A reply to Dimiter Kunnev's new abiogenesis paper
https://reasonandscience.catsboard.com/t3060-a-reply-to-dimiter-kunnev-s-new-abiogenesis-paper
Origin of Life: The Point of No Return
https://www.mdpi.com/2075-1729/10/11/269/htm
DK: “As we have presented it here, the key distinction between the origin of life and other ‘emergent’ transitions is the onset of distributed information control, enabling context-dependent causation, where an abstract and non-physical, systemic entity (algorithmic information) effectively becomes a causal agent capable of manipulating its material substrate”
Reply: Thank you for confirming my point, and disproving Speeds claim, that biological information is not physical, but abstract - non-physical. Of course, once it is non-physical, it must be of mental origin - aka, intelligence.
DK: Although an information repository is an attribute of life and certainly needs management, it is not clear what force(s) establishes this relationship.
Reply: Of course, from a materialistic viewpoint, that question finds no satisfactory answer. But from a Intelligent Design perspective, that question is perfectly answerable.
https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence
1. A code is a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.
2. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning in order to establish communication, trough encoding, sending, and decoding. Semantics, Synthax, and pragmatics are always set up by intelligence.
3. We see that precisely in cells, where information is encoded through the genetic code which is a set of rules, stored in DNA sequences of nucleotide triplets called codons. They are used to translate genetic information into amino acid polypeptide sequences, which make proteins ( the molecular machines, the working horses of the cell ). The assignment of codons (triplet nucleotides) to amino acids must be pre-established by a mind. And so, the information which is sent through the system, as well as the communication channels that permit encoding, sending, and decoding, which in life is done by over 25 extremely complex molecular machine systems, which do as well error check and repair to maintain genetic stability, 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 life began because life depends on it. The origin of such complex communication systems is best explained by an intelligent designer.
https://www.youtube.com/watch?v=X_tYrnv_o6A
DK: The mechanism for the transition of informational storage is rooted in the process of Darwinian evolution itself.
Reply: How is this possible, if biological information depends on the hardware and software fully operational, and in place?
DK: Looking at what constitutes Darwinian evolution, we naturally reach the opposite conclusion. Darwinian evolution has the innate ability to define the transition from non-life to life. The process of Darwinian evolution and “life” are the same phenomenon.
Reply: Dimiter, who did that peer-review? That is a unwarranted claim, a just so assertion, and not confirmed by any scientist i know of.... Darwinian evolution has nothing to do with chemical evolution, nor the origin of life.
DK: The “metabolism first” hypothesis postulates that CO2 and NH3 fixation plus energy lead to the synthesis of amino acids and nucleotides.
Reply: There are huge problems with the metabolism first scenarios, as i outline here:
Carbon metabolism, which is the most basic aspect of life: by design, or chemical evolution ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#7746
Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle: 26 January 2015
https://www.nature.com/articles/srep08009
The rTCA cycle that is found in bacteria is catalyzed by enzymes with high degrees of substrate selectivity. 28 The reaction substrates and the reaction sequence of the enzymatic rTCA cycle are conserved ( not evolved ) On the other hand, the transformations of pre biological chemistry are assumed to occur under the effect of chemical catalysts. The latter, however, are typically active with respect to certain types of chemical transformations and lack the high substrate selectivity characteristic of enzyme catalysts. The smallest supernetwork that includes rTCA cycle is designated the rTCA supernetwork. It contains 175 molecules and 444 reactions. We conclude that the rTCA cycle should have a low probability of a random realization. We also notice that its length and cost are close to extreme values. Selection for the extreme values implies an optimization process. Is there any evidence so far that such optimization will inevitably lead to the rTCA cycle?
DK: Lipid vesicles or lamellae may sustain integrity, but positive feedback from the vesicle structure to an information source capable of determining the synthesis of the same stable lipid vesicles is unspecified.
Reply: Somehow, that envelope had to create a homeostatic environment, diminishing the calcium concentration in the cell 10000 times below the external environment, to permit signaling. At the same time, a signaling code would have had to be established, and immediately begin to function, with a common agreement between sender and receiver................energy supply would have been a major problem, since almost all life forms depend on the supply of glucose, which is a product of complex metabolic pathways, and not readily available on the prebiotic earth. Most proteins require active metal clusters in their reaction centers.
DK: Due to the obligatory dependency of the information and structure subject to Darwinian evolution, these components must be locked in their origin. It is evident that the three components cannot originate independently and must be established in the same physicochemical set of processes. The assembly of information cannot arise separately in another system different from the existing one. It is obvious that all components from Figure 1 (information, structure, and the rule for their interactions) are “locked” and inter-reliant in their origin and must be formed within the same group of processes and within the same timeframe.
It is evident that the three components cannot originate independently and must be established in the same physicochemical set of processes. The assembly of information cannot arise separately in another system different from the existing one. It is obvious that all components (information, structure, and the rule for their interactions) are “locked” and inter-reliant in their origin and must be formed within the same group of processes and within the same timeframe.
Reply: Agreed. The four interdependent requirements to have an information transmission system
https://reasonandscience.catsboard.com/t3030-the-four-interdependent-requirements-to-have-an-information-transmission-system
Information is what is conveyed or represented by a particular arrangement or sequence of things. To have an information transmission system, following things are indispensable, essential, and required ( if any of those is missing, information transmission cannot be established - all have to be precisely defined in advance before any form of communication can be possible at all):
1. A language, 2. the information (message) produced upon that language, the 3 .information storage mechanism ( a hard disk, paper etc.), 4. an information transmission system, that is: encoding - sending and decoding) and eventually fifth, sixth, and seventh ( not essential): translation, conversion, and transduction
1. The rules or protocol of any informational communication and information system must be preestablished and agreed in advance between those that communicate with each other, through establishing in common agreement of the meaning where a symbol, letters, words, waves or frequency variations, sounds, pulses, or a combination of those are assigned to something else, otherwise the transmission of information is not possible. A message can only be created once a language has been established. A code is an abstract, immaterial, nonphysical set of rules. Statistics, Semantics, Synthax, and Pragmatics are used according to combinatorial, context-dependent, and content-coherent rules.
2. This set of rule, code, or language, permits to produce a blueprint, which contains instructional complex information, that permits to produce goods for specific purposes, control or maintain the operation of factories.
3. Then there has to be a device, that is the harddisk, a paper, or any hardware upon which the information can be recorded.
4. And there has to be a system to encode, send, and decode the message.
5. Eventually, during the transmission of information, it can be translated from one language to another. That requires a system of translation/cipher. It’s like when you visit a Russian website and your browser has the language plug-in for Russian. Conveying meaning of the Russian and english language must be established in advance, that is the alphabet (symbols), syntax (grammar), and semantics (meaning) before any translation can take place. Otherwise, it would never be certain that what the transmitter is communicating is the same as what the receiver is understanding.
6. Eventually signal conversion ( digital-analog conversion, modulators, amplifiers)
7. Eventually signal transduction converting the nonelectrical signals into electrical signals
In Cells, we see all these things.
DK: What distinguishes a living entity from matter that is not alive? How did life originate? These questions have accompanied us through human history.
Reply: What is life ?
https://reasonandscience.catsboard.com/t1435-paul-davies-what-is-life
NASA’s current working definition of life
is “a self-sustaining chemical system capable of Darwinian evolution.”
Szent-Györgyi, who was awarded the 1937 Nobel Prize in Physiology or Medicine for his discovery of the action of ascorbic acid:
“In my hunt for the secret of life, I started research in histology. Unsatisfied by the information that cellular morphology could give me about life, I turned to physiology. Finding physiology too complex I took up pharmacology. Still finding the situation too complicated I turned to bacteriology. But bacteria were even too complex, so I descended to the molecular level, studying chemistry and physical chemistry. After twenty years' work, I was led to conclude that to understand life we have to descend to the electronic level, and to the world of wave mechanics. But electrons are just electrons, and have no life at all. Evidently, on the way I lost life; it had run out between my fingers.”
Paul Davies:
http://www.nytimes.com/books/first/d/davies-miracle.html
Reproduction.
Metabolism.
Homeostasis
Nutrition.
Complexity.
Organization.
Growth and development.
Information content.
Hardware/software entanglement.
Permanence and change.
DK: In searching for the first living cell, at some moment, a proto-cell(s) capable of evolving should emerge.
Reply: There was most likely never a so-called protocell.
The cell is irreducibly complex
https://reasonandscience.catsboard.com/t1299-abiogenesis-the-cell-is-irreducibly-complex
Abiogenesis? Impossible !!
https://www.youtube.com/watch?v=ycJblRcgqXk
The cell is the irreducible, minimal unit of life 5
https://sci-hub.st/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8
Chemistry and the Missing Era of Evolution: A. Graham Cairns-Smith
We can see that at the time of the common ancestor, this system must already have been fixed in its essentials, probably through a critical interdependence of subsystems. (Roughly speaking in a domain in which everything has come to depend on everything else nothing can be easily changed, and our central biochemistry is very much like that.
https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/18260066
chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity
https://sixdaysblog.com/2013/07/06/protocells-may-have-formed-in-a-salty-soup/
If we are to assume all life came from a single cell way in the past, then that cell, from it's very first moment had to have all the machinery capable of :
1. reproduction
2. the means of obtaining energy in whatever form that may have been
3. the means of converting that energy source to a useable form
4. the means of ridding itself of toxic waste
5. the means of protecting itself from environmental dangers ex, radiation, temperature fluctuations, acid/base conditions
6. means of cellular repair of all of these mechanisms
7. The means of intracellular communication between all its parts the prior knowledge that it would need all these components and the ability of ALL of these to function fully and simultaneously from day one because malfunctions of, or incomplete versions or not fully "evolved" parts would have lead to immediate or almost immediate death.
DK: The newly established proto-cell must have a relatively simple structure with heredity and a primordial metabolism. However, the process leading to the formation of a proto-cell must consist of a multi-step process that begins with the precursors of nucleic acids, peptides, lipids, and energy followed by polymer interactions and enzymatic metabolic reactions.
Reply: There is no evidence whatsoever that prebiotic catalysis would/could have led to the emergence of the basic building blocks of life withouty enzymatic catalists. And there is no evidence of nor a plausible hypothesis of a transition from noncatalitic to enzymatic production of the building blocks. There is a huge unbridgeable gap.
I have listed 27 open questions in regard to the origin of RNA and DNA on the early earth, 14 unsolved problems in regard to the origin of amino acids on the early earth, 12 in regard to phospholipid synthesis, and also unsolved problems in regard to carbohydrate production. The open problems are in reality far greater. This is just a small list. It is not just an issue of things that have not yet been figured out by abiogenesis research, but deep conceptual problems, like the fact that there were no natural selection mechanisms in place on the early earth.
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759
DK: Based on our understanding of evolution, we can picture a scenario where multiple variants of proto-cells initially emerged but most adapted, survived, and evolved
Reply: What does survive even mean in the context of "proto-cells" ? Live starts once a threshold is achieved, where cell can live freely (independently from a living host, like mycoplasma in humans ), and being able to perform all tasks mentioned and described previously. Anything that is not capable to perform those tasks, cannot be described as alive.
DK: An obvious question is “What are the critical steps for living matter to emerge?” Is it possible, therefore, to find a boundary between chemistry and biology if we look at all the events leading up to LUCA?
Reply: What might be a Cell’s minimal requirement of parts ?
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts
The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells. It has complete biosynthetic pathways for all 20 amino acids. These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. 14 That would be the size of a book with 400 pages, each page with 3000 characters. They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells. If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help.
Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55.
The argument of the cell
1. At least 1300 proteins are required as building blocks for the simplest living cell to come into existence.
2. Proteins are highly complex structures.
3. The probability of random creation of complex proteins, the assemblage of the needed 1300 in one place in nature without any control is less than 10^700,000 or impossible.
4. If you leave the molecules required to make the four basic building blocks of life, they will just randomize, and become asphalts.
4. Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. The impossibility of chance indicates the necessity of an intelligent designer to explain the origin of life.
DK: The formation of RNA and peptides depends on the previous steps of the prebiotic synthesis of nucleotides and amino acids. Polymer interactions and the emergence of sustained proto-cellular structure depend on previously synthesized polymers made of monomers; therefore, there is no specific single event that is recognized to have paramount importance for the beginning of life.
Reply: Agreed. Many tasks would have to be accomplished already to get to that stage.
The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated
https://reasonandscience.catsboard.com/t2997-the-problem-of-the-origin-of-the-hardware-and-software-in-the-cell-is-far-greater-than-commonly-appreciated
- Getting the basic elements to make the building blocks of life
- RNA world
- RNA and DNA synthesis
- Polymerization through catalysts on clay
- The Eigen threshold
- The transition from the RNA world, to the DNA world
- Obtaining the genetic Code
- The genetic code is optimal amongst 1 million
- The second, overlapping code in DNA
- The amazing information storage capacity of DNA
- Getting the information in the genome
- Getting the gene expression machinery to make proteins
- Origin of the 37 gene codes: Did they evolve?
DK: If we investigate the chain of events from the first polymers to the formation of the first proto-cells, there must be a moment where heredity starts to play a significant role.
Reply: Heredity starts, when life starts to self-replicate. And for that to happen, DNA replication has to be in place. The problem faced by evolutionary biology is however, that DNA replication requires a minimal set of proteins, which word interdependently together:
DNA replication, and its mind boggling nano technology that defies naturalistic explanations
https://reasonandscience.catsboard.com/t1849-dna-replication-of-prokaryotes
The Argument of the Original Replicator
In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule.
Each of these proteins is essential and required for the proper replicating process. Not a single one of these proteins can be missing, otherwise the whole process breaks down, and is unable to perform its task correctly. DNA repair mechanisms must also be in place, fully functional and working properly, otherwise the mutation rate will be too high, and the cell dies. 18
The individual parts and proteins require by themselves complex assembly proteins to be built.
The individual parts, assembly proteins, and proteins individually would have no function by their own. They have only function interconnected in the working whole.
The individual parts must be readily available on the construction site of the rna replication complex, being correctly interlocked, interlinked, and have the right interface compatibility to be able to interact correctly together. All this requires information and meta information ( information that directs the expression of the genomic information for construction of the individual proteins, and correct timing of expression, and as well the information of the correct assembly sequence. )
Evolution is not a capable driving force to make the dna replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.
DNA replication requires coded, complex, specified information and meta-information, and the DNA replication process is irreducibly complex.
Therefore, DNA replication is best explained through design.
DK: The establishment of heredity defines the emergence of adaptation and diversification toward more complex structures, i.e., Darwinian evolution. All events that occur before this moment are governed only by environmental conditions, where more complicated structures are synthesized simply by chance with no “recollection” of previously existing ones. The forces of degradation could roll back the initial state.
Reply: That is one of the main reasons why abiogenesis is not possible.
Paradoxes in the Origin of Life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-virtually-impossible#7309
Steven A. Benner
https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/25608919
Discussed here is an alternative approach to guide research into the origins of life, one that focuses on “paradoxes”, pairs of statements, both grounded in theory and observation, that (taken together) suggest that the “origins problem” cannot be solved.
The Asphalt Paradox
Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”. the literature reports (to our knowledge) exactly ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution.
Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.
DK: The development of Darwinian evolution may not have been a sudden process; it would have involved many trials and errors but would have made an enormous difference after it was established.
Reply: The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells. It has complete biosynthetic pathways for all 20 amino acids. These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. 14 They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells. If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000.
DK: The task here is to define the minimum number of components working on the molecular level necessary for selection to occur, so these might be utilized in the further origin of life research.
Reply: Trying to shift Darwinian evolution to the field of the origin of life makes no sense whatsoever. Koonin, the logic of chance, page 266
Evolution by natural selection and drift can begin only after replication with sufficient fidelity is established. Even at that stage, the evolution of translation remains highly problematic. The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible . The synthesis of nucleotides and (at least) moderate-sized polynucleotides could not have evolved biologically and must have emerged abiogenically—that is, effectively by chance abetted by chemical selection, such as the preferential survival of stable RNA species.
DK: All three components: the information, the structure/function, and the rule between them are mutually dependent for their existence, i.e., the components are attributes of each other and cannot be analyzed independently
Reply: Unintentionally, Dimiter is making an argument for intelligent design. :=)) Interdependence is the hallmark of design, and requires fore-planning.
DK: If we take the information, for example, it cannot exist without resolving the structure/function component, otherwise, the string of units (e.g., nucleotides of RNA) would be random and without information.
Reply: The hardware and software of the cell, evidence of design
https://reasonandscience.catsboard.com/t2221-the-hardware-and-software-of-the-cell-evidence-of-design
Paul Davies: the fifth miracle page 62
Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it. 1
We need to explain the origin of both the hardware and software aspects of life, or the job is only half finished. Explaining the chemical substrate of life and claiming it as a solution to life’s origin is like pointing to silicon and copper as an explanation for the goings-on inside a computer. It is this transition where one should expect to see a chemical system literally take-on “a life of its own”, characterized by informational dynamics which become decoupled from the dictates of local chemistry alone (while of course remaining fully consistent with those dictates). Thus the famed chicken-or-egg problem (a solely hardware issue) is not the true sticking point. Rather, the puzzle lies with something fundamentally different, a problem of causal organization having to do with the separation of informational and mechanical aspects into parallel causal narratives. The real challenge of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics.
Software and hardware are irreducible complex and interdependent. There is no reason for information processing machinery to exist without the software, and vice versa.
Systems of interconnected software and hardware are irreducibly complex. 2
DK: It would be like the working of a mechanical clock without installed hands: you would never know what time it is. In order for the information to determine the structural/functional component, it needs a rule to execute the process of transfer of the information, i.e., genetic code or Watson-Crick base-pair, therefore the rule should exist also with the information and with the structure/function.
Reply: The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin
1. The assignment of a word to represent something, like the word chair to an object to sit down, is always of mental origin.
2. The translation of a word in one language, to another language, is always of mental origin. For example the assignment of the word chair, in English, to xizi, in Chinese, can only be made by intelligence upon common agreement of meaning.
3. In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
4. Since we know only of intelligence to be able to do so, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.
Origin and evolution of the genetic code: the universal enigma
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/
After this excellent paper ( and my review ) it can be concluded with high certainty, that there is no return to the abiogenesis hypothesis. Intelligent Design rules !!
https://reasonandscience.catsboard.com/t3060-a-reply-to-dimiter-kunnev-s-new-abiogenesis-paper
Origin of Life: The Point of No Return
https://www.mdpi.com/2075-1729/10/11/269/htm
DK: “As we have presented it here, the key distinction between the origin of life and other ‘emergent’ transitions is the onset of distributed information control, enabling context-dependent causation, where an abstract and non-physical, systemic entity (algorithmic information) effectively becomes a causal agent capable of manipulating its material substrate”
Reply: Thank you for confirming my point, and disproving Speeds claim, that biological information is not physical, but abstract - non-physical. Of course, once it is non-physical, it must be of mental origin - aka, intelligence.
DK: Although an information repository is an attribute of life and certainly needs management, it is not clear what force(s) establishes this relationship.
Reply: Of course, from a materialistic viewpoint, that question finds no satisfactory answer. But from a Intelligent Design perspective, that question is perfectly answerable.
https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence
1. A code is a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.
2. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning in order to establish communication, trough encoding, sending, and decoding. Semantics, Synthax, and pragmatics are always set up by intelligence.
3. We see that precisely in cells, where information is encoded through the genetic code which is a set of rules, stored in DNA sequences of nucleotide triplets called codons. They are used to translate genetic information into amino acid polypeptide sequences, which make proteins ( the molecular machines, the working horses of the cell ). The assignment of codons (triplet nucleotides) to amino acids must be pre-established by a mind. And so, the information which is sent through the system, as well as the communication channels that permit encoding, sending, and decoding, which in life is done by over 25 extremely complex molecular machine systems, which do as well error check and repair to maintain genetic stability, 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 life began because life depends on it. The origin of such complex communication systems is best explained by an intelligent designer.
https://www.youtube.com/watch?v=X_tYrnv_o6A
DK: The mechanism for the transition of informational storage is rooted in the process of Darwinian evolution itself.
Reply: How is this possible, if biological information depends on the hardware and software fully operational, and in place?
DK: Looking at what constitutes Darwinian evolution, we naturally reach the opposite conclusion. Darwinian evolution has the innate ability to define the transition from non-life to life. The process of Darwinian evolution and “life” are the same phenomenon.
Reply: Dimiter, who did that peer-review? That is a unwarranted claim, a just so assertion, and not confirmed by any scientist i know of.... Darwinian evolution has nothing to do with chemical evolution, nor the origin of life.
DK: The “metabolism first” hypothesis postulates that CO2 and NH3 fixation plus energy lead to the synthesis of amino acids and nucleotides.
Reply: There are huge problems with the metabolism first scenarios, as i outline here:
Carbon metabolism, which is the most basic aspect of life: by design, or chemical evolution ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#7746
Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle: 26 January 2015
https://www.nature.com/articles/srep08009
The rTCA cycle that is found in bacteria is catalyzed by enzymes with high degrees of substrate selectivity. 28 The reaction substrates and the reaction sequence of the enzymatic rTCA cycle are conserved ( not evolved ) On the other hand, the transformations of pre biological chemistry are assumed to occur under the effect of chemical catalysts. The latter, however, are typically active with respect to certain types of chemical transformations and lack the high substrate selectivity characteristic of enzyme catalysts. The smallest supernetwork that includes rTCA cycle is designated the rTCA supernetwork. It contains 175 molecules and 444 reactions. We conclude that the rTCA cycle should have a low probability of a random realization. We also notice that its length and cost are close to extreme values. Selection for the extreme values implies an optimization process. Is there any evidence so far that such optimization will inevitably lead to the rTCA cycle?
DK: Lipid vesicles or lamellae may sustain integrity, but positive feedback from the vesicle structure to an information source capable of determining the synthesis of the same stable lipid vesicles is unspecified.
Reply: Somehow, that envelope had to create a homeostatic environment, diminishing the calcium concentration in the cell 10000 times below the external environment, to permit signaling. At the same time, a signaling code would have had to be established, and immediately begin to function, with a common agreement between sender and receiver................energy supply would have been a major problem, since almost all life forms depend on the supply of glucose, which is a product of complex metabolic pathways, and not readily available on the prebiotic earth. Most proteins require active metal clusters in their reaction centers.
DK: Due to the obligatory dependency of the information and structure subject to Darwinian evolution, these components must be locked in their origin. It is evident that the three components cannot originate independently and must be established in the same physicochemical set of processes. The assembly of information cannot arise separately in another system different from the existing one. It is obvious that all components from Figure 1 (information, structure, and the rule for their interactions) are “locked” and inter-reliant in their origin and must be formed within the same group of processes and within the same timeframe.
It is evident that the three components cannot originate independently and must be established in the same physicochemical set of processes. The assembly of information cannot arise separately in another system different from the existing one. It is obvious that all components (information, structure, and the rule for their interactions) are “locked” and inter-reliant in their origin and must be formed within the same group of processes and within the same timeframe.
Reply: Agreed. The four interdependent requirements to have an information transmission system
https://reasonandscience.catsboard.com/t3030-the-four-interdependent-requirements-to-have-an-information-transmission-system
Information is what is conveyed or represented by a particular arrangement or sequence of things. To have an information transmission system, following things are indispensable, essential, and required ( if any of those is missing, information transmission cannot be established - all have to be precisely defined in advance before any form of communication can be possible at all):
1. A language, 2. the information (message) produced upon that language, the 3 .information storage mechanism ( a hard disk, paper etc.), 4. an information transmission system, that is: encoding - sending and decoding) and eventually fifth, sixth, and seventh ( not essential): translation, conversion, and transduction
1. The rules or protocol of any informational communication and information system must be preestablished and agreed in advance between those that communicate with each other, through establishing in common agreement of the meaning where a symbol, letters, words, waves or frequency variations, sounds, pulses, or a combination of those are assigned to something else, otherwise the transmission of information is not possible. A message can only be created once a language has been established. A code is an abstract, immaterial, nonphysical set of rules. Statistics, Semantics, Synthax, and Pragmatics are used according to combinatorial, context-dependent, and content-coherent rules.
2. This set of rule, code, or language, permits to produce a blueprint, which contains instructional complex information, that permits to produce goods for specific purposes, control or maintain the operation of factories.
3. Then there has to be a device, that is the harddisk, a paper, or any hardware upon which the information can be recorded.
4. And there has to be a system to encode, send, and decode the message.
5. Eventually, during the transmission of information, it can be translated from one language to another. That requires a system of translation/cipher. It’s like when you visit a Russian website and your browser has the language plug-in for Russian. Conveying meaning of the Russian and english language must be established in advance, that is the alphabet (symbols), syntax (grammar), and semantics (meaning) before any translation can take place. Otherwise, it would never be certain that what the transmitter is communicating is the same as what the receiver is understanding.
6. Eventually signal conversion ( digital-analog conversion, modulators, amplifiers)
7. Eventually signal transduction converting the nonelectrical signals into electrical signals
In Cells, we see all these things.
DK: What distinguishes a living entity from matter that is not alive? How did life originate? These questions have accompanied us through human history.
Reply: What is life ?
https://reasonandscience.catsboard.com/t1435-paul-davies-what-is-life
NASA’s current working definition of life
is “a self-sustaining chemical system capable of Darwinian evolution.”
Szent-Györgyi, who was awarded the 1937 Nobel Prize in Physiology or Medicine for his discovery of the action of ascorbic acid:
“In my hunt for the secret of life, I started research in histology. Unsatisfied by the information that cellular morphology could give me about life, I turned to physiology. Finding physiology too complex I took up pharmacology. Still finding the situation too complicated I turned to bacteriology. But bacteria were even too complex, so I descended to the molecular level, studying chemistry and physical chemistry. After twenty years' work, I was led to conclude that to understand life we have to descend to the electronic level, and to the world of wave mechanics. But electrons are just electrons, and have no life at all. Evidently, on the way I lost life; it had run out between my fingers.”
Paul Davies:
http://www.nytimes.com/books/first/d/davies-miracle.html
Reproduction.
Metabolism.
Homeostasis
Nutrition.
Complexity.
Organization.
Growth and development.
Information content.
Hardware/software entanglement.
Permanence and change.
DK: In searching for the first living cell, at some moment, a proto-cell(s) capable of evolving should emerge.
Reply: There was most likely never a so-called protocell.
The cell is irreducibly complex
https://reasonandscience.catsboard.com/t1299-abiogenesis-the-cell-is-irreducibly-complex
Abiogenesis? Impossible !!
https://www.youtube.com/watch?v=ycJblRcgqXk
The cell is the irreducible, minimal unit of life 5
https://sci-hub.st/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8
Chemistry and the Missing Era of Evolution: A. Graham Cairns-Smith
We can see that at the time of the common ancestor, this system must already have been fixed in its essentials, probably through a critical interdependence of subsystems. (Roughly speaking in a domain in which everything has come to depend on everything else nothing can be easily changed, and our central biochemistry is very much like that.
https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/18260066
chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity
https://sixdaysblog.com/2013/07/06/protocells-may-have-formed-in-a-salty-soup/
If we are to assume all life came from a single cell way in the past, then that cell, from it's very first moment had to have all the machinery capable of :
1. reproduction
2. the means of obtaining energy in whatever form that may have been
3. the means of converting that energy source to a useable form
4. the means of ridding itself of toxic waste
5. the means of protecting itself from environmental dangers ex, radiation, temperature fluctuations, acid/base conditions
6. means of cellular repair of all of these mechanisms
7. The means of intracellular communication between all its parts the prior knowledge that it would need all these components and the ability of ALL of these to function fully and simultaneously from day one because malfunctions of, or incomplete versions or not fully "evolved" parts would have lead to immediate or almost immediate death.
DK: The newly established proto-cell must have a relatively simple structure with heredity and a primordial metabolism. However, the process leading to the formation of a proto-cell must consist of a multi-step process that begins with the precursors of nucleic acids, peptides, lipids, and energy followed by polymer interactions and enzymatic metabolic reactions.
Reply: There is no evidence whatsoever that prebiotic catalysis would/could have led to the emergence of the basic building blocks of life withouty enzymatic catalists. And there is no evidence of nor a plausible hypothesis of a transition from noncatalitic to enzymatic production of the building blocks. There is a huge unbridgeable gap.
I have listed 27 open questions in regard to the origin of RNA and DNA on the early earth, 14 unsolved problems in regard to the origin of amino acids on the early earth, 12 in regard to phospholipid synthesis, and also unsolved problems in regard to carbohydrate production. The open problems are in reality far greater. This is just a small list. It is not just an issue of things that have not yet been figured out by abiogenesis research, but deep conceptual problems, like the fact that there were no natural selection mechanisms in place on the early earth.
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759
DK: Based on our understanding of evolution, we can picture a scenario where multiple variants of proto-cells initially emerged but most adapted, survived, and evolved
Reply: What does survive even mean in the context of "proto-cells" ? Live starts once a threshold is achieved, where cell can live freely (independently from a living host, like mycoplasma in humans ), and being able to perform all tasks mentioned and described previously. Anything that is not capable to perform those tasks, cannot be described as alive.
DK: An obvious question is “What are the critical steps for living matter to emerge?” Is it possible, therefore, to find a boundary between chemistry and biology if we look at all the events leading up to LUCA?
Reply: What might be a Cell’s minimal requirement of parts ?
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts
The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells. It has complete biosynthetic pathways for all 20 amino acids. These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. 14 That would be the size of a book with 400 pages, each page with 3000 characters. They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells. If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help.
Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55.
The argument of the cell
1. At least 1300 proteins are required as building blocks for the simplest living cell to come into existence.
2. Proteins are highly complex structures.
3. The probability of random creation of complex proteins, the assemblage of the needed 1300 in one place in nature without any control is less than 10^700,000 or impossible.
4. If you leave the molecules required to make the four basic building blocks of life, they will just randomize, and become asphalts.
4. Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. The impossibility of chance indicates the necessity of an intelligent designer to explain the origin of life.
DK: The formation of RNA and peptides depends on the previous steps of the prebiotic synthesis of nucleotides and amino acids. Polymer interactions and the emergence of sustained proto-cellular structure depend on previously synthesized polymers made of monomers; therefore, there is no specific single event that is recognized to have paramount importance for the beginning of life.
Reply: Agreed. Many tasks would have to be accomplished already to get to that stage.
The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated
https://reasonandscience.catsboard.com/t2997-the-problem-of-the-origin-of-the-hardware-and-software-in-the-cell-is-far-greater-than-commonly-appreciated
- Getting the basic elements to make the building blocks of life
- RNA world
- RNA and DNA synthesis
- Polymerization through catalysts on clay
- The Eigen threshold
- The transition from the RNA world, to the DNA world
- Obtaining the genetic Code
- The genetic code is optimal amongst 1 million
- The second, overlapping code in DNA
- The amazing information storage capacity of DNA
- Getting the information in the genome
- Getting the gene expression machinery to make proteins
- Origin of the 37 gene codes: Did they evolve?
DK: If we investigate the chain of events from the first polymers to the formation of the first proto-cells, there must be a moment where heredity starts to play a significant role.
Reply: Heredity starts, when life starts to self-replicate. And for that to happen, DNA replication has to be in place. The problem faced by evolutionary biology is however, that DNA replication requires a minimal set of proteins, which word interdependently together:
DNA replication, and its mind boggling nano technology that defies naturalistic explanations
https://reasonandscience.catsboard.com/t1849-dna-replication-of-prokaryotes
The Argument of the Original Replicator
In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule.
Each of these proteins is essential and required for the proper replicating process. Not a single one of these proteins can be missing, otherwise the whole process breaks down, and is unable to perform its task correctly. DNA repair mechanisms must also be in place, fully functional and working properly, otherwise the mutation rate will be too high, and the cell dies. 18
The individual parts and proteins require by themselves complex assembly proteins to be built.
The individual parts, assembly proteins, and proteins individually would have no function by their own. They have only function interconnected in the working whole.
The individual parts must be readily available on the construction site of the rna replication complex, being correctly interlocked, interlinked, and have the right interface compatibility to be able to interact correctly together. All this requires information and meta information ( information that directs the expression of the genomic information for construction of the individual proteins, and correct timing of expression, and as well the information of the correct assembly sequence. )
Evolution is not a capable driving force to make the dna replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.
DNA replication requires coded, complex, specified information and meta-information, and the DNA replication process is irreducibly complex.
Therefore, DNA replication is best explained through design.
DK: The establishment of heredity defines the emergence of adaptation and diversification toward more complex structures, i.e., Darwinian evolution. All events that occur before this moment are governed only by environmental conditions, where more complicated structures are synthesized simply by chance with no “recollection” of previously existing ones. The forces of degradation could roll back the initial state.
Reply: That is one of the main reasons why abiogenesis is not possible.
Paradoxes in the Origin of Life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-virtually-impossible#7309
Steven A. Benner
https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/25608919
Discussed here is an alternative approach to guide research into the origins of life, one that focuses on “paradoxes”, pairs of statements, both grounded in theory and observation, that (taken together) suggest that the “origins problem” cannot be solved.
The Asphalt Paradox
Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”. the literature reports (to our knowledge) exactly ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution.
Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.
DK: The development of Darwinian evolution may not have been a sudden process; it would have involved many trials and errors but would have made an enormous difference after it was established.
Reply: The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells. It has complete biosynthetic pathways for all 20 amino acids. These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. 14 They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells. If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000.
DK: The task here is to define the minimum number of components working on the molecular level necessary for selection to occur, so these might be utilized in the further origin of life research.
Reply: Trying to shift Darwinian evolution to the field of the origin of life makes no sense whatsoever. Koonin, the logic of chance, page 266
Evolution by natural selection and drift can begin only after replication with sufficient fidelity is established. Even at that stage, the evolution of translation remains highly problematic. The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible . The synthesis of nucleotides and (at least) moderate-sized polynucleotides could not have evolved biologically and must have emerged abiogenically—that is, effectively by chance abetted by chemical selection, such as the preferential survival of stable RNA species.
DK: All three components: the information, the structure/function, and the rule between them are mutually dependent for their existence, i.e., the components are attributes of each other and cannot be analyzed independently
Reply: Unintentionally, Dimiter is making an argument for intelligent design. :=)) Interdependence is the hallmark of design, and requires fore-planning.
DK: If we take the information, for example, it cannot exist without resolving the structure/function component, otherwise, the string of units (e.g., nucleotides of RNA) would be random and without information.
Reply: The hardware and software of the cell, evidence of design
https://reasonandscience.catsboard.com/t2221-the-hardware-and-software-of-the-cell-evidence-of-design
Paul Davies: the fifth miracle page 62
Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it. 1
We need to explain the origin of both the hardware and software aspects of life, or the job is only half finished. Explaining the chemical substrate of life and claiming it as a solution to life’s origin is like pointing to silicon and copper as an explanation for the goings-on inside a computer. It is this transition where one should expect to see a chemical system literally take-on “a life of its own”, characterized by informational dynamics which become decoupled from the dictates of local chemistry alone (while of course remaining fully consistent with those dictates). Thus the famed chicken-or-egg problem (a solely hardware issue) is not the true sticking point. Rather, the puzzle lies with something fundamentally different, a problem of causal organization having to do with the separation of informational and mechanical aspects into parallel causal narratives. The real challenge of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics.
Software and hardware are irreducible complex and interdependent. There is no reason for information processing machinery to exist without the software, and vice versa.
Systems of interconnected software and hardware are irreducibly complex. 2
DK: It would be like the working of a mechanical clock without installed hands: you would never know what time it is. In order for the information to determine the structural/functional component, it needs a rule to execute the process of transfer of the information, i.e., genetic code or Watson-Crick base-pair, therefore the rule should exist also with the information and with the structure/function.
Reply: The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin
1. The assignment of a word to represent something, like the word chair to an object to sit down, is always of mental origin.
2. The translation of a word in one language, to another language, is always of mental origin. For example the assignment of the word chair, in English, to xizi, in Chinese, can only be made by intelligence upon common agreement of meaning.
3. In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
4. Since we know only of intelligence to be able to do so, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.
Origin and evolution of the genetic code: the universal enigma
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/
After this excellent paper ( and my review ) it can be concluded with high certainty, that there is no return to the abiogenesis hypothesis. Intelligent Design rules !!
Last edited by Otangelo on Tue Nov 03, 2020 1:19 pm; edited 9 times in total
