Abiogenesis is impossible

http://web.pdx.edu/~niles/Lehman_Lab_at_PSU/Chem_460_560_files/CH460_Sp12_slides_final.pdf

There is a pdf of the book available on the internet with full color illustrations!

Yuri I Wolf and Eugene V Koonin (2007) On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization, Biol Direct. 2007; 2: 14. Free access. Here the authors show that what I call ‘the Koonin threshold’ is based on the Eigen threshold. There is no mentioning of the 1,800 threshold, but there is a qualitative statement: “Indeed, we are unaware of translation being possible without the involvement of ribosomes, the complete sets of tRNA and aminoacyl-tRNA synthetases (aaRS), and (at least, for translation to occur at a reasonable rate and accuracy) several translation factors”. They also discuss ID, irreducible complexity.

Eugene V Koonin (2007) The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life, Biol Direct. 2007; 2: 15. (This is essentially Appendix B of the book.)

“The origin of life is one of the hardest problems in all of science, but it is also one of the most important. Origin-of-life research has evolved into a lively, interdisciplinary field, but other scientists often view it with skepticism and even derision. This attitude is understandable and, in a sense, perhaps justified, given the “dirty,” rarely mentioned secret: Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure – we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth.” (Koonin, p. 391). 
This text has been quoted by the uncommon descent intelligent design blog (Nov 13, 2011). The fact that the ID community is happy quoting Koonin without specifying a detailed ID alternative, demonstrates they are not interested in science, but only in attacking and ridiculing science. Why don’t IDists want to know how the designer did it?

All this is not to suggest that OORT [origins of replication and translation] is a problem of “irreducible complexity” and that the systems of replication and translation could not emerge by means of biological evolution. It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally. However, it is clear that OORT is not just the hardest problem in all of evolutionary biology but one that is qualitatively distinct from the rest. For all other problems, the basis of biological evolution, genome replication, is in place but, in the case of OORT, the emergence of this mechanism itself is the explanandum. Thus, it is of interest to consider radically different scenarios for OORT…
The MWO [“many worlds in one” – VJT] version of the cosmological model of eternal inflation could suggest a way out of this conundrum because, in an infinite multiverse with a finite number of distinct macroscopic histories (each repeated an infinite number of times), emergence of even highly complex systems by chance is not just possible but inevitable.

http://www.uncommondescent.com/intelligent-design/rna-the-origin-of-life-and-the-gullibility-of-the-science-media/#Note2

Abiogenesis is impossible

http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible

Evolution Impossible Dr. John F. Ashton, PhD page 41
For the first life to start from nonliving matter, thousands of specialized large complex molecules must somehow be synthesized in very large numbers from simple small inorganic molecules. These molecules then have to come together randomly over and over again until somehow the structure of the cell is formed. This remarkable and complex structure would still, however, not be alive. To become alive, hundreds of metabolic reactions would have to be initiated, with the metabolic intermediates already in place at just the right concentrations so that the reactions went the right way. Common sense tells us that these sorts of reactions just don’t happen by chance — in fact, we cannot even make them happen. To make the complex cell machine start up, we  have to change the concentration of hundreds of the metabolic intermediates back to just the right concentrations simultaneously. That is, we have to reinstate steady state nonequilibrium where the rate at which metabolites are formed is balanced perfectly with the rate they are required to be used by the next process. We know what to do, but even with our best technology we cannot achieve this — it is impossible. Once even a simple organism is dead it cannot be made alive again. This is a straightforward scientific observation. Evolution, however, requires not only the equivalent of a dead organism being made alive, but that the organism and its complex components and information systems must form in the first place by random processes. Then it must quickly be made alive before it has a chance to decompose or be damaged by other chemicals. Thus, the proponents of chemical evolution have to show that under the conditions that supposedly existed in a hypothetical primordial earth:

1. biomonomers (basic building block molecules) could form
2. biopolymers could form from these biomonomers
3. connected metabolic pathways could form
4. a live cell forms where chemical reactions are taking place in steady state ( i.e., perfectly balanced) nonequilibrium

To date, scientists have been able to replicate in the laboratory most of the reactions required for step 1. However, scientists have run into major problems trying to perform step 2. Small biopolymers only a fraction of the size required have been produced under ideal conditions using chemically reactive versions of nucleotides. These small, random molecules are a long, long way from the giant information encoded molecules required for life . The genetic information problem also has not been addressed in these experiments. Step 2 requires not only formation of biopolymers but also information to be encoded into these molecules to prepare for step 3. The evolutionary model requires this encoded information to occur as a result of nondirected random processes.

Dembski has shown mathematically that chance can be eliminated as a plausible explanation for a specified system when it exceeds the available probabilistic resources.  For the known universe, this is calculated
to be one chance in ten to the power 150, i.e., 10^150. The latter number is a 1 followed by 150 zeros. (Note 1 billion is 10^9, i.e., 1 followed by 9 zeros or 1,000,000,000.)

Consider the probability of a short, specifically coded protein molecule 100 amino acids in length arising by chance from its amino acid building blocks. To make the protein chain, all the amino acids must form a specific type of chemical bond known as a peptide bond with each other. However, other non-peptide bonds are possible and occur with approximately equal probability. This means that at any given site along the growing chain, the probability of having a peptide bond is one in two or ½. Therefore, the probability of having four peptide bonds in a four-link chain is ½ x ½ x ½ x ½ = (½)4 = 1/16 or 1 chance in 16. The probability of building a 100 amino acid chain with only peptide bonds is (½)99, which calculates to be around 1 chance in 10^30.

the chance of getting 100 L-amino acids forming a chain with only peptide bonds is now roughly one chance in 10^60 attempts

The probability of getting the right amino acid in the right site is 1 chance out of 20 possibilities. Therefore, the probability of forming a particular protein 100 amino acids long by chance would be (1/20)100, which is around 1 chance in 10^130.

A typical biological protein consists of about 300 amino acid units, and some are much longer. Biochemists at Cambridge University and MIT have published more detailed calculations of the probability of a functional sequence of amino acids arising by chance, and have come up with probabilities equivalent to finding a particular single atom in the universe!

From studies of single-celled organisms, scientists have estimated that the simplest possible living organism would require a genome containing a minimum of 250 to 400 genes. Thus, the improbability of life occurring in the simplest cells with the corresponding molecular complexity vastly exceeds 1 chance in 10^150. In other words, abiogenesis is absolutely impossible. That is, a living organism cannot arise by chance from nonliving matter.

plausible prebiotic synthesis

https://www.science.gov/topicpages/p/plausible+prebiotic+synthesis.html

What can we know about how life began ? 

http://reasonandscience.heavenforum.org/t1279p50-abiogenesis-is-impossible#5352

Nobody knows for sure. When it comes to historical sciences, nobody was there in the past to see what happened. But upon abductive reasoning, and the growing evidence and knowledge of chemistry, biochemistry, molecular biology, cell biology, evolutionary biology, genetics, epigenetics, and developmental biology, amount of knowledge about how life works, how it have might began and diversified,  is growing. That permits us more than ever before to make informed inferences. My take on abiogenesis is that we can make safe inferences based on what we DO  know.  Douglas Futuyma admits as much:

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

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

chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity

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

Mainstream scientific papers confirm indirectly that cells are irreducibly complex and interdependent. At the paper :

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

That means, a minimal number of genes, proteins, and metabolic network is essential to be there to give life a first go, as to turn the car's engine on. In the same manner, as if you are sitting in a car, and try to turn it on if the pistons in the car are missing, or even if a tiny electric cable is broken and you turn the car key, nothing goes. But life did not have a helping hand to fix the problem, check what part was missing, and pluck a broken cable in. For self-replication to start, a minimal set of proteins was absolutely essential to start self-replication:

http://reasonandscience.heavenforum.org/t1849-dna-replication-of-prokaryotes?highlight=dna+replication

So if only one protein, as helicase, for example, is missing, nothing goes. But why would a prebiotic soup produce a helicase protein by a lucky accident? Helicase by its own has no function, only when inserted and finely adjusted to do its job in the DNA replication mechanism.  Intelligent agents have foresight. Such agents can determine or select functional goals before they are physically instantiated. That's a huge problem for natural mechanisms, where no intelligence is in place. 

A minimal metabolic set was also required:

http://reasonandscience.heavenforum.org/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design

a proeminent proposal, the so often mentioned RNA world, has also unbridgeable flaws, and cannot explain the origin of life adequately:

http://reasonandscience.heavenforum.org/t2024-the-rna-world-and-the-origins-of-life

The software/hardware in the cell, that is DNA, mRNA, RNA polymerase, tRNA's, the ribosome, tRNA Synthetases, protein chaperones etc, AND the software, that is the genetic code and translation mechanism,  had to emerge fully setup and TOGETHER, since one would have had no use without the other. That's a classic catch22 problem:

http://reasonandscience.heavenforum.org/t2221-the-hardware-and-software-of-the-cell-evidence-of-design?highlight=hardware

amongst many other catch22 situations that plague OOL researchers:

http://reasonandscience.heavenforum.org/t2059-catch22-chicken-and-egg-problems-in-biology-and-biochemistry

Furthermore, you need homeostasis and a functional signaling network right from the start:

http://reasonandscience.heavenforum.org/t2448-howintracellular-calcium-signaling-gradient-and-its-role-as-a-universal-intracellular-regulator-points-to-design?highlight=calcium

the ability of uptake of nutrients and its availability was also essential. That illustrates the tremendous difficulties that abiogenesis research faces. As for example: where did glucose come from?

http://reasonandscience.heavenforum.org/t2419-where-did-glucose-come-from-in-a-prebiotic-world?highlight=glucose

Then you need a set of proteins that use in their action centers metal clusters. To make them is an enormous feat and requires whole production lines and irreducible multistep biosynthesis processes: 

http://reasonandscience.heavenforum.org/t2445-amazing-molecular-assembly-lines-and-non-ribosomal-amino-acid-chain-formation-pathways-come-to-light

Another huge task is to create various cell codes, amongst them prominently the genetic code. The task is to create the code system itself, the director that plays the genetic piano, that is the gene expression network which determines which genes to turn on and off and express, find them in the genome, and express them at the right time, then encoding, transmission, and decoding of the information, and a translation system, where the genetic information is used to get useful proteins, the workhorses in the cell. The genetic code is more robust than one in a million:

 http://reasonandscience.heavenforum.org/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin

Furthermore, you need error check and repair systems all along the production line: DNA replication errors are reduced 10.000.000.000 times !! 

5ʹ => 3ʹ polymerization 1 in 100.000
3ʹ => 5ʹ exonucleolytic proofreading 1 in 100
Strand-directed mismatch repair 1 in 1000
Combined 1 in 10.000.000.000

Maintaining the genetic stability that an organism needs for its survival requires not only an extremely accurate mechanism for replicating DNA but also mechanisms for repairing the many accidental lesions that occur continually in DNA.

http://reasonandscience.heavenforum.org/t2043-dna-and-rna-error-checking-and-repair-amazing-evidence-of-design?highlight=error

the cell membrane could not have emerged as a simple vesicle, as Szostak et al try to popularize. Cell membranes are ENORMOUSLY COMPLEX, and membrane proteins for various functions are essential right from the start. Membranes and membrane proteins are interdependent and had to emerge together. I have various topics on the issue:

http://reasonandscience.heavenforum.org/f62-cell-membrane-and-membrane-proteins

Abiogenesis is a huge topic. There are essentially two possibilities. Either life was created, or it was not. If it was not created, all that is left, are random, unguided, lucky events that brought to the most complex self-replicating factory in the universe, full of molecular machines and production lines. 

Would you say that it is plausible that a tornado over a junkyard could produce a self-replicating machine, like John von Neumann's Universal Constructor?
Would you say that it is plausible that mindless random chance can write a book like a random letter generator using a computer pseudo-random number generator? if you see a message on a sand dune, like " John loves Sandy ". Would you intuitively and immediately recognize that someone past there a short time ago, and wrote the message on the sand dune? Or would you consider that rain and wind wrote the message randomly on the dune? The cell is far more complex than the most complex machine made by man, and the simplest cell stores as much information as contained in a CD. 

There are numerous other topics on the issue, which cannot be mentioned here. But this small resume gives a picture..... 

Sorry, I have not enough faith to be an atheist and believe, all this arose from a lucky accident. 

Abiogenesis is impossible

http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible

It’s Easy to Be an Atheist if You Ignore Science

Although the general public is disconcertingly unaware of it, it is a fact that scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a conscious creative force.

Here are just a few well-chosen statements on the Origin of Life:

(2016) “[There is] collective cluelessness…those who say this is well worked out, they know nothing, nothing about chemical synthesis…Those who think that scientists understand the details of life’s origin are wholly uninformed. Nobody understands…when will the scientific community confess to the world that they are clueless on life’s origin, that the emperor has no clothes?” James Tour — Professor of Chemistry, Rice University (Synthetic chemist and among the top ten most cited chemists in the world)
(2011) “The Origin of Life field is a failure.” Eugene Koonin, microbiologist at the National Center for Biotechnology Information
(2011) “With respect to the Origin of Life, I find the more we learn about cells, the more complex they seem; they are just incredibly complex things, and to go from what we can see today and try to reason where it came from, I think is really impossible.” Lee Hartwell, Nobel Prize in Medicine, 2001
(2007) “How? [did life begin] I have no idea.” George Whitesides, Professor of Chemistry, Harvard University, Winner of the Priestley Medal in Chemistry (second only to the Nobel Prize)
(2001) “The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication.” Franklin Harold, Professor Emeritus, Department of Biochemistry and Molecular Biology, Colorado State University
(1983) “In short, there is not a shred of objective evidence to support the hypothesis that life began in an organic soup here on earth.” Sir Fred Hoyle, distinguished British astronomer, physicist, mathematician (without question one of the greatest scientific minds of the 20th century)
(1981) “Since Science does not have the faintest idea how life on earth originated…it would only be honest to confess this to other scientists, to grantors, and to the public at large.” Hubert Yockey, physicist and renowned information theorist
Out of consideration for the reader, I won’t go back further than 35 years to illustrate the seamless ignorance of science and scientists regarding a naturalistic origin of life. Suffice it to say that not only has science not progressed in this area since Darwin published his famous treatise in 1859, but — on the contrary — it has slid backwards by many orders of magnitude.

SEPTEMBER 16, 2016 2:04 AM1
Were God Merely to ‘Exist,’ Our Prayers Would Be Meaningless
“God is a circle whose center is everywhere and circumference nowhere,” said Voltaire. Indeed, trying to describe God is like trying to...

What I mean by backwards becomes clear if we plot the Origin of Life dilemma on a standard x-y graph; with the horizontal X axis representing the understanding of a naturalistic origin of life from 1859 until the present. It is a straight line starting at zero (our understanding in 1859) and ending at zero (our understanding in 2016). Let the Y axis represent the level of understanding since 1859 of the magnitude of the problem that needs to be solved. In 1859 it was thought to be a relatively trivial issue (i.e. close to zero); however due to the astounding breakthroughs in genetics, biochemistry, and microbiology since then, the line of the Y axis is now off the graph.

As Biochemist Klaus Dose wrote: “Experimentation on the origin of life…has led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution.” Researchers Carl Woese and Gunter Wachtershauser concur: “While we do not have a solution, we now have an inkling of the magnitude of the problem.”

Why are researchers having such difficulties discovering a naturalistic Origin of Life? Let’s let the aforementioned  and atheist microbiologist Eugene Koonin answer this question: “Certainly this is not due to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the Origin of Life…these make the final outcome seem almost like a miracle.”

Translation for the lay-person: Discovering how unguided naturalistic forces could assemble a living cell — a molecular machine that is more sophisticated and functionally complex than anything human technology has ever produced — is a problem of nightmarish proportions.

Imagine a LEGO set designed to build a model of the Brooklyn Bridge, with hundreds of blocks specifically designed to construct it; imagine you are then assigned the task of finding a pathway to a successful assembly of the model using only unguided, naturalistic forces (i.e. heat, lightning, sunlight, wind, radiation, etc.) Would you agree with Koonin and describe that as a problem of “extraordinary intrinsic difficulty”? Actually, Koonin’s description is quite appropriate for the LEGO problem, but is a gross understatement when we are talking about something as frighteningly complex as a living cell and its DNA-based genetic code and digital information processing system:

The living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life giving molecule but a genetic data bank that transmits its information using a mathematical code. Most of the workings of the cell are best described as…information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level. (Dr. Paul Davies, Origin of Life expert, Physicist, Arizona State University)

When one dispassionately contemplates the enormous difficulties involved in a naturalistic origin of life, it is not surprising at all that one often suggested solution is Intelligent Design or Divine Creation. In fact, any number of world class scientists themselves have brought up the issue:

“Abiogenesis [life from non-life] strikes many as virtually miraculous…you might get the impression from what I have written not only that the origin of life is virtually impossible, but that life itself is impossible…So what is the answer? Is life a miracle after all?” (Dr. Paul Davies)
“[We have no naturalistic explanation for] the origin of life, which is unknown so far…As long as the origin of life can’t be explained in natural terms, the hypothesis of an instant Divine creation of life cannot objectively be ruled out.” (Dr. Christian DeDuve, Nobel Prize-Medicine, 1974)
“There are only two possibilities as to how life arose. One is spontaneous generation arising to evolution; the other is a supernatural creative act of God. There is no third possibility.” (George Wald, Nobel Prize-Medicine, 1967)
“Although a biologist, I must confess I do not understand how life came about…I consider that life only starts at the level of a functional cell. The most primitive cells may require at least several hundred different specific biological macro-molecules. How such already quite complex structures may have come together remains a mystery to me. The possibility of the existence of a Creator, of God, represents to me a satisfactory solution to this problem.” (Dr. Werner Arber, Nobel Prize-Medicine, 1978)
“From my earliest training as a scientist I was very strongly brainwashed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it; it is just not possible that life could have originated from a chemical accident.” (Chandra Wickramasinghe, mathematician, astronomer, astrobiologist – longtime collaborator of Sir Fred Hoyle)
“Indeed, such a theory [Intelligent Design] is so obvious that one wonders why it is not widely accepted as being self-evident. The reasons are psychological rather than scientific.” “A common sense interpretation of the facts suggests that a super intellect has monkeyed with the laws of physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature.” (Sir Fred Hoyle)
The Merriam-Webster Dictionary defines “atheism” as “a disbelief in the existence of the deity” or “the doctrine that there is no deity.” If one approaches the Origin of Life issue “objectively,” as Nobel Prize-winning biologist Christian DeDuve put it, there is no way that any rational person can rule out the very real possibility of a Creator of life. It is certainly reasonable to suggest or raise the possibility that the reason why scientists cannot find a naturalistic answer is because there is no naturalistic answer. Perhaps the reason why many people deny Intelligent Design as the answer to Origin of Life is a psychological reason not a scientific reason, as Sir Fred Hoyle has suggested. Perhaps the reason why a “common sense interpretation of the facts” suggests that a super-intellect has monkeyed with the universe, is because a super-intellect has monkeyed with the universe.

If a rational, truth-seeking individual is asked: “How did life begin; naturalistic, unguided forces or Divine Creation?” There are only two possible answers: (a) Divine Creation or (b) I don’t know, the jury is still out; but atheism – a denial of the existence of a Creator of life — is not possible anymore….unless, of course, as I stated in the title of this article, you are prepared to ignore science and scientists. And if so, you might just as well go and play children’s games and with children’s toys, like…..LEGO blocks.

https://www.algemeiner.com/2016/08/10/its-easy-to-be-an-atheist-if-you-ignore-science/

Bernd Rosslenbroich, On the Origin of Autonomy page 43

http://reasonandscience.heavenforum.org/t1279p50-abiogenesis-is-impossible#5666

The essential aspect of the theory presented here is that at some time and somehow life established biochemical functions that were not identical with the processes of the surrounding inorganic environment.

An essential part of early evolution must have been the origin of a system that carries and replicates information. Again, not much is known about the first principles of the biological storage of information. The essential characteristic of life is not so much the interacting matter but the information about how to use it to establish new islands of life. Information is immaterial, but it needs a material medium. Information is the source for building a higher degree of order than exists within the environment, as long as life functions are maintained. 

DNA repair systems contribute to the stabilization of the genome. They are present already from the prokaryotes on and eliminate mistakes in the genetic code with high efficacy. For example, the permanently working repair systems eliminate mistakes that result just from thermic fluctuations. Thus, every day about 5,000 purine bases from the DNA of each human cell are lost as their bondings to deoxyribose are hydrolyzed (depurination). In addition, spontaneous deaminations from cytosine to uracil occur through interactions with metabolic products and environmental influences (chemicals, light). The genetic autonomy must constantly be defended against destructive influences. In particular, the principle of the double helix enables repair because two copies of the information are available. One copy can be used as the backup copy to repair the other copy. Therefore, the principle of the double helix contributes to the independence and stability of the genome. 

If there was a prebiotic environment with some interaction of organic molecules as forerunners of the first cells, as some hypotheses assume, at some time a closed membrane must have appeared to form the principle of the cell. It must have enclosed a compartment for the concentration of biochemical molecules and their reactions. The encapsulation of such protoplasm in membranes is an essential question for any considerations about early evolution. If metabolic networks were somehow included in some sort of capsule, there would have been problems of permeation. Capsules or vesicles would have the effect of transferring the metabolic networks without a transition from an existence within a totally open surrounding into a completely sealed situation, which would bring these networks to a standstill. The question is how the remarkable balance between a relative separation from the environment and an intensive, but regulated, exchange of substances and energy evolved. emerged Modern cells solve this problem through a combination of the lipid bilayer with integrated membrane proteins. Not only is the transport through the membrane is regulated actively, partly through the consumption of energy, but also the properties of the lipid bilayer itself are regulated. Some authors postulate that from the beginning some sort of a protocell must have been involved.

I have noticed that both Dawkins and Coyne say that some sort of 'self-replicating molecule' is the most plausible - or perhaps least implausible - starting point. Do you happen to know what they mean by this? Is it a) RNA? b) something simpler, which then supposedly sets up a random mutation natural selection means of progression.

With regard to the latter I see Dawkins has made reference to Rebek's work in both River out of Eden and The Ancestor's Tale. (Wikipedia Julius_Rebek)

This doesn't seem to be of any use for getting to an RNA or RNA-DNA system.

Andrew

Andrew Chapman wrote:I have noticed that both Dawkins and Coyne say that some sort of 'self-replicating molecule' is the most plausible - or perhaps least implausible - starting point. Do you happen to know what they mean by this? Is it a) RNA? b) something simpler, which then supposedly sets up a random mutation natural selection means of progression.

With regard to the latter I see Dawkins has made reference to Rebek's work in both River out of Eden and The Ancestor's Tale. (Wikipedia Julius_Rebek)

This doesn't seem to be of any use for getting to an RNA or RNA-DNA system.

Andrew

Andrew, they mean the RNA hypothesis, which is not compelling at all. 

THE RNA WORLD,  AND THE ORIGINS OF LIFE

http://reasonandscience.heavenforum.org/t2024-the-rna-world-and-the-origins-of-life

Paul Davies The Algorithmic Origins of Life
Despite the conceptual elegance of the RNA world, the hypothesis faces problems, primarily due to the immense challenge of synthesizing RNA nucleotides under plausible prebiotic conditions and the susceptibility of RNA oligomers to degradation via hydrolysis 21 Due to the organizational structure of systems capable of processing algorithmic (instructional) information, it is not at all clear that a monomolecular system – where a single polymer plays the role of catalyst and informational carrier – is even logically consistent with the organization of information flow in living systems, because there is no possibility of separating information storage from information processing (that being such a distinctive feature of modern life). As such, digital–first systems (as currently posed) represent a rather trivial form of information processing that fails to capture the logical structure of life as we know it. 

Replicator first, and metabolism first scenarios
http://reasonandscience.heavenforum.org/t1428-replicator-first-and-metabolism-first-scenarios

No evidence that RNA molecules ever had the broad range of catalytic activities
http://reasonandscience.heavenforum.org/t2243-no-evidence-that-rna-molecules-ever-had-the-broad-range-of-catalytic-activities

The hardware and software of the cell, evidence of design
http://reasonandscience.heavenforum.org/t2221-the-hardware-and-software-of-the-cell-evidence-of-design

The origin of replication and translation and the RNA World
http://reasonandscience.heavenforum.org/t2234-the-origin-of-replication-and-translation-and-the-rna-world

Tom Robbins: The time argument is worthless. As over time, organic molecules break apart as fast as they form - thus the monkey's on a typewriter argument does not work, as the INFORMATION represented on the paper when they strike a key, disappears off the paper as they type. Given enough time, CERTAIN things will probably happen, but only things that are not impossible (and of course there was a finite amount of time from the creation of the earth). Nature can't create specified, dedicated, self-replicating, self-repairing, self-editing information - THE ONLY source that we know of that can do this, is MIND..

"We propose that the transition from non-life to life is unique and definable," added Davies. "We suggest that life may be characterized by its distinctive and active use of information, thus providing a roadmap to identify rigorous criteria for the emergence of life. This is in sharp contrast to a century of thought in which the transition to life has been cast as a problem of chemistry, with the goal of identifying a plausible reaction pathway from chemical mixtures to a living entity."

In a nutshell, the authors shift attention from the "hardware" – the chemical basis of life – to the "software" – its information content. To use a computer analogy, chemistry explains the material substance of the machine, but it won't function without a program and data. Davies and Walker suggest that the crucial distinction between non-life and life is the way that living organisms manage the information flowing through the system.
"When we describe biological processes we typically use informational narratives – cells send out signals, developmental programs are run, coded instructions are read, genomic data are transmitted between generations and so forth," Walker said. "So identifying life's origin in the way information is processed and managed can open up new avenues for research."

Paul Davies, an ASU Regents' Professor and director of the Beyond Center for Fundamental Concepts in Science, and Sara Walker, a NASA post-doctoral fellow at the Beyond Center.

What Davies missed to point out, is, that this information input could have come only from an intelligent designer.

http://www.dailygalaxy.com/my_weblog/2013/10/radical-theory-says-transition-from-inorganic-to-organic-life-was-based-on-information-not-chemistry.html

Admin wrote:"We propose that the transition from non-life to life is unique and definable," added Davies. "We suggest that life may be characterized by its distinctive and active use of information, thus providing a roadmap to identify rigorous criteria for the emergence of life. This is in sharp contrast to a century of thought in which the transition to life has been cast as a problem of chemistry, with the goal of identifying a plausible reaction pathway from chemical mixtures to a living entity."

In a nutshell, the authors shift attention from the "hardware" – the chemical basis of life – to the "software" – its information content. To use a computer analogy, chemistry explains the material substance of the machine, but it won't function without a program and data. Davies and Walker suggest that the crucial distinction between non-life and life is the way that living organisms manage the information flowing through the system.
"When we describe biological processes we typically use informational narratives – cells send out signals, developmental programs are run, coded instructions are read, genomic data are transmitted between generations and so forth," Walker said. "So identifying life's origin in the way information is processed and managed can open up new avenues for research."

Paul Davies, an ASU Regents' Professor and director of the Beyond Center for Fundamental Concepts in Science, and Sara Walker, a NASA post-doctoral fellow at the Beyond Center.

What Davies missed to point out, is, that this information input could have come only from an intelligent designer.

Hadn't this been pointed out by 1966 at the Wistar Institute, and certainly by Hubert Yockey by 1981?

Andrew Chapman wrote:

Hadn't this been pointed out by 1966 at the Wistar Institute, and certainly by Hubert Yockey by 1981?

Yes.

A calculation of the probability of spontaneous biogenesis by information theory
Hubert P. Yockey
The Darwin-Oparin-Haldane “warm little pond” scenario for biogenesis is examined by using information theory to calculate the probability that an informational biomolecule of reasonable biochemical specificity, long enough to provide a genome for the “protobiont”, could have appeared in 109 years in the primitive soup. Certain old untenable ideas have served only to confuse the solution of the problem. Negentropy is not a concept because entropy cannot be negative. The role that negentropy has played in previous discussions is replaced by “complexity” as defined in information theory. A satisfactory scenario for spontaneous biogenesis requires the generation of “complexity” not “order”. Previous calculations based on simple combinatorial analysis over estimate the number of sequences by a factor of 105. The number of cytochrome c sequences is about 3·8 × 10^61. The probability of selecting one such sequence at random is about 2·1 ×10^65. The primitive milieu will contain a racemic mixture of the biological amino acids and also many analogues and non-biological amino acids. Taking into account only the effect of the racemic mixture the longest genome which could be expected with 95 % confidence in 109 years corresponds to only 49 amino acid residues. This is much too short to code a living system so evolution to higher forms could not get started. Geological evidence for the “warm little pond” is missing. It is concluded that belief in currently accepted scenarios of spontaneous biogenesis is based on faith, contrary to conventional wisdom.
http://www.sciencedirect.com/science/article/pii/0022519377900443

By chance? - Not a chance !!

http://reasonandscience.heavenforum.org/t1279p50-abiogenesis-is-impossible#5764

Single proteins do not have any function on their own unless interconnected correctly in a living cell. In order for life to begin naturally, all essential proteins required for life to start would have had to emerge randomly on a prebiotic earth, protein super-complexes like ribosomes would have had to join the subparts together to get the right protein-protein interactions, like lock and key. A miracle would have had to prevent them to be burned by UV radiation. Then start to interconnect in the correct order to create a functional metabolic network and multi-protein production lines , where the joint venture of several enzymes began to produce functional products, hand them over to carrier mechanisms, tag them in order to be transported to the right locations. Somehow, all this would have had to begin in a protected environment, so a protective envelope would have had to exist.

Somehow, that envelope had to create a homeostatic environment, diminishing the calcium concentration in the cell 10000 times below the external environment, to permit signaling. At the same time, a signaling code would have had to be established, and immediately begin to function, with a common agreement between sender and receiver................energy supply would have been a major problem, since almost all life forms depend on the supply of glucose, which is a product of complex metabolic pathways, and not readily available on a prebiotic earth. Most proteins require active metal clusters in their reaction centers.

These clusters are in most cases ultracomplex, each cluster had to have the right atoms interconnected in the right way, and get the correct 3-dimensional form. They require the complex uptake of the basic materials, like iron and sulfur, molybdenum, and complex biosynthesis processes, and after the correct assembling, the insertion in the right way and form inside the proteins. All these processes require energy, in form of ATP, not readily available - since ATP is the product of complex nano-factories, like ATP synthase - which by themselves depend on a proton gradient. Sorry------- not by chance !!

From Primordial Soup to the Prebiotic Beach

An interview with exobiology pioneer, Dr. Stanley L. Miller, University of California San Diego

1n 1953, a University of Chicago graduate student named Stanley Miller working in Harold Urey's lab flipped a switch sending electric current through a chamber containing a combination of methane, ammonia, hydrogen and water. The experiment yielded organic compounds including amino acids, the building blocks of life, and catapulted a field of study known as exobiology into the headlines. Since that time a new understanding of the workings of RNA and DNA, have increased the scope of the subject. Moreover, the discovery of prebiotic conditions on other planets and the announcement of a bacterial fossil originating on Mars has brought new attention to the study of life's origins. I spoke with Dr. Miller in his lab at UCSD about the field he has helped to make famous, exobiology.

Let start with the basics. Can you give a simple definition of exobiology?
The term exobiology was coined by Nobel Prize-winning scientist Joshua Lederberg. What it means is the study of life beyond the Earth. But since there's no known life beyond the Earth people say its a subject with no subject matter. It refers to the search for life elsewhere, Mars, the satellites of Jupiter and in other solar systems. It is also used to describe studies of the origin of life on Earth, that is, the study of pre-biotic Earth and what chemical reactions might have taken place as the setting for life's origin.

Some 4.6 billion years ago the planet was a lifeless rock, a billion years later it was teeming with early forms of life. Where is the dividing line between pre-biotic and biotic Earth and how is this determined?
We start with several factors. One, the Earth is fairly reliably dated to 4.55 billion years. The earliest evidence for life was 3.5 billion years based on findings at the Apex formation in Western Australia. A new discovery reported in the journal Nature indicates evidence for life some 300 million years before that. We presume there was life earlier, but there is no evidence beyond that point.
We really don't know what the Earth was like three or four billion years ago. So there are all sorts of theories and speculations. The major uncertainty concerns what the atmosphere was like. This is major area of dispute. In early 1950's, Harold Urey suggested that the Earth had a reducing atmosphere, since all of the outer planets in our solar system- Jupiter, Saturn, Uranus and Neptune- have this kind of atmosphere. A reducing atmosphere contains methane, ammonia, hydrogen and water. The Earth is clearly special in this respect, in that it contains an oxygen atmosphere which is clearly of biological origin.
Although there is a dispute over the composition of the primitive atmosphere, 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.

So while these are potential sources of organic compounds they are not essential for the creation of life on Earth?
As long as you have those basic chemicals and a reducing atmosphere, you have everything you need. People often say maybe some of the special compounds came in from space, but they never say which ones. If you can make these chemicals in the conditions of cosmic dust or a meteorite, I presume you could also make them on the Earth. I think the idea that you need some special unnamed compound from space is hard to support.
You have to consider separately the contributions of meteors, dust and comets. 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. It ultimately doesn't make much difference where it comes from. I happen to think prebiotic synthesis happened on the Earth, but I admit I could be wrong.
There is another part of the story. In 1969 a carbonaceous meteorite fell in Murchison Australia. It turned out the meteorite had high concentrations of amino acids, about 100 ppm, and they were the same kind of amino acids you get in prebiotic experiments like mine. This discovery made it plausible that similar processes could have happened on primitive Earth, on an asteroid, or for that matter, anywhere else the proper conditions exist.



Doesn't the Panspermia theory looks at the question of ultimate origins of life in a slightly different way?
That's a different controversy. There are different versions of the theory. One idea is that there was no origin of life, that life, like the universe, has always existed and got to the Earth through space. That idea doesn't seem very reasonable since we know that the universe has not always existed, so life has to happen some time after the big bang 10 or 20 billion years ago.
It may be that life came to Earth from another planet. That may or may not be true, but still doesn't answer the question of where life started. You only transfer the problem to the other solar system. Proponents say conditions may have been more favorable on the other planet, but if so, they should tell us what those conditions were.
Along these lines, 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.

What about submarine vents as a source of prebiotic compounds?
I have a very simple response to that . Submarine vents don't make organic compounds, they decompose them. Indeed, these vents are one of the limiting factors on what organic compounds you are going to have in the primitive oceans. At the present time, the entire ocean goes through those vents in 10 million years. So all of the organic compounds get zapped every ten million years. That places a constraint on how much organic material you can get. Furthermore, it gives you a time scale for the origin of life. If all the polymers and other goodies that you make get destroyed, it means life has to start early and rapidly. If you look at the process in detail, it seems that long periods of time are detrimental, rather than helpful.

Can you review with us some of the history and basic background of your original prebiotic experiments?
In the 1820's a German chemist named Woeller announced the synthesis of urea from ammonium cyanate, creating a compound that occurs in biology. That experiment is so famous because it is considered the first example where inorganic compounds reacted to make a biological compound. They used to make a distinction between organic, meaning of biological origin, and inorganic- CO₂, CO and graphite. We now know that there is no such distinction.
However, it remained a mystery how you could make organic compounds under geological conditions and have them organized into a living organism. There were all sorts of theories and speculation. It was once thought that if you took organic material, rags, rotting meat, etc, and let it sit, that maggots, rats etc. would arise spontaneously. It's not as crazy as it seems, considering DNA hadn't been discovered. It was then reasonable to hold those views if you consider living organisms as protoplasm, a life substance. This all changed in 1860 when Pasteur showed that you don't get living organisms except from other living organisms. This disproved the idea of spontaneous generation.
But spontaneous generation means two things. One is the idea that life can emerge from a pile of rags. The other is that life was generated once, hundreds of millions of years ago. Pasteur never proved it didn't happen once, he only showed that it doesn't happen all the time.
A number of people tried prebiotic experiments. But they used CO₂F, nitrogen and water. When you use those chemicals, nothing happens. It's only when you use a reducing atmosphere that things start to happen.

Who came up with the idea of the reducing atmosphere?
Oparin, a Russian scientist, began the modern idea of the origin of life when he published a pamphlet in 1924. His idea was called the heterotrophic hypothesis: that the first organisms were heterotrophic, meaning they got their organic material from the environment, rather than having to make it, like blue-green algae. This was an important idea. Oparin also suggested that the less biosynthesis there is, the easier it is to form a living organism. Then he proposed the idea of the reducing atmosphere where you might make organic compounds.
He also proposed that the first organisms were coacervates, a special type of colloid. Nobody takes that last part very seriously anymore, but in 1936, this was reasonable since DNA was not known to be the genetic material..
In 1951, unaware of Oparin's work, Harold Urey came to the same conclusion about the reducing atmosphere. He knew enough chemistry and biology to figure that you might get the building blocks of life under these conditions.

Tell us about the famous electrical discharge experiment.
The experiments were done in Urey's lab when I was a graduate student. Urey gave a lecture in October of 1951 when I first arrived at Chicago and suggested that someone do these experiments. So I went to him and said, "I'd like to do those experiments". The first thing he tried to do was talk me out of it. Then he realized I was determined. He said the problem was that it was really a very risky experiment and probably wouldn't work, and he was responsible that I get a degree in three years or so. So we agreed to give it six months or a year. If it worked out fine, if not, on to something else. As it turned out I got some results in a matter of weeks. 

Next he exposed the gases to a continuous electrical discharge ("lightning"), causing the gases to interact. Water-soluble products of those reactions then passed through a condenser and dissolved in the mock ocean. The experiment yielded many amino acids and enabled Miller to explain how they had formed. For instance, glycine appeared after reactions in the atmosphere produced simple compounds - formaldehyde and hydrogen cyanide. Years after this experiment, a meteorite that struck near Murchison, Australia, was shown to contain a number of the same amino acids that Miller identified and in roughly the same relative amounts. Such coincidences lent credence to the idea that Miller's protocol approximated the chemistry of the prebiotic earth. More recent findings have cast some doubt on that conclusion.

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You must have been excited to get such dramatic results so quickly, and with what, at the time, must have seemed like an outlandish hypothesis?
Oh yes. Most people thought I was a least a little bit crazy. But if you look at methane/ammonia vs CO₂/nitrogen there was no doubt in my mind. It was very clear that if you want to make organic compounds it would be easier with methane. It's easy to say that but it is quite a bit more difficult to get organized and do the experiment.
The surprise of the experiment was the very large yield of amino acids. We would have been happy if we got traces of amino acids, but we got around 4 percent. Incidentally, this is probably the biggest yield of any similar prebiotic experiment conducted since then. The reason for that has to do with the fact that amino acids are made from even simpler organic compounds such as hydrogen cyanide and aldehydes.
That was the start. It all held together and the chemistry turned out to be not that outlandish after all.

What was the original reaction to your work in the science community?
There was certainly surprise. One of the reviewers simply didn't believe it and delayed the review process of the paper prior to publication. He later apologized to me. It was sufficiently unusual, that even with Urey's backing it was difficult to get it published. If I'd submitted it to "Science" on my own, it would still be on the bottom of the pile. But the work is so easy to reproduce that it wasn't long before the experiment was validated.
Another scientist was sure that there was some bacterial contamination of the discharge apparatus. When you see the organic compounds dripping off the electrodes, there is really little room for doubt. But we filled the tank with gas, sealed it, put it in an autoclave for 18 hours at 15 psi. Usually you would use 15 minutes. Of course the results were the same.
Nobody questioned the chemistry of the original experiment, although many have questioned what the conditions were on pre-biotic Earth. The chemistry was very solid.

How much of a role did serendipity play in the original setup?
Fortunately, Urey was so adamant at the time about methane that I didn't explore alternate gas mixtures. Now we know that any old reducing gases will do. CO₂/hydrogen and nitrogen will do the trick, although not as well.
There was some serendipity in how we handled the water. If we hadn't boiled it and run it for a week, we wouldn't have gotten such good yields of amino acids. We knew right away that something happened rather quickly because you could see a color change after a couple of days.
The fact that the experiment is so simple that a high school student can almost reproduce it is not a negative at all. That fact that it works and is so simple is what is so great about it. If you have to use very special conditions with a very complicated apparatus there is a question of whether it can be a geological process.

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

You are talking about some kind of pre-RNA?
Exactly a kind of pre-RNA. RNA has four asymmetric carbons in it. This pre-RNA must have somehow developed into RNA. There is a considerable amount of research now to try and figure out what that pre-RNA compound was, that is, what was the precursor to the RNA ribose-phosphate.

Peter E. Nielsen of the University of Copenhagen has proposed a polymer called peptide nucleic acid (PNA) as a precursor of RNA. Is this is where PNA comes in?
Exactly, PNA looks prebiotic. Currently that is the best alternative to ribose phosphate. Whether it was the original material or not is another issue.

Can you clarify one thing? Have all of the amino acids been synthesized in pre-biotic experiments, along with all the necessary components for making life?
Just turning on the spark in a basic pre-biotic experiment will yield 11 out of 20 amino acids. If you count asparagine and glutamine you get thirteen basic amino acids. We don't know how many amino acids there were to start with. Asparagine and glutamine, for example, do not look prebiotic because they hydrolyze. The purines and pyrimidines can alos be made, as can all of the sugars, although they are unstable.

Your original work was published only a month apart from Watson and Crick's description of the DNA molecule. How has the field of molecular biology influenced the field of exobiology?
The thing that has probably changed the outlook the most is the discovery of ribozymes, the catalytic RNA. This means you can have an organism with RNA carrying out both the genetic functions and catalytic functions. That gets around the problem of protein synthesis, which is this incredibly complicated thing. There is a problem with RNA as a prebiotic molecule because the ribose is unstable. This leads us to the pre-RNA world.
The idea of the pre-RNA world is essentially the same as the RNA world, except you have a different molecule that replicates. Another thing worth remembering is that all these pre-biotic experiments produce amino acids. To have these amino acids around and not use them in the first living organism would be odd. So the role of amino acids in the origin of life is unknown but still likely.

Tell us about your recent work and the lagoon idea.
The primitive Earth had big oceans, but it also had lakes, lagoons and beaches. Our hypothesis is that the conditions may have been ideal on these beaches or drying lagoons for prebiotic reactions to occur, for the simple reason that the chemicals were more concentrated in these sites than in the middle of the ocean.

Is this because of the temperatures and also the presence of minerals as well?
Temperature is an important factor. Minerals have been thought by some to play a role in the origin of life, but they really haven't done much for us so far. People talk about how minerals might have helped catalyze reactions, but there are few examples where the mineral makes any difference.
Our most recent research tackled the problem of making pyrimidines- uracil and cytosine, in prebiotic conditions. For some reason it just doesn't work very well under dilute conditions. We showed that it works like a charm once you get things concentrated and dry it out a bit. This changed my outlook on where to start looking for prebiotic reactions.
Another example is our work with co-enzyme A. The business end of co-enzyme A is called pantetheine. We showed you could make this under these kind of pre-biotic "dry beach" conditions. We found that you didn't need it to be very hot, you can make it at 40 degrees C. This indicates the ease with which some of this chemistry can take place.

Temperature seems to be a talking point regarding prebiotic hypotheses.
We know we can't have a very high temperature, because the organic materials would simply decompose. For example, ribose degrades in 73 minutes at high temperatures, so it doesn't seem likely. Then people talk about temperature gradients in the submarine vent. I don't know what these gradients are supposed to do. My thinking is that a temperature between 0 and 10 degrees C would be feasible. The minute you get above 25 degrees C there are problems of stability.

How does the discovery of the Martian meteorite factor in to the discussion? Are you convinced these are the fossilized remains of extraterrestrial microorganisms?
I think the data is interesting and suggestive, but not yet conclusive. Let's accept that the meteorite does come from Mars. You have apparently got very small bacterial fossils also iron sulfide and magnetite sitting next to each other. Then there are these PAHs (polycyclic aromatic hydrocarbons). All of this is suggestive but not compelling.
There are just two possibilities. Either there was life on Mars or there was not. I have no problem with the idea of life on Mars, the question remains whether this evidence is adequate. If it is correct, it has an implication for one of the big questions of prebiotic research. That is, is it easy or difficult to produce life from prebiotic compounds in prebiotic conditions? It seems that it would be difficult on Mars. If it turns out to be the case on Mars, where the conditions do not look very favorable, then it should apply to anywhere in the universe, or any planet with a suitable atmosphere and temperature.

Can you tell us about the field of exobiology today in context of the world of science research?
It is a very small field. There is a society, the International Society for the Study of the Origin of Life. It has only 300 members, a rather small society. My own lab is part of program called NSCORT (NASA Specialized Center of Research and Training). This program is conducted in close cooperation with NASA and supports five researchers along with graduate students, post-docs and undergraduate students.
The more important research are the experiments these days, rather than the trading of ideas. Good ideas are those that when reduced to an experiment end up working. Our approach is to do experiments and demonstrate things, not just talk about possibilities.

What advice do you have for students interested in pursuing studies in exobiology?
Well we are talking about solving chemical problems. Therefore a background in basic chemistry is essential along with knowledge in the fields of organic chemistry, biochemistry and some background in geology and physics. Exobiology is a small field with a lot of interaction. It is one of few fields where an undergraduate would be able to work with top people in the field almost immediately.
This interview was conducted in October, 1996


1. https://web.archive.org/web/20080518054852/http://www.accessexcellence.org/WN/NM/miller.php