How Did Protein Amino Acids Get Left-Handed: Fill & Download for Free

The origin of life is a huge unsolved problem. It won’t be completely solved in the next decade but aspects of the problem look solvable.This answer could be hard for people who haven’t taken a course in Biochemistry.Anyone who has looked casually at the field could easily get the impression that the problem is mostly solved. Look at this diagram from two of the best scientists in the field, Koonin and Martin.[1] It describes how life could have originated from undersea alkaline hydrothermal vents. The chart is detailed, comprehensive, specific, and scientifically plausible.There’s just one flaw in it. Nearly every step is purely hypothetical, lacking in empirical support. Nobody knows whether any of these steps actually occurred or even whether they can happen as described.[2]One of the authors of that chart, Koonin, isn’t very confident about that concept. He coauthored a paper describing an entirely different, incompatible, theory.[3]But this doesn’t mean that progress is impossible. There is one bit that’s widely accepted and has a firm scientific foundation. It’s called the RNA World. At some point, there were organisms that used RNA instead of DNA as their genetic material. The evidence for that rests on the following facts:Key portions of the genetic machinery in modern cells rely on RNA.[4]RNA strands are able to catalyze some of the reactions that are necessary for life.[5]Components of RNA, like ATP, are used by many biochemical pathways in most organisms.Some modern organisms, viroids, resemble hypothetical RNA world organisms. They use RNA as their genetic material and lack protein-coding genes.[6]Unsolved RNA World problemsWhere did the RNA nucleotides and nucleosides come from? There is no known nonbiological process which produces both the pyrimidine and purine ribonucleotides in reasonable amounts.[7] Some scientists are optimistic about solving this problem.[8]What was the catalyst for RNA replication? Without that, you can’t have reproduction or evolution. It could have been an RNA ribozyme that no one has discovered yet. Or it could have been inorganic chemicals that are naturally present.[9]How did RNA organisms activate nucleosides into nucleotides? Modern living forms must activate nucleotides by adding phosphate before they can be used. Adenosine, for example, is converted to ATP by adding three phosphate groups. It takes energy to add them but they allow RNA to be created from individual units. Nobody knows how an RNA organism might have done that.How did life evolve right-handed RNA? Modern biochemical machinery requires the correct enantiomeric forms of RNA nucleotides but abiotic processes produce both left- and right-handed versions.[10] One possibility is that some natural process separated out right- and left-handed versions of nucleotides. Another possibility is that primitive enzymes or ribozymes could work with both left- and right-handed forms.[11]How did RNA organisms evolve the ability to create and use proteins? Modern organisms use a very complicated system in which transfer RNA brings amino acids to ribosomes so they can be added to a protein chain. The exact amino acid to be used is defined by a complex genetic code. Koonin describes some possible evolutionary pathways in his book, The Logic of Chance.[12]How did the RNA World transform into the modern DNA world?Evolution requires a sequence of individual steps but there aren’t any obvious small steps when switching from RNA to DNA. The DNA replication machinery is different in the two main branches of life, archaea and bacteria.[13] That suggests that the common ancestor of those two branches might have been an RNA organism.General unsolved problemsWhere did life originate? That matters because each location provides different chemistry. Some investigators think it arose in undersea alkaline vents as shown in the first chart of this answer.[14] [15][16] But other investigators have raised serious objections to that idea.[17] Life could have arisen in anoxic geothermal fields. [18][19] Alternatively, Szostak proposed that life began in small ponds.[20]What sort of container did the earliest biochemical systems live in? Living things must be enclosed somehow. This chart lists some possibilities: among ice crystals, pores in rocks, within a droplet of water within oil, or within a membrane consisting of fatty acids.[21]What happened before RNA appeared? There are lots of proposals for self-replicating entities that existed before RNA. Nick Lane proposed that micells might appear on the edges of hydrothermal vents. These might have the ability to grow and split into new micells producing a sort of non-biological self-replicating entity. [22][23] Here’s a picture of one.What did the first organisms and their ancestors eat? You can’t have life without a source of energy. Martin and Lane proposed that biochemical systems used the pH difference between the inside and outside of pore in a hydrothermal vent as shown in this diagram.[24] But that wouldn’t work if life originated somewhere else. Early biochemical systems could have used UV light or maybe simply eat the biochemicals in the primordial soup. Later on, it may have used Hydrogen to convert CO2 to methane and acetate, if Hydrogen was available.[25]How did the molecular machinery in the first cells arise? Here are the structures of the two kinds of ATPase. [26] These structures, or something like them, must have existed in the very first cells. Nobody has any idea as to how they evolved.OddsHow likely is life to arise a planet having the right conditions? Is it so certain that living things will appear on every planet that resembles Earth? Or is there a big element of chance involved? Koonin discussed the possibility that life might be very rare. He computed that the probability of the DNA to protein translation and replication machinery might occur by chance in the observable universe is less than 10^–1,018.[27] That would mean that nearly all universes have no life at all. He suspects that there are many universes, so we just happen to live in one of the lucky ones. (You may have noticed that Koonin has proposed other theories that make life more certain.)More to readThere’s a lot more to know but this answer is already too long. This article does a first-rate job of defining major unsolved issues.http://n.ethz.ch/~nbennett/download/Reading_NEW/Catalytic%20RNA/Joyce.pdfFootnotes[1] https://www.molevol.hhu.de/fileadmin/redaktion/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Biologie/Institute/Molekulare_Evolution/Dokumente/135.pdf[2] Ancient Living Organisms Escaping from, or Imprisoned in, the Vents?[3] Origin of first cells at terrestrial, anoxic geothermal fields[4] The Ancestor Within: Michael Yarus: 9780674060715: Amazon.com: Books[5] The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a[6] https://www.researchgate.net/profile/Santiago_Elena/publication/263741076_Viroids_Survivors_from_the_RNA_World/links/543bb1ec0cf2d6698be31328/Viroids-Survivors-from-the-RNA-World.pdf[7] Origins of building blocks of life: A review[8] Researchers may have solved origin-of-life conundrum[9] The eightfold path to non-enzymatic RNA replication[10] Chiral Key Found to Origin of Life | Quanta Magazine[11] A cross-chiral RNA polymerase ribozyme[12] Medicine & Health Science Books @ Amazon.com[13] DNA Replication in the Archaea[14] https://www.molevol.hhu.de/fileadmin/redaktion/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Biologie/Institute/Molekulare_Evolution/Dokumente/135.pdf[15] Extreme accumulation of nucleotides in simulated hydrothermal pore systems[16] Proton gradients at the origin of life - Lane - 2017 - BioEssays - Wiley Online Library[17] Ancient Living Organisms Escaping from, or Imprisoned in, the Vents?[18] Open Questions on the Origin of Life at Anoxic Geothermal Fields[19] Origin of first cells at terrestrial, anoxic geothermal fields[20] https://www.scientificamerican.com/article/how-did-life-begin1/?redirect=1[21] https://scholar.google.com/scholar_url?url=https://www.researchgate.net/profile/Philipp_Holliger/publication/315052808_Nucleic_acids_Function_and_potential_for_abiogenesis/links/5af15ca5458515c283754b67/Nucleic-acids-Function-and-potential-for-abiogenesis.pdf&hl=en&sa=T&oi=gsb-gga&ct=res&cd=0&d=11395180778409664887&ei=KQ8IXYygKonemQHCs4o4&scisig=AAGBfm0lj9GdueACLdoKcTbEI9aNvHaj8Q[22] https://scholar.google.com/scholar_url?url=https://link.springer.com/article/10.1186/1759-2208-3-2&hl=en&sa=T&oi=gsb-gga&ct=res&cd=0&d=18256795192388354411&ei=QxEIXfSlKMGomQHH367YCw&scisig=AAGBfm3oLtoAxiapSLl7aY9ydPWGOYVRtA[23] https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2016.0419[24] http://nick-lane.net/wp-content/uploads/2016/12/LAM-BioEssays.pdf[25] The physiology and habitat of the last universal common ancestor[26] The mechanism of rotating proton pumping ATPases[27] Israel Ramirez's answer to What is an unpopular but plausible theory on abiogenesis?

There are chemical reactions that will convert CO2, N2, and H2O to organic molecules. One is lightning. This is the Miller-Urey experiments. The original experiments used CH4, H2, N2, NH4, and some other molecules in what is called a “reducing” atmosphere.Since then, the experiments have been re-run in more “oxidizing” atmospheres like I listed above. They have even been run in today’s atmosphere. The result of those reactions are the organic molecules of amino acids, sugars, and bases (adenine, thymine, etc.)The same type of reactions can happen at underwater hydrothermal vents where the temperature is 700° F. The reactions also happen in space, in that the organic compounds are detected on comets and meteorites.So now there are amino acids. Heat a solution of amino acids and you get proteins:This can be dry heat, as in an evaporating tidal pool. Or it happens in hydrothermal vents. That high temperature drives the reaction.It turns out that the thermal proteins will spontaneously make cells:This is the dry heated (tidal pool). The protein is bottom left. A salt solution is being added (tide comes back). The circles in the upper right are the cells, and you can see the interface where the cells are forming. The cells are the size of bacteria.These cells composed of salt solution and thermal proteins are called “protocells” The proteins serve as cell membrane and as enzymes catalyzing chemical reactions. The protocells 1) metabolize, 2) grow, 3) respond to stimuli, and 4) reproduce (they divide by fission like bacteria). Those 4 activities are what defines “alive”. The protocells are alive.Here is a picture of the protocells dividing (reproducing):You can see all the stages. The protocells divide like bacteria or your cells: by fission.Now you have gone from inorganic chemicals to replicating cells that make new proteins, RNA or DNA, sugars, and lipids.Just for fun, Fox and co-workers artificially fossilized protocells and then compared them to actual fossils of the oldest cells found:The actual fossils are in left hand column, while the right hand column are the fossilized protocells.If you want to learn more, you can start with these sources:1. My Scientific Discussions of Evolution for the Pope and His Scientists (My Scientific Discussions of Evolution for the Pope and His Scientists)1a. Experimental retracement of the origins of a protocell (Experimental retracement of the origins of a protocell) website for protoneuron1b, . Visually Retracing the Emergence of the Evolvable Protocell (Visually Retracing the Emergence of the Evolvable Protocell) pictures of formation of protocells1c. Origin of Life (Origin of Life) college course teaching protocells1d. The Emergence of Life: Darwinian Evolution from the Inside by Sidney W. Fox (1988-04-03): Sidney W. Fox: Online Shopping for Electronics, Apparel, Computers, Books, DVDs & more: Books (The Emergence of Life: Darwinian Evolution from the Inside by Sidney W. Fox (1988-04-03): Amazon.com: Books)

Is there any evidence that God created humans or the other way around?There is no direct evidence God created humans—God didn’t leave any fingerprints or notes behind—but the options are limited aren’t they? And since none of us can go back in time and observe, what we are all—everyone of us—left with, is a choice. We try to make the best choice based on the best evidence we can find and the best logic we can employ, but it still comes down to making a choice between the only two real options: God or chance.Since the late 1920s, naturalistically-minded scientists have worked to explain the origin of the first cellular life as the result of an undirected process of ‘‘chemical evolution’’: chance.The problems are formidable. Bruce Alberts, President of the National Academy of Sciences, stated:“The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. . . . Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.”They appear designed. Naturalist scientists insist it is not actual design we are seeing—it just looks like design. What is the difference? Without that time machine, how is it possible to tell that the appearance of design isn’t actual design?This kind of complexity creates problems for naturalism to explain because the parts are meaningless—have no value for survival—until they are all put together: it’s the machine that has value and the machine works as a complex unit. The parts do nothing on their own. So how did they get created?The components of the molecular machines are proteins; proteins are made of long nonrepetitive sequences of amino acids—like colored beads on a string. Proteins also exhibit an irregular three-dimensional shape— a twisting, turning, tangled chain of those colored beads, amino acids. Proteins also have a specific function that depends upon the complex but very specific sequencing of these ‘colored beads’—something akin to one set of amino acids in the “hammer” protein being blue-red-green-blue, and another set in the “screwdriver” protein being red-red-blue-green. Any slight alteration in sequencing can quickly result in loss of function.A functioning protein’s three-dimensional shape gives it a ‘‘hand-in-glove’’ fit with other molecules in the cell... one protein cannot usually substitute for another any more than one tool can substitute for another: an axe cannot do the work of a soldering iron.The nucleotide bases in DNA—more different colored beads—function like letters in an alphabet or characters in a machine code.As Dawkins notes, ‘‘The machine code of the genes is uncannily computer-like.’’ Or, as software innovator Bill Gates explains, ‘‘DNA is like a computer program, but far, far more advanced than any software we’ve ever created.’’Various methods of calculating the probabilities of this [happening by chance] have been offered.The probability of achieving a functional sequence of amino acids in several known proteins at random is roughly 1 chance in 10⁶⁵ — (There are 10⁶⁵ atoms in our entire galaxy.) If one also factors in the need for proper bonding and homochirality, the probability of constructing a short functional protein at random becomes so small (1 chance in 10¹²⁵) as to approach the universal probability bound of 1 chance in 10¹⁵⁰, the point at which appeals to chance become absurd.The probability of generating a protein of 150 amino acids in length exceeds 1 chance in 10¹⁸⁰, well beyond the most conservative estimates for the small probability bound given our multi-billion-year-old universe.In other words, given the complexity of proteins, it is extremely unlikely that a random search through all the possible amino acid sequences could generate even a single relatively short functional protein in the time available since the beginning of the universe (let alone the time available on the early earth).…What justifies the elimination of chance is not just the occurrence of a highly improbable event, but the occurrence of a highly improbable event that also conforms to an independently discernible pattern.A single, freak, highly improbable event can conceivably happen. Many highly improbable events—drawing a winning lottery number or the distribution of playing cards in a hand of bridge— happen all the time.But a string of improbable events…does not happen naturally. (Christian de Duve)In 2001, biochemist Franklin Harold stated in an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations."This can be seen as a “God of the gaps” argument with scientists saying they will figure it out someday, but that is a faith I don’t have. For me, life, the cell, DNA— there are too many coincidences, and too many unspoken assumptions in naturalism, and too many loose strings and unanswerable questions, and too darn many improbable events to accept naturalism as having any real credibility as an explanation for life itself. I love and respect science, and even most scientists, but buying into the idea life happened by accident just strains credulity in my mind. Some things have to be accepted on faith either way. I have placed mine in a Being I can feel and know.With that, the other half of the question becomes moot. If God created us—we did not create Him.References: Signature in the Cell by Stephen C. Meyer; ID's Top Six — The Origin of Irreducibly Complex Molecular Machines | Evolution News; Franklin M. Harold, The Way of the Cell: Molecules, Organisms and the Order of Life, page 205 (Oxford University Press, 2001).