Abiogenesis or biopoiesis, is the natural process of life arising from non-living matter, such as simple organic compounds.
Synopsis
The Origins of Life
Protocells; Encasing Molecules Without Membranes
The Universe moves in a direction in which entropy increases, yet life is distinguished by its great degree of organization. Therefore, a boundary is needed to separate life processes from nonliving matter... The Dresden droplet discoveries by Brangwynn and collaborators... that they are liquid droplets in subcellular structures... the droplets believed to be from Oparin's 1924 protocell theory and “may still be alive and well, safe within our cells" ...a viable path from nonlife to life starts to come into focus.
Protocells; Fostering Complex Organic Compounds.
The biophysicist Jeremy England made waves in 2013 with a new theory that cast the origin of life as an inevitable outcome of thermodynamics. England said this restructuring effect of atoms due to entropy, which he calls dissipation-driven adaptation, fosters the growth of complex structures, including living things. exercises in non-equilibrium statistical mechanics... as long as you can harvest energy from your environment, order will spontaneously arise and self-tune.
Cell Membranes
Competition for membrane molecules would favour stabilized membranes, suggesting a selective advantage for the evolution of crosslinked fatty acids and even the phospholipids of today. The main advantages of encapsulation include the increased solubility of the contained cargo within the capsule and the storage of energy in the form of a electrochemical gradient.
Before DNA There Was Only RNA
Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems.
DNA-RNA-protein world, LIFE!
"Ur-organism" is the term loosely given to the hypothetical "first life" species, from which all other life presumably evolved. It is therefore the ancestor of the LUA. It is estimated to have lived some 3.9 to 4.1 billion years ago.
LUCA; To Which All Surviving Life Is Related
The last universal common ancestor (LUCA), is the most recent population of organisms from which all organisms now living on Earth have a common descent. LUCA is the most recent common ancestor of all current life on Earth.
RESEARCH
The Dresden droplet discoveries began in 2009, when Brangwynne and collaborators demystified the nature of little dots known as “P granules” in C. elegans germline cells, which undergo division into sperm and egg cells. During this division process, the researchers observed that P granules grow, shrink and move across the cells via diffusion. The discovery that they are liquid droplets, reported in Science, prompted a wave of activity as other subcellular structures were also identified as droplets. It didn’t take long for Brangwynne and Tony Hyman, head of the Dresden biology lab where the initial experiments took place, to make the connection to Oparin’s 1924 protocell theory. In a 2012 essay about Oparin’s life and seminal book, The Origin of Life, Brangwynne and Hyman wrote that the droplets (proto cells) he theorized about “may still be alive and well, safe within our cells, like flies in life’s evolving amber.”...The primordial plotline hinges, of course, on the outcome of future experiments, which will determine how robust and relevant the predicted droplet division mechanism really is. Can chemicals be found with the right two states, A and B, to bear out the theory? If so, then a viable path from nonlife to life starts to come into focus. The luckiest part of the whole process, in Jülicher’s opinion, was not that droplets turned into cells, but that the first droplet — our globule ancestor — formed to begin with. Droplets require a lot of chemical material to spontaneously arise or “nucleate,” and it’s unclear how so many of the right complex macromolecules could have accumulated in the primordial soup to make it happen. But then again, Jülicher said, there was a lot of soup, and it was stewing for eons. “It’s a very rare event. You have to wait a long time for it to happen,” he said. “And once it happens, then the next things happen more easily, and more systematically.”
The biophysicist Jeremy England made waves in 2013 with a new theory that cast the origin of life as an inevitable outcome of thermodynamics. His equations suggested that under certain conditions, groups of atoms will naturally restructure themselves so as to burn more and more energy, facilitating the incessant dispersal of energy and the rise of “entropy” or disorder in the universe. England said this restructuring effect, which he calls dissipation-driven adaptation, fosters the growth of complex structures, including living things. The existence of life is no mystery or lucky break, he told Quanta in 2014, but rather follows from general physical principles and “should be as unsurprising as rocks rolling downhill.”... Eugene Shakhnovich, a professor of chemistry and chemical biology at Harvard who supervised England’s undergraduate research, sharply emphasized the divide between his former student’s work and questions in biology. “He started his scientific career in my lab and I really know how capable he is,” Shakhnovich said, but “Jeremy’s work represents potentially interesting exercises in non-equilibrium statistical mechanics of simple abstract systems.” Any claims that it has to do with biology or the origins of life, he added, are “pure and shameless speculations.” Even if England is on the right track about the physics, biologists want more particulars — such as a theory of what the primitive “protocells” were that evolved into the first living cells, and how the genetic code arose. England completely agrees that his findings are mute on such topics. “In the short term, I’m not saying this tells me a lot about what’s going in a biological system, nor even claiming that this is necessarily telling us where life as we know it came from,” he said. Both questions are “a fraught mess” based on “fragmentary evidence,” that, he said, “I am inclined to steer clear of for now.” He is rather suggesting that in the tool kit of the first life- or proto-life-forms, “maybe there’s more that you can get for free, and then you can optimize it using the Darwinian mechanism.” Sarpeshkar seemed to see dissipation-driven adaptation as the opening act of life’s origin story. “What Jeremy is showing is that as long as you can harvest energy from your environment, order will spontaneously arise and self-tune,” he said. Living things have gone on to do a lot more than England and Horowitz’s chemical reaction network does, he noted. “But this is about how did life first arise, perhaps — how do you get order from nothing.”
"Primordial soup" hypothesis
...Certain organic compounds that are necessary building blocks for the evolution of life.. Oparin argued that a "primeval soup" of organic molecules could be created in an oxygenless atmosphere through the action of sunlight. These would combine in ever more complex ways until they formed coacervate droplets. These droplets would "grow" by fusion with other droplets, and "reproduce" through fission into daughter droplets, and so have a primitive metabolism in which factors that promote "cell integrity" survive, and those that do not become extinct. Many modern theories of the origin of life still take Oparin's ideas as a starting point...
"'Coacervation"' is a unique type of electrostatically-driven liquid-liquid phase separation, resulting from association of oppositely charged macro-ions. The term "coacervate" is sometimes used to refer to spherical aggregates of colloidal droplets held together by hydrophobic forces...
This theory proposes that metabolism predated information replication, although the discussion as to whether metabolism or molecules capable of Template replication came first in the origins of life remains open...
One of the most important pieces of experimental support for the "soup" theory came in 1952. Stanley L. Miller and Harold C. Urey performed an experiment that demonstrated how organic molecules could have spontaneously formed from inorganic precursors under conditions like those posited by the Oparin-Haldane hypothesis. The now-famous Miller–Urey experiment used a highly reducing mixture of gases – methane, ammonia, and hydrogen, as well as water vapour – to form basic organic monomers such as amino acids. The mixture of gases was cycled through an apparatus that delivered electrical sparks to the mixture. After one week, it was found that about 10% to 15% of the carbon in the system was then in the form of a racemic mixture of organic compounds, including amino acids, which are the building blocks of proteins. This provided direct experimental support for the second point of the "soup" theory...
the first molecules constituting the earliest cells "were synthesized under natural conditions by a slow process of molecular evolution, and these molecules then organized into the first molecular system with properties with biological order".
Chemical synthesis
While features of self organization and self replication are often considered the hallmark of living systems, there are many instances of abiotic molecules exhibiting such characteristics under proper conditions. Stan Palasek suggested based on a theoretical model that self assembly of ribonucleic acid (RNA) molecules can occur spontaneously due to physical factors in hydrothermal vents. Virus self assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self assembling organic molecules.
Protocells
A protocell is a self organized, self ordered, spherical collection of lipids proposed as a stepping stone to the origin of life. A central question in evolution is how simple protocells first arose and differed in reproductive contribution to the following generation driving the evolution of life. Although a functional protocell has not yet been achieved in a laboratory setting, there are scientists who think the goal is well within reach.
Self assembled vesicles are essential components of primitive cells. The second law of thermodynamics requires that the Universe move in a direction in which entropy increases, yet life is distinguished by its great degree of organization. Therefore, a boundary is needed to separate life processes from nonliving matter. Researchers Irene A. Chen and Jack W. Szostak amongst others, suggest that simple physicochemical properties of elementary protocells can give rise to essential cellular behaviours, including primitive forms of differential reproduction competition and energy storage. Such cooperative interactions between the membrane and its encapsulated contents could greatly simplify the transition from simple replicating molecules to true cells. Furthermore, competition for membrane molecules would favour stabilized membranes, suggesting a selective advantage for the evolution of crosslinked fatty acids and even the phospholipids of today. Such microencapsulation would allow for metabolism within the membrane, the exchange of small molecules but the prevention of passage of large substances across it. The main advantages of encapsulation include the increased solubility of the contained cargo within the capsule and the storage of energy in the form of a electrochemical gradient.
RNA world
The RNA world hypothesis describes an early Earth with self-replicating and catalytic RNA but no DNA or proteins. It is generally accepted that current life on Earth descends from an RNA world, although RNA-based life may not have been the first life to exist....
The structure of the ribosome has been called the "smoking gun," as it showed that the ribosome is a ribozyme, with a central core of RNA and no amino acid side chains within 18 angstroms of the active site where peptide bond formation is catalyzed...
The ribosome is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunit, which reads the RNA, and the large subunit, which joins amino acids to form a polypeptide chain. Each subunit is composed of one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus...
Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonstrated that RNA can be both genetic material (like DNA) and a biological catalyst (like protein enzymes), and contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems. The most common activities of natural or in vitro-evolved ribozymes are the cleavage or ligation of RNA and DNA and peptide bond formation. Within the ribosome, ribozymes function as part of the large subunit ribosomal RNA to link amino acids during protein synthesis. They also participate in a variety of RNA processing reactions, including RNA splicing, viral replication, and transfer RNA biosynthesis. Examples of ribozymes include the hammerhead ribozyme, the VS ribozyme, Leadzyme and the hairpin ribozyme.
Investigators studying the origin of life have produced ribozymes in the laboratory that are capable of catalyzing their own synthesis from activated monomers under very specific conditions, such as an RNA polymerase ribozyme...
Relatively short RNA molecules have been artificially produced in labs, which are capable of replication. Such replicase RNA, which functions as both code and catalyst provides its own template upon which copying can occur. Jack W. Szostak has shown that certain catalytic RNAs can join smaller RNA sequences together, creating the potential for self-replication...
It had been a firmly established belief in biology that catalysis was reserved for proteins. However, the idea of RNA catalysis is motivated in part by the old question regarding the origin of life: Which comes first, enzymes that do the work of the cell or nucleic acids that carry the information required to produce the enzymes? The concept of "ribonucleic acids as catalysts" circumvents this problem. RNA, in essence, can be both the chicken and the egg...
Depending on the specific definition used, life can be considered to have emerged when RNA chains began to express the basic conditions necessary for natural selection to operate as conceived by Darwin: heritability, variation of type, and differential reproductive output...
The RNA world would have eventually been replaced by the DNA-RNA-protein world...
"Ur-organism" is the term loosely given to the hypothetical "first life" species, from which all other life presumably evolved. The term was used first by Charles Darwin, and has been picked up by various subsequent thinkers addressing the same questions of origin of species. Not to be confused with the Last universal ancestor (LUA), the term "ur-organism" refers to the first universal ancestor common to all life existing on earth today. It is therefore the ancestor of the LUA. The ur-organism is not necessarily the first instance of life arising abiogenically on Earth. As with the concept of the " Mitochondrial Eve, "the existence of the ur-organism does not imply the existence of a population bottleneck or a first organism. It is estimated to have lived some 3.9 to 4.1 billion years ago.
The last universal common ancestor (LUCA), is the most recent population of organisms from which all organisms now living on Earth have a common descent. LUCA is the most recent common ancestor of all current life on Earth...
Genetically sequencing of decendants, suggest that the LUCA inhabited an anaerobic hydrothermal vent setting in a geochemically active environment...
At the beginnings of life, ancestry was not as linear as it is today because the genetic code took time to evolve.Before high fidelity replication, organisms could not be easily mapped on a phylogenetic tree. Not to be confused with the Ur-organism, however, the LUCA lived after the genetic code and at least some rudimentary early form of molecular proofreading had already evolved. It was not the very first cell, but rather, the one whose descendants survived beyond the very early stages of microbial evolution...
Monophyly
In cladistics, a monophyletic group is a taxon (group of organisms) which forms a clade, meaning that it consists of an ancestral species and all its descendants.
Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. One possibility is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes...
Bacteria common noun bacteria, singular bacterium) constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals... Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.[99] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes... Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.
The Archaea (ar-KEE-ə or ar-KAY-ə) constitute a domain and kingdom of single-celled microorganisms. These microbes (archaea; singular archaeon) are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells... Archaea and bacteria have generally similar cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles.[51] Like bacteria, the cell membranes of archaea are usually bounded by a cell wall and they swim using one or more flagella... Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis does not occur...
Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is outdated. Archaeal cells have unique properties separating them from the other two domains of life, Bacteria and Eukaryota...
Archaea, however, were later discovered in less hostile environments, and are now believed to be more closely related to eukaryotes than bacteria, although many details are still unknown.
A eukaryote (yoo-KARR-ee-oht or yoo-KARR-ee-ət) is any organism whose cells have a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eucarya or Eukaryota. The defining feature that sets eukaryotic cells apart from prokaryotic cells (Bacteria and Archaea) is that they have membrane-bound organelles, especially the nucleus, which contains the genetic material and is enclosed by the nuclear envelope. The presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ (eu, "well" or "true") and κάρυον (karyon, "nut" or "kernel"). Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus. In addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular. Only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion.
Researching online about the Ur-organism, the designation given to the 'hypothetical first life species from which all other life presumably evolved', discovering this meme. 'You keep using that word. I do not think it means what you think it means.'
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