Intelligent Design, the best explanation of Origins

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The possible mechanisms to explain the origin of life

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The possible mechanisms to explain the origin of life

In an attempt to explain the origin of life, scientists propose a two-stage process of natural chemical evolution:  formation of organic molecules, which combine to make larger biomolecules; self-organization of these molecules into a living organism. The origin of life can not be explained through biological nor chemical evolution. Adaptation, mutation, and natural selection depend on DNA replication. Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication. Neither can it be explained through physical laws. Life depends on codes and instructional complex information. This information can only be generated by when the arrangement of the code is free and unconstrained, and any of the four bases of the genetic code can be placed in any of the positions in the sequence to generate the information. The only alternative, if the action of a creative agency is excluded, would be spontaneous self-assembly by orderly aggregation of prebiotic elements and building blocks in a sequentially correct manner without external direction.

Natural selection is not a possible mechanism to explain the origin of life, since evolution depends on DNA replication

When we consider how life might have arisen from nonliving matter, we must take into account the properties of the young Earth’s atmosphere, oceans, and climate, all of which were very different than they are today. Biologists postulate that complex biological molecules first arose through the random physical association of chemicals in that environment.
LIFE The Science of Biology, TENTH EDITION, page 3

Neither Evolution nor physical necessity are a driving force prior dna replication. The only two alternatives are either a) creation by an intelligent agency, or b) Random, unguided, undirected natural events by a lucky "accident". 

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. Translation is thought to have evolved later via an ad hoc selective process.  Did you read this ???!! An ad-hoc process ?? 

Without code there can be no self-replication. Without self-replication, you can’t have reproduction. Without reproduction, you can’t have evolution or natural selection.

Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication.  ( Furusawa, 1998 ) We hypothesize that the origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis. ( Vaneechoutte M )

Ann N Y Acad Sci. 2000;901:139-47.
The scientific origin of life. Considerations on the evolution of information, leading to an alternative proposal for explaining the origin of the cell, a semantically closed system
We hypothesize that the origin of life, that is, the origin of the first cell, cannot be explained by natural selection among self-replicating molecules, as is done by the RNA-world hypothesis.
The hypothesis espoused here states that it is virtually impossible that the highly complicated system cell developed gradually around simple self-replicating molecules (RNA-hypercycles or autocatalytic peptide networks) by means of natural selection; as is proposed by, for example, the RNA-world hypothesis.  Despite searching quadrillions of molecules, it is clear that a spontaneous RNAreplicator is unlikely to occur. Reports of nucleotide and peptide self-replication still depend upon human intervention (for instance, by changing the environmental conditions between two rounds of replication or by denaturing the double strands). The problem of denaturing the double-nucleotide strand in a nonenzymatic manner has been overlooked and has contributed to a failure to establish molecular self-replication. The first cell, life, was born and natural selection (selection among variations on the theme of autonomous duplication) commenced.

Natural selection requires pre-existing life.

Chance and necessity do not explain the origin of life
Selection pressure cannot select nucleotides at the digital programming level where primary structures form. Genomes predetermine the phenotypes which natural selection only secondarily favors. Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming. No new informationis provided by such tautologies. The argument simply says it happened. As such, it is nothing more than blind belief. Science must provide rational theoretical mechanism, empirical support, prediction fulfillment, or some combination of these three. If none of these three are available, science should reconsider that molecular evolution of genetic cybernetics is a proven fact and press forward with new research approaches which are not obvious at this time. 5

B.Alberts, Molecular Biology of the Cell, 5th edition, page 406
Self-Replicating Molecules Undergo Natural Selection
The three-dimensional folded structure of a polynucleotide affects its stability, its actions on other molecules, and its ability to replicate. Therefore, certain polynucleotides will be especially successful in any self-replicating mixture. Because errors inevitably occur in any copying process, new variant sequences of these polynucleotides will be generated over time.

Stephen Meyer, Darwins doubt, page 6: 
Natural selection assumes 
the existence of living organisms with a capacity to reproduce. Yet self-replication in all extant cells depends upon information-rich proteins and nucleic acids (DNA and RNA), and the origin of such  information-rich molecules is precisely what origin-of-life research needs to explain. That’s why Theodosius Dobzhansky, one of the founders of the modern neo-Darwinian synthesis, can state flatly, “Pre-biological natural selection is a contradiction in terms.”5 Or, as Nobel Prize–winning molecular biologist and origin-of-life researcher Christian de Duve explains, theories of prebiotic natural selection fail because they “need information which implies they have to presuppose what is to be explained in the first place.

That means, evolution was not a driving force and acting for the emergence and origin of the first living organisms. The only remaining possible mechanisms are chemical reactions acting upon unregulated, aleatory events ( luck,chance), or physical necessity.  ( where chemical reactions are  forced into taking a certain course of action. )  

Physical necessity & Physical laws

Life's Irreducible Structure, Michael Polanyi
Science mag, 1968
In Galileo's experiments on balls rolling down a slope, the angle of the slope was not derived from the laws of mechanics, but was chosen by Galileo. And as this choice of slopes was extraneous to the laws of mechanics, so is the shape and manufacture of test tubes extraneous to the laws of chemistry. The same thing holds for machinelike boundaries; their structure cannot be defined in terms of the laws which they harness. Nor can a vocabulary determine the content of a text, and so on. Therefore, if the structure of living things is a set of boundary conditions, this structure is extraneous to the laws of physics and chemistry which the organism is harnessing. Thus the morphology of living things transcends the laws of physics and chemistry.the codelike structure of DNA must be assumed to have come about by a sequence of chance variations established by natural selection. But this evolutionary aspect is irrelevant here; whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page. As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule. It is this physical indeterminacy of the sequence that produces the improbability of occurrence of any particular sequence and thereby enables it to have a meaning-a meaning that has a mathematically determinate information content equal to the numerical improbability of the arrangement.

A deterministic answer assumes that the laws of physics and chemistry have causally and sequentially determined the obligatory series of events leading from inanimate matter to life – that each step is causally linked to the previous one and to the next one by the laws of nature. In principle, in a strictly deterministic situation, the state of a system at any point in time determines the future behavior of the system – with no random influences. To invoke a guided determinism toward the formation of life would only make sense if the construction of life was demonstrably a preferential, highly probable natural pathway.
Luisi, The Emergence of Life; From Chemical Origins to Synthetic Biology, page 21

Just like computer codes, the genetic code is arbitrary. There is no law of physics that says “1” has to mean “on” and “0” has to mean “off.” There’s no law of physics that says 10000001 has to code for the letter “A.” Similarly, there is no law of physics that says three Guanine molecules in a row have to code for Glycine. In both cases, the communication system operates from a freely chosen, fixed set of rules.
In all communication systems it is possible to label the encoder, the message and the decoder and determine the rules of the code.
The rules of communication systems are defined in advance by conscious minds. There are no known exceptions to this. Therefore we have 100% inference that the Genetic Code was designed by a conscious mind.

Physical laws which result in physical constraints,  where chemical reactions are forced into taking a certain course of action is an often cited possible mechanism for the origin of life. 
We are moving from chemistry to biology. Henceforward, life, it goes without saying, is independent of its chemical substrate, and its evolution does not follow paths that are predictable solely based on the laws of physics.
M. Gargaud · H. Martin · P. López-García T. Montmerle · R. Pascal Young Sun, Early Earth and the Origins of Life, page 95

Laurent Boiteau Prebiotic Chemistry: From Simple Amphiphiles to Protocell Models, page 3:
Spontaneous self-assembly occurs when certain compounds associate through noncovalent hydrogen bonds, electrostatic forces, and nonpolar interactions that stabilize orderly arrangements of small and large molecules.  The argument that chemical reactions in a primordial soup would not act upon pure chance, and that  chemistry is not a matter of "random chance and coincidence , finds its refutation by the fact that the information stored in DNA is not constrained by chemistry. Yockey shows that the rules of any communication system are not derivable from the laws of physics.  He continues : “there is nothing in the physicochemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” In other words, nothing in nonliving physics or chemistry obeys symbolic instructions.

Information theory cannot normally be used to predict how chemicals will react because some chemicals react with each other readily, and others only react very slowly. Others do not react with each other at all. Thus, the likelihood of two chemicals joining together depends on both the quantity of the chemicals present and their chemical properties. Information theory can easily deal with the effects of quantity, but it has no way to deal with chemical properties.
Stuart Pullen, Intelligent Design or Evolution? Why the Origin of Life and the Evolution of Molecular Knowledge Imply Design, page 88

Stephen C. Meyer observed:
“There are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the base sequencing that constitutes the information in the DNA molecule”
(Signature in the Cell, 243).

As Paul Davies lamented,
“We are still left with the mystery of where biological information comes from.… If the normal laws of physics can’t inject information, and if we are ruling out miracles, then how can life be predetermined and inevitable rather than a freak accident? How is it possible to generate random complexity and specificity together in a lawlike manner? We always come back to that basic paradox”
(Fifth Miracle, 258).

A law of nature could not alone explain how life began, because no conceivable law would compel a legion of atoms to follow precisely a prescribed sequence of assemblage.
Paul Davies, The origin of Life, page 17

Werner Gitt summarized it this way:
“A necessary requirement for generating meaningful information is the ability to select from alternatives and this requires an intelligent, volitional entity.… Unguided, random processes cannot do this—not in any amount of time because this selection process demands continuous guidance by intelligent beings that have a purpose”
(Without Excuse, 50–51).

Let's assume that we begin with the sequence R-T-X, and will add two amino acids "B" and "A" to it. If amino acid "B" is the most reactive amino acid, the sequence would be R-T-X-B-A. However, if "A" is the most reactive amino acid, then the sequence would be R-T-X-A-B. In a random chemical reaction, the sequence of amino acids would be determined by the relative reactivity of the different amino acids. The polymer chain found in natural proteins and DNA has a very precise sequence that does not correlate with the individual components' reaction rates. Since all of the amino acids have relatively similar structures, they all have similar reaction rates; they will all react at about the same rate making the precise sequence by random chemical reactions unthinkably unlikely. This is the problem of Chemical Reactivity.

The Genetic Code
DNA contains a true code. Being a true code means that the code is free and unconstrained; any of the four bases can be placed in any of the positions in the sequence of bases. Their sequence is not determined by the chemical bonding. There are hydrogen bonds between the base pairs and each base is bonded to the sugar phosphate backbone, but there are no bonds along the longitudional axis of DNA. The bases occur in the complementary base pairs A-T and G-C, but along the sequence on one side the bases can occur in any order, like the letters of a language used to compose words and sentences. Since nucleotides can be arranged freely into any informational sequence, physical necessity could not be a driving mechanism.

Abiogenesis is the process by which life arises naturally from non-living matter. Scientists speculate that life may have arisen as a result of random chemical processes happening to produce self-replicating molecules.

Paul Davies conceded, “Unfortunately, before Darwinian evolution can start, a certain minimum level of complexity is required. But how was this initial complexity achieved? When pressed, most scientists wring their hands and mutter the incantation ‘Chance.’ So, did chance alone create the first self-replicating molecule?” (Fifth Miracle, 138).

If design or physical necessity is discarded, the only remaining possible mechanism for the origin of life is chance/luck.

Calculations of life beginning through unguided, natural, random events.

Last edited by Admin on Mon Aug 13, 2018 3:59 pm; edited 31 times in total

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Roscoe T Kane Life might well be an inevitable consequence of the laws of nature. Consider the Everett Interpretation of Quantum Mechanics. In it, life needs no maker and has no luck, everything that could possibly happen must happen in some world.

Dynamic kinetic stability (DKS) 1

Recently, one of us (A.P.) has described a new stability kind in nature, seemingly overlooked in modern scientific thought, which we have termed dynamic kinetic stability (DKS) . That stability kind, applicable solely to persistent replicating systems, whether chemical or biological, derives directly from the powerful kinetic character and the inherent unsustainability of the replication process. However, for the replication reaction to be kinetically unsustainable, the reverse reaction, in which the replicating system reverts back to its component building blocks, must be very slow when compared with the forward reaction; the replication reaction must be effectively irreversible. That condition, in turn, means the system must be maintained in a far-from-equilibrium state , and that continuing requirement is satisfied through the replicating system being open and continually fed activated component building blocks. Note that the above description is consistent with Prigogine's non-equilibrium thermodynamic approach, which stipulates that self-organized behaviour is associated with irreversible processes within the nonlinear regime . From the above, it follows that the DKS term would not be applicable to an equilibrium mixture of some oligomeric replicating entity together with its interconverting component building blocks.


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3 Selforganization on Wed May 31, 2017 5:44 am


Selforganization 1

In the book: Young Sun, Early Earth and the Origins of Life, we read:
Every living being consists of a collection of molecules that are constantly renewed and which appear to coordinate their evolution. We are therefore dealing with organized systems, the emergence of which, perforce, implies a process of self-organization. However, the spontaneous formation of an ordered system from disorder contradicts our everyday experience. We all know that over time, the most beautiful building is inevitably reduced to ruins. In physical or chemical terms, this tendency is expressed as a quantity, entropy, which expresses the degree of disorder in a system. The second law of thermodynamics expresses the idea that the entropy of an isolated system increases, and thus that disorder tends to increase. An isolated chemical system must, therefore, evolve towards an equilibrium state in which the concentration of different chemical species will be determined by their individual energy levels and the laws of statistics. So how could a system that was as disordered as that of the primitive Earth, with an incredible diversity of forms and structures, give rise to life? The answer lies in the fact that the process of self-organization, which is linked to the emergence and development of life, concerns only one part of the system. Hence, the formation of an ordered structure in a sub-system will be compensated by an increase in disorder in its environment, such that overall, the entropy does not decrease. That means then that exchanges of energy and matter are the basis of the dynamics of self-organization.

Since the authors apply methodological naturalism and exclude design a priori, they are left with the only alternative to design, that is self-organisation. Mount Improbable is, however, higher to climb, to get life the first go, then keep it going. That implies a paradox: If the inorganic matter had the unbound drive to get self-organized and become alive, why do thermodynamic mechanisms, and evolution, permit life to die? Why the cycle oself-replication, , which had to be fully setup as well right from the beginning, to perpetuate life for millennia, if not millions of years, but living organisms die? If the unbound drive of atoms to self-organize and get alive, why not the unbound drive to KEEP alive? We know for instance, that lobsters don't die. They just get bigger. Turtles live for centuries. If the struggle is for survival, why do not more species steal DNA from other species like bdelloids? why can Glass Sponges live for 15 thousand years, but evolution has not helped us to get so far?   Turritopsis doohmii jellyfish  has found a way to cheat death by actually reversing its aging process. If the jellyfish is injured or sick, it returns to its polyp stage over a three-day period, transforming its cells into a younger state that will eventually grow into adulthood all over again. If and molecules drive for survival, why have not many more organisms evolved in a convergent manner, and adopted this extraordinary mechanism? 

Moreover, the inescapable evolution towards disorder and the state of thermodynamic equilibrium does not predict in any way the duration of the chemical reactions involved, which may occur in a fraction of a second or, on the other hand, over a period that is reckoned in millions of years. The speed of this evolution depends on the dynamics of the reaction (the subject of chemical kinetics) and not on thermodynamics, which only predicts the sense in which it unfolds. In chemistry, it is difficult to envisage self-organization without having recourse to the heterogeneous nature of matter on a microscopic scale, that is to the fact that matter is not indefinitely divisible. If that were the case, how could it form complex structures? It was undoubtedly this type of reasoning that led, in antiquity, certain philosophers, the best known of which remains Democritus, to postulate the existence of atoms as being the basis of matter. The difficulty comes in passing from this microscopic heterogeneity to a single macroscopic entity that involves a coordination in the arrangement or the movement of a multiplicity of atoms or molecules (either within a three-dimensional structure or within an entire organism). The properties that molecules have of associating with one another may give rise to the formation of crystals or other macroscopic structures such as vesicles (such as those that form cellular membranes ) or the micelles of surfactants. Structures that have a dynamical character may also appear through amplification mechanisms that are highly efficient, such as replication or autocatalysis. These mechanisms are at work in what are known as oscillating reactions, which are often considered chemical curiosities, such as the Belousov-Zhabotinsky reaction . The concentration of certain intermediates then varies until the reagents are exhausted, in a cyclic or stochastic

1. M. Gargaud · H. Martin · P. López-García -  Young Sun, Early Earth and the Origins of Life page 92

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