ElShamah - Reason & Science: Defending ID and the Christian Worldview
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ElShamah - Reason & Science: Defending ID and the Christian Worldview

Welcome to my library—a curated collection of research and original arguments exploring why I believe Christianity, creationism, and Intelligent Design offer the most compelling explanations for our origins. Otangelo Grasso


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Abiogenesis: The cell is irreducibly complex

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The cell is irreducibly complex

https://reasonandscience.catsboard.com/t1299-abiogenesis-the-cell-is-irreducibly-complex

Albert-László Barabási: Various types of interaction webs, or networks, (including protein-protein interaction, metabolic, signaling and transcription-regulatory networks) emerge from the sum of these interactions. None of these networks are independent, instead, they form a ‘network of networks that is responsible for the behavior of the cell. the architectural features of molecular interaction networks within a cell are shared to a large degree by other complex systems, such as the Internet, computer chips, and society. This unexpected universality indicates that similar laws may govern most complex networks in nature, which allows the expertise from large and well-mapped non-biological systems to be used to characterize the intricately interwoven relationships that govern cellular functions. t the quantifiable tools of network theory offer unforeseen possibilities to understand the cell’s internal organization and evolution, fundamentally altering our view of cell biology. The emerging results are forcing the realization that, notwithstanding the importance of individual molecules, cellular function is a contextual attribute of strict and quantifiable patterns of interactions between the myriad of cellular constituents. Although uncovering the generic organizing principles of cellular networks is fundamental to our understanding of the cell as a system, it also needs to develop relevance for the experimental biologist, helping to elucidate the role of individual molecules in various cellular processes. A highly modular structure is a fundamental design attribute. Biology is full of examples of modularity. Instead of chance and randomness, we have found a high degree of internal order that governs the cell’s molecular organization.
https://sci-hub.wf/10.1038/nrg1272

Graham Cairns-Smith: Fine-tuning in living systems: early evolution and the unity of biochemistry   11 November 2003
We are all descended from some ancient organisms or group of organisms within which much of the machinery now found in all forms of life on Earth was already essentially fixed and, as part of that, hooked on today’s so-called ‘molecules of life’. This machinery is enormously sophisticated, depending for its operation on many collaborating parts. The multiple collaboration provides an explanation for why the present system is so frozen now and has been for so long.  So we are left wondering how the whole DNA/RNA/protein control system, on which evolution now so utterly depends, could itself have evolved.

It is hard to see primitive geochemical processes maintaining the clean supplies of nucleotides required for the replication of molecules like RNA. Nucleotides are not easy to make, as organic chemists know, and as is evidenced by the long pathways to nucleotides within biochemistry today.
https://www.cambridge.org/core/journals/international-journal-of-astrobiology/article/abs/finetuning-in-living-systems-early-evolution-and-the-unity-of-biochemistry/193313763244F9E6D085A3F062110389

Doug Sharp (1977): Macromolecules in the cell such as DNA, RNA, and proteins are interdependent for mutual synthesis. Within the cell, proteins used for enzyme catalysis, structural components, energy generation, and digestion of food, are produced through an amazing manufacturing process, involving DNA as a template for the three types of RNA (MRNA, TRNA, and RRNA), which in turn act as different components in the synthesis and coding of each protein molecule. But, each step in this complicated synthesis is catalyzed by an enzyme, which, since it is a protein, would have had to be synthesized by the same process! In other words, the end products of this reaction aid in the synthesis of the starting components and catalyzes each reaction along,the way, making up a complicated series of interrelationships. In order to explain life, then, the appearance of this entire machinery must be explained.
https://www.creationresearch.org/enzymes/

ADDY PROSS: What is Life? How Chemistry becomes Biology
The living cell is a highly organized entity. We can compare it to a familiar mechanical entity, a clock. Both are organized in the sense that all of the component parts contribute to the operation of the holistic entity. The parts of the clock enable it to fulfill its function of telling the time, and the parts of the cell enable it to fulfill its function and become two cells. Of course, the clock is an organized entity that has been constructed to fulfil its particular function—it is man-made, then how can the bacterial cell have somehow come about on its own accord? The living cell, the basic unit comprising all life, is a highly complex set of these reactions somehow integrated into a coordinated whole.
What is Life?: How Chemistry Becomes Biology  2012

Martina Preiner: The Future of Origin of Life Research: Bridging Decades-Old Divisions 2020 Feb 26
The emergence of metabolism and inherited information as complex systems was most likely interdependent and simultaneous. This directly leads to the fundamental question of how and when metabolism and information storage became linked. Nature’s elegant solution is the genetic code, the origin of which remains a true enigma. The question of which class of biomolecules initiated the OoL is a loaded question. All known living cells contain DNA, RNA, proteins, lipids, coenzymes, and other metabolites—and the earliest cells as those known on Earth would have had to fulfill these minimal cell requirements. There is a strong argument to be made for the emergence of essential biomolecules to have been (at least to some extent) contemporaneous and interdependent. Cells are not mere collections of their chemical components, but highly dynamic, complex systems with multiple interlocked processes involving those components.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151616/

Jim Bendewald Irreducible Complexity  SEPTEMBER 21, 2019
The cell is the ultimate example of irreducible complexity. My book Evolution Shot Full of Holes with co-author Frank Sherwin, contains a chapter on the topic of the origin of life. [/size]The cell is an interdependent functional city. We state, “The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.” The notion of the theoretical first cell arising by natural causes is a perfect example of irreducibly complexity. Life cannot exist without many numerous interdependent complex systems, each irreducibly complex on their own, working together to bring about a grand pageant for life to exist.
https://evidencepress.com/irreducible-complexity/

Sanders Heuristic View on Quantum Bio-Photon Cellular Communication  2017
The cell is the irreducible, minimal unit of life 
https://sci-hub.st/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8

A. Graham Cairns-Smith Chemistry and the Missing Era of Evolution 2008
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

Wilhelm Huck chemist , 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/

Renato Fani: The Origin and Evolution of Metabolic Pathways: Why and How did Primordial Cells Construct Metabolic Routes? 15 September 2012
The extant cells are quite complex entities constituted from a myriad of different molecules that, however, have to act and interact in a concerted manner in order to assure the survival and reproduction of cells (and multicellular organisms).
https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-012-0439-5

Charles W Carter, Jr (2017): Studies of gene–replicase–translatase (GRT) systems reveal that gene replication and coded expression are interdependent. Living systems now produce proteins from information encoded in genes using protein translatases whose genes are copied using protein polymerases. Could self-organization of both processes be so strongly coupled that they emerged simultaneously?
https://academic.oup.com/mbe/article/35/2/269/4430325

ROBERT F. SERVICE Researchers may have solved origin-of-life conundrum 16 MAR 2015
The origin of life on Earth is a set of paradoxes. In order for life to have gotten started, there must have been a genetic molecule — something like DNA or RNA — capable of passing along blueprints for making proteins, the workhorse molecules of life. But modern cells can’t copy DNA and RNA without the help of proteins themselves. To make matters more vexing, none of these molecules can do their jobs without fatty lipids, which provide the membranes that cells need to hold their contents inside. And in yet another chicken-and-egg complication, protein-based enzymes (encoded by genetic molecules) are needed to synthesize lipids.
https://www.science.org/content/article/researchers-may-have-solved-origin-life-conundrum

What good is a one-cylinder motor for without a piston?
What good is a piston for, if not used fully mounted in the cylinder with the right size to fit and interconnected, to fulfill its task? Ok. You could use it as an Ashtray. But for that, you would not need to produce it highly specified with piston rings, connecting rods etc.
What good is a production line of pistons for, if the end product, the piston, has no place to be employed?
What good is a transport system for, if there is no place to deliver the goods, and a communication system to direct them to the right place?

If we are to assume all life came from a single cell way in the past, then that cell, from its 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.

Following  irreducible processes and parts  are required to keep cells alive, and illustrate mount improbable to get life a first go: 
Reproduction. Reproduction is essential for the survival of all living things.
Metabolism. Enzymatic activity allows a cell to respond to changing environmental demands and regulate its metabolic pathways, both of which are essential to cell survival. 
Nutrition. This is closely related to metabolism. Seal up a living organism in a box for long enough and in due course it will cease to function and eventually die. Nutrients are essential for life. 
Complexity. All known forms of life are amazingly complex. Even single-celled organisms such as bacteria are veritable beehives of activity involving millions of components. 
Organization. Maybe it is not complexity per se that is significant, but organized complexity. 
Growth and development. Individual organisms grow and ecosystems tend to spread (if conditions are right). 
Information content. In recent years scientists have stressed the analogy between living organisms and computers. Crucially, the information needed to replicate an organism is passed on in the genes from parent to offspring. 
Hardware/software entanglement. All life of the sort found on Earth stems from a deal struck between two very different classes of molecules: nucleic acids and proteins. 
Permanence and change. A further paradox of life concerns the strange conjunction of permanence and change.
Sensitivity. All organisms respond to stimuli— though not always to the same stimuli in the same ways.
Regulation. All organisms have regulatory mechanisms that coordinate internal processes.

Paul Davies, The origin of life, 2003 page 52
Acknowledging the inter-dependability of the component molecules within a living organism immediately presents us with a stark philosophical puzzle. If everything needs everything else, how did the community of molecules ever arise in the first place? As most large molecules needed for life are produced only by living organisms and are not found outside the cell, how did they come to exist originally, without the help of a meddling scientist? Could we seriously expect a Miller – Urey type of soup to make them all at once, given the hit-and-miss nature of its chemistry? 

You might get the impression from what I have written that not only is the origin of life virtually impossible, but that life itself is impossible. If fragile biomolecules are continually being attacked and disintegrated, surely our own bodies would rapidly degenerate into chemical mayhem spelling certain death? Fortunately for us, our cells contain sophisticated chemical repair and construction mechanisms, handy sources of chemical energy to drive processes uphill, and enzymes with special properties that can smoothly assemble complex molecules from fragments. Also, proteins fold into protective balls that prevent water from attacking their delicate chemical bonds. As fast as the second law tries to drag us downhill, this cooperating army of specialized molecules tugs the other way. So long as we remain open systems, exchanging energy and entropy with our environment, the degenerative consequences of the second law can be avoided. But the primordial soup lacked these convenient cohorts of cooperating chemicals. No molecular repair gangs stood ready to take on the second law. The soup had to win the battle alone, against odds that are not just heavy, but mind-numbingly huge.
https://3lib.net/book/3321550/5e1ca9

The Cell and Irreducible Complexity
1.  Up until this past Century, we had no idea just how complex and interactively dependent biological systems are…
2.  A cell is like a very complex factory. Many different ‘molecular machines’, like the golgi-apparatus, the endoplasmic reticulum, the mitochondria and many more, take care of various processes within the cell. The processes are all part of one system, which means that the one process cannot function without other processes. You could say there is a certain cooperation between the various organelles within the cell.
3.The cell is yet another example of something that is irreducibly complex
4. The point is the evolutionary processes would not produce such complexity by definition – biological processes according to evolution will weed out that which is useless or detrimental. Unless, you have each of the parts showing up at the exact same time in the same life form – the individual components would serve no purpose.
https://web.archive.org/web/20170522092740/http://christianevidences.org/scientific-evidence/hematology/the-cell-and-irreducible-complexity/

To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis

Iris Fry The role of natural selection in the origin of life  21 April 2010
Unlike living systems that are products of and participants in evolution, these prebiotic chemical structures were not products of evolution. Not being yet intricately organized, they could have emerged as a result of ordinary physical and chemical processes.
https://sci-hub.ren/10.1007/s11084-010-9214-1

Cellular biologists have discovered that not even the simplest cell can exist without a completely, intact internal structure as complicated as New York City--including the DNA helix etc. It is called "irreducible complexity" which means each cell must exist as a whole from the beginning in order to live. (There is no building up part by part over millions of years.)
[Michael J. Behe, DARWIN'S BLACK BOX; The Biochemical Challenge to Evolution, 1996, Simon and Schuster, NY, p. 39.]

Georg Fuchs Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life? July 6, 2011
Regarding the essential parts, biologists allege that the biochemical unity that underlies the living world makes sense only if most of the central metabolic intermediates and pathways were already present in the common ancestor. This appears to be the blueprint of primordial metabolism: a network of a dozen common organic molecules (central precursor metabolites) from which all building blocks derive and which are transformed and interconnected by
only a few reactions.
https://sci-hub.ren/https://www.annualreviews.org/doi/10.1146/annurev-micro-090110-102801

Christos A Ouzounis A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective 19 December 2005
A truly minimal estimate of the gene content of the last universal common ancestor, obtained by three different tree construction methods and the inclusion or not of eukaryotes (in total, there are 669 ortholog families distributed in 561 functional annotation descriptions ( proteins) , including 52 which remain uncharacterized)
https://www.ncbi.nlm.nih.gov/pubmed/16431085

Emily Singer How Structure Arose in the Primordial Soup May 19, 2015
About 4 billion years ago, molecules began to make copies of themselves, an event that marked the beginning of life on Earth. A few hundred million years later, primitive organisms began to split into the different branches that make up the tree of life. In between those two seminal events, some of the greatest innovations in existence emerged: the cell, the genetic code and an energy system to fuel it all. ALL THREE of these are ESSENTIAL to life as we know it, yet scientists know disappointingly little about how any of these remarkable biological innovations came about.
https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/

Claim: Irreducible complexity has been demonstrated to not be valid.
Response: As soon as the evidence points to a system, that requires a minimal number of essential parts, where, if one of them is removed, the system becomes non-functional, the system is irreducibly complex.
Even science peer reviewed papers of science journals mention many such systems. Many laboratories and science teams for example have dedicated considerable efforts to investigate and elucidating what might be the minimal number of parts to have a primordial cell, which would require several functions all at once, and together, that is reproduction, obtaining energy, getting rid of toxic waste, protecting itself from environmental dangers ex, radiation, temperature fluctuations, acid/base conditions, self replication, and means of cellular repair of all of these mechanisms, 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 functional parts would have lead to immediate or almost immediate death.

Information has independent existence from the structures. The information, the code, and hardware to process the information and to use it to accomplish a specific task all need to appear simultaneously. None have value without the others in place. This requires single step first appearance of all of them. Required tasks for simultaneous first appearance include replication, information storage and processing, metabolism, organic compartments with active transport, and various additional miscellaneous functions 4

chicken and egg scenarios in cellular function can be discovered at will. The essential components of a minimal cell cooperate with each other, such that when all work together life appears and missing any one of them prevents its appearance. If one tries to explain the appearance of any component through the gradual step by step process of natural selection, he will quickly find himself facing a chicken and egg scenario, a catch-22 situation, a paradox, a conundrum. Ignoring the fact that natural selection doesn’t work for large genome systems before replication appears, there is another basic issue. How could natural selection define a proper genetic structure to produce a protein so that the protein could provide a step in the production of an essential product before all of the other proteins for the others steps have appeared? There is a long list of products essential to the appearance of the first cell. Pick any one of them and try to explain how this product could appear apart from single-step, sudden first appearance. You will find that emergence leads you straight to the chicken and egg scenario. This is the impact of emergence on abiogenesis.

Behes definition of  Irreducible complexity can be expanded, and applied not only  to biological systems, but also to systems , machines and factories created by man,  that require a minimal number of parts to exercise a specific function, and this minimal number of parts cannot be reduced to keep the basic function. The term applies as well  to processes, production methods and proceedings of various sorts. To reach a certain goal, a minimal number of manufacturing  steps must be gone through. That applies in special to  processes in living cells, where  a minimal set of basic processes must be fully functional and operational, in order to maintain cells alive.

Let's suppose an immensely unlikely random accident would produce a self-replicating RNA molecule in a prebiotic world. That molecule would have no function on its own, in the same manner as a piston has no function by its own unless fully mounted with the right fit in the cylinder. In the same manner, as a water turbine has no function on its own unless mounted at the river with the energy gradient, and all other parts to make energy, there would be no function for it. In the same manner, the energy turbine of life, ATP synthase, would have no function on its own, unless a proton gradient is established in the cell, and for that, a membrane to establish the gradient is required. Had the cell membrane, the energy gradient, and ATP synthase not to be fully setup together right from the beginning, otherwise, one could not bear any function on its own, together with the other parts?  Let's suppose you have a car. You enter the car, turn the key, but the cable that connects the signal to the battery, the car's engine will not turn on. Intelligence is required to find out, which cable has to connect, to solve the problem. But in cells, even if one protein, as tiny as it might seem, is missing, cells cannot become alive either. A cell without any of the key enzymes to make energy, will not function. But all enzymes and proteins are intricately complex and must be interconnected in a metabolic network, to bear function.

Mainstream scientific papers confirm indirectly that cells are irreducible complex. The paper: Determination of the Core of a Minimal Bacterial Gene Set says: Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes. Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell.

Eugene V. Koonin. How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept 2000
Several theoretical and experimental studies have endeavored to derive the minimal set of genes that are necessary and sufficient to sustain a functioning cell under ideal conditions, that is, in the presence of unlimited amounts of all essential nutrients and in the absence of any adverse factors, including competition. A comparison of the first two completed bacterial genomes, those of the parasites Haemophilus influenzae and Mycoplasma genitalium, produced a version of the minimal gene set consisting of ~250 genes.
https://www.ncbi.nlm.nih.gov/books/NBK2227/

DIANA YATES Last Universal Common Ancestor had a complex cellular structure OCT 5, 2011
New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct. The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study.
https://news.illinois.edu/view/6367/205221

http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf

Albert Voie Biological function and the genetic code are interdependent 2006
Functional parts are only meaningful within a whole, in other words, it is the whole that gives meaning to its parts. 
Parts require a blueprint in order to be made upon specified complex instructional information. The information is based on a language system wich must be pre-established.
In order to define a sign or a code (which can be a symbol, an index, or an icon) a whole cluster of self-referring concepts is presupposed, that is, the definition cannot be given on a priori grounds, without implicitly referring to this cluster of conceptual agents. In other words, to define a specific subpart of a machine that requires a specific shape, size, material etc. the initial requirement is a 1. language or code system, and 2. the information based on that language to specify the part in question. Intelligent agents think with an "end goal" in mind, allowing them to solve complex problems by taking many parts and arranging them in intricate patterns that perform a specific function 2  They need to be able to organize parts availability, synchronization, manufacturing and assembly coordination and interface compatibility of the single parts and subunits. The individual parts must precisely fit together.
Biological function and sign systems, resemble the complexity of computer programs.  There cannot be information without an interpreter,  there is no message coming from the genes without the cell machinery in place that interprets the genes. Catch 22. On the other hand the cell machinery must be rooted causally ( or have their origin ) in the symbolic codes for at least two reasons. Firstly, the cell machinery consists of different parts that have to be produced in a number of copies depending on a memory ( instructions stored in dna ). Secondly, functionality of the cell machinery implies a three-dimensional folding, which is determined by the intrinsic properties of the building blocks e.g. amino acids. In addition there are control mechanisms for protein folding. The production of proteins presupposes a control mechanism involving the genes that secures ( and defines ) the entire sequence of amino acids before the folding takes place.  This leaves us with two mutually dependent categories of chemical structures or events (symbols and cell machinery), which does not fit with the axioms of probability that only considers one-way dependency. Thus, the structure of life has a probability to emerge randomly of zero.
Life express both function and sign systems, which indicates that it is not a subsystem of the universe, since chance and necessity cannot explain sign systems, meaning, purpose, and goals 

Now lets apply that to biology.
What good would DNA, mRNA, RNA polymerase, tRNA's, Ribosomes and chaperones be good for by their own, if not interconnected in a working cell ? Why would a prebiotic soup produce these molecular machines ? They would only become functional with the instructions encoded in DNA, defining and specifying how they would have to be interconnected The thing is, there's no driver for any of the pieces to emerge individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of a planning organizing creative intelligence.  
Biological systems are functionally organized , integrated into an interdependent network, and complex, like human-made machines and factories. The wiring of an electrical device equals to metabolic pathways. A minimal metabolic network is required in every cell, and must have emerged prior life began. For the assembly of a biological system of multiple parts, not only the origin of the genome information to produce all subunits and assembly cofactors must be explained, but also parts availability ( The right materials must be transported to the building site. Often these materials in their raw form are unusable. Other complex machines come into play to transform the raw materials into usable form.  All this requires specific information. )  synchronization, ( these parts must be read at hand at the building site )  manufacturing and assembly coordination ( which required the information of how to assemble each single part correctly, at the right place, at the right moment, and in the right position ) , and interface compatibility ( the parts must fit together correctly, like lock and key ) . Unless the origin of all these steps are properly explained, functional complexity as existing in biological systems has not been addressed adequately.

The immense challenge to unguided, random mechanisms becomes, even more, evidence, once you remove the delusional crutches of evolution, and look into the origin of the first self-replicating cell. The solutions to overcome problems like DNA replication errors or damage must all be pre-programmed, and the repair "working horses" to resolve the problem must be ready in place and "know" what to do how, and when, and able to compare between what is right, and what is in error.  If a robot in a factory assembly line fails, employees are ready to detect the error and make the repair. In the cell, the malfunction of any part even as tiny and irrelevant as it might seem, can be fatal, and if the repair mechanisms are not functioning correctly and fully in place right from the start, the repair can't be done, and life ceases.  These repair enzymes which cleave, join, add, replace etc. must be programmed in order to function properly right from the start. Aberrantly processed pre-tRNAs, for example, are eliminated through a nuclear surveillance pathway by degradation of their 3′ ends, whereas mature tRNAs lacking modifications are degraded from their 5′ends in the cytosol.
https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf

J. Warner Wallace  The Irreducible Complexity of a Protein July 13, 2015
Now let’s take a look again at the simple protein and see how it is assembled out of amino acids. These acids have to come together in a specific way and if they do, then they begin to fold up onto themselves to form the specific shapes and clusters that we call proteins. But ask yourself the question: how do these amino acids know how to join to each other? Is there a natural attraction between the acids that acts like magnets coming together? No.. When scientists discovered DNA, they unlocked a powerful secret within the cell. They realized that the acids come together in response to INFORMATION and DIRECTION from the DNA molecule which exists alongside the acids and proteins! The DNA directs the assembly of the acids and provides a blueprint for the operation! And DNA is the most densely packed molecule in the known universe. It is a highly complex, highly ordered and extremely large assembly of information containing more data than the largest human library and posing a far greater problem for evolutionists to explain that the most complicated proteins!
http://coldcasechristianity.com/2012/christianity-promotes-rational-and-evidential-exploration/

Craig Rusbult, Ph.D. Irreducible Complexity: Definition & Evaluation 2002
DNA poses a dilemma. Proteins cannot form without the DNA information and direction. But DNA is highly complex, ordered and informational. Where does it come from? As it turns out, the DNA molecule is filled with specific information that directs the assembly of the overall organism. And it is required for the protein to exist. The ‘irreducible complexity’ of the protein is not just a number of simple amino acid chemicals. The ‘irreducible complexity’ of the protein also includes the most complex known molecule in the universe: the DNA molecule. ‘Irreducible complexity’ of the protein demonstrates that the random forces of nature cannot explain the origin of life.
http://www.asa3.org/ASA/education/origins/ic-cr.htm

The DNA - Enzyme System is Irreducibly Complex
Which came first? DNA needs enzymes to replicate, but the enzymes are encoded by DNA. DNA needs protection provided by the cell wall, but the cell wall is also encoded by the DNA. The answer is that none came “first” for all are required in DNA-based life. These fundamental components form an irreducibly complex system in which all components must have been present from the start. This presents a challenge to the step-by-step evolution required by Darwin’s theory.

Hitching, p. 66.
The amino acids must link together to form proteins, and the other chemicals must join up to make nucleic acids, including the vital DNA. The seemingly insurmountable obstacle is the way the two reactions are inseparably linked—one can’t happen without the other. Proteins depend on DNA for their formation. But DNA cannot form without pre-existing protein.

John C. Walton, (Lecturer in Chemistry, University of St. Andrews, Fife, Scotland,Organization and the Origin of Life,” Origins, Vol. 4, No. 1, 1977, pp. 30–31.
The origin of the genetic code presents formidable unsolved problems. The coded information in the nucleotide sequence is meaningless without the translation machinery, but the specification for this machinery is itself coded in the DNA. Thus without the machinery the information is meaningless, but without the coded information the machinery cannot be produced! This presents a paradox of the ‘chicken and egg’ variety, and attempts to solve it have so far been sterile.
http://www.ideacenter.org/contentmgr/showdetails.php/id/845

Joseph W. Francis Peering into Darwin's Black Box: The cell divsion processes required for bacterial life  27.6.2001
There is good evidence to suggest that the process of cell division is indeed irreducibly complex, for the steps involved are interdependent and highly coordinated. For example, crucial steps such as DNA transcription require proteins (see Figure 1)—while protein synthesis in turn is dependent upon transcription. Moreover, evidence suggests that the processes involved in cell division are highly regulated and coordinated in a sequential fashion. For instance, in bacteria, cytokinesis does not proceed until DNA replication is complete, so that the DNA is precisely partitioned into the developing daughter cells. Each process itself is complex and if any one of the processes is inhibited, cell division ceases. This interdependence fits the criteria of an irreducibly complex system.
http://www.arn.org/docs/odesign/od201/peeringdbb201.htm

Chuck Missler The Origin of Information
The chicken-egg dilemma has confounded scientists for decades. Chemist John Walton noted the dilemma in 1977 when he stated:
"The origin of the genetic code presents formidable unsolved problems. The coded information in he nucleotide sequence is meaningless without the translation machinery, but the specification for his machinery is itself coded in the DNA. Thus without the machinery the information is meaningless, but without the coded information, the machinery cannot be produced. This presents a paradox of the 'chicken and egg' variety, and attempts to solve it have so far been sterile."

The Chicken or the Egg?
Any discussion of the origin of life would not be complete without a look at the greatest paradox of all: What came first, DNA or the proteins essential for the production of DNA?
Since the structure of DNA was deciphered in 1953, biologists have discovered that the process of duplicating DNA requires as many as twenty specific protein enzymes. These enzymes function to unwind, un-zip, copy, and rewind the DNA molecule. There are even enzymes that screen and correct for copying errors!
The instructions for the production of all proteins, including these enzymes, are in turn stored on the DNA molecule. So which came first: The DNA molecule or the proteins necessary to make DNA? You can't make DNA without highly specific proteins. But you can't make proteins unless you have a system in place to code for and build those proteins in the first place. And that means DNA.

Harold Blum recognized this  when he stated:
"...The riddle seems to be: How, when no life existed, did substances come into being which, today, are absolutely essential to living systems, yet which can only be formed by those systems?...A number of major properties are essential to living systems as we see them today, the origin of any of which from a 'random' system is difficult enough to conceive, let alone the simultaneous origin of all."
http://xwalk.ca/origin2.html

Shapiro, R., "Origins: A Skeptic's Guide to the Creation of Life on Earth," Summit Books: New York NY, 1986, p.135)
"Genes and enzymes are linked together in a living cell two interlocked systems, each supporting the other. It is difficult to see how either could manage alone. Yet if we are to avoid invoking either a Creator or a very large improbability, we must accept that one occurred before the other in the origin of life. But which one was it? We are left with the ancient riddle: Which came first, the chicken or the egg? In its biochemical form, protein versus nucleic acid, the question is a new one, dating back no further than Watson and Crick and our knowledge of the structure and function of the gene. In its essence, however, the question is much older, and has provoked passion and acrimony that extend beyond the boundaries of science. In an earlier, broader form, the question asked whether the gene or protoplasm had primacy, not only in the origin but also in the development of life."
It's nice to talk about replicating DNA molecules arising in a soupy sea, but in modern cells this replication requires the presence of suitable enzymes. ... [T]he link between DNA and the enzyme is a highly complex one, involving RNA and an enzyme for its synthesis on a DNA template; ribosomes; enzymes to activate the amino acids; and transfer-RNA molecules. ... How, in the absence of the final enzyme, could selection act upon DNA and all the mechanisms for replicating it? It's as though everything must happen at once: the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don't see them at the moment.
https://creationevolutiondesign.blogspot.com/2007/01/mullers-theory-and-nucleic-acid-theory.html


For a nonliving system, questions about irreducible complexity are even more challenging for a totally natural non-design scenario, because natural selection — which is the main mechanism of Darwinian evolution — cannot exist until a system can reproduce.  For an origin of life we can think about the minimal complexity that would be required for reproduction and other basic life-functions.  Most scientists think this would require hundreds of biomolecular parts, not just the five parts in a simple mousetrap or in my imaginary LMNOP system.  And current science has no plausible theories to explain how the minimal complexity required for life (and the beginning of biological natural selection) could have been produced by natural process before the beginning of biological natural selection.
The cell is an interdependent functional city. We state, “The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.” The notion of the theoretical first cell arising by natural causes is a perfect example of irreducibly complexity. Life cannot exist without many numerous interdependent complex systems, each irreducibly complex on their own, working together to bring about a grand pageant for life to exist.
Another huge problem is that information is useless unless it can be read. But the decoding machinery is itself encoded on the DNA. The leading philosopher of science, Karl Popper (1902–1994), expressed the huge problem:
‘What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But … the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.

A classic example of interdependence is that of DNA and proteins. Within each cell, proteins manufacture, repair, and access DNA. So, DNA depends on proteins. But DNA provides the blueprints for protein structure, so proteins also depend on DNA. These two system parts stand and function only when working together, and they fall apart when separated from each other.
“The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.”
A specific example described in the book is the interdependence of DNA, RNA and protein. We summarize the issue, “DNA, RNA and proteins cannot do their jobs without the help of at least one of the other two. DNA is a library of detailed information for the various structures within the cell. It has the information for the manufacture of each protein. RNA is a copy of instructions from the DNA and is sent as a messenger to the ribosomes for making proteins. There are two types of proteins; functional proteins such as enzymes, and structural proteins, which compose the organelles. Living cells need all three molecules at the same time. The chance, simultaneous natural appearance of the three distinct, interdependent complex systems is just not possible.” Not only are these three needed for life, but an organism also needs a cell membrane, usable energy, reproduction and all left-handed amino acids. The cell itself is a tremendous and irrefutable example of irreducible complexity.
Considering the cell as being the ultimate irreducibly complex system, there is no conceivable way that life could arise by natural causes. Darwin’s theory of numerous, successive, slight modifications simply does not work when discussing the origin of life. The problem that irreducibly complexity brings to evolution is clearly daunting for evolutionists. Their way to deal with the problem is to dismiss it as nonscientific, pseudoscience or religion dressed in a tuxedo. However, when one looks at the issue of origin of life through the lens of irreducible complexity, it simply brings one with a reasonable mind to his or her knees, admitting life cannot begin by natural causes.

Cellular transport systems:
Gated transport is called thus due to it's similarity to our everyday experience of passing through a guarded (electronically or otherwise) gate. This system require three basic components to work: an identification tag, a scanner (to verify identification) and a gate (that is activated by the scanner). The system needs all three components to work otherwise it will not work. Thus in a cell, when a protein is to be manufactured, one of the first steps is for the mRNA [c] to be transported out from the nucleus into the cytoplasm. This requires gated transport of the mRNA at the nuclear pore. Proteins in the pore reads a signal from the RNA (the scanner reads the identification tag) and opens the pore (gate is opened).

DNA and information
The structure of DNA polymerase is determined by information stored on DNA, but it takes DNA polymerase and other proteins to make DNA.  Furthermore, information to make DNA polymerase must be transferred to RNA before it can be used to make proteins from amino acids.  Making the RNA copy also requires proteins.
Can you see where the process has a beginning?  Could any of it function before the whole system was complete?
This system will not work unless all the components are present and functioning.  This means that in order to start life you must have proteins and RNA and DNA.

The irreducible, code-instructed process to make cell factories and machines points to intelligent design
https://reasonandscience.catsboard.com/t2364-the-irreducible-code-instructed-process-to-make-cell-factories-and-machines-points-to-intelligent-design

All cellular functions are  irreducibly complex
https://reasonandscience.catsboard.com/t2179-the-cell-is-a-interdependent-irreducible-complex-system

The Cell membrane, irreducible complexity
https://reasonandscience.catsboard.com/t2128-membrane-structure#3798

The Interdependency of Lipid Membranes and Membrane Proteins
https://reasonandscience.catsboard.com/t2397-the-interdependency-of-lipid-membranes-and-membrane-proteins

Factory and machine planning and design, and what it tells us about cell factories and molecular machines
https://reasonandscience.catsboard.com/t2245-factory-and-machine-planning-and-design-and-what-it-tells-us-about-cell-factories-and-molecular-machines

Genome information, protein synthesis,  the biosynthesis pathways in biologiy, and the analogy of human programming, engeneering, and factory robotic assembly lines
https://reasonandscience.catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines

What might be a Cell’s minimal requirement of parts ?  
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts

How Cellular Enzymatic and Metabolic networks  point to design
https://reasonandscience.catsboard.com/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design

Abiogenesis: The cell is irreducibly complex Wt2k3dW
Abiogenesis: The cell is irreducibly complex Cell-hematology


Abiogenesis: The cell is irreducibly complex O0Igjrbl


Abiogenesis: The cell is irreducibly complex Lyfe10

A Venn diagram of the four pillars of lyfe. Sublyfe (regions 1–8 ) is any system that performs some but not all of the pillars, while lyfe (region 9) is any system that performs all four. 
My comment: This is a nice illustration why life is irreducibly complex. 
https://sci-hub.st/https://www.mdpi.com/2075-1729/10/4/42

Abiogenesis: The cell is irreducibly complex Frank_10

ScienceDaily: Protocells may have formed in a salty soup July 2, 2013
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity," said Huck
https://www.sciencedaily.com/releases/2013/07/130702100115.htm

http://christianevidences.org/scientific-evidence/hematology/the-cell-and-irreducible-complexity/
https://web.archive.org/web/20130329104258/http://www.rejectionofpascalswager.net/behe.html

1. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf
2. http://www.evolutionnews.org/2011/03/a_closer_look_at_one_scientist045311.html
3. http://complex.upf.es/~andreea/2006/Bib/MonnardDeamer.NutrientUptakeByProtocells.pdf
4. https://osf.io/p5nw3/
5. https://sci-hub.tw/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8[/size]



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Essential parts and functions in the cell

The mechanism by which chromosomal DNA molecules are held together: entrapment within cohesin rings?

mysterious has been the trigger for what is arguably the most dramatic and one of the most highly regulated events in the life of a eukaryotic cell, the sudden disjunction of sister chromatids at the metaphase to anaphase transition. 1

Work in our lab has shown that sister chromatids are held together by a multi-subunit complex called cohesin whose Smc1 and Smc3 subunits are rod shaped proteins with ABC-like ATPases at one end of 50nm long intra-molecular anti-parallel coiled coils. At the other ends are pseudo-symmetrical hinge domains that interact to create V shaped Smc1/Smc3 heterodimers. N- and C-terminal domains within cohesin’s third subunit, known as α kleisin, bind to Smc3 and Smc1 ATPase heads respectively, thereby creating a huge tripartite ring whose integrity is essential for holding sister DNAs together. A thiol protease called separase opens the cohesin ring by cleaving its α kleisin subunit, which causes cohesin’s dissociation from chromosomes and triggers sister chromatid disjunction.


Regulation of chromosome condensation and segregation. 2

Regulated and controlled chromosome condensation and segregation is essential for the transmission of genetic information from one generation to the next. A myriad of techniques has been utilized over the last few decades to identify proteins required for the organized compaction of the massive length of a cell's DNA. A full understanding of the components and processes involved relies on further work, exploiting biochemical, genetic, cytological, and proteomics approaches to complete the picture of how a cell packages and partitions its genome during the cell cycle.

Condensins: universal organizers of chromosomes with diverse functions 3

Condensins are multisubunit protein complexes that play a fundamental role in the structural and functional organization of chromosomes in the three domains of life. Most eukaryotic species have two different types of condensin complexes, known as condensins I and II, that fulfill nonoverlapping functions and are subjected to differential regulation during mitosis and meiosis.

The multisubunit condensin complex is essential for the structural organization of eukaryotic chromosomes during their segregation by the mitotic spindle 4


Recruitment of the conserved centromeric protein shugoshin is essential for biorientation, but its exact role has been enigmatic. 5

A mystery surrounding tubulin, the protein that plays a crucial role in the passing of genetic material from a parent cell to daughter cells, has been at least partially solved. 6 Nogales and her colleagues also identified a region in Dam1 essential for the regulation of the complex, by spindle-checkpoint kinase enzymes. "These kinases are signaling proteins that, based on tension in the spindles, tell the ring when the time is right for it to let go of the microtubules," Nogales says. "We have found that without this region, the ability of the Dam1 to form a ring is reduced."

All eukaryotic cells must segregate their chromosomes equally between two daughter cells at each division. This process needs to be robust, as errors in the form of loss or gain of genetic material have catastrophic effects on viability. Chromosomes are captured, aligned, and segregated to daughter cells via interaction with spindle microtubules mediated by the kinetochore. 7

Topoisomerase II enzymes are essential in the separation of entangled daughter strands during replication. This function is believed to be performed by topoisomerase II in eukaryotes and by topoisomerase IV in prokaryotes. Failure to separate these strands leads to cell death.

Controlled transport of macromolecules between the cytoplasm and nucleus is essential for homeostatic regulation of cellular functions. For instance, gene expression entails coordinated nuclear import of transcriptional regulators to activate transcription and nuclear export of the resulting messenger RNAs for cytoplasmic translation. Thus, Ddx19 participates in mRNA export, translation and nuclear import of a key transcriptional regulator. 9

Cell membranes are crucial to the life of the cell. 10

Nucleo-cytoplasmic transport of RNAs and proteins is essential for eukaryotic gene expression. 11


The field of mitochondrial ion channels has recently seen substantial progress, including the molecular identification of some of the channels. An integrative approach using genetics, electrophysiology, pharmacology, and cell biology to clarify the roles of these channels has thus become possible. It is by now clear that many of these channels are important for energy supply by the mitochondria and have a major impact on the fate of the entire cell as well. 12

Mammalian mtDNA only encodes 13 proteins, but these are nevertheless essential for cell viability as they are crucial components of the oxidative phosphorylation system, located in the inner mitochondrial membrane 13

In eukaryotes, lipid metabolism requires the function of peroxisomes. These multitasking organelles are also part of species-specific pathways such as the glyoxylate cycle in yeast and plants or the synthesis of ether lipid in mammals.Peroxisomal function is essential for life. 14

Fatty acids are aliphatic acids fundamental to energy production and storage, cellular structure and as intermediates in the biosynthesis of hormones and other biologically important molecules. 15

Coenzyme A (CoA) is an essential cofactor in numerous metabolic and energy-yielding reactions and is involved in the regulation of key metabolic enzymes 16

γ-tubulin is essential for normal microtubule organization in every organism in which it has been studied, and it is nearly ubiquitous throughout the eukaryotes 17

Su48 represents a previously unrecognized centrosome protein that is essential for cell division18

The ab tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. 19

Presently, the best studied are the mitotic Kinesin-13 proteins. Studies in both D. melanogaster and human cells suggest a division of labor between Kinesin-13 family members, such that different proteins contribute microtubule depolymerizing activity to the centrosome and centromere  during mitosis. These activities have been shown to be essential for spindle morphogenesis and chromosome segregation.  20

During cell division, mitotic spindles are assembled by microtubule-based motor proteins1, 2. The bipolar organization of spindles is essential for proper segregation of chromosomes, and requires plus-end-directed homotetrameric motor proteins of the widely conserved kinesin-5 (BimC) family  21

The various functions of the Endoplasmic Reticulum are essential to every cell, their relative importance varies greatly between individual cell types.

Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. 22

Telomeres, the specialized nucleoprotein structures that cap the ends of linear chromosomes, are essential for genome integrity and hence cell viability because they protect chromosome ends from fusions and degradation.  23

Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset.


DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied. 


1) http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=591
2) http://www.ncbi.nlm.nih.gov/pubmed/12672496
3) http://genesdev.cshlp.org/content/26/15/1659.full
4) http://www.nature.com/nsmb/journal/v18/n8/full/nsmb.2087.html?WT.ec_id=NSMB-201108
5) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063673/
6) http://www2.lbl.gov/Science-Articles/Archive/sabl/2007/Oct/onering.html
7) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216659/
8 ) https://en.wikipedia.org/wiki/Type_II_topoisomerase
9) http://www.nature.com/ncomms/2015/150114/ncomms6978/full/ncomms6978.html
10) http://reasonandscience.heavenforum.org/t2128-membrane-structure#3789
11) file:///E:/Downloads/genes-06-00163.pdf
12) http://physrev.physiology.org/content/94/2/519
13) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105550/
14) http://www.springer.com/us/book/9783709117873
15) http://reasonandscience.heavenforum.org/t2168-lipids-fatty-acids-and-the-origin-of-life?highlight=fatty+acids
16) http://mbe.oxfordjournals.org/content/21/7/1242.full
17) http://www.nature.com/nrm/journal/v12/n11/full/nrm3209.html#B10
18) http://creationsafaris.com/crev200604.htm
19) http://www2.lbl.gov/tt/publications/1706pub.pdf
20) http://labs.cellbio.duke.edu/kinesin/MTdisassembly.html
21) http://www.nature.com/nature/journal/v435/n7038/full/nature03503.html
22) http://www.ncbi.nlm.nih.gov/pubmed/14985753
23) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251085/
24) http://www.nature.com/nature/journal/v519/n7543/full/nature14239.html       Nature 519, 321–326 (19 March 2015) doi:10.1038/nature14239

25) http://www.nature.com/scitable/definition/helicase-307



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http://telicthoughts.com/the-irreducible-complexity-of-dna-replication/

Replication must begin somewhere. Why not at the origin of replication with the formation of a replication fork. A prepriming complex of proteins forms. Included are DnaA proteins and single stranded binding proteins. Also involved are DNA helicases to separate the strands, DNA topoisomerases to respond to supercoils, DNA polymerase and DNA ligase.

Don't bother making semantic arguments about how to define irreducible complexity. There are multiple parts needed for function. The challenge lies in demonstrating the incremental evolution of these components.

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http://www.uncommondescent.com/intelligent-design/yet-another-irreducible-complexity-no-brainer-twisted-ropes/

I find the phenomenon of the DNA supercoiling problem and its biochemical solution even more compelling than examples like protein synthesis and the bacterial flagellum, since twisted ropes are familiar to everyone. This might make for another highly persuasive ID mascot.

How could random variation and natural selection come up with a pair of biochemical scissors and a repair mechanism that cuts and splices the twisted DNA molecule in order to relieve torsional tension? What would be the functional, naturally-selectable intermediate steps in a hypothetical stochastically generated evolutionary process? It is clear that there could not possibly be any.

I’m suffering from a state of extreme cognitive dissonance. How can educated, intelligent scientists continue to defend the obviously indefensible, in light of what is now known about the nature of living systems (at all levels, not just the biochemical)? Richard Dawkins has remarked that biology was once a mystery, but “Darwin solved that.” Really?

http://www.creationscience.com/onlinebook/LifeSciences39.html

DNA cannot function without hundreds of preexisting proteins,but proteins are produced only at the direction of DNA. Because each needs the other, a satisfactory explanation for the origin of one must also explain the origin of the other. Therefore, the components of these manufacturing systems must have come into existence simultaneously. This implies creation.



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http://www.arn.org/docs/odesign/od201/peeringdbb201.htm

Cell division and the protocell

One of the more popular theories of protocell evolution, presented in biology textbooks, involves the encapsulation of the basic processes of biopolymer synthesis in a membrane (Cooper, 1997). It is then postulated that the protocell began to divide by a simple mechanism. In other words, it is assumed that all the cell functions required for life, perhaps even those required for cell division, were pre-manufactured and pre-functioning processes sequestered together by a cell membrane. (One barrier to cell division that the early protocell would encounter is that in an aqueous environment there is a natural physical resistance to the membrane disruption needed for cell division. For the sake of discussion, we will assume that the dividing protocell was in a membrane-disrupting environment that promoted some type of membrane blebing or stressing so that new cells could bud or pinch off the protocell.)

There are several fundamental problems with the encapsulation theory. First, how does a cytokinesis process develop before the membrane forms the cell? Cytokinesis requires a membrane-enclosed cytoplasmic space and could only develop after encapsulation. Yet in that case—if cytokinesis evolved only after encapsulation—then it would have to evolve rapidly, otherwise the cell would not reproduce and its long-term survival would be questionable. One possible postulate is that the early cytokinesis process was a much simpler process compared with the complex cytokinesis mechanism observed in bacteria today. That would imply, however, that there was very little regulation or no coordination between DNA replication and cytokinesis and other cell systems, which in turn implies that the division of the membrane and successful transfer of genetic material was haphazard and inefficient. The protocell would partition its DNA into new daughter bacteria, and then divide, by random uncoordinated processes.

There is good evidence to suggest that the process of cell division is indeed irreducibly complex, for the steps involved are interdependent and highly coordinated. For example, crucial steps such as DNA transcription require proteins (see Figure 1)—while protein synthesis in turn is dependent upon transcription. Moreover, evidence suggests that the processes involved in cell division are highly regulated and coordinated in a sequential fashion. For instance, in bacteria, cytokinesis does not proceed until DNA replication is complete, so that the DNA is precisely partitioned into the developing daughter cells. Each process itself is complex and if any one of the processes is inhibited, cell division ceases. This interdependence fits the criteria of an irreducibly complex system.

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https://releasingthetruth.wordpress.com/tag/irreducible-complexity/

How could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function? Absurd “chicken-egg” paradox! Also, consider that ATP synthase is made by processes that all need ATP—such as the unwinding of the DNA helix with helicase to allow transcription and then translation of the coded information into the proteins that make up ATP synthase. And manufacture of the 100 enzymes/machines needed to achieve this needs ATP! And making the membranes in which ATP synthase sits needs ATP, but without the membranes it would not work. This is a really vicious circle for evolutionists to explain.

https://www.youtube.com/watch?v=XI8m6o0gXDY

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http://dialogue.adventist.org/articles/15_2_ward_e.htm

The primordial cell, like any other, would depend on its energy-generating biochemistry in order to operate crucial metabolic processes and synthesize essential molecules. As mentioned, information for molecular synthesis is stored in DNA. Energy generated by the cell is required for DNA synthesis and cellular replication. DNA synthesis depends upon enzymes whose blueprint is contained in DNA. None of these systems could function if it were not for the cell membrane separating the cell's biochemical reactions from the external environment. Indeed, enzymes encoded by information in DNA direct synthesis of the membrane itself--irreducible complexity at its best.

In his book, Behe analyzes published scientific literature on mechanisms of molecular and biochemical evolution. He also examines papers published in the Journal of Molecular Evolution (JME) since its founding in 1971. His conclusion: None of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual, step-by-step Darwinian fashion

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Douglas Futuyma, a prominent American biologist admits as much:

“Organisms either appeared on the earth fully developed or they did not. If they did not, they must have developed from preexisting species by some process of modification. If they did appear in a fully developed state, they must indeed have been created by some omnipotent intelligence” (Futuyma, 1983, p. 197).

In fact, Futuyma’s words underline a very important truth. He writes that when we look at life on Earth, if we see that life emerges all of a sudden, in its complete and perfect forms, then we have to admit that life was created, and is not a result of chance. As soon as naturalistic explanations are proven to be invalid, then creation is the only explanation left.

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

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Karen Fliegel MacDougall 

The very first cell must have had all of these from day one:

1) The means to obtain energy in whatever form that may be
2) The means to convert that energy into a usable source
3) The means to rid itself of deadly waste product
4) The means to protect itself from the environment such as temperature fluctuations, pH balance and radiation
5) The means to repair all of those mechanisms
6) then means within itself for all of those systems to communicate
7) The means to replicate
8  ) The knowledge in advance that it would need ALL of those mechanisms fully functioning simultaneously from day one in order for the cell to survive and create the next generation.

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Catch22 Origin of Life problems - checkmake for Abiogenesis

Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

This is very true. But we can go a step further:

To go from the existence of the basic building blocks on early earth to Cell assembly of complex carbohydrates, lipids, proteins, nucleic acids, metals and seven non-metal elements from monomers is less of a step than to go from the existence of these small organic molecules synthesized in Cells to a fully working self-replicating Cell. This might be surprising, but not when someone knows the efforts taken by cells to synthesize these building blocks, which is truly remarkable.

One of the most dramatic evidence why abiogenesis fails is the fact that to make these basic building blocks of life, the cell machinery which is made upon these very basic building blocks must be fully set up and operating. That creates a catch22 situation:

It takes Proteins to make the basic building blocks of life. But it takes the basic building blocks of life to make proteins.
It takes ATP to make proteins. But it takes proteins to make ATP.
It takes proteins to make amino acids. But it takes amino acids to make proteins
It takes DNA to make proteins. But it takes proteins to make DNA.
Cell duplication and DNA replication are essential for the survival and perpetuation of all living things. It takes over 30 specialized irreducible proteins for DNA replication. But it takes the DNA to RNA transcription and RNA translation to make proteins. What came first?
It takes proteins to make the error-check and correction proteins that reduce the DNA replication error rate 10.000.000.000 times. These error check and correction proteins had to be checked too. How did the process start?
But it takes DNA transcription and translation to make proteins. What came first?
It takes a full setup signaling network for cells to adapt to ecological variations, like heat-shock proteins to adapt to climate variation and temperatures. How did that system start, if it is non-functional, if not fully setup?
It takes fully synthesized Fe/S ( Iron sulfur) clusters for a majority of proteins used in oxidation-reduction reactions, essential for all life forms. But it takes complex uptake and synthesis processes to make these metal clusters through veritable nano-molecular non-ribosomal peptide synthetase (NRPS) assembly lines for iron uptake. What came first: These manufacturing assembly lines, or the proteins that make them?
The central metabolic pathways like glycolysis or the Citric Acid cycle are essential to make Adenine triphosphate ( ATP ), the energy currency in the cell, and amino acids, the basic building blocks of proteins. These metabolic pathways use enzymes, which are made through ATP and amino acids. How did these pathways emerge?
It takes DNA and proteins to make phospholipids for Cell membranes. But the Cell membrane must be fully set up and permit a closed, protected environment, for the very own processes to operate that synthesize Cell membranes.
The Lipid membrane would be useless without membrane proteins but how could membrane proteins have emerged in the absence of functional membranes?

Carbohydrates are metabolized to provide energy and are stored in muscle and liver as glycogen. Six-carbon glucose molecules are degraded by a series of chemical reactions to three-carbon pyruvate by the reactions of glycolysis; pyruvate. The core structure of the metabolic network is very similar across all organisms. Centrally located within this network are the sugar-phosphate reactions of glycolysis and the pentose phosphate pathway. Together with the overlapping reactions of the Entner–Doudoroff pathway and of the Calvin cycle, they provide the precursor metabolites required for the synthesis of RNA, DNA, lipids, energy, and redox coenzymes and amino acids—key molecules required for life.

Cells use hierarchical levels of organization, where the function and proper set up of the higher level depend on the lower level. And that lower level, as shown above, depends on irreducible biochemical synthesis processes. That is an all or nothing business, which could not be set up if not by intelligent setup.



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11Abiogenesis: The cell is irreducibly complex Empty Uncovering the Genomic Origins of Life Fri Mar 08, 2019 10:12 am

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Uncovering the Genomic Origins of Life



There’s been no direct phylogenetic evidence indicating whether membranes or RNAs came first. Given our new ability to generate genomic based phylogenies within the OLD, we can now ask whether RNAs came before or after membranes. If RNAs came before DNA, we would also like to know which of the RNAs appeared first (mRNA, tRNA, or rRNA).

https://academic.oup.com/gbe/article/10/7/1705/5045876

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In order to explain the origin of first life one must explain the coming into existence of a cell, the basic unit of life. The cell is a prime example of an incredibly complex machine which contains biomolecules like proteins and incredibly complex genetic code on RNA and DNA. Incredibly complex genetic information is useless without some kind of incredibly complex translation and copying machinery. So a cell is irreducibly complex which means that it won't function if any of its many complex subparts is not present and in its proper specific order.

Abiogenesis: The cell is irreducibly complex Cell_110

http://www.basfeijen.nl/worldview/evolution/abiogenesis.htm

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13Abiogenesis: The cell is irreducibly complex Empty Essential parts and functions in the cell Fri Jul 09, 2021 7:13 pm

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Essential parts and functions in the cell

https://reasonandscience.catsboard.com/t1299-abiogenesis-the-cell-is-irreducibly-complex#8784

1. The mechanism by which chromosomal DNA molecules are held together: entrapment within cohesin rings?
mysterious has been the trigger for what is arguably the most dramatic and one of the most highly regulated events in the life of a eukaryotic cell, the sudden disjunction of sister chromatids at the metaphase to anaphase transition. 1
2. Work in our lab has shown that sister chromatids are held together by a multi-subunit complex called cohesin whose Smc1 and Smc3 subunits are rod shaped proteins with ABC-like ATPases at one end of 50nm long intra-molecular anti-parallel coiled coils. At the other ends are pseudo-symmetrical hinge domains that interact to create V shaped Smc1/Smc3 heterodimers. N- and C-terminal domains within cohesin’s third subunit, known as α kleisin, bind to Smc3 and Smc1 ATPase heads respectively, thereby creating a huge tripartite ring whose integrity is essential for holding sister DNAs together. A thiol protease called separase opens the cohesin ring by cleaving its α kleisin subunit, which causes cohesin’s dissociation from chromosomes and triggers sister chromatid disjunction.
3. Regulation of chromosome condensation and segregation. 2
4. Regulated and controlled chromosome condensation and segregation is essential for the transmission of genetic information from one generation to the next. A myriad of techniques has been utilized over the last few decades to identify proteins required for the organized compaction of the massive length of a cell's DNA. A full understanding of the components and processes involved relies on further work, exploiting biochemical, genetic, cytological, and proteomics approaches to complete the picture of how a cell packages and partitions its genome during the cell cycle.
Condensins: universal organizers of chromosomes with diverse functions 3
5. Condensins are multisubunit protein complexes that play a fundamental role in the structural and functional organization of chromosomes in the three domains of life. Most eukaryotic species have two different types of condensin complexes, known as condensins I and II, that fulfill nonoverlapping functions and are subjected to differential regulation during mitosis and meiosis.
The multisubunit condensin complex is essential for the structural organization of eukaryotic chromosomes during their segregation by the mitotic spindle 4
6. Recruitment of the conserved centromeric protein shugoshin is essential for biorientation, but its exact role has been enigmatic. 5
7. A mystery surrounding tubulin, the protein that plays a crucial role in the passing of genetic material from a parent cell to daughter cells, has been at least partially solved. 6 Nogales and her colleagues also identified a region in Dam1 essential for the regulation of the complex, by spindle-checkpoint kinase enzymes. "These kinases are signaling proteins that, based on tension in the spindles, tell the ring when the time is right for it to let go of the microtubules," Nogales says. "We have found that without this region, the ability of the Dam1 to form a ring is reduced."
All eukaryotic cells must segregate their chromosomes equally between two daughter cells at each division. This process needs to be robust, as errors in the form of loss or gain of genetic material have catastrophic effects on viability. Chromosomes are captured, aligned, and segregated to daughter cells via interaction with spindle microtubules mediated by the kinetochore. 7
8. Topoisomerase II enzymes 8  are essential in the separation of entangled daughter strands during replication. This function is believed to be performed by topoisomerase II in eukaryotes and by topoisomerase IV in prokaryotes. Failure to separate these strands leads to cell death.
9. Controlled transport of macromolecules between the cytoplasm and nucleus is essential for homeostatic regulation of cellular functions. For instance, gene expression entails coordinated nuclear import of transcriptional regulators to activate transcription and nuclear export of the resulting messenger RNAs for cytoplasmic translation. Thus, Ddx19 participates in mRNA export, translation and nuclear import of a key transcriptional regulator. 9
10. Cell membranes are crucial to the life of the cell. 10
11. Nucleo-cytoplasmic transport of RNAs and proteins is essential for eukaryotic gene expression. 11
12. The field of mitochondrial ion channels has recently seen substantial progress, including the molecular identification of some of the channels. An integrative approach using genetics, electrophysiology, pharmacology, and cell biology to clarify the roles of these channels has thus become possible. It is by now clear that many of these channels are important for energy supply by the mitochondria and have a major impact on the fate of the entire cell as well. 12
13. Mammalian mtDNA only encodes 13 proteins, but these are nevertheless essential for cell viability as they are crucial components of the oxidative phosphorylation system, located in the inner mitochondrial membrane 13
14. In eukaryotes, lipid metabolism requires the function of peroxisomes. These multitasking organelles are also part of species-specific pathways such as the glyoxylate cycle in yeast and plants or the synthesis of ether lipid in mammals.Peroxisomal function is essential for life. 14
15. Fatty acids are aliphatic acids fundamental to energy production and storage, cellular structure and as intermediates in the biosynthesis of hormones and other biologically important molecules. 15
16. Coenzyme A (CoA) is an essential cofactor in numerous metabolic and energy-yielding reactions and is involved in the regulation of key metabolic enzymes 16
17. γ-tubulin is essential for normal microtubule organization in every organism in which it has been studied, and it is nearly ubiquitous throughout the eukaryotes 17
18. Su48 represents a previously unrecognized centrosome protein that is essential for cell division18
19. The ab tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. 19
20. Presently, the best studied are the mitotic Kinesin-13 proteins. Studies in both D. melanogaster and human cells suggest a division of labor between Kinesin-13 family members, such that different proteins contribute microtubule depolymerizing activity to the centrosome and centromere  during mitosis. These activities have been shown to be essential for spindle morphogenesis and chromosome segregation.  20
21. During cell division, mitotic spindles are assembled by microtubule-based motor proteins1, 2The bipolar organization of spindles is essential for proper segregation of chromosomes, and requires plus-end-directed homotetrameric motor proteins of the widely conserved kinesin-5 (BimC) family  21
22. The various functions of the Endoplasmic Reticulum are essential to every cell, their relative importance varies greatly between individual cell types.
Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. 22
23. Telomeres, the specialized nucleoprotein structures that cap the ends of linear chromosomes, are essential for genome integrity and hence cell viability because they protect chromosome ends from fusions and degradation.  23
Initiation of cellular DNA replication is tightly controlled to sustain genomic integrity. In eukaryotes, the heterohexameric origin recognition complex (ORC) is essential for coordinating replication onset.
DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied. 


1) http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=591
2) http://www.ncbi.nlm.nih.gov/pubmed/12672496
3) http://genesdev.cshlp.org/content/26/15/1659.full
4) http://www.nature.com/nsmb/journal/v18/n8/full/nsmb.2087.html?WT.ec_id=NSMB-201108
5) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063673/
6) http://www2.lbl.gov/Science-Articles/Archive/sabl/2007/Oct/onering.html
7) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216659/
8 ) https://en.wikipedia.org/wiki/Type_II_topoisomerase
9) http://www.nature.com/ncomms/2015/150114/ncomms6978/full/ncomms6978.html
10) http://reasonandscience.heavenforum.org/t2128-membrane-structure#3789
11) file:///E:/Downloads/genes-06-00163.pdf
12) http://physrev.physiology.org/content/94/2/519
13) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105550/
14) http://www.springer.com/us/book/9783709117873
15) http://reasonandscience.heavenforum.org/t2168-lipids-fatty-acids-and-the-origin-of-life?highlight=fatty+acids
16) http://mbe.oxfordjournals.org/content/21/7/1242.full
17) http://www.nature.com/nrm/journal/v12/n11/full/nrm3209.html#B10
18) http://creationsafaris.com/crev200604.htm
19) http://www2.lbl.gov/tt/publications/1706pub.pdf
20) http://labs.cellbio.duke.edu/kinesin/MTdisassembly.html
21) http://www.nature.com/nature/journal/v435/n7038/full/nature03503.html
22) http://www.ncbi.nlm.nih.gov/pubmed/14985753
23) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251085/
24) http://www.nature.com/nature/journal/v519/n7543/full/nature14239.html       
25) http://www.nature.com/scitable/definition/helicase-307

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Ricard V. Sole Synthetic protocell biology: from reproduction to computation February 16, 2015
´
Cells are the building blocks of biological complexity. They are complex systems sustained by the coordinated cooperative dynamics of several biochemical networks. Their replication, adaptation, and computational features emerge as a consequence of appropriate molecular feedbacks that somehow define what life is.
https://sci-hub.ee/10.1098/rstb.2007.2065

My comment: Several keywords stand out here: complex systems, coordination, cooperative dynamics, computational features, and feedback systems.

The Cambridge dictionary describes coordination as: " involved in a plan or activity work together in an organized way ". Molecules do not have the aim to do any such things. They have no goals. Molecules do not organize themselves, they simply act based on natural forces, the laws of nature, and stochastically, in an unorganized manner. Attributing the action of those things to molecules is anthropomorphizing them, which is senseless, and not what we observe molecules doing.

Wikipedia describes computing as: "any goal-oriented activity requiring, benefiting from, or creating computing machinery. It includes the study and experimentation of algorithmic processes and the development of both hardware and software. It has scientific, engineering, mathematical, technological, and social aspects" Molecules have no goals, no goal-directedness, no foresight, and so, no will do benefit in some way from anything. Attributing the origin and ability of computing of cells to the random action of molecules is not supported by evidence.

Wiki describes feedback systems as follows: Feedback occurs when outputs of a system are routed back as inputs as part of a chain of cause-and-effect that forms a circuit or loop. The system can then be said to feed back into itself. The notion of cause-and-effect has to be handled carefully when applied to feedback systems: They are Self-regulating mechanisms.
Self-regulation is a goal-oriented process. It requires management skills. It means self-optimization. It is evolution on steroids. Life is a constant process of self-evolution and change. Molecules have no goals. They have no goal to become alive and to keep alive through self-regulation, managing a specific high-order state of affairs, which is life-essential.

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https://arxiv.org/ftp/arxiv/papers/1706/1706.02902.pdf

Dr. Indrajit Patra: The Complex and the Miraculous: A Closer Look at the Irreducible Complexity of Cell
https://www.annalsofrscb.ro/index.php/journal/article/view/884/756

Andrew H. Knoll Fundamentals of Geobiology 2012 page 323

Metabolism versus genetic mechanisms
The problem with understanding origins is that metabolism and genetic mechanisms constitute two separate, chemically distinct systems in cells. Nevertheless, metabolism and genetic mechanisms are inextricably linked in modern life. DNA holds genetic instructions to make hundreds of molecules essential to metabolism, while metabolism provides both the energy and the basic building blocks to make DNA and other genetic materials. Like the dilemma of which came first, the chicken or the egg, it is difficult to imagine back to a time when metabolism and genetic mechanisms were not intertwined. Consequently, origins-of-life researchers engage in an intense ongoing debate about whether these two aspects of life arose simultaneously or independently and, if the latter, which one came first. 
 Most experts seem to agree that the simultaneous emergence of metabolism and genetic mechanisms is unlikely. The chemical processes are just too different, and they rely on completely different sets of molecules. It’s much easier to imagine life arising one small step at a time, but what is the sequence of emergent steps? Those who favor genetics first argue on the basis of life’s remarkable complexity; they point to the astonishing intricacy of even the simplest living cell. Without a genetic mechanism, there would be no way to ensure the faithful reproduction of all that complexity. Metabolism without a genetic mechanism may be viewed as nothing more than a collection of overactive chemicals. Other scientists are persuaded by the principle that life emerged through stages of increasing complexity. Metabolic chemistry, at its core, is vastly simpler than genetic mechanisms because it requires relatively few small molecules that work in concert to duplicate themselves. In this view, the core metabolic cycle – the citric acid cycle that lies at the heart of every modern cell’s metabolic processes – survives as a biochemical fossil from life’s beginning. This comparatively simple chemical cycle is an engine that can bootstrap all of life’s biochemistry, including the key genetic molecules. Origins-of-life scientists are not shy about voicing their opinions on the metabolism- vs. genetics-first problem, which will probably remain a central controversy in the field for some time.

Self-replicating molecular systems 
The simplest imaginable self-replicating system consists of one type of molecule that makes exact copies of itself. Under just the right chemical environment, such an isolated molecule will become two copies, then four, then eight molecules, and so on in a geometrical expansion. Such an ‘autocatalytic’ molecule must act as a template that attracts and assembles smaller building blocks from an appropriate chemical broth. Single self-replicating molecules are intrinsically complex in structure, but organic chemists have managed to devise several varieties of these curious beasts, including small peptides (made of amino acids) and short strands of DNA. Nevertheless, these self-replicating molecules don’t meet anyone’s minimum requirements for life on at least two counts. These systems require a steady input of smaller highly specialized molecules – synthetic chemicals that must be supplied by the researchers. Under no plausible natural environment could these idiosyncratic ‘food’ molecules arise independently in nature. Furthermore – and this is a key point in distinguishing life from non-life – these particular self-replicating molecules can’t change and evolve, any more than a photocopy can evolve from an original. More relevant to biological metabolism are systems of two or more molecules that form a self-replicating cycle or network. In the simplest system, two molecules (call them AA and BB) form from smaller feedstock molecules A and B. If AA catalyzes the formation of BB, and BB, in turn, catalyzes the formation of AA, then the system will sustain itself as long as researchers maintain a reliable supply of food molecules A and B. The well-known polymerase chain reaction (PCR) of crime scene investigation fame is an important example of such a self-replicating molecular system. A strand of DNA is added to a solution of nucleotides, a primer that targets a specific DNA sequence, and the enzyme polymerase that helps to assemble DNA. Each cycle of heating (to separate DNA strands) and cooling (to trigger assembly of double-stranded DNA) doubles the number of copies of DNA. Twenty cycles can thus produce more than a million copies of a single piece of DNA. Theorists elaborate on such a model with networks of many molecules, each of which promotes the production of another species in the system. What separates living systems from simple self-replicating collections of molecules? The answer in part is complexity; living systems require numerous interacting molecules. In addition, a living metabolic cycle must incorporate a certain degree of sloppiness. Only through such copying ‘mistakes’ can the system experiment with new, more efficient reaction pathways and thus evolve – an essential attribute of living systems. A dramatic gap exists between plausible theory and actual experiment. Metabolism is a special kind of cyclical chemical process with two requisite inputs. Living cells undergo chemical reactions, not unlike burning in which two chemicals (oxygen and fuel) react and release energy. However, the trick in metabolism, unlike an open fire, is to capture part of that released energy to make new useful molecules that reinforce the cycle. So metabolism requires a sequence of chemical reactions that work in concert.

https://www.amazon.com.br/Fundamentals-Geobiology-Andrew-H-Knoll/dp/1405187522

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Jean-Paul Douliez: Fatty acid vesicles and coacervates as model prebiotic protocells 2021

A protocell can be defined as the most primitive compartment that would have led to the emergence of a living cell. Based on seminal theoretical models of the simplest living chemical systems in the 1970s by Kauffman[55] (autocatalytic set model), Eigen[56] (hypercycle model) and Ganti[57] (chemoton model), it is now acknowledged that a living protocell should contain (at least) three key ingredients: a compartment, to delimit the inner self from the outer environment; a metabolism, defined as an ensemble of out-of-equilibrium reactions coupled to an external source of energy; and a process of self-replication by which the protocell makes copies of itself based on error-prone duplication, paving the way to population-level Darwinian evolution. The de novo self-assembly of a living protocell therefore requires the integration of these three modules to produce a selfsustained growing and duplicating minimal compartment able to store and transfer information to the next protocell generation. While such a complex, integrated system has not been realized yet, a few studies have started coupling two of the three key Life’s ingredients.

Abiogenesis: The cell is irreducibly complex Interd11
Theories proposing a purely metabolic or genomic starting point actually encounter numerous theoretical and experimental objections, mainly because the type of initial system they propose has a much higher probability to fall into equilibrium than to originate a sustainable, kinetically driven process leading to life.
https://sci-hub.ee/10.1021/cr2004844

https://sci-hub.ee/10.1002/syst.202100024

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God spoke, and life arose
With all machinery in place, it was wise
To have the means of reproduction
And ways to obtain energy without reduction

Converting it to a usable form
And ridding waste to keep it warm
Radiation, temperature, and pH, it did all strive

The cellular repair was also in its domain
A complete mechanism, nothing in vain
Intracellular communication, is a must
To keep all parts functioning, a thrust

All these components, from day one
Fully functioning, or else undone
Malfunctions or incomplete versions, fatal fate
Immediate death, nothing to negotiate

The machinery of life, standing tall
From this humble beginning, we all came
A marvel of God's design, life's eternal flame.

Up until this century, we never knew
Just how complex life is, so true
Biological systems, interactively dependent
A marvel of God's design, quite transcendent

A cell, a complex factory indeed
Molecular machines, taking the lead
Golgi-apparatus, mitochondria, and more
Each process is linked, a correlation to adore

Cooperation, the key to this system
Organelles working, in perfect rhythm
Irreducibly complex, a fact to behold
The intricacy of life, a story untold

Evolutionary processes, unable to create
With such complexity, it's not up for debate
Unless each part, shows up in perfect sync
Together in a life form, able to link
Individual components, purposeless they'll be

The point is clear, for all to see
Life, a mystery, we're yet to unfold
Complexity beyond measure, so bold
A cell, a testament to God's design
A true wonder, for all time.

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The Irreducible Complexity of Minimal Cells: Challenges in Understanding the Origin of Life

Abstract

This paper examines the concept of irreducible complexity in minimal cells through an analysis of 21 essential life processes. We argue that the high degree of interdependence among these processes, their lack of individual functionality in isolation, and the challenges of prebiotic emergence present significant obstacles to explaining the origin of life through gradual, step-wise evolution. The study highlights the need for comprehensive models that can account for the simultaneous or rapid sequential emergence of multiple, interconnected cellular processes.

1. Introduction

The origin of life remains one of the most profound and challenging questions in science. Central to this question is understanding how the first minimal cells - the simplest self-replicating entities capable of evolution - could have emerged from prebiotic chemistry. This paper explores the concept of irreducible complexity in minimal cells by examining 21 processes considered essential for life.

2. Methods

We conducted a comprehensive literature review and theoretical analysis of 21 life-essential processes. Each process was evaluated for its individual importance and its interdependencies with other processes. We then considered the implications of these interdependencies for the concept of irreducible complexity and the challenges they present to the origin of life theories.

3. Results

3.1 Essential Processes

We identified and analyzed 21 processes considered essential for life, including closed-loop recycling, energy-efficient processes, selective permeability, environmental sensing, efficient energy storage, parallel processing, self-replication, catalysis, information storage and transfer, adaptability, compartmentalization, molecular recognition, error correction, energy transduction, metabolism, nutrition, organization, growth and development, information processing, hardware/software integration, and balancing permanence and change.

3.2 List of processes that were likely life-essential and present when life began, along with explanations for their importance

1. Closed-loop recycling: The ability to break down and reuse components. This is vital for early life to conserve limited resources and maintain itself in resource-poor environments.
2. Energy-efficient processes: Reactions occurring at low temperatures and pressures. This is essential because early life forms likely had limited energy available and needed to operate under a wide range of environmental conditions.
3. Selective permeability: The ability to control what enters and exits a cell. This is crucial for maintaining a distinct internal environment and for resource acquisition.
4. Environmental sensing: The capacity to detect and respond to environmental changes. This is essential for survival in variable conditions and for efficiently utilizing available resources.
5. Efficient energy storage: The ability to store energy in accessible forms. This is vital for sustaining life processes during periods when external energy sources are unavailable.
6. Parallel processing: The ability to conduct multiple chemical reactions simultaneously. This is essential for carrying out the complex set of reactions necessary for even the simplest forms of life.
7. Self-replication: The ability to create copies of oneself. This is fundamental for life to persist and evolve over time, allowing for the propagation of successful adaptations.
8. Catalysis: The use of catalysts to speed up chemical reactions. This is crucial for enabling life processes to occur at rates fast enough to sustain living systems.
9. Information storage and transfer: The capacity to store and pass on genetic information. This is essential for maintaining the identity of an organism and allowing for heredity and evolution.
10. Adaptability: The ability to adjust to changing environmental conditions. This is vital for survival in the face of fluctuating external factors and limited resources.
11. Compartmentalization: The creation of distinct spaces within a cell. This is important for maintaining different chemical environments and optimizing various cellular processes.
12. Molecular recognition: The ability of molecules to specifically interact with one another. This is crucial for the precise control of cellular processes and for maintaining cellular organization.
13. Error correction: Mechanisms to identify and fix mistakes in cellular processes. This is essential for maintaining the integrity of genetic information and cellular functions over time.
14. Energy transduction: The conversion of one form of energy to another. This is vital for harnessing environmental energy sources to power life processes.
15. Metabolism: The ability to process chemicals through complicated sequences of reactions, liberating energy for various life processes. This is fundamental for organisms to "do something" and sustain themselves.
16. Nutrition: The capacity to take in matter and energy from the environment. This continual throughput is crucial for maintaining life processes over time.
17. Organization: The ability to maintain organized complexity, where components cooperate to function as a coherent unity. This is essential for the emergence of life from simpler chemical systems.
18. Growth and development: The capacity for individual organisms to grow and for populations to develop and adapt over time. This is crucial for the evolution and persistence of life.
19. Information processing: The ability to use and respond to meaningful information within a specific context. This goes beyond mere information storage and is essential for life's complex functions.
20. Hardware/software integration: The capacity to link information-storing molecules (like nucleic acids) with functional molecules (like proteins) through a communication channel or code. This integration is fundamental to life as we know it.
21. Balancing permanence and change: The ability to maintain genetic stability while also allowing for variation and adaptation. This balance is crucial for life's long-term survival and evolution.

Based on the 21 points listed, we can argue that a minimal cell is irreducibly complex because each of these processes is essential for life, and the absence of any one of them would make life as we know it impossible. 

3.3 Irreducible Complexity


1. Without closed-loop recycling, early life forms would quickly deplete their limited resources and cease to function.
2. Without energy-efficient processes, life would consume energy too quickly to sustain itself in most environments.
3. Without selective permeability, cells couldn't maintain their internal environment or control resource acquisition, leading to dissolution.
4. Without environmental sensing, organisms couldn't adapt to changes, leading to death in variable conditions.
5. Without efficient energy storage, life processes would halt during periods of resource scarcity.
6. Without parallel processing, the complex reactions necessary for life couldn't occur simultaneously, making even basic life functions impossible.
7. Without self-replication, life couldn't persist beyond a single generation or evolve.
8. Without catalysis, chemical reactions would be too slow to support life processes.
9. Without information storage and transfer, there would be no heredity or evolution, and organisms couldn't maintain their identity.
10. Without adaptability, life would fail to survive in changing environments.
11. Without compartmentalization, cells couldn't optimize different processes or maintain distinct chemical environments.
12. Without molecular recognition, precise control of cellular processes would be impossible.
13. Without error correction, genetic information and cellular functions would degrade over time.
14. Without energy transduction, organisms couldn't harness environmental energy to power life processes.
15. Without metabolism, organisms couldn't process chemicals or liberate energy for life processes.
16. Without nutrition, there would be no input of matter and energy to sustain life processes.
17. Without organization, the complexity necessary for life couldn't emerge or be maintained.
18. Without growth and development, life couldn't persist or evolve over time.
19. Without information processing, organisms couldn't respond appropriately to their environment or internal states.
20. Without hardware/software integration, there would be no link between information storage and functional molecules.
21. Without the balance of permanence and change, life couldn't maintain stability while also adapting and evolving.

The irreducible complexity of a minimal cell is evident because these processes are not only essential but also interdependent. For example:

- Metabolism (15) requires catalysis ( 8 ), energy transduction (14), and organization (17).
- Self-replication (7) depends on information storage and transfer (9), error correction (13), and molecular recognition (12).
- Adaptability (10) relies on environmental sensing (4), information processing (19), and the balance of permanence and change (21).

3.4 Interdependencies with other points

1. Closed-loop recycling:
  - Interdependent with 15 (Metabolism): Recycling is a key part of metabolic processes.
  - Interdependent with 16 (Nutrition): Recycling allows for efficient use of limited nutrients.
  - Interdependent with 10 (Adaptability): Recycling helps adapt to resource-poor environments.

2. Energy-efficient processes:
  - Interdependent with 5 (Efficient energy storage): Both contribute to overall energy efficiency.
  - Interdependent with 14 (Energy transduction): Efficient processes rely on effective energy conversion.
  - Interdependent with 15 (Metabolism): Energy efficiency is crucial for sustainable metabolic processes.

3. Selective permeability:
  - Interdependent with 16 (Nutrition): Controls intake of nutrients.
  - Interdependent with 11 (Compartmentalization): Both contribute to maintaining distinct environments.
  - Interdependent with 4 (Environmental sensing): Permeability can be adjusted based on environmental cues.

4. Environmental sensing:
  - Interdependent with 10 (Adaptability): Sensing enables adaptive responses.
  - Interdependent with 19 (Information processing): Sensing provides information to be processed.
  - Interdependent with 3 (Selective permeability): Sensing informs permeability adjustments.

5. Efficient energy storage:
  - Interdependent with 2 (Energy-efficient processes): Both contribute to overall energy efficiency.
  - Interdependent with 15 (Metabolism): Stored energy fuels metabolic processes.
  - Interdependent with 16 (Nutrition): Energy storage compensates for fluctuations in nutrient availability.

6. Parallel processing:
  - Interdependent with 15 (Metabolism): Enables complex metabolic pathways.
  - Interdependent with 17 (Organization): Requires organized complexity to function effectively.
  - Interdependent with 11 (Compartmentalization): Different processes can occur in different compartments.

7. Self-replication:
  - Interdependent with 9 (Information storage and transfer): Replication requires accurate information transfer.
  - Interdependent with 18 (Growth and development): Replication is a key aspect of growth.
  - Interdependent with 21 (Balancing permanence and change): Replication must balance fidelity with variation.

8. Catalysis:
  - Interdependent with 15 (Metabolism): Catalysts are crucial for metabolic reactions.
  - Interdependent with 2 (Energy-efficient processes): Catalysts make processes more energy-efficient.
  - Interdependent with 12 (Molecular recognition): Catalysts work through specific molecular interactions.

9. Information storage and transfer:
  - Interdependent with 7 (Self-replication): Information transfer is crucial for replication.
  - Interdependent with 13 (Error correction): Ensures accuracy of stored and transferred information.
  - Interdependent with 20 (Hardware/software integration): Information storage (software) must integrate with functional molecules (hardware).

10. Adaptability:
   - Interdependent with 4 (Environmental sensing): Adaptation requires sensing environmental changes.
   - Interdependent with 21 (Balancing permanence and change): Adaptability requires a balance between stability and change.
   - Interdependent with 18 (Growth and development): Adaptability drives evolutionary development.

11. Compartmentalization:
   - Interdependent with 3 (Selective permeability): Compartments require selective barriers.
   - Interdependent with 6 (Parallel processing): Enables different processes to occur simultaneously in different compartments.
   - Interdependent with 17 (Organization): Compartmentalization is a key aspect of cellular organization.

12. Molecular recognition:
   - Interdependent with 8 (Catalysis): Many catalysts work through specific molecular recognition.
   - Interdependent with 19 (Information processing): Molecular recognition is a form of information processing at the chemical level.
   - Interdependent with 20 (Hardware/software integration): Enables communication between information-storing and functional molecules.

13. Error correction:
   - Interdependent with 9 (Information storage and transfer): Ensures accuracy of genetic information.
   - Interdependent with 7 (Self-replication): Maintains fidelity during replication.
   - Interdependent with 21 (Balancing permanence and change): Helps maintain genetic stability while allowing for some variation.

14. Energy transduction:
   - Interdependent with 2 (Energy-efficient processes): Efficient energy conversion is crucial for energy-efficient processes.
   - Interdependent with 15 (Metabolism): Energy transduction is a key aspect of metabolism.
   - Interdependent with 5 (Efficient energy storage): Converted energy often needs to be stored efficiently.

15. Metabolism:
   - Interdependent with 1 (Closed-loop recycling): Metabolic processes often involve recycling of components.
   - Interdependent with 8 (Catalysis): Metabolic reactions rely heavily on catalysts.
   - Interdependent with 16 (Nutrition): Metabolism processes nutrients taken in from the environment.

16. Nutrition:
   - Interdependent with 3 (Selective permeability): Controls intake of nutrients.
   - Interdependent with 15 (Metabolism): Provides the raw materials for metabolic processes.
   - Interdependent with 1 (Closed-loop recycling): Efficient nutrition involves recycling of materials.

17. Organization:
   - Interdependent with 11 (Compartmentalization): Organization often involves compartmentalization.
   - Interdependent with 6 (Parallel processing): Organized systems can perform multiple processes simultaneously.
   - Interdependent with 20 (Hardware/software integration): Organization requires integration of information and function.

18. Growth and development:
   - Interdependent with 7 (Self-replication): Growth often involves replication at the cellular level.
   - Interdependent with 10 (Adaptability): Development involves adapting to changing conditions.
   - Interdependent with 21 (Balancing permanence and change): Development requires both stability and change.

19. Information processing:
   - Interdependent with 4 (Environmental sensing): Processing of environmental information.
   - Interdependent with 12 (Molecular recognition): Information processing at the molecular level.
   - Interdependent with 9 (Information storage and transfer): Processing of stored genetic information.

20. Hardware/software integration:
   - Interdependent with 9 (Information storage and transfer): Integration of information-storing molecules with functional molecules.
   - Interdependent with 12 (Molecular recognition): Enables communication between different types of molecules.
   - Interdependent with 17 (Organization): Integration is a key aspect of cellular organization.

21. Balancing permanence and change:
   - Interdependent with 13 (Error correction): Maintains stability while allowing for some variation.
   - Interdependent with 10 (Adaptability): Allows for adaptation while maintaining core functions.
   - Interdependent with 7 (Self-replication): Ensures both faithful replication and introduction of variations.

These interdependencies create a complex web of processes that must all be present and functioning for life to exist. The removal of any single process would cause the entire system to fail, as the remaining processes depend on it in some way. Even the simplest form of life requires a minimum set of interrelated processes that cannot be reduced further without losing the essential characteristics of life. This supports the concept of irreducible complexity in minimal cells, as all these processes must have emerged together for life to begin, presenting a significant challenge in understanding the origin of life. We can indeed consider the unlikelihood of these 21 components emerging prebiotically in isolation:

1. Interconnected nature: These 21 processes are highly interdependent. For example, energy-efficient processes (2) rely on selective permeability (3), which in turn requires compartmentalization (11). This interconnectedness suggests that these processes would need to emerge as a system rather than individually.
2. Lack of individual function: Many of these processes, in isolation, would serve no purpose. For instance, information storage and transfer (9) would be meaningless without self-replication (7) or information processing (19). This lack of individual function reduces the likelihood of their independent emergence and persistence.
3. Prebiotic stability issues: As you mentioned, experiments have shown that organic molecules left on their own tend to break down rather than build up into more complex structures. This tendency, often referred to as the "asphalt problem," poses a significant challenge to the idea of these components emerging and persisting independently in a prebiotic environment.
4. Synergistic complexity: The functionality of a minimal cell emerges from the synergistic interaction of these 21 processes. For example, adaptability (10) requires the integration of environmental sensing (4), information processing (19), and the balance of permanence and change (21). This level of complexity is difficult to account for through gradual, step-wise emergence.
5. Chicken-and-egg problems: Many of these processes present chicken-and-egg dilemmas. For instance, metabolism (15) is necessary for nutrition (16), but nutrition is required to fuel metabolism. Such interdependencies make it challenging to explain how these processes could have emerged separately.
6. Environmental context: Many of these processes only make sense in the context of a living system. For example, error correction (13) presupposes the existence of a system complex enough to make errors that need correcting. This contextual requirement further reduces the likelihood of independent prebiotic emergence.
7. Energetic considerations: Maintaining these processes requires a constant input and efficient management of energy. Without the overarching system to capture and direct energy (as in points 2, 5, and 14), individual processes would likely dissipate rather than persist or develop further.
8. Information paradox: The development of such a complex, interconnected system seems to require a level of information processing and storage that is itself one of the system's outputs. This paradox adds to the difficulty of explaining how these processes could have emerged independently.

Given these considerations, the argument for irreducible complexity in minimal cells gains strength. The high degree of interdependence, the lack of individual functionality, and the tendency towards breakdown rather than spontaneous complexity in prebiotic conditions all point to the improbability of these 21 essential processes emerging independently and then integrating into a functional cellular system. This line of reasoning suggests that the origin of life, particularly the emergence of the first minimal cells, remains a significant scientific puzzle. It underscores the need for comprehensive models that can account for the simultaneous or rapid sequential emergence of multiple, interconnected cellular processes.

3.5 Challenges to Independent Emergence

Several factors make the independent emergence of these processes unlikely:
- Lack of individual function: Many processes serve no purpose in isolation.
- Prebiotic stability issues: Organic molecules tend to break down rather than build up in prebiotic conditions.
- Synergistic complexity: The functionality of a minimal cell emerges from the interaction of multiple processes.
- Chicken-and-egg problems: Many processes present circular dependencies.
- Environmental context: Some processes only make sense within an already living system.
- Energetic considerations: Maintaining these processes requires constant energy input and management.
- Information paradox: The system's development seems to require a level of information processing that is itself one of the system's outputs.

4. Discussion

The high degree of interdependence among the 21 essential processes supports the concept of irreducible complexity in minimal cells. The removal of any single process would likely cause the entire system to fail, as the remaining processes depend on it in some way. This presents a significant challenge to explaining the origin of life through gradual, step-wise processes. 

Graham Cairns-Smith (2003):  We are all descended from some ancient organisms or group of organisms within which much of the machinery now found in all forms of life on Earth was already essentially fixed and, as part of that, hooked on today’s so-called ‘molecules of life’. This machinery is enormously sophisticated, depending for its operation on many collaborating parts. The multiple collaboration provides an explanation for why the present system is so frozen now and has been for so long.  So we are left wondering how the whole DNA/RNA/protein control system, on which evolution now so utterly depends, could itself have evolved. It is hard to see primitive geochemical processes maintaining the clean supplies of nucleotides required for the replication of molecules like RNA. Nucleotides are not easy to make, as organic chemists know, and as is evidenced by the long pathways to nucleotides within biochemistry today. 2

The prebiotic emergence of these processes in isolation seems highly improbable due to their lack of individual function and the tendency of organic molecules to break down in prebiotic conditions. 

Steven A. Benner (2014): The Asphalt Paradox:  An enormous amount of empirical data have established, as a rule, that organic 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. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that 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. Lipids that provide tidy compartments under the close supervision of a graduate student (supporting a protocell first model for origins) are quite non-robust with respect to small environmental perturbations, such as a change in the salt concentration, the introduction of organic solvents, or a change in temperature.1

Furthermore, the synergistic nature of cellular functionality suggests that these processes would need to emerge as an integrated system rather than as individual components. These findings underscore the need for comprehensive models in origin of life research that can account for the simultaneous or rapid sequential emergence of multiple, interconnected cellular processes. Such models would need to explain how a minimal set of interdependent processes could arise and stabilize in a prebiotic environment.

5. Conclusion

Our analysis of 21 essential life processes reveals a high degree of irreducible complexity in minimal cells. The extensive interdependencies among these processes, their lack of individual functionality, and the challenges of prebiotic emergence present significant obstacles to explaining the origin of life through gradual, step-wise emergence. These findings highlight the need for new, comprehensive approaches to understanding the emergence of cellular life. While this study supports the concept of irreducible complexity in minimal cells, it does not argue for or against any particular explanation for the origin of life. Rather, it aims to clarify the challenges that origin of life theories must address and to stimulate further research in this field. Future work should focus on developing and testing models that can account for the simultaneous or rapid sequential emergence of multiple, interconnected cellular processes. Such research may provide new insights into the conditions and mechanisms that could have given rise to the first living cells.

References

1. Benner, Steven A. (2014). Paradoxes in the Origin of Life. Origins of Life and Evolution of Biospheres, 44(4), 339–343. doi:10.1007/s11084-014-9379-0

2. Meyer-Ortmanns, H. (2003). Fine-tuning in living systems: early evolution and the unity of biochemistry. *International Journal of Astrobiology*, 2(4), 231-243. Link. (This paper discusses the fine-tuning observed in biological systems, focusing on early evolutionary processes and the biochemical unity across diverse forms of life.)

The Complex and the Miraculous: A Closer Look at the Irreducible Complexity of CellDr. Indrajit Patra, Annals of R.S.C.B., ISSN:1583-6258, Vol. 25, Issue 1, 2021, Pages. 7127-7136 Link

Saugata, Basu. (2002). The Combinatorial and Topological Complexity of a Single Cell. Discrete and Computational Geometry,  doi: 10.1007/S00454-002-2799-Z

William, A., Dembski. (2003). Irreducible Complexity Revisited.   

Michael, J., Behe. (2003). Irreducible Complexity: Obstacle to Darwinian Evolution.   doi: 10.1017/CBO9780511804823.020

Andrew, Reynolds. (2010). The redoubtable cell. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences,  doi: 10.1016/J.SHPSC.2010.07.011

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Refuting the Oversimplification of First Cell Requirements in Libretext 5.6

Claim: Libretext 5.6: What was needed for the first cell? Some sort of membrane surrounding organic molecules? Probably. How organic molecules such as RNA developed into cells is not known for certain. Scientists speculate that lipid membranes grew around the organic molecules. The membranes prevented the molecules from reacting with other molecules, so they did not form new compounds. In this way, the organic molecules persisted, and the first cells may have formed.Figure below shows a model of the hypothetical first cell. Were these first cells the first living organisms? Were they able to live and reproduce while passing their genetic information to the next generation? If so, then yes, these first cells could be considered the first living organisms. The first cells consisted of little more than an organic molecule such as RNA inside a lipid membrane.

Response: The claim from Libretext 5.6 oversimplifies the requirements for the first cell and does not accurately represent the complexity involved in the origin of life. Based on our current understanding of minimal cell requirements, we can refute this claim on several grounds:

1. Complexity of Minimal Cells
Even the simplest form of life requires numerous essential processes far more complex than just "a membrane surrounding organic molecules." These include:
• Metabolism
• Energy transduction
• Information storage and processing
• Self-replication
• Homeostasis
• Response to stimuli
The interdependence and complexity of these processes suggest that a simple lipid membrane encapsulating RNA would be far from sufficient for life.

2. Irreducible Complexity
The concept of irreducible complexity argues that all essential cellular processes are interdependent, and removing any single process would likely cause the entire system to fail. This contradicts the simplistic view presented in the Libretext claim. For example:
• DNA replication requires proteins
• Protein synthesis requires DNA
• Both processes require energy from metabolism
• Metabolism requires enzymes (proteins)
This intricate web of dependencies challenges the idea of a simple, stepwise origin of life.

3. Prebiotic Challenges
There are significant challenges to the prebiotic emergence of cellular components:
• The "asphalt problem": Organic molecules tend to break down rather than build up in prebiotic conditions
• Chirality: Life uses specific molecular orientations, but prebiotic chemistry produces mixed orientations
• Concentration problem: Dilute prebiotic oceans make molecular interactions unlikely
• Incompatibility of RNA and peptide syntheses: Different conditions are required for these crucial processes

4. Information Processing and Replication
The Libretext claim does not address the crucial aspects of information processing and replication:
• Information storage (e.g., DNA or RNA)
• Information transfer (e.g., transcription, translation)
• Information processing (e.g., gene regulation)
• Self-replication of the entire system
These are essential for life according to both the NASA definition and other criteria.

5. Energy and Metabolism
The claim overlooks the critical roles of energy transduction and metabolism:
• Energy capture (e.g., photosynthesis or chemosynthesis)
• Energy storage (e.g., ATP)
• Energy utilization for cellular processes
• Metabolic pathways for biosynthesis and breakdown of molecules
Without these processes, no cellular functions could be sustained.

6. Adaptability and Evolution
While the Libretext mentions passing genetic information, it does not adequately address the requirements for adaptability and Darwinian evolution, which are central to NASA's definition of life. This includes:
• Mechanisms for generating genetic variation
• Selection processes
• Inheritance of adaptive traits

7. Synergistic Functionality
The functionality of a minimal cell emerges from the synergistic interaction of multiple processes, not just from the encapsulation of molecules. This synergy includes:
• Coordinated regulation of gene expression
• Feedback loops in metabolic pathways
• Integration of sensory information with cellular responses
• Coupling of energy production with cellular functions

Conclusion
While the Libretext claim provides a very basic starting point for thinking about the origin of life, it grossly underestimates the complexity and requirements for the first living cells. The emergence of life likely required the simultaneous or rapid sequential development of multiple, interconnected cellular processes, presenting a far more challenging puzzle than the simple encapsulation of organic molecules within a lipid membrane.

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The Irreducible Complexity of Minimal Cells: Challenges in Understanding the Origin of Life

Abstract

This paper examines the concept of irreducible complexity in minimal cells through an analysis of 26 essential life processes. We argue that the high degree of interdependence among these processes, their lack of individual functionality in isolation, and the challenges of prebiotic emergence present significant obstacles to explaining the origin of life through gradual, step-wise processes. The study highlights the need for comprehensive models that can account for the simultaneous or rapid emergence of multiple, interconnected cellular parts.

1. Introduction

The origin of life remains one of the most strident and challenging questions in science. Central to this question is understanding how the first minimal cells - the simplest self-replicating entities capable of evolution - could have emerged from prebiotic chemistry. This paper explores the concept of irreducible complexity in minimal cells by examining 26 processes considered essential for life.

2. Methods

We conducted a comprehensive literature review and theoretical analysis of 26 life-essential processes. Each process was evaluated for its individual importance and its interdependencies with other processes. We then considered the implications of these interdependencies for the concept of irreducible complexity and the challenges they present to the origin of life theories.

3. Results

3.1 Essential Processes

We identified and analyzed the following 26 processes considered essential for life, along with explanations for their importance:

1. Closed-loop recycling: The ability to break down and reuse components. This is vital for early life to conserve limited resources and maintain itself in resource-poor environments.
2. Energy-efficient processes: Reactions occurring at low temperatures and pressures. This is essential because early life forms likely had limited energy available and needed to operate under a wide range of environmental conditions.
3. Selective permeability: The ability to control what enters and exits a cell. This is crucial for maintaining a distinct internal environment and for resource acquisition.
4. Environmental sensing: The capacity to detect and respond to environmental changes. This is essential for survival in variable conditions and for efficiently utilizing available resources.
5. Efficient energy storage: The ability to store energy in accessible forms. This is vital for sustaining life processes during periods when external energy sources are unavailable.
6. Parallel processing: The ability to conduct multiple chemical reactions simultaneously. This is essential for carrying out the complex set of reactions necessary for even the simplest forms of life.
7. Self-replication: The ability to create copies of oneself. This is fundamental for life to persist and evolve over time, allowing for the propagation of successful adaptations.
8. Catalysis: The use of catalysts to speed up chemical reactions. This is crucial for enabling life processes to occur at rates fast enough to sustain living systems.
9. Information storage and transfer: The capacity to store and pass on genetic information. This is essential for maintaining the identity of an organism and allowing for heredity and evolution.
10. Adaptability: The ability to adjust to changing environmental conditions. This is vital for survival in the face of fluctuating external factors and limited resources.
11. Compartmentalization: The creation of distinct spaces within a cell. This is important for maintaining different chemical environments and optimizing various cellular processes.
12. Molecular recognition: The ability of molecules to specifically interact with one another. This is crucial for the precise control of cellular processes and for maintaining cellular organization.
13. Error correction: Mechanisms to identify and fix mistakes in cellular processes. This is essential for maintaining the integrity of genetic information and cellular functions over time.
14. Energy transduction: The conversion of one form of energy to another. This is vital for harnessing environmental energy sources to power life processes.
15. Metabolism: The ability to process chemicals through complicated sequences of reactions, liberating energy for various life processes. This is fundamental for organisms to "do something" and sustain themselves.
16. Nutrition: The capacity to take in matter and energy from the environment. This continual throughput is crucial for maintaining life processes over time.
17. Organization: The ability to maintain organized complexity, where components cooperate to function as a coherent unity. This is essential for the emergence of life from simpler chemical systems.
18. Growth and development: The capacity for individual organisms to grow and for populations to develop and adapt over time. This is crucial for the evolution and persistence of life.
19. Information processing: The ability to use and respond to meaningful information within a specific context. This goes beyond mere information storage and is essential for life's complex functions.
20. Hardware/software integration: The capacity to link information-storing molecules (like nucleic acids) with functional molecules (like proteins) through a communication channel or code. This integration is fundamental to life as we know it.
21. Balancing permanence and change: The ability to maintain genetic stability while allowing for variation and adaptation. This balance is crucial for life's long-term survival and evolution.
22. Ion transport and homeostasis: The maintenance of proper ion gradients across membranes and regulation of internal conditions. This is essential for energy generation, cellular signaling, and maintaining proper chemical environments for biochemical processes.
23. Cell division machinery: The physical processes and molecular mechanisms required for accurate cell division. This includes the coordinated separation of genetic material and cellular components, essential for reproduction and growth.
24. Protein quality control: Systems for maintaining proper protein folding, preventing aggregation, and removing damaged proteins. This is crucial for maintaining cellular function and preventing toxic accumulations.
25. Cell wall/membrane synthesis: The processes for constructing and maintaining cellular boundaries and structural components. This is essential for cell integrity, growth, and division.
26. Translation quality control: Systems ensuring accurate protein synthesis and maintaining translation fidelity. This is crucial for proper protein function and cellular survival.[/size]

3.2 Interdependencies

Each process forms multiple interdependencies with others:

1. Closed-loop recycling:
- Interdependent with 15 (Metabolism): Recycling is a key part of metabolic processes
- Interdependent with 16 (Nutrition): Recycling allows for efficient use of limited nutrients
- Interdependent with 10 (Adaptability): Recycling helps adapt to resource-poor environments
- Interdependent with 24 (Protein quality control): Recycling of damaged proteins
- Interdependent with 25 (Cell wall/membrane synthesis): Reuse of membrane components

2. Energy-efficient processes:
- Interdependent with 5 (Efficient energy storage): Both contribute to overall energy efficiency
- Interdependent with 14 (Energy transduction): Efficient processes rely on effective energy conversion
- Interdependent with 15 (Metabolism): Energy efficiency is crucial for sustainable metabolic processes
- Interdependent with 22 (Ion transport): Efficient maintenance of ion gradients
- Interdependent with 23 (Cell division): Energy-efficient division processes

3.3 Irreducible Complexity

The irreducible complexity of a minimal cell is evident because these processes are not only essential but also interdependent. For example:

1. Without closed-loop recycling, early life forms would quickly deplete their limited resources and cease to function.
2. Without energy-efficient processes, life would consume energy too quickly to sustain itself in most environments.[/size][/size]
3. Without selective permeability, cells couldn't maintain their internal environment or control resource acquisition, leading to dissolution.
4. Without environmental sensing, organisms couldn't adapt to changes, leading to death in variable conditions.
5. Without efficient energy storage, life processes would halt during periods of resource scarcity.
6. Without parallel processing, the complex reactions necessary for life couldn't occur simultaneously, making even basic life functions impossible.
7. Without self-replication, life couldn't persist beyond a single generation or evolve.
8. Without catalysis, chemical reactions would be too slow to support life processes.
9. Without information storage and transfer, there would be no heredity or evolution, and organisms couldn't maintain their identity.
10. Without adaptability, life would fail to survive in changing environments.
11. Without compartmentalization, cells couldn't optimize different processes or maintain distinct chemical environments.
12. Without molecular recognition, precise control of cellular processes would be impossible.
13. Without error correction, genetic information and cellular functions would degrade over time.
14. Without energy transduction, organisms couldn't harness environmental energy to power life processes.
15. Without metabolism, organisms couldn't process chemicals or liberate energy for life processes.
16. Without nutrition, there would be no input of matter and energy to sustain life processes.
17. Without organization, the complexity necessary for life couldn't emerge or be maintained.
18. Without growth and development, life couldn't persist or evolve over time.
19. Without information processing, organisms couldn't respond appropriately to their environment or internal states.
20. Without hardware/software integration, there would be no link between information storage and functional molecules.
21. Without the balance of permanence and change, life couldn't maintain stability while also adapting and evolving.
22. Without ion transport and homeostasis, cells would be unable to maintain essential chemical gradients, causing collapse of energy generation systems and loss of cellular function.
23. Without cell division machinery, cells could not reproduce accurately, leading to failure of generational continuity and evolution.
24. Without protein quality control, misfolded proteins would accumulate and aggregate, disrupting cellular processes and leading to cell death.
25. Without cell wall/membrane synthesis, cells would lose structural integrity and boundary control, leading to cellular collapse.
26. Without translation quality control, protein synthesis errors would accumulate, leading to dysfunction of all protein-dependent processes.

3.4 Interdependencies with other points

1. Closed-loop recycling:
- Interdependent with 15 (Metabolism): Recycling is a key part of metabolic processes
- Interdependent with 16 (Nutrition): Recycling allows for efficient use of limited nutrients
- Interdependent with 10 (Adaptability): Recycling helps adapt to resource-poor environments
- Interdependent with 24 (Protein quality control): Coordinates disposal and recycling of damaged proteins
- Interdependent with 25 (Cell wall/membrane synthesis): Enables reuse of membrane components

2. Energy-efficient processes:
- Interdependent with 5 (Efficient energy storage): Both contribute to overall energy efficiency
- Interdependent with 14 (Energy transduction): Efficient processes rely on effective energy conversion
- Interdependent with 15 (Metabolism): Energy efficiency is crucial for sustainable metabolic processes
- Interdependent with 22 (Ion transport): Powers efficient maintenance of ion gradients
- Interdependent with 23 (Cell division): Enables energy-efficient division processes

3. Selective permeability:
- Interdependent with 16 (Nutrition): Controls intake of nutrients
- Interdependent with 11 (Compartmentalization): Both contribute to maintaining distinct environments
- Interdependent with 4 (Environmental sensing): Permeability can be adjusted based on environmental cues
- Interdependent with 22 (Ion transport): Controls ion flow across membranes
- Interdependent with 25 (Cell wall/membrane synthesis): Requires proper membrane construction

4. Environmental sensing:
- Interdependent with 10 (Adaptability): Sensing enables adaptive responses
- Interdependent with 19 (Information processing): Sensing provides information to be processed
- Interdependent with 3 (Selective permeability): Sensing informs permeability adjustments
- Interdependent with 22 (Ion transport): Monitors ion gradients and cellular conditions
- Interdependent with 24 (Protein quality control): Detects cellular stress conditions

5. Efficient energy storage:
- Interdependent with 2 (Energy-efficient processes): Both contribute to overall energy efficiency
- Interdependent with 15 (Metabolism): Stored energy fuels metabolic processes
- Interdependent with 16 (Nutrition): Energy storage compensates for fluctuations in nutrient availability
- Interdependent with 22 (Ion transport): Supports maintenance of ion gradients
- Interdependent with 23 (Cell division): Provides energy for division processes

6. Parallel processing:
- Interdependent with 15 (Metabolism): Enables complex metabolic pathways
- Interdependent with 17 (Organization): Requires organized complexity to function effectively
- Interdependent with 11 (Compartmentalization): Different processes can occur in different compartments
- Interdependent with 24 (Protein quality control): Multiple quality control processes occur simultaneously
- Interdependent with 26 (Translation quality control): Multiple quality checks during protein synthesis

7. Self-replication:
- Interdependent with 9 (Information storage and transfer): Replication requires accurate information transfer
- Interdependent with 18 (Growth and development): Replication is a key aspect of growth
- Interdependent with 21 (Balancing permanence and change): Replication must balance fidelity with variation
- Interdependent with 23 (Cell division): Physical process of cellular replication
- Interdependent with 25 (Cell wall/membrane synthesis): Required for daughter cell formation

8. Catalysis:
- Interdependent with 15 (Metabolism): Catalysts are crucial for metabolic reactions
- Interdependent with 2 (Energy-efficient processes): Catalysts make processes more energy-efficient
- Interdependent with 12 (Molecular recognition): Catalysts work through specific molecular interactions
- Interdependent with 24 (Protein quality control): Protein-based catalysts require quality control
- Interdependent with 26 (Translation quality control): Ensures proper synthesis of catalytic proteins

9. Information storage and transfer:
- Interdependent with 7 (Self-replication): Information transfer is crucial for replication
- Interdependent with 13 (Error correction): Ensures accuracy of stored and transferred information
- Interdependent with 20 (Hardware/software integration): Information storage must integrate with functional molecules
- Interdependent with 23 (Cell division): Accurate distribution of genetic information
- Interdependent with 26 (Translation quality control): Ensures accurate protein synthesis from stored information

10. Adaptability:
- Interdependent with 4 (Environmental sensing): Adaptation requires sensing environmental changes
- Interdependent with 21 (Balancing permanence and change): Adaptability requires balance between stability and change
- Interdependent with 18 (Growth and development): Adaptability drives evolutionary development
- Interdependent with 22 (Ion transport): Adaptation to osmotic changes
- Interdependent with 24 (Protein quality control): Adaptation to stress conditions

11. Compartmentalization:
- Interdependent with 3 (Selective permeability): Compartments require selective barriers
- Interdependent with 6 (Parallel processing): Enables different processes to occur simultaneously
- Interdependent with 17 (Organization): Compartmentalization is key to cellular organization
- Interdependent with 25 (Cell wall/membrane synthesis): Creates and maintains compartments
- Interdependent with 22 (Ion transport): Maintains distinct ionic environments

12. Molecular recognition:
- Interdependent with 8 (Catalysis): Many catalysts work through specific molecular recognition
- Interdependent with 19 (Information processing): Recognition is a form of information processing
- Interdependent with 20 (Hardware/software integration): Enables communication between molecules
- Interdependent with 24 (Protein quality control): Recognition of misfolded proteins
- Interdependent with 26 (Translation quality control): Recognition of correct amino acids

13. Error correction:
- Interdependent with 9 (Information storage and transfer): Ensures accuracy of genetic information
- Interdependent with 7 (Self-replication): Maintains fidelity during replication
- Interdependent with 21 (Balancing permanence and change): Helps maintain genetic stability
- Interdependent with 24 (Protein quality control): Correction of protein folding errors
- Interdependent with 26 (Translation quality control): Correction of translation errors

14. Energy transduction:
- Interdependent with 2 (Energy-efficient processes): Efficient energy conversion
- Interdependent with 15 (Metabolism): Energy transduction is key to metabolism
- Interdependent with 5 (Efficient energy storage): Converted energy needs efficient storage
- Interdependent with 22 (Ion transport): Powers ion gradient maintenance
- Interdependent with 23 (Cell division): Provides energy for division processes

15. Metabolism:
- Interdependent with 1 (Closed-loop recycling): Metabolic processes involve recycling
- Interdependent with 8 (Catalysis): Metabolic reactions rely on catalysts
- Interdependent with 16 (Nutrition): Metabolism processes nutrients
- Interdependent with 24 (Protein quality control): Metabolic enzymes require quality control
- Interdependent with 22 (Ion transport): Metabolic energy powers ion transport

16. Nutrition:
- Interdependent with 3 (Selective permeability): Controls nutrient intake
- Interdependent with 15 (Metabolism): Provides raw materials for metabolism
- Interdependent with 1 (Closed-loop recycling): Efficient nutrition involves recycling
- Interdependent with 22 (Ion transport): Nutrient transport requires ion gradients
- Interdependent with 25 (Cell wall/membrane synthesis): Provides building blocks

17. Organization:
- Interdependent with 11 (Compartmentalization): Organization involves compartmentalization
- Interdependent with 6 (Parallel processing): Organized systems enable parallel processing
- Interdependent with 20 (Hardware/software integration): Organization requires integration
- Interdependent with 23 (Cell division): Organized distribution of components
- Interdependent with 24 (Protein quality control): Maintains protein organization

18. Growth and development:
- Interdependent with 7 (Self-replication): Growth involves cellular replication
- Interdependent with 10 (Adaptability): Development involves adaptation
- Interdependent with 21 (Balancing permanence and change): Development requires both
- Interdependent with 23 (Cell division): Physical process of growth
- Interdependent with 25 (Cell wall/membrane synthesis): Required for expansion

19. Information processing:
- Interdependent with 4 (Environmental sensing): Processing of environmental information
- Interdependent with 12 (Molecular recognition): Processing at molecular level
- Interdependent with 9 (Information storage and transfer): Processing stored information
- Interdependent with 22 (Ion transport): Processing of ionic signals
- Interdependent with 26 (Translation quality control): Processing of translation signals

20. Hardware/software integration:
- Interdependent with 9 (Information storage and transfer): Integration of information molecules
- Interdependent with 12 (Molecular recognition): Communication between molecules
- Interdependent with 17 (Organization): Integration requires organization
- Interdependent with 24 (Protein quality control): Hardware maintenance
- Interdependent with 26 (Translation quality control): Software-to-hardware conversion

21. Balancing permanence and change:
- Interdependent with 13 (Error correction): Maintains stability while allowing variation
- Interdependent with 10 (Adaptability): Allows adaptation while maintaining core functions
- Interdependent with 7 (Self-replication): Balance in replication fidelity
- Interdependent with 24 (Protein quality control): Protein stability vs turnover
- Interdependent with 26 (Translation quality control): Translation accuracy vs speed

22. Ion transport and homeostasis:
- Interdependent with 3 (Selective permeability): Control of ion flow
- Interdependent with 14 (Energy transduction): Powers ion gradients
- Interdependent with 15 (Metabolism): Supports metabolic processes
- Interdependent with 25 (Cell wall/membrane synthesis): Requires proper membranes
- Interdependent with 4 (Environmental sensing): Monitors ion balance

23. Cell division machinery:
- Interdependent with 7 (Self-replication): Physical process of replication
- Interdependent with 17 (Organization): Organized distribution of components
- Interdependent with 25 (Cell wall/membrane synthesis): New cell boundaries
- Interdependent with 14 (Energy transduction): Energy for division
- Interdependent with 9 (Information storage and transfer): DNA segregation

24. Protein quality control:
- Interdependent with 1 (Closed-loop recycling): Recycling damaged proteins
- Interdependent with 12 (Molecular recognition): Recognition of defects
- Interdependent with 13 (Error correction): Correction of protein errors
- Interdependent with 26 (Translation quality control): Coordination with synthesis
- Interdependent with 15 (Metabolism): Maintenance of metabolic enzymes

25. Cell wall/membrane synthesis:
- Interdependent with 11 (Compartmentalization): Creates compartments
- Interdependent with 3 (Selective permeability): Builds permeable barriers
- Interdependent with 16 (Nutrition): Requires building blocks
- Interdependent with 23 (Cell division): New cell boundaries
- Interdependent with 22 (Ion transport): Supports ion gradient maintenance

26. Translation quality control:
- Interdependent with 13 (Error correction): Correction of synthesis errors
- Interdependent with 20 (Hardware/software integration): Accurate protein synthesis
- Interdependent with 24 (Protein quality control): Coordination of quality systems
- Interdependent with 12 (Molecular recognition): Recognition of correct components
- Interdependent with 9 (Information storage and transfer): Accurate information use

3.5 Challenges to Independent Emergence

Several factors make the independent emergence of these 26 processes highly unlikely:

1. Interconnected nature:
- All 26 processes are highly interdependent
- Each process requires multiple others to function
- Example: Energy-efficient processes (2) rely on selective permeability (3), which requires compartmentalization (11), which needs cell wall/membrane synthesis (25)
- Ion transport (22) requires both membrane synthesis (25) and energy transduction (14)
- This interconnectedness suggests these processes must emerge as a system rather than individually

2. Lack of individual function:
- Many processes serve no purpose in isolation
- Information storage (9) is meaningless without self-replication (7) or information processing (19)
- Translation quality control (26) has no function without protein synthesis
- Protein quality control (24) requires both proteins to check and mechanisms to correct errors
- Cell division machinery (23) is useless without all the components needed for a viable daughter cell

3. Prebiotic stability issues:
- Organic molecules tend to break down rather than build up in prebiotic conditions (the "asphalt problem")
- Complex machinery like ion transport systems (22) would degrade without maintenance
- Cell membranes (25) would be unstable without continuous synthesis and repair
- Protein quality control systems (24) would themselves degrade without error correction
- Translation machinery (26) requires precise molecular interactions that are unlikely to persist

4. Synergistic complexity:
- System functionality emerges from multiple interacting processes
- Adaptability (10) requires integration of:
 - Environmental sensing (4)
 - Information processing (19)
 - Balance of permanence and change (21)
 - Ion transport (22) for response
 - Protein quality control (24) for stress response
- Such complexity is difficult to explain through gradual emergence

5. Chicken-and-egg problems:
- Many processes present circular dependencies
- Metabolism (15) needs nutrition (16), but nutrition requires metabolism
- Cell walls (25) need proteins, but protein synthesis needs containment
- Ion transport (22) needs energy, but energy generation needs ion gradients
- Translation quality control (26) needs proteins, but protein synthesis needs quality control

6. Environmental context:
- Many processes only make sense within an existing living system
- Error correction (13) presupposes a system complex enough to make errors
- Quality control systems (24, 26) require defined "correct" states
- Ion transport (22) requires pre-existing membrane organization
- Cell division machinery (23) needs an existing cell to divide

7. Energetic considerations:
- Maintaining these processes requires constant energy input and management
- Ion gradients (22) constantly dissipate without energy input
- Quality control systems (24, 26) require energy to operate
- Cell wall/membrane synthesis (25) needs energy for assembly
- Without the overarching system to capture and direct energy (2, 5, 14), individual processes would dissipate

8. Information paradox:
- System development seems to require information processing that is itself an output
- Translation quality control (26) needs information about correct protein structures
- Protein quality control (24) requires recognition of proper folding states
- Cell division (23) needs information about proper component distribution
- Ion transport (22) requires regulation information

9. Maintenance requirements:
- Complex processes need constant maintenance to avoid degradation
- Quality control systems (24, 26) themselves need quality control
- Cell walls/membranes (25) need continuous repair and renewal
- Ion transport systems (22) require ongoing maintenance
- This creates a recursive need for maintenance of maintenance systems

10. Coordination complexity:
- Multiple processes must be precisely coordinated
- Cell division (23) must coordinate with DNA replication and membrane synthesis (25)
- Ion transport (22) must coordinate with metabolism (15) and energy systems
- Quality control systems (24, 26) must coordinate with multiple cellular processes
- This coordination itself requires additional control systems

11. System Integration Requirements:
- Each process requires precise integration with multiple others
- Integration needs its own control mechanisms
- System-wide feedback loops must be established
- Example: Cell division machinery (23) must integrate with membrane synthesis (25), DNA replication, and protein distribution
- Integration mechanisms themselves need coordination

12. Temporal Coordination:
- Processes must occur in precise temporal sequences
- Timing mechanisms needed for coordination
- Cell cycle events must be synchronized
- Example: Translation quality control (26) must operate in real-time with protein synthesis
- Temporal control systems must themselves be regulated

13. Spatial Organization:
- Processes require specific spatial arrangements
- Cellular components need precise positioning
- Compartmentalization must be maintained
- Example: Ion transport systems (22) must be correctly positioned in membranes
- Spatial organization itself requires organizational mechanisms

14. Resource Allocation:
- Limited resources must be distributed effectively
- Competition between processes must be managed
- Resource priorities must be established
- Example: Protein quality control (24) competes with protein synthesis for energy
- Resource allocation systems themselves need resources

15. Error Cascade Prevention:
- Errors in one process affect multiple others
- Error prevention systems must be robust
- Recovery mechanisms must exist
- Example: Translation errors affect all protein-dependent processes
- Error prevention systems themselves can fail

16. Environmental Response Coordination:
- Multiple processes must respond to environmental changes
- Responses must be coordinated
- Adaptation mechanisms must be integrated
- Example: Ion transport (22) must coordinate with osmotic stress responses
- Response systems must themselves be adaptable

17. Growth Management:
- All processes must scale with cell growth
- Growth must be coordinated across systems
- Resource allocation must adjust with size
- Example: Membrane synthesis (25) must match growth rate
- Growth control systems must themselves grow

18. Component Replacement:
- All components have limited lifespans
- Replacement must be continuous
- Old components must be recycled
- Example: Protein quality control (24) must manage protein turnover
- Replacement systems themselves need replacement

19. System Redundancy:
- Critical processes need backup systems
- Redundancy requires additional resources
- Backup systems must be maintained
- Example: Translation quality control (26) has multiple error-checking mechanisms
- Redundancy systems themselves need redundancy

20. Information Management:
- Complex information must be maintained and transmitted
- Information systems must be robust
- Multiple information types must be coordinated
- Example: Cell division (23) requires accurate information distribution
- Information systems themselves need information

21. Energy Distribution:
- Energy must be distributed efficiently
- Energy priorities must be established
- Energy systems must be maintained
- Example: Ion transport (22) requires continuous energy supply
- Energy distribution systems need energy

22. Component Assembly:
- Complex components must be assembled correctly
- Assembly must be coordinated
- Quality control must be maintained
- Example: Membrane synthesis (25) requires precise component assembly
- Assembly systems themselves need assembly

23. System Stability:
- Overall stability must be maintained
- Destabilizing factors must be controlled
- Stability mechanisms must exist
- Example: Ion gradients must be stable despite fluctuations
- Stability systems must themselves be stable

24. Process Synchronization:
- Multiple processes must be synchronized
- Timing mechanisms must be precise
- Synchronization must be maintained
- Example: Cell division (23) requires multiple synchronized events
- Synchronization systems need synchronization

25. Evolutionary Stability:
- Systems must be stable enough to persist
- Changes must not disrupt essential functions
- Evolution must maintain functionality
- Example: Quality control systems must remain functional while evolving
- Stability mechanisms must themselves evolve

26. System Emergence:
- All systems must emerge in a viable state
- Initial functionality must be sufficient
- Minimal systems must be complete
- Example: Translation (26) requires full functionality from the start
- Emergence mechanisms must themselves emerge simultaneously

Each of these factors compounds the improbability of independent emergence, creating a complex web of requirements that suggests the necessity of simultaneous or rapid sequential emergence of multiple, interconnected processes. The addition of quality control systems (24, 26), ion transport (22), cell division machinery (23), and membrane synthesis (25) further increases this complexity by introducing additional layers of interdependence and regulation requirements.

4. Discussion

The high degree of interdependence among the 26 essential processes strongly supports the concept of irreducible complexity in minimal cells. The removal of any single process would likely cause the entire system to fail, as the remaining processes depend on it in some way. This presents a significant challenge to explaining the origin of life through gradual, step-wise processes.

Graham Cairns-Smith (2003) provides an important insight: "We are all descended from some ancient organisms or group of organisms within which much of the machinery now found in all forms of life on Earth was already essentially fixed and, as part of that, hooked on today's so-called 'molecules of life'. This machinery is enormously sophisticated, depending for its operation on many collaborating parts. The multiple collaboration provides an explanation for why the present system is so frozen now and has been for so long. So we are left wondering how the whole DNA/RNA/protein control system, on which evolution now so utterly depends, could itself have evolved. It is hard to see primitive geochemical processes maintaining the clean supplies of nucleotides required for the replication of molecules like RNA. Nucleotides are not easy to make, as organic chemists know, and as is evidenced by the long pathways to nucleotides within biochemistry today."

This observation becomes even more significant when considering the additional processes we've identified. The presence of sophisticated quality control systems (both for proteins and translation), ion transport mechanisms, cell division machinery, and membrane synthesis systems adds multiple layers of complexity to the already challenging picture. These systems not only need to function individually but must also integrate seamlessly with all other cellular processes.

Steven A. Benner (2014) highlights what he terms "The Asphalt Paradox": "An enormous amount of empirical data have established, as a rule, that organic 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."

This paradox becomes even more pronounced when considering the quality control systems required for minimal cell function. The very existence of protein quality control (24) and translation quality control (26) systems suggests that cellular processes are inherently prone to errors and require sophisticated correction mechanisms. Yet these correction mechanisms themselves are complex molecular machines that would need to emerge alongside the systems they monitor.

The addition of ion transport and homeostasis (22) introduces another layer of complexity. Modern cells maintain precise ion gradients across membranes, requiring continuous energy input and sophisticated control mechanisms. These gradients are essential for energy generation, cellular signaling, and maintaining proper chemical environments for biochemical processes. The emergence of such systems presents several challenges:

1. The need for sophisticated membrane proteins for ion transport
2. The requirement for energy coupling mechanisms
3. The necessity of regulatory systems to maintain proper gradients
4. The interdependence with membrane synthesis and maintenance

Cell division machinery (23) presents its own set of challenges. The process of cell division requires:
- Precise coordination of multiple events
- Accurate distribution of cellular components
- Integration with membrane synthesis
- Energy management
- Quality control systems

The presence of membrane synthesis systems (25) adds another dimension to the complexity:
- Requires sophisticated enzymatic machinery
- Must coordinate with cell growth and division
- Needs quality control mechanisms
- Depends on precise lipid composition
- Must maintain proper membrane fluidity and functionality

These additional processes demonstrate that the challenge of explaining life's origin goes beyond the traditional focus on information storage and metabolism. A minimal cell requires multiple layers of quality control, precise ion regulation, sophisticated division machinery, and continuous membrane maintenance – all working in concert from the start.

Furthermore, the interdependencies between these processes create what might be called "regulatory loops within regulatory loops." For example:
- Ion transport requires energy from metabolism, which requires proper ion gradients
- Quality control systems need to be quality-controlled themselves
- Cell division requires membrane synthesis, which requires properly divided cells
- Translation quality depends on properly folded proteins, which require quality translation

This level of interconnectedness suggests that these processes could not have emerged gradually or independently. Instead, they must have appeared as an integrated system, capable of maintaining its own complexity from the start.

The prebiotic emergence of these processes in isolation seems highly improbable due to:
1. Their lack of individual function
2. The tendency of organic molecules to break down in prebiotic conditions
3. The need for sophisticated quality control from the beginning
4. The requirement for precise ion regulation
5. The complexity of membrane synthesis and maintenance
6. The necessity of coordinated cell division

The synergistic nature of cellular functionality suggests that these processes would need to emerge as an integrated system rather than as individual components. These findings underscore the need for comprehensive models in origin of life research that can account for:
- The simultaneous emergence of multiple, interconnected processes
- The establishment of quality control systems
- The development of ion regulation mechanisms
- The coordination of cell division and growth
- The maintenance of membrane integrity and functionality

Such models would need to explain not only how these processes could arise but also how they could immediately integrate into a functional whole. The challenge is particularly acute given that many of these processes, such as quality control systems and ion transport, appear to be necessary for the stability and function of the very systems that would need to create them.

These considerations suggest that the origin of life represents an even greater scientific challenge than previously recognized. The requirement for multiple, sophisticated quality control systems, precise ion regulation, coordinated cell division, and continuous membrane maintenance indicates that even the simplest possible cell is extraordinarily complex and highly integrated.

5. Conclusion

Our analysis of 26 essential life processes reveals a profound and extensive degree of irreducible complexity in minimal cells. These processes, ranging from fundamental operations like closed-loop recycling and energy transduction to sophisticated quality control systems and ion transport mechanisms, demonstrate an intricate web of interdependencies that challenges our understanding of life's origins.

The extensive interdependencies among these processes, their lack of individual functionality, and the challenges of prebiotic emergence present significant obstacles to explaining the origin of life through gradual, step-wise emergence. Our findings reveal several critical insights:

1. Quality control systems, ion transport mechanisms, cell division machinery, and membrane synthesis processes represent sophisticated regulatory and maintenance systems that themselves require regulation and maintenance, illustrating multiple layers of cellular complexity.
2. Each of the 26 processes is not only essential but also deeply integrated with multiple other processes, creating a network of dependencies that appears impossible to reduce further. The removal of any single process would trigger cascade failures throughout the system.
3. The requirement for sophisticated quality control mechanisms (both for proteins and translation) suggests that even the most primitive cells needed complex error-detection and correction systems from the start.
4. Ion transport and homeostasis mechanisms demonstrate that precise molecular control and energy management were essential features of early life, requiring complex membrane systems and regulatory networks.
5. Cell division machinery and membrane synthesis systems reveal that even the most basic form of cellular reproduction required intricate molecular coordination and precise spatial organization.

These findings highlight the need for new, comprehensive approaches to understanding the emergence of cellular life. Traditional models proposing gradual, step-wise evolution of cellular processes appear insufficient to explain how such an interconnected system could arise. Instead, our analysis suggests that early cells must have possessed a minimal complexity threshold below which life would have been impossible.

The interdependencies we have identified raise fundamental questions about the mechanisms that could have enabled the emergence of such a complex, integrated system. Future research should focus on:

- Developing models that can account for the simultaneous or rapid sequential emergence of multiple, interconnected cellular processes
- Understanding how quality control systems could have arisen alongside the processes they regulate
- Investigating potential mechanisms for the coordinated emergence of membrane systems, ion transport, and cellular division
- Exploring how protein synthesis and quality control could have co-evolved
- Examining the minimal requirements for maintaining ion gradients in early cells

While this study supports the concept of irreducible complexity in minimal cells, it does not argue for or against any particular explanation for the origin of life. Rather, it aims to clarify the challenges that origin of life theories must address and to stimulate further research in this field. The findings underscore the remarkable sophistication of even the simplest possible living systems and highlight the significant challenges in explaining their emergence.

Our analysis emphasizes that the question of life's origins remains one of science's most profound challenges. Understanding how these 26 essential processes could have emerged and integrated into functional cellular systems continues to be a frontier of scientific investigation. Future work in this field must grapple with not only the complexity of individual processes but also their intricate interdependencies and the requirements for their coordinated function.


References

1. Benner, Steven A. (2014). Paradoxes in the Origin of Life. Origins of Life and Evolution of Biospheres, 44(4), 339–343. doi:10.1007/s11084-014-9379-0

2. Meyer-Ortmanns, H. (2003). Fine-tuning in living systems: early evolution and the unity of biochemistry. *International Journal of Astrobiology*, 2(4), 231-243. Link. (This paper discusses the fine-tuning observed in biological systems, focusing on early evolutionary processes and the biochemical unity across diverse forms of life.)

The Complex and the Miraculous: A Closer Look at the Irreducible Complexity of CellDr. Indrajit Patra, Annals of R.S.C.B., ISSN:1583-6258, Vol. 25, Issue 1, 2021, Pages. 7127-7136 Link

Saugata, Basu. (2002). The Combinatorial and Topological Complexity of a Single Cell. Discrete and Computational Geometry,  doi: 10.1007/S00454-002-2799-Z

William, A., Dembski. (2003). Irreducible Complexity Revisited.   

Michael, J., Behe. (2003). Irreducible Complexity: Obstacle to Darwinian Evolution.   doi: 10.1017/CBO9780511804823.020

Andrew, Reynolds. (2010). The redoubtable cell. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences,  doi: 10.1016/J.SHPSC.2010.07.011

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