Analogy Viewed from Science
https://reasonandscience.catsboard.com/t2809-analogy-viewed-from-science
Etymologically, metaphor (the Greek metafora, 'carry over') means 'transfer', 'convey', the transference of an often figurative expression from one area to another, and analogy (Gr. analogia, 'relation', from ana, 'up' + logos, 'thought') means 'similarity', or 'accordance'. Both terms are found in Aristotle, with a sense fairly similar to the present use. It is hardly feasible in any unequivocal way to delimit the concepts of model, analogy and metaphor in science. Model, however, is the most general term, and analogy and metaphor can be defined as special kinds of models. Any theory can be seen as a model system. An analogy is a relation between two descriptions of objects (or subject areas) which allows inferences to be made about one on the basis of the other (e.g. studying cell membrane diffusion on artificial membranes), or one to be understood in terms of the other (e.g. the solar system model of atomic structure). The analogy may be formal or material, and complete or partial. In formal analogy there is similarity of form, logical or mathematical structure or syntax; in material analogy of content, substance, function or semantics as well.
https://www.nbi.dk/~emmeche/cePubl/91a.frolan.html
The Argument from Simple Analogy
https://iep.utm.edu/design/#SH1b
David Hume is the most famous critic of these arguments. In Part II of his famous Dialogues Concerning Natural Religion, Hume formulates the argument as follows:
Look round the world: contemplate the whole and every part of it: you will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines, which again admit of subdivisions to a degree beyond what human senses and faculties can trace and explain. All these various machines, and even their most minute parts, are adjusted to each other with an accuracy which ravishes into admiration all men who have ever contemplated them. The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human designs, thought, wisdom, and intelligence. Since, therefore, the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of Nature is somewhat similar to the mind of man, though possessed of much larger faculties, proportioned to the grandeur of the work which he has executed. By this argument a posteriori, and by this argument alone, do we prove at once the existence of a Deity, and his similarity to human mind and intelligence.
If the causes are known that are efficacious in those other, similar phenomena, then this may give us clues concerning the causes in the phenomenon under consideration. Of course, whether this strategy works depends on the availability of closely analogous phenomena that are already explained (Herschel [1830] 1987, p. 148). Herschel (ibid., p. 149) wrote:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”
Let us suppose we arrive at a parking lot, and a car is parked there. It is from a well-known American car maker, and you know the model, type, when it was made, etc. Then, you observe a second object, which you immediately recognize as a car as well. It is far far better build, with similar functionalities, but of unknown manufacturer. Now someone approaches you and asks: Hey, what do you think, was the second car made by another car manufacturer, or did some natural unguided processes build the car? We will obviously without thinking twice answer: What a foolish question. It is OBVIOUS that an unknown car maker made the Car. Biological Cells use instructional codes to make the building blocks of life and are full of molecular machines, which resemble machines made by humans through intelligent design with specific goals. We can, therefore, infer that, since like effects have most probably similar causes, that the agency which created biological Cells, and life, must be of intelligent nature.
1. Intelligent minds make blueprints of factories full of machines with specific functions, set up for specific purposes. Each factory eventually will be full of robotic production lines where the product of one factory is handed over to the next for further processing until the end product is made. Each of the intermediate steps is essential. If any is mal or non-functioning, like energy supply, or supply of the raw materials, the factory as a whole ceases its production.
2. Biological cells are a factory complex of interlinked high-tech fabrics, fully automated and self-replicating, hosting up to over 2 billion molecular machines like Ribosomes & chemical production lines, full of protein machines that act like robots, each with a specific task or function, and completing each other, the whole system has the purpose to survive and perpetuate life. At least 1350 proteins and a fully setup genome, metabolome, and interactome is required, and they are interdependent. The probability, that such complex nano-factory complex could have emerged by unguided chemical reactions, no matter in what primordial environment, is beyond the chance of one to
10^750000. The universe hosts about 10^80 atoms.
3. Biological Cells are of unparalleled gigantic complexity and adaptive design, vastly more complex and sophisticated than any man-made factory complex. Self-replicating cells are, therefore, with extremely high probability, the product of an intelligent agency with purpose and intent.
David Hume Dialogues Concerning Natural Religion
Look round the world: contemplate the whole and every part of it: you will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines, which again admit of subdivisions to a degree beyond what human senses and faculties can trace and explain. All these various machines, and even their most minute parts, are adjusted to each other with an accuracy which ravishes into admiration all men who have ever contemplated them. The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human designs, thought, wisdom, and intelligence. Since, therefore, the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of Nature is somewhat similar to the mind of man, though possessed of much larger faculties, proportioned to the grandeur of the work which he has executed. By this argument a posteriori, and by this argument alone, do we prove at once the existence of a Deity, and his similarity to human mind and intelligence.
SCIENTIFIC MODEL S IN PHILOSOPHY OF SCIENCE, page 48
Nobody would doubt that analogy can play a considerable role in arguments, for developing or for illustrating points. This use of analogy can be found in different intellectual pursuits, such as literature, historiography, or philosophy, and there exist many examples in science —some of which are presented in section. However, analogies were not just used in science; some scientists from the nineteenth century on also discussed their use.John Herschel, mathematician, chemist, and astronomer, published a philosophical treatise in 1830 called A Preliminary Discourse on the Study of Natural Philosophy. In it, he highlights the role of analogy in science. Herschel ([1830] 1987, p. 94) wrote that “parallels and analogies” can be traced between different branches of science, and doing so “terminate[s] in a perception of their dependence on some common phenomenon of a more general and elementary nature than that which form the subject of either separately.” In short, analogy enables us to link different branches of science, seeking something more general that joins them. Herschel’s example of the search for and finding of such a common nature is electromagnetism, demonstrated by Hans Oërsted (1777–1851), relying on similarities between electricity and magnetism. Another example Herschel mentions is the analogy between light and sound. He concludes that, when confronted with an unexplained phenomenon, we need to find and study similar phenomena.
The example Herschel gives for this kind of analogical inference is a stone being whirled around on a string on a circular orbit around the hand holding the string. Whoever is holding the string is able to feel the force pulling on the string due to the stone being kept on its circular orbit by the string. One may, therefore, according to Herschel, infer that a similar force must be exerted on the moon by the Earth to keep the moon on its orbit around the Earth, even if there is no string present in the case of the moon and the Earth. Herschel obviously views this strategy of drawing analogies as a legitimate path toward scientific knowledge when he concludes from this example: “It is thus that we are continually acquiring a knowledge of the existence of causes acting under circumstances of such concealment as effectually to prevent their direct discovery” (ibid., p. 149).
The aim is to find the mechanisms that constitute the hidden processes producing certain phenomena (ibid., p. 191). In the course of this search, different hypotheses may be formed about the mechanism and, in fact, different theorists may well form different hypotheses about a phenomenon (ibid., p. 194), perhaps based on different analogies employed. Herschel is adamant that, despite the dilemmas that might occur due to competing hypotheses, forming hypotheses is still highly beneficial for scientific exploration: “they [hypotheses with respect to theories] afford us motives for searching into analogies” (ibid., p. 196). In particular,
“it may happen (and it has happened in the case of the undulatory doctrine of light) that such a weight of analogy and probability may become accumulated on the side of a hypothesis, that we are compelled to admit one of two things; either that it is an actual statement of what really passes in nature, or that the reality, whatever it be, must run so close a parallel with it, as to admit of some mode of expression common to both, at least in so far as the phenomena actually known are concerned” (ibid., pp. 196–197).
Making such an inference is not only a theoretical undertaking, but it also has practical consequences. It leads to experiments: “[W]e may be thus led to the trial of many curious experiments, and to the imagining of many useful and important contrivances, which we should never otherwise have thought of, and which, at all events, if verified in practice, are real additions to our stock of knowledge and to the arts of life” (ibid., p. 197). In sum, analogies in science, according to Herschel, establish links between different areas of investigation. Moreover, they may aid explaining a new phenomenon on the basis of the causes acting in an analogous phenomenon already explained.
As such, analogies lead to the formulation of hypotheses (and the stronger the analogy, the more evidence for the hypothesis). Finally, they may guide the experimental testing of such hypotheses, thus promoting theory development.
I discussed Maxwell’s vortex model, his model of field lines, and mechanical understanding of physics in the last chapter. I now specifically consider his reflections on the use of analogy in science. One place where he explicitly considered the use of analogy in science is his “Address to the Mathematical and Physical Sections of the British Association” in Liverpool in 1870 (Maxwell [1870] 1890).³ He had in mind what we would today call a cognitive function of analogy. Maxwell’s emphasis is on the illustrations provided by analogies. The scientist should “try to understand the subject by means of well-chosen illustrations derived from subjects with which he is more familiar” (ibid., p. 219). The aim is “to enable the mind to grasp some conception or law in one branch of science, by placing before it a conception or a law in a different branch of science and directing the mind to lay hold of that mathematical form which is common to the corresponding ideas in the two sciences, leaving out of account for the present the difference between the physical nature of the real phenomena” (ibid., p. 219). An analogy is more than a teaching aid or dispensable illustration and can tell us what the system under study is like:
“the recognition of the formal analogy between the two systems of ideas leads to a knowledge of both, more profound than could be obtained by studying each system separately” (ibid., p. 219).
Maxwell voices reasons why analogies are useful in science. Using an analogy can be a strategy toward understanding an as yet not understood subject and hence contribute to generating knowledge by guiding the mind. Understanding, knowledge generation, and creativity are issues that have been investigated quite systematically in the cognitive sciences. Maxwell was also a great practitioner of the use of analogy in physics. Analogy was deliberately and systematically used in an effort to understand electrical effects that were not mechanical by nature. (Frequently these were analogies to mechanical models, see chapter 2, section 2.1, but not inevitably.) Maxwell not only devised the vortex model. An earlier and very instructive example is Maxwell’s model of electrical field lines that quite obviously exploits an analogy (Maxwell [1855] 1890). There, the field lines are represented by tubes in which an incompressible fluid moves, a model also broadly based on Thomson’s analogy between the flow of heat and the flow of electrical force. Maxwell’s aim in using this analogy is not to say what electrical field lines are physically like—they do not consist of a fluid—but how one might imagine them in accordance with the analogy guiding their theoretical description. Maxwell (ibid., pp. 157–158) wrote: “By the method which I adopt, I hope to render it evident . . . that the limit of my design is to show how, by strict application of the ideas and methods of Faraday, the connexion of the very different orders of phenomena which he has discovered may be clearly placed before the mathematical mind.”
Here Maxwell makes explicit how analogies, and analogies to classical mechanics, in particular, aid understanding. One beneficial point is that “the mathematical forms of the relations of the quantities are the same in both systems, though the physical nature of the quantities may be utterly different” (Maxwell [1870] 1890, p. 218).
Analogical reasoning is fundamental to human thought and, arguably, to some nonhuman animals as well. Historically, analogical reasoning has played an important, but sometimes mysterious, role in a wide range of problem-solving contexts. The explicit use of analogical arguments, since antiquity, has been a distinctive feature of scientific, philosophical and legal reasoning. This article focuses primarily on the nature, evaluation and justification of analogical arguments.
https://plato.stanford.edu/entries/reasoning-analogy/
Machines, robots, fully automated manufacturing production lines, transport carriers, turbines, transistors, computers, and factories are always set up by intelligent designers
Science has discovered, that cells are literally chemical nano factories, that operate based on molecular machines, protein robots, kinesin protein carriers, autonomous self-regulated production lines, generate energy through turbines, neuron transistors, and computers
Therefore, most probably, Cell factories containing all those things are the product of an intelligent designer.
https://reasonandscience.catsboard.com/t2809-analogy-viewed-from-science#7675
Molecular machines
https://reasonandscience.catsboard.com/t1289-molecular-machines-in-biology
https://en.wikipedia.org/wiki/Molecular_machine
Science papers:
1.“Biological machines: from mills to molecules,” Nature Reviews Molecular Cell Biology, Vol. 1:149-153 (November, 2000).
2.Thomas Köcher & Giulio Superti-Furga, "Mass spectrometry-based functional proteomics: from molecular machines to protein networks," Nature Methods (October, 2007).
3."Crystalline Molecular Machines: A Quest Toward Solid-State Dynamics and Function," Accounts of Chemical Research, Vol. 39(6):413-422 (2006).
4."Molecular Machines," Annual Review of Biomedical Engineering, Vol. 6:363-395 (2004).
5."The Closest Look Ever At The Cell's Machines,” ScienceDaily.com (January 24, 2006).
6."The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, Vol. 92:291 (February 6, 1998).
7.Walter Neupert, "Highlight: Molecular Machines," Biological Chemistry, Vol. 386:711(August, 2005).
8.Seiji Kojima and David F. Blair, “The Bacterial Flagellar Motor: Structure and Function of a Complex Molecular Machine,” International Review of Cytology, Vol. 233:93-134 (2004).
9.Hugo ten Cate, “The blood coagulation system as a molecular machine,” BioEssays, Vol. 25:1220-1228 (2003).
10.John L Woolford, Jr, “Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines,” Current Opinion in Cell Biology, Vol. 21(1):109-118 (February, 2009).
11.Reinhard Lührmann, "The Spliceosome: Design Principles of a Dynamic RNP Machine," Cell, Vol. 136: 701-718 (February 20, 2009).
12.Timothy W. Nilsen, "The spliceosome: the most complex macromolecular machine in the cell?," BioEssays, Vol. 25:1147-1149 (2003).
13.L. Yarmush, "Molecular Machines," Annual Review of Biomedical Engineering, Vol. 6:363-395 (2004);
14.Paul D. Boyer, "The ATP Synthase--A Splendid Molecular Machine," Vol. 66:717-749 (1997);
15.Steven M. Block, "Real engines of creation," Nature, Vol. 386:217-219 (March 20, 1997).
16.C. Mavroidis, A. Dubey, and M.L. Yarmush, "Molecular Machines," Annual Review of Biomedical Engineering, Vol. 6:363-395 (2004)
17.Ronald D. Vale, “The Molecular Motor Toolbox for Intracellular Transport,” Cell, Vol. 112:467-480 (February 21, 2003).
18.Sharyn A. Endow, “Kinesin motors as molecular machines,” BioEssays, Vol. 25:1212-1219 (2003).
19.Michiel Meijer, “Mitochondrial biogenesis: The Tom and Tim machine,” Current Biology, Vol. 7:R100-R103 (1997).
20.Maurizio Brunori, "Structure and function of a molecular machine: cytochrome c oxidase," Biophysical Chemistry, Vol. 54: 1-33 (1995).
21.Robert T. Sauer, “Structures of Asymmetric ClpX Hexamers Reveal Nucleotide-Dependent Motions in a AAA+ Protein-Unfolding Machine,” Cell, Vol. 139:744-756 (November 13, 2009).
Proteins are robots
Nature's robots: A history of proteins: Tanford, C., Reynolds, J
Shape-shifting molecular robots respond to DNA signals
When Nature's Robots Go Rogue: Exploring Protein ...
- Document - Nature's Robots: a History of Proteins - Gale
Bio-Inspired Self-Organizing Robotic Systems
GACR - Proteins - Multi-robot Systems
Buy Nature's Robots: A History of Proteins Book Online at Low ...
Molecular production lines
A molecular production line | Nature Chemistry
molecular assembly line | News and features
The molecular biology of production cell lines. - NCBI
Cell-Like 'Molecular Assembly Lines' of ... - Cordis
Biologically inspired molecular assembly lines - MIT Media Lab
DNA-based assembly lines and nanofactories
Cell factories
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument
Microbial cell factory is an approach to bioengineering which considers microbial cells as a production facility in which the optimization process largely depends on metabolic engineering
https://en.wikipedia.org/wiki/Microbial_cell_factory
Science papers:
The Molecular Fabric of Cells BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
Plant Cells as Chemical Factories: Control and Recovery of Valuable Products
Fine Tuning our Cellular Factories: Sirtuins in Mitochondrial Biology
Cells As Molecular Factories
Eukaryotic cells are molecular factories in two senses: cells produce molecules and cells are made up of molecules.
Ribosome: Lessons of a molecular factory construction
Nucleolus: the ribosome factory
Ribosome: The cell city's factories
The Cell's Protein Factory in Action
What looks like a jumble of rubber bands and twisty ties is the ribosome, the cellular protein factory.
Chloroplasts are the microscopic factories on which all life on Earth is based.
Visualization of the active expression site locus by tagging with green fluorescent protein shows that it is specifically located at this unique pol I transcriptional factory.
There are millions of protein factories in every cell. Surprise, they’re not all the same
Rough ER is also a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane.
Endoplasmic reticulum: Scientists image 'parking garage' helix structure in protein-making factory
Theoretical biologists at Los Alamos National Laboratory have used a New Mexico supercomputer to aid an international research team in untangling another mystery related to ribosomes -- those enigmatic jumbles of molecules that are the protein factories of living cells.
The molecular factory that translates the information from RNA to proteins is called the "ribosome"
Quality control in the endoplasmic reticulum protein factory
The endoplasmic reticulum (ER) is a factory where secretory proteins are manufactured, and where stringent quality-control systems ensure that only correctly folded proteins are sent to their final destinations. The changing needs of the ER factory are monitored by integrated signalling pathways that constantly adjust the levels of folding assistants.
Molecular factories: The combination between nature and chemistry is functional
The brain is a " Uber-Computer "
https://reasonandscience.catsboard.com/t2734-the-brain-is-a-uber-computer-far-more-sophisticated-that-man-made-computers
The Cell is a super computer
https://reasonandscience.catsboard.com/t2712-the-cell-is-a-super-computer?highlight=computer
Your Cortex Contains 17 Billion Computers
Yes, the brain is a computer…
An 83,000-Processor Supercomputer Can Only Match 1% of Your Brain
Why cells are like computers—And how ‘hacking’ them could lead to new diagnostic tools
Hidden Computational Power Found in the Arms of Neurons
Dendritic action potentials and computation in human layer 2/3 cortical neurons
Single neuron dynamics and computation
What can a single neuron compute?
Brain-Inspired Computing Could Lead to Better Neuroscience
Neurons are transistors
Synaptic transistor
https://en.wikipedia.org/wiki/Synaptic_transistor
Neuron transistor behaves like a brain neuron - Phys.org
Digital: From Neurons to Transistors - LinkedIn
Capacitive neural network with neuro-transistors | Nature
A neuron-astrocyte transistor-like model for neuromorphic dressed neurons.
Electrolyte-gated organic synapse transistor interfaced ... - arXiv
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Hi, I recently started a new YouTube channel: The God-talk: It has the purpose to do debates & chats between believers and unbelievers. I would like to invite you to have a chat, either formal or not in regards to Gods existence ( or not )
https://www.youtube.com/channel/UC0nEzsU2UOrx1eXGw-Kjw4w?view_as=subscriber
The God-talk: This channel has the purpose to talk about God. Promoting debates & chats between believers and unbelievers.
https://www.youtube.com/channel/UC0nEzsU2UOrx1eXGw-Kjw4w?view_as=subscriber
https://reasonandscience.catsboard.com/t2809-analogy-viewed-from-science
Etymologically, metaphor (the Greek metafora, 'carry over') means 'transfer', 'convey', the transference of an often figurative expression from one area to another, and analogy (Gr. analogia, 'relation', from ana, 'up' + logos, 'thought') means 'similarity', or 'accordance'. Both terms are found in Aristotle, with a sense fairly similar to the present use. It is hardly feasible in any unequivocal way to delimit the concepts of model, analogy and metaphor in science. Model, however, is the most general term, and analogy and metaphor can be defined as special kinds of models. Any theory can be seen as a model system. An analogy is a relation between two descriptions of objects (or subject areas) which allows inferences to be made about one on the basis of the other (e.g. studying cell membrane diffusion on artificial membranes), or one to be understood in terms of the other (e.g. the solar system model of atomic structure). The analogy may be formal or material, and complete or partial. In formal analogy there is similarity of form, logical or mathematical structure or syntax; in material analogy of content, substance, function or semantics as well.
https://www.nbi.dk/~emmeche/cePubl/91a.frolan.html
The Argument from Simple Analogy
https://iep.utm.edu/design/#SH1b
David Hume is the most famous critic of these arguments. In Part II of his famous Dialogues Concerning Natural Religion, Hume formulates the argument as follows:
Look round the world: contemplate the whole and every part of it: you will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines, which again admit of subdivisions to a degree beyond what human senses and faculties can trace and explain. All these various machines, and even their most minute parts, are adjusted to each other with an accuracy which ravishes into admiration all men who have ever contemplated them. The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human designs, thought, wisdom, and intelligence. Since, therefore, the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of Nature is somewhat similar to the mind of man, though possessed of much larger faculties, proportioned to the grandeur of the work which he has executed. By this argument a posteriori, and by this argument alone, do we prove at once the existence of a Deity, and his similarity to human mind and intelligence.
If the causes are known that are efficacious in those other, similar phenomena, then this may give us clues concerning the causes in the phenomenon under consideration. Of course, whether this strategy works depends on the availability of closely analogous phenomena that are already explained (Herschel [1830] 1987, p. 148). Herschel (ibid., p. 149) wrote:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”
Let us suppose we arrive at a parking lot, and a car is parked there. It is from a well-known American car maker, and you know the model, type, when it was made, etc. Then, you observe a second object, which you immediately recognize as a car as well. It is far far better build, with similar functionalities, but of unknown manufacturer. Now someone approaches you and asks: Hey, what do you think, was the second car made by another car manufacturer, or did some natural unguided processes build the car? We will obviously without thinking twice answer: What a foolish question. It is OBVIOUS that an unknown car maker made the Car. Biological Cells use instructional codes to make the building blocks of life and are full of molecular machines, which resemble machines made by humans through intelligent design with specific goals. We can, therefore, infer that, since like effects have most probably similar causes, that the agency which created biological Cells, and life, must be of intelligent nature.
1. Intelligent minds make blueprints of factories full of machines with specific functions, set up for specific purposes. Each factory eventually will be full of robotic production lines where the product of one factory is handed over to the next for further processing until the end product is made. Each of the intermediate steps is essential. If any is mal or non-functioning, like energy supply, or supply of the raw materials, the factory as a whole ceases its production.
2. Biological cells are a factory complex of interlinked high-tech fabrics, fully automated and self-replicating, hosting up to over 2 billion molecular machines like Ribosomes & chemical production lines, full of protein machines that act like robots, each with a specific task or function, and completing each other, the whole system has the purpose to survive and perpetuate life. At least 1350 proteins and a fully setup genome, metabolome, and interactome is required, and they are interdependent. The probability, that such complex nano-factory complex could have emerged by unguided chemical reactions, no matter in what primordial environment, is beyond the chance of one to
10^750000. The universe hosts about 10^80 atoms.
3. Biological Cells are of unparalleled gigantic complexity and adaptive design, vastly more complex and sophisticated than any man-made factory complex. Self-replicating cells are, therefore, with extremely high probability, the product of an intelligent agency with purpose and intent.
David Hume Dialogues Concerning Natural Religion
Look round the world: contemplate the whole and every part of it: you will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines, which again admit of subdivisions to a degree beyond what human senses and faculties can trace and explain. All these various machines, and even their most minute parts, are adjusted to each other with an accuracy which ravishes into admiration all men who have ever contemplated them. The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human designs, thought, wisdom, and intelligence. Since, therefore, the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of Nature is somewhat similar to the mind of man, though possessed of much larger faculties, proportioned to the grandeur of the work which he has executed. By this argument a posteriori, and by this argument alone, do we prove at once the existence of a Deity, and his similarity to human mind and intelligence.
SCIENTIFIC MODEL S IN PHILOSOPHY OF SCIENCE, page 48
Nobody would doubt that analogy can play a considerable role in arguments, for developing or for illustrating points. This use of analogy can be found in different intellectual pursuits, such as literature, historiography, or philosophy, and there exist many examples in science —some of which are presented in section. However, analogies were not just used in science; some scientists from the nineteenth century on also discussed their use.John Herschel, mathematician, chemist, and astronomer, published a philosophical treatise in 1830 called A Preliminary Discourse on the Study of Natural Philosophy. In it, he highlights the role of analogy in science. Herschel ([1830] 1987, p. 94) wrote that “parallels and analogies” can be traced between different branches of science, and doing so “terminate[s] in a perception of their dependence on some common phenomenon of a more general and elementary nature than that which form the subject of either separately.” In short, analogy enables us to link different branches of science, seeking something more general that joins them. Herschel’s example of the search for and finding of such a common nature is electromagnetism, demonstrated by Hans Oërsted (1777–1851), relying on similarities between electricity and magnetism. Another example Herschel mentions is the analogy between light and sound. He concludes that, when confronted with an unexplained phenomenon, we need to find and study similar phenomena.
The example Herschel gives for this kind of analogical inference is a stone being whirled around on a string on a circular orbit around the hand holding the string. Whoever is holding the string is able to feel the force pulling on the string due to the stone being kept on its circular orbit by the string. One may, therefore, according to Herschel, infer that a similar force must be exerted on the moon by the Earth to keep the moon on its orbit around the Earth, even if there is no string present in the case of the moon and the Earth. Herschel obviously views this strategy of drawing analogies as a legitimate path toward scientific knowledge when he concludes from this example: “It is thus that we are continually acquiring a knowledge of the existence of causes acting under circumstances of such concealment as effectually to prevent their direct discovery” (ibid., p. 149).
The aim is to find the mechanisms that constitute the hidden processes producing certain phenomena (ibid., p. 191). In the course of this search, different hypotheses may be formed about the mechanism and, in fact, different theorists may well form different hypotheses about a phenomenon (ibid., p. 194), perhaps based on different analogies employed. Herschel is adamant that, despite the dilemmas that might occur due to competing hypotheses, forming hypotheses is still highly beneficial for scientific exploration: “they [hypotheses with respect to theories] afford us motives for searching into analogies” (ibid., p. 196). In particular,
“it may happen (and it has happened in the case of the undulatory doctrine of light) that such a weight of analogy and probability may become accumulated on the side of a hypothesis, that we are compelled to admit one of two things; either that it is an actual statement of what really passes in nature, or that the reality, whatever it be, must run so close a parallel with it, as to admit of some mode of expression common to both, at least in so far as the phenomena actually known are concerned” (ibid., pp. 196–197).
Making such an inference is not only a theoretical undertaking, but it also has practical consequences. It leads to experiments: “[W]e may be thus led to the trial of many curious experiments, and to the imagining of many useful and important contrivances, which we should never otherwise have thought of, and which, at all events, if verified in practice, are real additions to our stock of knowledge and to the arts of life” (ibid., p. 197). In sum, analogies in science, according to Herschel, establish links between different areas of investigation. Moreover, they may aid explaining a new phenomenon on the basis of the causes acting in an analogous phenomenon already explained.
As such, analogies lead to the formulation of hypotheses (and the stronger the analogy, the more evidence for the hypothesis). Finally, they may guide the experimental testing of such hypotheses, thus promoting theory development.
I discussed Maxwell’s vortex model, his model of field lines, and mechanical understanding of physics in the last chapter. I now specifically consider his reflections on the use of analogy in science. One place where he explicitly considered the use of analogy in science is his “Address to the Mathematical and Physical Sections of the British Association” in Liverpool in 1870 (Maxwell [1870] 1890).³ He had in mind what we would today call a cognitive function of analogy. Maxwell’s emphasis is on the illustrations provided by analogies. The scientist should “try to understand the subject by means of well-chosen illustrations derived from subjects with which he is more familiar” (ibid., p. 219). The aim is “to enable the mind to grasp some conception or law in one branch of science, by placing before it a conception or a law in a different branch of science and directing the mind to lay hold of that mathematical form which is common to the corresponding ideas in the two sciences, leaving out of account for the present the difference between the physical nature of the real phenomena” (ibid., p. 219). An analogy is more than a teaching aid or dispensable illustration and can tell us what the system under study is like:
“the recognition of the formal analogy between the two systems of ideas leads to a knowledge of both, more profound than could be obtained by studying each system separately” (ibid., p. 219).
Maxwell voices reasons why analogies are useful in science. Using an analogy can be a strategy toward understanding an as yet not understood subject and hence contribute to generating knowledge by guiding the mind. Understanding, knowledge generation, and creativity are issues that have been investigated quite systematically in the cognitive sciences. Maxwell was also a great practitioner of the use of analogy in physics. Analogy was deliberately and systematically used in an effort to understand electrical effects that were not mechanical by nature. (Frequently these were analogies to mechanical models, see chapter 2, section 2.1, but not inevitably.) Maxwell not only devised the vortex model. An earlier and very instructive example is Maxwell’s model of electrical field lines that quite obviously exploits an analogy (Maxwell [1855] 1890). There, the field lines are represented by tubes in which an incompressible fluid moves, a model also broadly based on Thomson’s analogy between the flow of heat and the flow of electrical force. Maxwell’s aim in using this analogy is not to say what electrical field lines are physically like—they do not consist of a fluid—but how one might imagine them in accordance with the analogy guiding their theoretical description. Maxwell (ibid., pp. 157–158) wrote: “By the method which I adopt, I hope to render it evident . . . that the limit of my design is to show how, by strict application of the ideas and methods of Faraday, the connexion of the very different orders of phenomena which he has discovered may be clearly placed before the mathematical mind.”
Here Maxwell makes explicit how analogies, and analogies to classical mechanics, in particular, aid understanding. One beneficial point is that “the mathematical forms of the relations of the quantities are the same in both systems, though the physical nature of the quantities may be utterly different” (Maxwell [1870] 1890, p. 218).
Analogical reasoning is fundamental to human thought and, arguably, to some nonhuman animals as well. Historically, analogical reasoning has played an important, but sometimes mysterious, role in a wide range of problem-solving contexts. The explicit use of analogical arguments, since antiquity, has been a distinctive feature of scientific, philosophical and legal reasoning. This article focuses primarily on the nature, evaluation and justification of analogical arguments.
https://plato.stanford.edu/entries/reasoning-analogy/
Machines, robots, fully automated manufacturing production lines, transport carriers, turbines, transistors, computers, and factories are always set up by intelligent designers
Science has discovered, that cells are literally chemical nano factories, that operate based on molecular machines, protein robots, kinesin protein carriers, autonomous self-regulated production lines, generate energy through turbines, neuron transistors, and computers
Therefore, most probably, Cell factories containing all those things are the product of an intelligent designer.
https://reasonandscience.catsboard.com/t2809-analogy-viewed-from-science#7675
Molecular machines
https://reasonandscience.catsboard.com/t1289-molecular-machines-in-biology
https://en.wikipedia.org/wiki/Molecular_machine
Science papers:
1.“Biological machines: from mills to molecules,” Nature Reviews Molecular Cell Biology, Vol. 1:149-153 (November, 2000).
2.Thomas Köcher & Giulio Superti-Furga, "Mass spectrometry-based functional proteomics: from molecular machines to protein networks," Nature Methods (October, 2007).
3."Crystalline Molecular Machines: A Quest Toward Solid-State Dynamics and Function," Accounts of Chemical Research, Vol. 39(6):413-422 (2006).
4."Molecular Machines," Annual Review of Biomedical Engineering, Vol. 6:363-395 (2004).
5."The Closest Look Ever At The Cell's Machines,” ScienceDaily.com (January 24, 2006).
6."The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, Vol. 92:291 (February 6, 1998).
7.Walter Neupert, "Highlight: Molecular Machines," Biological Chemistry, Vol. 386:711(August, 2005).
8.Seiji Kojima and David F. Blair, “The Bacterial Flagellar Motor: Structure and Function of a Complex Molecular Machine,” International Review of Cytology, Vol. 233:93-134 (2004).
9.Hugo ten Cate, “The blood coagulation system as a molecular machine,” BioEssays, Vol. 25:1220-1228 (2003).
10.John L Woolford, Jr, “Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines,” Current Opinion in Cell Biology, Vol. 21(1):109-118 (February, 2009).
11.Reinhard Lührmann, "The Spliceosome: Design Principles of a Dynamic RNP Machine," Cell, Vol. 136: 701-718 (February 20, 2009).
12.Timothy W. Nilsen, "The spliceosome: the most complex macromolecular machine in the cell?," BioEssays, Vol. 25:1147-1149 (2003).
13.L. Yarmush, "Molecular Machines," Annual Review of Biomedical Engineering, Vol. 6:363-395 (2004);
14.Paul D. Boyer, "The ATP Synthase--A Splendid Molecular Machine," Vol. 66:717-749 (1997);
15.Steven M. Block, "Real engines of creation," Nature, Vol. 386:217-219 (March 20, 1997).
16.C. Mavroidis, A. Dubey, and M.L. Yarmush, "Molecular Machines," Annual Review of Biomedical Engineering, Vol. 6:363-395 (2004)
17.Ronald D. Vale, “The Molecular Motor Toolbox for Intracellular Transport,” Cell, Vol. 112:467-480 (February 21, 2003).
18.Sharyn A. Endow, “Kinesin motors as molecular machines,” BioEssays, Vol. 25:1212-1219 (2003).
19.Michiel Meijer, “Mitochondrial biogenesis: The Tom and Tim machine,” Current Biology, Vol. 7:R100-R103 (1997).
20.Maurizio Brunori, "Structure and function of a molecular machine: cytochrome c oxidase," Biophysical Chemistry, Vol. 54: 1-33 (1995).
21.Robert T. Sauer, “Structures of Asymmetric ClpX Hexamers Reveal Nucleotide-Dependent Motions in a AAA+ Protein-Unfolding Machine,” Cell, Vol. 139:744-756 (November 13, 2009).
Proteins are robots
Nature's robots: A history of proteins: Tanford, C., Reynolds, J
Shape-shifting molecular robots respond to DNA signals
When Nature's Robots Go Rogue: Exploring Protein ...
- Document - Nature's Robots: a History of Proteins - Gale
Bio-Inspired Self-Organizing Robotic Systems
GACR - Proteins - Multi-robot Systems
Buy Nature's Robots: A History of Proteins Book Online at Low ...
Molecular production lines
A molecular production line | Nature Chemistry
molecular assembly line | News and features
The molecular biology of production cell lines. - NCBI
Cell-Like 'Molecular Assembly Lines' of ... - Cordis
Biologically inspired molecular assembly lines - MIT Media Lab
DNA-based assembly lines and nanofactories
Cell factories
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument
Microbial cell factory is an approach to bioengineering which considers microbial cells as a production facility in which the optimization process largely depends on metabolic engineering
https://en.wikipedia.org/wiki/Microbial_cell_factory
Science papers:
The Molecular Fabric of Cells BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
Plant Cells as Chemical Factories: Control and Recovery of Valuable Products
Fine Tuning our Cellular Factories: Sirtuins in Mitochondrial Biology
Cells As Molecular Factories
Eukaryotic cells are molecular factories in two senses: cells produce molecules and cells are made up of molecules.
Ribosome: Lessons of a molecular factory construction
Nucleolus: the ribosome factory
Ribosome: The cell city's factories
The Cell's Protein Factory in Action
What looks like a jumble of rubber bands and twisty ties is the ribosome, the cellular protein factory.
Chloroplasts are the microscopic factories on which all life on Earth is based.
Visualization of the active expression site locus by tagging with green fluorescent protein shows that it is specifically located at this unique pol I transcriptional factory.
There are millions of protein factories in every cell. Surprise, they’re not all the same
Rough ER is also a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane.
Endoplasmic reticulum: Scientists image 'parking garage' helix structure in protein-making factory
Theoretical biologists at Los Alamos National Laboratory have used a New Mexico supercomputer to aid an international research team in untangling another mystery related to ribosomes -- those enigmatic jumbles of molecules that are the protein factories of living cells.
The molecular factory that translates the information from RNA to proteins is called the "ribosome"
Quality control in the endoplasmic reticulum protein factory
The endoplasmic reticulum (ER) is a factory where secretory proteins are manufactured, and where stringent quality-control systems ensure that only correctly folded proteins are sent to their final destinations. The changing needs of the ER factory are monitored by integrated signalling pathways that constantly adjust the levels of folding assistants.
Molecular factories: The combination between nature and chemistry is functional
The brain is a " Uber-Computer "
https://reasonandscience.catsboard.com/t2734-the-brain-is-a-uber-computer-far-more-sophisticated-that-man-made-computers
The Cell is a super computer
https://reasonandscience.catsboard.com/t2712-the-cell-is-a-super-computer?highlight=computer
Your Cortex Contains 17 Billion Computers
Yes, the brain is a computer…
An 83,000-Processor Supercomputer Can Only Match 1% of Your Brain
Why cells are like computers—And how ‘hacking’ them could lead to new diagnostic tools
Hidden Computational Power Found in the Arms of Neurons
Dendritic action potentials and computation in human layer 2/3 cortical neurons
Single neuron dynamics and computation
What can a single neuron compute?
Brain-Inspired Computing Could Lead to Better Neuroscience
Neurons are transistors
Synaptic transistor
https://en.wikipedia.org/wiki/Synaptic_transistor
Neuron transistor behaves like a brain neuron - Phys.org
Digital: From Neurons to Transistors - LinkedIn
Capacitive neural network with neuro-transistors | Nature
A neuron-astrocyte transistor-like model for neuromorphic dressed neurons.
Electrolyte-gated organic synapse transistor interfaced ... - arXiv
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Hi, I recently started a new YouTube channel: The God-talk: It has the purpose to do debates & chats between believers and unbelievers. I would like to invite you to have a chat, either formal or not in regards to Gods existence ( or not )
https://www.youtube.com/channel/UC0nEzsU2UOrx1eXGw-Kjw4w?view_as=subscriber
The God-talk: This channel has the purpose to talk about God. Promoting debates & chats between believers and unbelievers.
https://www.youtube.com/channel/UC0nEzsU2UOrx1eXGw-Kjw4w?view_as=subscriber
