, specify cell-fate, extend, provide structural links, form aspect ratio and size, form filament ends, etc.3. Codified signals and information directing the make of machines ( proteins) and factories ( cells) have only been observed to come from intelligent minds. Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic codes, and upon it, instructional information, is like suggesting that a rainbow can write poetry... it is never going to happen! Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating a conceptual semiotic information is a conscious intelligent mind. Life is no accident, the vast quantity of semiotic information in life provides powerful positive evidence that we have been designed.1. Single cell to man evolution is not a scientific theory. Science, observational science, begins with . . . observation. No human being anywhere ever saw any of the proposed steps from amoeba to multicellular invertebrates, to chordates, to fish, to amphibians to reptiles and birds, and to mammals and man. It is all speculation about what might have occurred in the unobserved, unobservable, unrepeatable and untestable past. You cannot do a controlled experiment on events of history.Modern molecular biology would suggest that any naturalistic origin of life from dirty pond water theory is nonsense.
2. Evolution is speculation based on naturalism, that everything must be required to have a natural cause, nothing supernatural can exist, and materialism. that matter and energy is absolutely all there is was, or ever can be amen.
3. Abductive reasoning permits the inference that life and biodiversity was created by the Creator of this Universe, and of man, which is extraordinarily brilliant and powerful.
1. Pre-programming and prescription of information to get an intended purposeful outcome requires foresight.
2. Foresight comes always from an intelligent agent.
3. Therefore, biodiversity is the result rather of divine intelligent design, than unguided evolution.
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"...Molecular Machines point to intelligent design
1. Living cells are full of Molecular machines, rotors, and engines, and they are made upon the same design principles as big machines. They are a pre-requisite for DNA replication. Life, according to a science paper from 2016, needs a minimum of 438 different, in part interdependent proteins in order to start, and they require to be fully in place before natural selection can be considered as a driving force to produce evolutionary novelties.
2. The emergence of machines for specific purposes, and assembly lines of machines working in a joint venture, have never been observed to emerge by lucky accidents, spontaneously through self-organization by unguided natural events in an orderly manner without external direction, purely physicodynamic processes, and reactions, but always through the direct intervention and creative force of an intelligent agency, a powerful creator.
3. Therefore, the origin of molecular machines is best explained by the ( past )creative act of an intelligent designer.The organization of the genome dictates protein assembly1. Proteins are synthesized in specific orders to assemble large protein complexes, such as microtubule, proteasome, ribosomes, and cellulosome. These protein complexes are assembled both inside and outside cells through the coordination of gene expression, protein transport, and binding processes. Protein complexes can compose of different cofactors and post-translational modifications. Multiple protein subunits have to come together to form protein complexes that play critical functional roles in a cell. There is a remarkable correspondence between gene order and protein assembly order. The gene order has a significant effect and helps in the protein subunit assembly. Operon gene order is optimized to match the order in which protein subunits assemble. There is a significant benefit from tightly coordinating gene expression and protein assembly. Genetic circuits, physical transport, and binding kinetic rates all modulate the distribution of protein complexes. The interplay between the circuit architecture and the genetic and physical rate kinetics together determine the protein assembly structure. 2. Foreknowledge is required for the protein multisubunit assembly that has to be performed and involving ordering principles which are known to come from an intelligent mind. Subunits confer no function unless their use is known in the heterogeneous organization, formed from multiple distinct protein subunits, and completed into the much larger system. There has to be a corresponding order. If gene sequences were formed stochastically by mutations, and if trial and error explored protein assembly space possibilities until a particular sequential functional order and finally functional heteromeric subunit combination of protein complexes was "discovered", the cell would have been producing a considerable number of nonfunctional proteins assembled in the wrong way. In that process, deleterious genetic mutations would probably be eliminated by selection, long before a new protein assembly sequence would be explored and become functional.3. Therefore, evolutionary principles and mutations are an inadequate explanation for the specific genetic order and genetic circuits. An intelligent designer instantiating protein assembly is the more case-adequate explanation.Dinoflagellates with multi-barrel Gatling guns
1. Nematodinium Dinoflagellates are the coolest cells. They are among the most complex single-celled organisms we know of.They have ballistic "nematocyst" organelles. The weaponry is complicated, savage, and unlike what’s seen in animals. These bugs are basically the battle tanks of the microbial world, with armor-piercing, multi-barrel Gatling guns capturing them with their harpoon-like weapons that pierce the prey and drag them in to be consumed. They have intricate weapons—including a microscopic version of a Gatling gun—to harpoon their dinners. They are hunters that eat other dinoflagellates, which themselves are bristling with armor, microscopic munitions and even chemical weapons. The tiny weapons are a unique invention
2. In order for their ballistic organelle to function, a capsule or nematocyst is required, which is composed of 9 essential elementary parts that compose the Gatling gun. This is an integrated interdependent system, where all parts must be in place in order to reach the higher end, that is to catch prey.
3. The origin of these sophisticated ballistic organelles that exceed those of animals in complexity are best explained through intelligent design.
https://reasonandscience.catsboard.com/t3055-a-dinoflagellate-protist-which-has-eyes-like-in-vertebrates-and-ballistic-multi-barrel-guns-for-taking-out-prey-by-design-or-evolutionCell fate determination and differentiation ( phenotype, or what cell type each one will become )1. Cell fate determination depends on various kinds of codified information, communication and feedback systems, signaling, and bar-code marking. These information systems prescribe, drive, direct, operate, control, and induce reacting to stimuli, provide patterning cues, regulation, determine and permit the making of decisions based on memory, control transcription, remodel chromatin structure and state, control cell-cell interactions, differential gene expression, regulate which genes are transcribed in a cell ( which genes are turned on and off ), influence the arrangement of different cell types during embryological development, give cues to cleavage patterns, create asymmetry from homogeneity, induce concentration gradients, cell positioning, and many more.
2. These are not simply chemical reactions, but actions directed by prescribed, instructional complex information input. This orchestration depends on a network of logic interactions programmed into the DNA sequence, epigenetic information, and signaling networks that amount essentially to a hardwired biological computational device. Animal forms depend on tightly integrated networks of genes, proteins, and other molecules to regulate their development.
3. Neither proponents of "evo-devo," nor proponents of other proposed materialistic theories of evolution, have identified a mutational mechanism capable of generating anything even remotely resembling a complex integrated circuit. In our experience, the functional integration of parts in complex systems generally—are known to be produced by intelligent agents—specifically, by engineers. Intelligence is the only known cause of such effects. Developing animals employ a form of integrated circuitry, and certainly one manifesting a tightly and functionally integrated system of parts and subsystems, and intelligence is the only known cause of these features. Once established, the complexity of integrated circuits and signaling networks makes them stubbornly resistant to mutational change. Disarming any one of these hierarchically structured systems produces some abnormality in expression.
The Ribosome1. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.
2. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency.
3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confesses that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.
Evidence of design in the ribosome1. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. For example, the functional group A2451, one single ribonucleotide which is not only of vital importance for peptide bond catalysis ( yeah, how did unguided events "discover" hot to place this one tiny molecule in the right place amongst 2900 of its peers ) but when the translation process is stalled, it signals to a dynamically coupled group in the exit tunnel of the product, the polypeptide chain: " we have a problem here" !! and the ribosome takes action. Ribosomes form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, they can halt the translation process on the fly, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential. Even more strikingly amazing, ribosomes occasionally get stalled when faulty messenger RNA molecules are read, for instance, for a messenger RNA that has broken and is thus is missing its stop codon. The ribosome uses an incredible piece of bio-engineering to rescue a stalled situation when they get stuck at the end of the truncated chain. They use a mechanism called Trans-translation. It is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. This mechanism is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors, mRNA damage, and translational frameshifting. This so-called Trans-Translation is performed by a ribonucleoprotein complex.2. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency. 3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confesses that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.Evidence of design in the ribosome1. Ribosomes have the purpose to translate genetic information into proteins. According to Craig Venter, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. It is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… They are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They can halt the translation process on the fly, and coordinate extremely complex movements. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.2. For the assembly of this protein-making factory, consisting of multiple parts, the following is required: genetic information to produce the ribosome assembly proteins, chaperones, all ribosome subunits, and assembly cofactors. a full set of tRNA's, a full set of aminoacyl tRNA synthetases, the signal recognition particle, elongation factors, mRNA, etc. The individual parts must be available, precisely fit together, and assembly must be coordinated. A ribosome cannot perform its function unless all subparts are fully set up and interlocked. 3. The making of a translation machine makes only sense if there is a source code, and information to be translated. Eugene Koonin: Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working. Design some machinery which behaves like this and I personally will build a temple to your name! Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. The origin of the ribosome is better explained through a brilliant intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories.Translation through the ribosome is an irreducible, integrated complex process1. The ribosome is the 3D printer of proteins. A human-made 3D printer is made of several functional parts, like the nozzle, the extruder, cooling fan, heated be, the painter's tape, etc. The 3D extruder has no use on its own. But only, when working inside the 3D printer in the right place. A bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs). This system includes the ribosome (consisting of fifty distinct protein parts), the twenty distinct tRNA synthetases, twenty distinct tRNA molecules with their specific anticodons, about 200 ribosome assembly proteins and 75 co-factors, chaperones, free-floating amino acids, ATP molecules (for energy), and—last, but not least—information-rich mRNA transcripts for directing protein synthesis. Many of the proteins in the translation system perform multiple functions and catalyze coordinated multistep chemical transformations.
2. In the same sense, as an engineer would not project, invent, create and make a blueprint of a 3D printer extruder with no use by its own, but only conjoined, and together with all other parts while projecting a whole printer, envisioning its end function and use, its evident that unguided random natural events without foresight would not come up with an assemblage of tiny molecular machines, enzymatic structures with unique contours, which bear no function by their own, but only when inserted as part of the ribosome with higher ends, being essential for cells to translate DNA information into proteins, and being a key part participating to perpetuate life. 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? Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal. 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.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex machines with little tolerance of change. Therefore, intelligent design constitutes the best explanations for the origin of the information guiding the making of the irreducible and integrated complex ribosome protein factory.
Evidence of design in the ribosome1. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. For example, the functional group A2451, one single ribonucleotide which is not only of vital importance for peptide bond catalysis ( yeah, how did unguided events "discover" hot to place this one tiny molecule in the right place amongst 2900 of its peers ) but when the translation process is stalled, it signals to a dynamically coupled group in the exit tunnel of the product, the polypeptide chain: " we have a problem here" !! and the ribosome takes action. Ribosomes form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, they can halt the translation process on the fly, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential. Even more strikingly, ribosomes occasionally get stalled when faulty messenger RNA molecules are read, for instance, for a messenger RNA that has broken and is thus is missing its stop codon. The ribosome uses an incredible piece of bio-engineering to rescue a stalled situation when they get stuck at the end of the truncated chain. They use a mechanism called Trans-translation. It is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. This mechanism is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors, mRNA damage, and translational frameshifting. This so-called Trans-Translation is performed by a ribonucleoprotein complex.2. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confesses that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: 3. An intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design?1. In cells, in a variety of biochemical processes, when something goes havoc for some reason, there is readily an armada of different error check and repair mechanisms with their "antenna" out to detect errors, and correct them, preventing lethal consequences.
2. Leaking Cells membranes need to be fixed. During DNA replication, and translation, error check and repair is essential. Cells are endowed with a wide variety of specialized DNA repair mechanisms to counteract daily attacks: base excision repair, nucleotide excision repair, homologous recombination repair, mismatch repair, photoreactivation, nonhomologous end joining, translesion synthesis, and processing by the MRN complex. The Ribosome alone has 13 different error-check and repair mechanisms. In addition to repairing damage to existing DNA, living organisms have mechanisms to correct errors during reproduction. Bacteria have three types of DNA polymerase, all capable of detecting an incorrect base pairing, backing up one step to excise the incorrect nucleotide, and then progressing forward in a process called proofreading. The proofreading step decreases the error rate in bacteria from approximately one error in 100,000 base pairs to one error in 10,000,000 base pairs.
3. Molecules don't care if they are assembled in a way to bear a specific function. And if they do and the function is damaged and breaks down, those molecules neither "care" that they cease bearing that function.
4. Know how to implement an error check and repair system requires foresight. The very concepts of proofreading and repair implies goal orientation and "know-how" to keep something working and going. Those things can only come from an intelligent agency which implements these systems for specific purposes.
Question: Let's suppose you see a machine made for specific functions. And you see nearby another machine, that is set up constantly to monitor the function of the first machine, and knows when it performs properly, and when an error occurs. And then, when something goes havoc, that machine knows immediately what error occurred, and has the know-how to fix it. Is it more rational to infer that intelligence was required to set up both machines, or rather that both are the product of random unguided events?
1. Organisms are constantly exposed to different environments, and in order to survive, require to be able to adapt to external conditions.
2. Life, in order to perpetuate, has to replicate. That includes DNA, which must be replicated with extreme accuracy. Somehow, the cell knows when DNA is accurately replicated, and when not. There are extremely complex quality control mechanisms in place, which constantly monitor the process. At least 3 error check and repair mechanisms keep error during replication down to 1 error in 10 billion nucleotides replicated.
3. These repair mechanisms, sophisticated proteins, are also encoded in DNA. So proteins are required to error check and repair DNA but accurately replicated DNA is necessary to make the proteins that repair DNA. 4. That is an all-or-nothing business. Therefore, these sophisticated systems had to emerge all at once, and require a designer. 1. The origin of life, and perpetuation of life, depends on the accurate replication of DNA. At least 3 error check and repair mechanisms keep error during replication down to 1 error in 10 billion nucleotides replicated.
2. That depends on very sophisticated error check and repair proteins, which had to be in operation from day one.
3. Instructions in DNA are required to make error check and repair proteins, but these proteins have to be there from day one to error check and repair DNA. That is an all or nothing business.
4. The complexity of the first living cell had to be set up fully formed right from the beginning, and that requires intelligence.
