Abiogenesis: The Miller Urey experiment

The Miller Urey experiment 1

https://reasonandscience.catsboard.com/t2170-abiogenesis-the-miller-urey-experiment

Claim: The Miller-Urey experiment provides evidence that Abiogenesis is a plausible explanation for the origin of life. 
Answer: It is remarkable that the Miller-Urey experiment is still mentioned after almost 70 years. There is a reason, why. 

Steve Benner, professor at Harvard University, one of the world’s leading authorities on abiogenesis: 
We are now 60 years into the modern era of prebiotic chemistry. That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology” …. For the most part, these papers report “success” in the sense that those papers define the term…. And yet, the problem remains unsolved

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.

The evidence of Urey-Miller experiment
1 Amino Acid Synthesis (1953). When Stanley Miller produced a few amino acids from chemicals, amid a continuous small sparking apparatus, newspaper headlines proclaimed: “Life has been created!” But naturalists hide the truth: The experiment had disproved the possibility that random emergence of the building blocks could occur. The amino acids were not biologically active, and the experiment only proved that a synthetic production of them would result in equal amounts of left- and right-handed amino acids. Since only left-handed ones exist in animals, accidental production could never produce a living creature.
2. Till nowadays life could not be created in any laboratory. Therefore, by eliminative induction, we can conclude life must have been created by God.
3. God most probably, exists.


If you can't make a brick, you can't make a house. Naturalistic scenarios are all based on ad-hoc anecdotal pseudo-scientific claims. In the Urey - Miller experiment, none of the following amino-acids were produced, all life essential: Cysteine Histidine Lysine Asparagine Pyrrolysine Proline Glutamine Arginine Threonine Selenocysteine Tryptophan Tyrosine

Never, in any simulated OOL experiment, the amino acid Tryptophan was synthesized. Why? The biosynthesis pathway to make tryptophan is the most biochemically expensive and most complicated process of all life essential amino acid pathways, and tightly regulated. Glucose feeds the Glycolysis pathway, which utilizes nine enzymatic steps and enzymes to produce phosphoenolpyruvate (PEP) and erythrose- 4-phosphate, which enter the Shikimake pathway, which uses another seven enzymes, to make chorismate, which enters the Tryptophan biosynthesis pathway, and after another five steps and enzymes, finally produces Tryptophan. So, in total, 21 enzymes.

But not any kind of enzyme. Some are highly sophisticated, veritable multienzyme nanomachines, like a paper called the bacterial tryptophan synthase, which channels the substrates through a long interconnecting tunnel with a clear logic: the substrate is not lost from the enzyme complex and diluted in the surrounding milieu. This phenomenon of direct transfer of enzyme-bound metabolic intermediates, or tunneling, increases the efficiency of the overall pathway by preventing loss and dilution of the intermediate. Smart, hah ??!!

You can have a closer look at the entire pathway to make tryptophan here:
https://reasonandscience.catsboard.com/t1740-origin-of-the-canonical-twenty-amino-acids-required-for-life#5939

From Primordial Soup to the Prebiotic Beach
An interview from 1998 with exobiology pioneer, Dr. Stanley L. Miller, University of California San Diego 3
We've shown that either you have a reducing atmosphere or you are not going to have the organic compounds required for life. If you don't make them on Earth, you have to bring them in on comets, meteorites or dust. Certainly, some material did come from these sources. In my opinion, the amount from these sources would have been too small to effectively contribute to the origin of life.

The amount of useful compounds you are going to get from meteorites is very small. The dust and comets may provide a little more. Comets contain a lot of hydrogen cyanide, a compound central to prebiotic synthesis of amino acids as well as purines. Some HCN came into the atmosphere from comets. Whether it survived impact, and how much, are open to discussion. I'm skeptical that you are going to get more than a few percent of organic compounds from comets and dust.

There is a consensus that life would have had a hard time making it here from another solar system, because of the destructive effects of cosmic rays over long periods of time.

Submarine vents don't make organic compounds, they decompose them. The original study raised many questions. What about the even balance of L and D (left and right oriented) amino acids seen in your experiment, unlike the preponderance of L seen in nature? How have you dealt with that question? All of these pre-biotic experiments yield a racemic mixture, that is, equal amounts of D and L forms of the compounds. Indeed, if you're results are not racemic, you immediately suspect contamination. The question is how did one form get selected. In my opinion, the selection comes close to or slightly after the origin of life. There is no way in my opinion that you are going to sort out the D and L amino acids in separate pools. My opinion or working hypothesis is that the first replicated molecule had effectively no asymmetric carbon

 “Running equations through a computer does not constitute an experiment,” Miller sniffed. Miller acknowledged that scientists may never know precisely where and when life emerged.

Miller has faith that biologists will know the answer to the riddle of life’s origin when they see it. But his belief rests on the premise that the answer will be plausible, if only retrospectively. Who said the origin of life on earth was plausible?

https://reasonandscience.catsboard.com/t2170-the-miller-urey-experiment




2


An important survey of the origin-of-life (OOL) field has been published in Scientific American.  Robert Shapiro, a senior prize-winning chemist, cancer researcher, emeritus professor and author of books in the field, debunks the Miller experiment, the RNA World and other popular experiments as unrealistic dead ends.  Describing the wishful thinking of some researchers, he said, “In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry.”
Shapiro had been explaining that millions of organic molecules can form that are not RNA nucleotides.  These are not only useless to life, they get in the way and clog up the beneficial reactions.  He went on to describe how extrapolation from the Miller Experiment produced an unearned sense of euphoria among researchers: “By extrapolation of these results, some writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies.  This is not the case,” he warned in a section entitled, “The Soup Kettle Is Empty.”  He said that no experiment has produced amino acids with more than three carbons (life uses some with six), and no Miller-type experiment has ever produced nucleotides or nucleosides, essential for DNA and RNA.
Shapiro described in some detail the difficult steps that organic chemists employ to synthesize the building blocks of RNA, using conditions highly unrealistic on the primitive earth.  “The point was the demonstration that humans could produce, however inefficiently, substances found in nature,” he said.  “Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA.”  Here, for instance, is how scientists had to work to create cytosine, one of the DNA bases:

I will cite one example of prebiotic synthesis, published in 1995 by Nature and featured in the New York Times.  The RNA base cytosine was prepared in high yield by heating two purified chemicals in a sealed glass tube at 100 degrees Celsius for about a day.  One of the reagents, a sealed glass tube at 100 degrees Celsius for about a day.  One of the reagents, cyanoacetaldehyde, is a reactive substance capable of combining with a number of common chemicals that may have been present on the early Earth.  These competitors were excluded.  An extremely high concentration was needed to coax the other participant, urea, to react at a sufficient rate for the reaction to succeed.  The product, cytosine, can self-destruct by simple reaction with water.  When the urea concentration was lowered, or the reaction allowed to continue too long, any cytosine that was produced was subsequently destroyed.  This destructive reactionhad been discovered in my laboratory, as part of my continuing research on environmental damage to DNA.  Our own cells deal with it by maintaining a suite of enzymes that specialize in DNA repair.

There seems to be a stark difference between the Real World and the imaginary RNA World.  Despite this disconnect, Shapiro describes some of the hype the RNA World scenario generated when Gilbert first suggested it in 1986.  “The hypothesis that life began with RNA was presented as a likely reality, rather than a speculation, in journals, textbooks and the media,” he said.  He also described the intellectual hoops researchers have envisioned to get the scenario to work: freezing oceans, drying lagoons, dry deserts and other unlikely environments in specific sequences to keep the molecules from destroying themselves.  This amounts to attributing wish-fulfillment and goal-directed behavior to inanimate objects, as Shapiro makes clear with this colorful analogy:

The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence.  He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time.  No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA.  Themajority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

Realistically, unfavorable molecules are just as likely to form.  These would act like terminators for any hopeful molecules, he says.  Shapiro uses another analogy.  He pictures a gorilla pounding on a huge keyboard containing not only the English alphabet, but every letter of every language and all the symbol sets in a typical computer.  “The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne.”  That’s why Gerald Joyce, Mr. RNA-World himself, and Leslie Orgel, a veteran OOL researcher with Stanley Miller, concluded that the spontaneous appearance of chains of RNA on the early earth “would have been a near miracle.”
Boy, and all this bad news is only halfway through the article.  Does he have any good news?  Not yet; we must first agree with a ground rule stated by Nobel laureate Christian de Duve, who called for “a rejection ofimprobabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry.”  That rules out starting with complex molecules like DNA, RNA, and proteins .

From that principle, Shapiro advocated a return to scenarios with environmental cycles involving simple molecules.  These thermodynamic or “metabolism first” scenarios are only popular among about a third of OOL researchers at this time.  Notable subscribers include Harold Morowitz, Gunter Wachtershauser, Christian de Duve, Freeman Dyson and Shapiro himself.  Their hypotheses, too, have certain requirements that must be met: an energy source, boundaries, ways to couple the energy to the organization, and a chemical network or cycle able to grow and reproduce.  (The problems of genetics and heredity are shuffled into the future in these theories.)  How are they doing?  “Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them,” Shapiro admits.  “In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle.”  In addition, “An understanding of the initial steps leading to life would not reveal the specific events that led to the familiar DNA-RNA-protein-based organisms of today.”  Nor would plausible prebiotic cycles prove that’s what happened on the early earth.  Success in the metabolism-first experiments would only contribute to hope that prebiotic cycles are plausible in principle, not that they actually happened. Nevertheless, Shapiro himself needed to return to the miracles he earlier rejected.  “Some chance event or circumstance may have led to the connection of nucleotides to form RNA,” he speculates.  Where did the nucleotides come from?  Didn’t he say their formation was impossibly unlikely?  How did they escape rapid destruction by water?  Those concerns aside, maybe nucleotides initially served some other purpose and got co-opted, by chance, in the developing network of life.  Showing that such thoughts represent little more than a pipe dream, though, he admits: “Many further steps in evolution would be needed to ‘invent’ the elaborate mechanisms for replication and specific protein synthesis that we observe in life today.”

Time for Shapiro’s grand finale.  For an article predominantly discouraging and critical, his final paragraph is surprisingly upbeat.  Recounting that the highly-implausible big-molecule scenarios imply a lonely universe, he offers hope with the small-molecule alternative.  Quoting Stuart Kauffman, “If this is all true, life is vastly more probable than we have supposed.  Not only are we at home in the universe, but we are far more likely to share it with unknown companions.” Letters to the editor appeared in Science the next day, debating the two leading theories of OOL.  The signers included most of the big names: Stanley Miller, Jeffrey Bada, Robert Hazen and others debating Gunter Wachtershauser and Claudia Huber.  After sifting through the technical jargon, the reader is left with the strong impression that both camps have essentially falsified each other.  On the primordial soup side, the signers picked apart details in a paper by the metabolism-first side.  Concentrations of reagants and conditions specified were called “implausible” and “exceedingly improbable.”

Wachtershauser and Huber countered that the “prebiotic soup theory” requires a “protracted, mechanistically obscure self-organization in a cold, primitive ocean,” which they claim is more improbable than the volcanic environment of their own “pioneer organism” theory (metabolism-first).  It’s foolish to expect prebiotic soup products to survive in the ocean, of all places, “wherein after some thousand or million years, and under all manner of diverse influences, the magic of self-organization is believed to have somehow generated an unspecified first form of life.”  That’s some nasty jabbing between the two leading camps.

The Miller Experiment, the RNA World, and all the hype of countless papers, articles, popular press pieces and TV animations are impossible myths. You know you cannot stay with small molecules forever.  You have not begun to bridge the canyon between metabolic cycles with small molecules to implausible genetic networks with large molecules (RNA, DNA and proteins).  Any way you try to close the gap, you are going to run into the very same criticisms you raised against the RNA-World storytellers.  You cannot invoke natural selection without accurate replication .

Funny how these people presume that if they can just get molecules to pull themselves up by their bootstraps to the replicator stage, Charlie and Tinker Bell will take over from there.  Before you can say 4 Gya, biochemists emerge! Shapiro  is very valuable for exposing the vast difference between the hype over origin of life and its implausibilities – nay, impossibilities – in the chemistry of the real world.  His alternative is weak and fraught with the very same difficulties.  If a golf ball is not going to finish holes 14-18 on its own without help, it is also not going to finish holes 1-5.  If a gorilla is not going to type a recipe in English for chili con carne from thousands of keys on a keyboard, it is not going to type a recipe for hot soup either, even using only 1% of the keys.  Furthermore, neither the gorilla nor the golf ball are going to want to proceed further on the evolutionist project.  We cannot attribute an “innate desire” to a gorilla, a golf ball, or a sterile planet of chemicals to produce coded languages and molecular machines. Sooner or later, all the machinery, the replicators, the genetic codes and complex entropy-lowering processes are going to have to show up in the accounting.  Once Shapiro realizes that his alternative is just as guilty as the ones he criticizes, we may have an ardent new advocate of intelligent design in the ranks.  Join the winning side, Dr. Shapiro, before sliding with the losers and liars into the dustbin of intellectual history. 

The proponents of the primordial soup theory for the origins of life had thought initially in terms of chemical synthesis in a presumed reductive atmosphere of the primitive Earth, The essential logic of all such experiments was straightforward. An initial reductive mixture of gases such as CH4 , NH3, H2 and H20 have their chemical bonds broken by high energy radiation, leading to an assembly of atoms and unstable free radicals. These then proceed to recombine into stable molecules through a multitude of chemical pathways. Most of the material returns to the original composition, but among the cascade of reactions that follows, some lead to the formation of trace quantities of more complex organic molecules.

Is It Time To Throw Out 'Primordial Soup' Theory?
February 7, 2010
Is the "primordial soup" theory — the idea that life emerged from a prebiotic broth — past its expiration date? Biochemist Nick Lane thinks so. The University College London writer and his colleagues argue that the 81-year-old notion just doesn't hold water.
https://www.npr.org/templates/story/story.php?storyId=123447937

https://www.youtube.com/watch?v=fS8yObX8tqs&feature=emb_title


1) http://creationsafaris.com/crev200702.htm#20070215a
2. LIFE The Science of Biology TENTH EDITION, page 70
3. https://web.archive.org/web/20080518054852/http://www.accessexcellence.org/WN/NM/miller.php

More:
Miller-Urey Experiment Amino Acids & The Origins of Life on Earth

Formation of nucleobases in a Miller–Urey reducing atmosphere

http://www.pnas.org/content/early/2017/04/04/1700010114.abstract

The Miller–Urey experiments pioneered modern research on the molecular origins of life, but their actual relevance in this field was later questioned because the gas mixture used in their research is considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the production of only amino acids has been taken as evidence of the limited relevance of the results. Here, we report an experimental work, combined with state-of-the-art computational methods, in which both electric discharge and laser-driven plasma impact simulations were carried out in a reducing atmosphere containing NH3 + CO. We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results.
Note that they have transformed the phrase "laser-driven plasma impact simulations" into "we show that RNA nucleobases are synthesized in these experiments ..." look at that - Virtual simulations through a computer program and  databases.   Can they tell us the if the amino acids got homochiral and biologically active ?

Below is a table of amino acids produced and identified in the "classic" 1952 experiment, as published by Miller in 1953, the 2008 re-analysis of vials from the volcanic spark discharge experiment,^[38] and the 2010 re-analysis of vials from the H₂S-rich spark discharge experiment.  1



1. https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment

Miller-Frankenstein Ghost Rises from the Dead 1

The tenacity with which naturalists cling to their icons would put a Buddhist monk to shame.  There are SO many problems with the Miller scenario, we weary ourselves to keep repeating them (search "Stanley Miller" in the search bar).  We”ll give them a whole earth made up of amino acids, combining and recombining at fantastically rapid rates (see online book): no life is going to happen.  Amino acids are nothing.  They are common little molecules, many of which are thermodynamically probable under certain natural conditions.  Some are found in meteorites.  It’s not the building blocks that characterize life.  It’s the way they are organized.  It’s the way they perform functions.  Organic chemists have to go to great lengths to get some of the building blocks under carefully controlled conditions.  Surely Bada et al are not suggesting that amino acids formed on land, perhaps on lava flows far from the oceans Miller required.  They can always dream up a scenario that keeps the molecules hopeful, but by the time they try to get the building blocks to join up in one-handed configuration and actually do something without a genetic code to direct them, they have to tweak the scenario to the point of absurdity.  Matter is fecund only in the imaginations of naturalists who will not permit information and direction into their world view.
    Their fascination with that phrase “building blocks of life” becomes more absurd with each announcement.  We have been told that water is a building block of life, and tailpipe soot is a building block of life.  Why stop there?  Why not call protons building blocks of life?  or quarks?  or superstrings?  The laws of chemistry militate against the formation of a functional biological apparatus.  In the lab, most of the organic ingredients for life have to be carefully shielded from oxygen.  Miller’s amino acids, even around Mother Volcano, would be subject to hydrolyzing radiation, oxidation, thermal destruction and dilution.  Astrobiologists have to imagine protected enclaves that could somehow concentrate and protect the exceedingly low yields.  Since amino acids do not polymerize in water, they have to imagine alternate waves of wetting and drying that somehow avoid washing the precious gems into the vast diluting sea (11/19/2004, 04/08/2008).  Then there need to be the right clay minerals to act as templates (but this won’t work; see 02/13/2006).  What if the next lava flow covers it up?  Sorry.  What if harmful cross-reactions dominate, as they would?  Sorry.  What if one wrong-handed amino acid joins the chain, as is immensely more probable (online book)?  Sorry.  It’s a sorry tale at every turn: improbabilities piled on improbabilities far beyond the limits of credibility.
    Don’t mistake commotion for progress.  You can listen to Robert Hazen’s cheerful [url=http://www.teach12.com/ttcx/CourseDescLong2.aspx?cid=1515&pc=Science and Mathematics]Teaching Company[/url] series “Origins of Life” in which he describes in detail all the commotion in origin-of-life studies, with nothing at the end to show for it than naturalistic bluffing, hope and hype.  The characters doing OOL research look like the bad guys in Home Alone trying to burglarize life’s secrets, only to come back with bumps and bruises and burned hands.  There’s even an international organization of the burglars, ISSOL (newly renamed the International Astrobiology Society), that gathers every 3 years to pool their ignorance and share tales of woe about their latest bruises in the lab.  Its members comprise a Who’s Who (or Who Cares) of all the big names in the field.  Go ahead.  Browse the dozens of abstracts from their Summer 2008 gathering at Florence, that began with the obligatory sacrifice to Stanley Miller, and you will find everything from confident claims to frustration and dead ends, each hopeful sign falsified a few pages later.  Is this science?  What if any other group of zealots suffered this many losing confrontation with nature?
    Miller was usually more honest about the difficulties of finding how life originated than many of his disciples.  His greatest success was not in solving any of the problems, but in producing a visual propaganda tool that facilitated the dissemination of a useful lie (05/02/2003).  That’s not a legacy any self-respecting scientist should wish to have. 

1. http://creationsafaris.com/crev200810.htm#20081020a

Organic soup scenarios stipulate that sufficient quantities of organic molecules may have been produced in Miller–Urey-type reactions to allow heterotrophy as the ancestral system of biomass production. Apart from all the controversy concerning the soundness of the starting conditions for Miller–Urey experiments, it has in the recent past been argued that organic soup scenarios for the origin of life are severely at odds with the second law of thermodynamics. More recent approaches to life's emergence have consequently concentrated on autotrophic carbon fixation and assumed that one or more of the known extant autotrophic pathways can serve as at least a partial model of how it was first achieved.

https://royalsocietypublishing.org/doi/10.1098/rstb.2012.0258

Regardless of how life originated and what the ancestral state of microbial metabolism is, the overall process of life’s emergence must have been thermodynamically favourable, otherwise it would not have occurred. 

https://www.tesble.com/10.1098/rstb.2006.1881

They bring up Urey/Miller, and tout that as evidence. They leave out oxygen because they know oxidation is the enemy. So they try ammonia and methane...unfortunately, ammonia would be dissolved in the oceans, and the methane should be found stuck to ancient (deep) sedimentary clays, but we don't find evidence of this. They've tried other "primordial atmospheres", but to no avail.

Add to this Miller used an electric spark, which produces some results...but the same spark that puts amino acids together also tears them apart. Miller knew that, so he created a mechanism to save the good product, and increase yield. But rather than prove it could happen in nature, he proved that it requires information/intelligence.

Another problem is that the aminos needed are alpha (short) and homochiral (all left-handed), but Miller's experiment produced long (beta, gamma, delta) aminos in equal left and right handed forms, so any likelihood of natural occurrence just went down the proverbial toilet, as this mix would be toxic to any potential organic development/organization.

Without information and the right enzymes and mechanisms, the process simply couldn't happen fast enough, if at all, before destabilizing and decaying. With the information, enzymes, etc., it can happen very, very fast.
If they're still with you at this point in the conversation, they probably saying "abiogenesis is not part of biological evolution". And once you start talking about the necessity for real, functional bilipid layers, including carbohydrates such as d-pyranose (with a trillion possible configurations but only one that works), and show that it goes far beyond the "protocell" garbage they propose, and could never form chemically, they want to move on as quickly as possible to "biological evolution" where they feel they can defend their sadly broken hypotheses.

As Angelo pointed out, there are huge issues with single to multicellular organisms, not the least of which is the Information for a Body Plan. And there's a difference between Mutualism, Commensalism, and Parasitism. I was surprised he used this as an argument for his position. If you pull a single parasite of the right kind out of his very complex body, it could kill him, as well. How does that provide any relevance or evidence to any kind of evolution from single-celled to multi-celled? And a symbiotic relationship would not prove anything for his position, either. It can't happen.

I didn't really see him provide any evidence for his position, but simply vague arguments that given enough time and enough raw materials, it could happen.
The other argument he made repeatedly was that we see replication and other things on the "life" list happen today. Well, yes, but there's information. Without it, you have nothing...and if it could all happen chemically, you would have no need for it, right?