15 open questions posed on origin of life

_{Denyse O'Leary

June 13, 2015

Intelligent Design, News, Origin Of Life}

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By working scientists. A friend writes to tell us: The International Institute for Advanced Studies (IIAS) (Web) Kizugawa, Kyoto, Japan, has proposed 15 open questions on the origin of life:

02. Why is the origin of life still a mystery?

Premise: Why is the origin of life still a mystery? Yes, we all in science accept 1924 Oparin’s idea that life on Earth originated from the inanimate matter via a series of chemical steps of increasing molecular complexity and functionality. However, the turning point nonlife-life has never been put into one experimental set up-actually it has never be clarified this from a conceptual point of view either. There are of course several hypotheses, and this plethora of ideas means already that we do not have a convincing one. The most popular is with the RNA-world prebiotic scenario, which has the advantage of providing on paper a theoretical series of imaginary events, each however with an unimaginably small probability (be the prebiotic production of a self-replicating RNA, and its eventual transformation into a catalyst for DNA and independently for protein synthesis-why should this happen, and what about the genetic code? Aside from the problem of experimental implementation, don’t you think we lack (until now) the capability of intellectually conceiving how the turning point really happened?

The friend note that it is an honest list of open questions posed by scientists working in the field.

And asks, Does anyone know of a similar list of open questions in evolution, provided by supporters of evolution? Readers?

See also: Why origin of life is such a problem

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Comments

harry: And what natural mechanism produces automated factories capable of churning out digital information-based, self-replicating nanotechnology the functional complexity of which is light years beyond our own? You seem to have forgotten your original claim, which was much more general than "digital information-based self-replicating nanotechnology". Here is your claim: h: “Energy that is not constructively harnessed by some mechanism only increases entropy." That statement is false, and we provided several counterexamples. While overall entropy increases whether harnessed or not, local entropy can decrease whether harnessed or not.Zachriel_{June 15, 2015
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And what natural mechanism produces automated factories capable of churning out digital information-based, self-replicating nanotechnology the functional complexity of which is light years beyond our own? Yeah, I know. If your mind had been present in the pre-life Universe, you would have looked around and said to yourself, "Hey! There is no way this stuff isn't going to turn into an automated factory that manufactures nanotechnology light years beyond that of which I can even conceive!"harry_{June 15, 2015
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harry: By the way, where is your example of energy decreasing entropy without some mechanism to harness it? Z: Emeralds, snowflakes, sunlight, tornadoes, are all low entropy occurrences in nature. There’s a mechanism involved, but the mechanism is natural.Zachriel_{June 15, 2015
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No, of course not. There is no reason to do that. By the way, where is your example of energy decreasing entropy without some mechanism to harness it? Think about reality for a while: Bombs and tornados destroy things, not build things. Your car wears out; it doesn't mysteriously develop new features it didn't have when you purchased it. Things tend to fall apart, not self-assemble. Unharnessed energy is destructive, not constructive.harry_{June 15, 2015
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harry: Sure they are. So you retract your statement that “Energy that is not constructively harnessed by some mechanism only increases entropy"?Zachriel_{June 15, 2015
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Sure they are. A very limited and simplistic mechanism to harness energy is built into some elements, and all they can produce are things like emeralds and snowflakes, not automated factories.harry_{June 15, 2015
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harry: Emeralds and snowflakes are the inevitable result of the laws of physics applied to a given environment. Yes, they are examples of decreases in entropy, something you suggested couldn't happen when you said, "Energy that is not constructively harnessed by some mechanism only increases entropy."Zachriel_{June 15, 2015
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Emeralds and snowflakes are the inevitable result of the laws of physics applied to a given environment. Digital information-based, self-replicating nanotechnology the functional complexity of which is light years beyond our own, is not. For life to emerge obviously took some planning the extent of which was much greater than that which goes into the construction of automated factories. Mindless, dumb matter just doesn't have the ability to do that kind of planning. To keep insisting the environment in which life emerged came about mindlessly and accidentally is more absurd than suggesting that an automated factory that churns out laptop PCs might come about mindlessly and accidentally. Meditate on Penrose's assertion that the odds of the Universe mindlessly and accidentally configuring itself such that life was a possibility was 1 chance in 10^10^123. Let that sink in. Some cogs in your brain will probably start rattling, and maybe some smoke will start coming out of your ears, but overall it will be good for you.harry_{June 15, 2015
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harry: Energy that is not constructively harnessed by some mechanism only increases entropy. Emeralds, snowflakes, sunlight, tornadoes, are all low entropy occurrences in nature. There's a mechanism involved, but the mechanism is natural.Zachriel_{June 15, 2015
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Hello Zachriel, Energy that is not constructively harnessed by some mechanism only increases entropy. That is why tornados destroy houses instead of build them. Unharnessed energy only increases entropy. Which is the reason I find so irritating facile assertions that energy from the Sun is all that was necessary to create life's obvious and exceptional resistance to the 2LoT. That is hogwash. How were the necessary energy-harnessing mechanisms arrived at? And please don't bring up photosynthesis, which is found in living things. An environment that would manufacture digital information-based, self-replicating nanotechnology would have to have the precision and durability of an automated factory. So how did the environment that produced the first life, which is digital information-based, self-replicating nanotechnology, become ordered enough to do that, since before there was life, there were no mechanisms to constructively harness energy? Without mechanisms to constructively harness the Sun's energy, all that energy is going to produce is increasing entropy, which is the opposite of creating what amounts to an automated factory that churns out nanotechnology light years beyond our own.harry_{June 15, 2015
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Z: While overall entropy increases whether harnessed or not, local entropy can decrease whether harnessed or not.Zachriel_{June 15, 2015
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harry: Unharnessed energy only increases entropy. While overall entropy increases whether harnessed or not, local entropy can increase whether harnessed or not.Zachriel_{June 15, 2015
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I am not all that impressed with that definition, but it illustrates a point: Life contains the energy-harnessing mechanisms that enable it to "sustain itself against the tendency to disorder" that is relentlessly imposed upon non-living matter. That being the case, how did non-living matter configure itself into the unlikely, low entropy state the prebiotic environment had to assume for life to emerge without such energy-harnessing mechanisms? Without them energy from to sun would only increase entropy.harry_{June 14, 2015
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Hawking:
One can define Life to be an ordered system that can sustain itself against the tendency to disorder, and can reproduce itself.
One can define life that way, but why would one?Mung_{June 14, 2015
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Mung @ 9,
Others?
I would submit a question, but it will take a minute to set the stage for it. ;o) Unharnessed energy only increases entropy. Setting aside the inventions of humanity, the complex mechanisms that are required to constructively harness energy and thereby decrease entropy are found only in low entropy living things. All inanimate matter can do is submit to the inexorable pressure of the 2nd Law of Thermodynamics and assume a more likely state. As Stephen Hawking put it here Life in the Universe:
It is a matter of common experience that things get more disordered and chaotic with time. This observation can be elevated to the status of a law, the so-called Second Law of Thermodynamics. This says that the total amount of disorder, or entropy, in the universe, always increases with time. However, the Law refers only to the total amount of disorder. The order in one body can increase, provided that the amount of disorder in its surroundings increases by a greater amount. This is what happens in a living being. One can define Life to be an ordered system that can sustain itself against the tendency to disorder, and can reproduce itself.
In light of the above, my question is: In the absence of energy-harnessing mechanisms such as those found only in living things, how did inanimate matter mindlessly and accidentally assemble itself into the extremely unlikely, low entropy state the prebiotic conditions on Earth would have to assume in order for life to emerge? In other words, how did the extremely unlikely and precise environment required for the emergence of life, "an ordered system that can sustain itself against the tendency to disorder," arrive in the absence of energy-harnessing systems that could sustain such an unlikely environment against the tendency to disorder?harry_{June 14, 2015
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So, what ARE some open questions in evolution? 1. What are the requirements for a system capable of Darwinian evolution? 2. Why does the genetic code appear to be frozen? 3. Why are the three domains of life so different? 4. If bacteria are so primitive, why are they so advanced? Others?Mung_{June 14, 2015
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01. How can we make ordered sequences of amino acids, or mononucleotides by prebiotic means?
Powner et al., Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, Nature 2009.Zachriel_{June 13, 2015
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DNA is life's blueprint? No, master controller of the cell - 13 June 2015 by Claire Ainsworth Everything we thought we knew about the genome is turning out to be wrong as The Deeper Genome and The Developing Genome make clear. New metaphors, anyone? Excerpt: ASK me what a genome is, and I, like many science writers, might mutter about it being the genetic blueprint of a living creature. But then I'll confess that "blueprint" is a lousy metaphor since it implies that the genome is two-dimensional, prescriptive and unresponsive. Now two new books about the genome show the limitation of that metaphor for something so intricate, complex, multilayered and dynamic. Both underscore the risks of taking metaphors too literally, not just in undermining popular understanding of science, but also in trammelling scientific enquiry. They are for anyone interested in how new discoveries and controversies will transform our understanding of biology and of ourselves. John Parrington is an associate professor in molecular and cellular pharmacology at the University of Oxford. In The Deeper Genome, he provides an elegant, accessible account of the profound and unexpected complexities of the human genome, and shows how many ideas developed in the 20th century are being overturned. Take DNA. It's no simple linear code, but an intricately wound, 3D structure that coils and uncoils as its genes are read and spliced in myriad ways. Forget genes as discrete, protein-coding "beads on a string": only a tiny fraction of the genome codes for proteins, and anyway, no one knows exactly what a gene is any more. A key driver of this new view is ENCODE, the Encyclopedia of DNA Elements, which is an ambitious international project to identify the functional parts of the human genome. In 2012, it revealed not only that the protein-coding elements of DNA can overlap, but that the 98 per cent of the genome that used to be labelled inactive "junk" is nothing of the sort. Some of it regulates gene activity, some churns out an array of different kinds of RNA molecules (RNAs for short), some tiny, some large, many of whose functions are hotly debated. Parrington quotes ENCODE scientist Ewan Birney as saying at the time, "It's a jungle in there. It's full of things doing stuff." And that is one of the most apt genome metaphors I've ever read. Recent insights into what some of this "stuff" is reveal problems with another classic idea: that DNA is the master controller of the cell, with information flowing in one direction from it, via RNA, to proteins. Some of ENCODE's mystery RNAs control gene activity, others make changes that the cell remembers and passes on when it divides, and which can even be passed down generations. The RNAs may be one way the environment alters the behaviour of genes without changing their DNA sequences, a phenomenon known as epigenetics. Growing evidence of the extent of epigenetic influence on the genome has led some researchers to argue that much of medical research, and indeed mainstream evolutionary theory, places too much importance on genes in determining an organism's characteristics. They think the environment plays a much bigger role in their emergence as an organism develops. This developmental view of the genome is a key theme in The Developing Genome by David Moore. He is a professor of psychology at Pitzer College, Claremont, California, with an interest in cognition in infants, and behavioural epigenetics – the study of how epigenetics shapes individual cognition, behaviour and mental health. This includes the famous studies by researchers Michael Meaney and Moshe Szyf, which showed that baby rats that are licked and groomed by their mothers grow up to be less sensitive to stress, and that this correlates with changes to the pup's neurobiology and the epigenetic alterations associated with certain genes. Behavioural epigenetics is a controversial field, with critics arguing that many of its findings are little more than correlation and conjecture. Moore is suitably sceptical without shying away from the more contentious areas, such as research suggesting that being abused as a child can cause long-term epigenetic changes in the brain. Some researchers speculate that this could be a mechanism by which the cycle of violence transmits down generations. But just as genes are not destiny, neither is epigenetics. Like Parrington, Moore warns against oversimplification. Epigenetic determinism is just as unhelpful as the deterministic gene-as-blueprint idea. "Do not assume you are trapped by your biology," he says. That genetics is complicated isn't news, but Parrington and Moore underline the limitations and the power of trying to understand its complexity by reducing it to simpler divisions. For example, the molecular and computing technologies spawned by such attempts are now giving researchers the potential to work out how to integrate it all to form a greater whole. Time, surely, to rip up the old metaphors and create some new ones. This article appeared in print under the headline "It's so last century!" Claire Ainsworth is a science writer http://www.newscientist.com/article/mg22630251.000-dna-is-lifes-blueprint-no-master-controller-of-the-cell.html#.VXySfUbcBCBbornagain77_{June 13, 2015
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15. What is the physical mechanisms underlying the assembly of primitive cell-like structures? The Premise: The transition from non-living to living systems involves, as a key step, the formation of a self-bounded physical system that contains interacting molecules. In many proposed scenarios, the complexity of such an event is often underestimated, and it is typically taken for granted, starting from the separated components. However, compared to the large amount of work done for understanding the emergence and the evolution of functional molecules and networks (ribozymes, catalytic peptides, simple metabolic cycles, self-replicating molecules, hypercycles and autocatalytic sets, etc.), much less has been done for understanding the physical mechanisms underlying the assembly of primitive cell-like structures. In particular, little attention has been given to go beyond the general and simplistic sentence ‘… and later became encapsulated in a membrane-based compartment’.
This is a favorite topic of mine, the cell membrane. It just is not the simple lipid bilayer that many posters seem to think it is. It is a very highly complex entity in it's own right, and we have no idea how it evolved. Just think of the issues involved in getting the basic molecules required for cellular function across the membrane.Mung_{June 13, 2015
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Does anyone know of a similar list of open questions in evolution, provided by supporters of evolution?
Excellent question News. None that I can find. Perhaps The Major Transitions in Evolution Revisited. Might have to look into Philosophy of Biology to find such a list. What Are the Top Ten Problems with Darwinian Evolution? Scientific Issues and Problems with Traditional Evolution Theory The Top Ten Scientific Problems with Biological and Chemical EvolutionMung_{June 13, 2015
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The question “how can we make by prebiotic means ordered sequences of amino acids, or mononucleotides?” is in fact never asked in the modern research on the origin of life.
Mung_{June 13, 2015
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The Formalism > Physicality (F > P) Principle - * David L. Abel - 2011 ABSTRACT: The F > P Principle states that “Formalism not only describes, but preceded, prescribed, organized, and continues to govern and predict Physicality.” The F > P Principle is an axiom that defines the ontological primacy of formalism in a presumed objective reality that transcends both human epistemology, our sensation of physicality, and physicality itself. The F > P Principle works hand in hand with the Law of Physicodynamic Incompleteness, which states that physicochemical interactions are inadequate to explain the mathematical and formal nature of physical law relationships. Physicodynamics cannot generate formal processes and procedures leading to nontrivial function. Chance, necessity and mere constraints cannot steer, program or optimize algorithmic/computational success to provide desired nontrivial utility. As a major corollary, physicodynamics cannot explain or generate life. Life is invariably cybernetic. The F > P Principle denies the notion of unity of Prescriptive Information (PI) with mass/energy. The F > P Principle distinguishes instantiation of formal choices into physicality from physicality itself. The arbitrary setting of configurable switches and the selection of symbols in any Material Symbol System (MSS) is physicodynamically indeterminate—decoupled from physicochemical determinism. https://www.academia.edu/12952944/The_F_P_Principle_The_Formalism_Physicality_Principle_bornagain77_{June 13, 2015
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What is Life? I have been reading Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Quite a bit of material I am not familiar with so not always an easy go, but I think well worth reading for anyone on either side of the ID debate. The bits on Newton's theory alone were an eye opener. Good stuff on scientific models. http://en.wikipedia.org/wiki/Robert_Rosen_(theoretical_biologist) http://www.people.vcu.edu/~mikuleck/RSNCYBRSPC2.htmlMung_{June 13, 2015
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as to:
07. What is the origin of genetic code?: Investigating design principle of aa-tRNA and aa-RS? The genetic code is most essential part for the genetic systems. In the context of the origin of life, a major issue on the genetic code is to understand how the materials relevant to genetic code that can translate the sequence of four bases into a polypeptide. In bacteria and cells, each of ~20 different amino-acyl tRNA synthethase (aa-RS) bind to a particular tRNA with high affinity and also has an specific binding to one of twenty amino acids. The aa-RS produces amino-acyl tRNA (aa-tRNA) that has the triplet of anti-codon in a loop of tRNA and a corresponding amino acid at 3’ end. How was a family of aa-tRNAs created without sophisticated enzymes? Although RNA-catalyzed self-aminoacylation and tRNA aminoacylation has been demonstrated experimentally, the possible evolutional pathway of genetic coding system is little understood. Can we find or design simple aa-RS and aa-tRNA from the cocktail of molecules (e.g., amino acid, tRNA(-like) molecule, and ATP), which might be relevant to the origin of translation and genetic code? What features are required as a mechanism that ensures robust translation?
Stephen Meyer states:
Dr. Stephen Meyer: Chemistry/RNA World/crystal formation can't explain genetic information - video Excerpt 5:00 minute mark: "If there is no chemical interaction here (in the DNA molecule) you can't invoke chemistry to explain sequencing" http://www.youtube.com/watch?v=yLeWh8Df3k8
Meyer (and Gitt) also state:
"Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source -- from a mind or personal agent." (Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).) "A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107." (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig),
also of note:
“Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature.” (Fazale Rana, -The Cell's Design - 2008 - page 177)
Of realated interest to these '15 questions' about the origin of life are these 'top problems' for the origin of life
Top Five Problems with Current Origin-of-Life Theories - Casey Luskin - December 12, 2012 Overview: Problem 1: No Viable Mechanism to Generate a Primordial Soup Problem 2: Forming Polymers Requires Dehydration Synthesis Problem 3: RNA World Hypothesis Lacks Confirming Evidence Problem 4: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code Problem 5: No Workable Model for the Origin of Life http://www.evolutionnews.org/2012/12/top_five_probl067431.html RNA world: Chemists Propose a Seemingly Unlikely Environment for the Origin of Life - February 27, 2013 Excerpt: Benner and his colleagues consider three major problems with the RNA-world model: *The "asphalt problem": Organic reactions often produce unreactive byproducts. These byproducts are a mixture of pieces of the product or polymerization of the product, but are chemically insignificant and otherwise unpromising. Hence the metaphor of "asphalt." Typically, avoiding the production of such byproducts requires very specific and controlled conditions, or post-reaction purification steps. *The "water problem": Many of the bonds in RNA will undergo hydrolysis. This occurs when water reacts with the bond, causing it to break apart. In a lab, the problem is easily addressed by using a different solvent. However, the environment of the early Earth could not draw on the resource of various organic solvents. *The "impossible bond problem": The authors refer here to the difficulty in forming certain bonds in RNA. Usually this follows from thermodynamic issues that prohibit bonds from spontaneously forming. Conspicuously missing from the authors' list of critiques are the "chirality problem" and the "information problem." Later in the paper, however, they concede that their model does not solve the enigma of chirality, and they allude to a potential "fatal flaw" in their proposition, namely that the kinds of RNA molecules that catalyze the destruction of RNA are more likely to emerge than RNA molecules that catalyze the synthesis of RNA. - http://www.evolutionnews.org/2013/02/death_valley_da068661.html Suzan Mazur: Origin of life shifting to “nonmaterial events”? - December 15, 2013 Excerpt: The first paradox is the tendency of organic matter to devolve and to give tar. If you can avoid that, you can start to try to assemble things that are not tarry, but then you encounter the water problem, which is related to the fact that every interesting bond that you want to make is unstable, thermodynamically, with respect to water. If you can solve that problem, you have the problem of entropy, that any of the building blocks are going to be present in a low concentration; therefore, to assemble a large number of those building blocks, you get a gene-like RNA — 100 nucleotides long — that fights entropy. And the fourth problem is that even if you can solve the entropy problem, you have a paradox that RNA enzymes, which are maybe catalytically active, are more likely to be active in the sense that destroys RNA rather than creates RNA. https://uncommondescent.com/origin-of-life/origin-of-life-shifting-to-nonmaterial-events/ Chemistry by Chance: A Formula for Non-Life by Charles McCombs, Ph.D. Excerpt: The following eight obstacles in chemistry ensure that life by chance is untenable. 1. The Problem of Unreactivity 2. The Problem of Ionization 3. The Problem of Mass Action 4. The Problem of Reactivity 5. The Problem of Selectivity 6. The Problem of Solubility 7. The Problem of Sugar 8. The Problem of Chirality The chemical control needed for the formation of a specific sequence in a polymer chain is just not possible through random chance. The synthesis of proteins and DNA/RNA in the laboratory requires the chemist to control the reaction conditions, to thoroughly understand the reactivity and selectivity of each component, and to carefully control the order of addition of the components as the chain is building in size. http://www.icr.org/article/chemistry-by-chance-formula-for-non-life/
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