52 Re: Abiogenesis is impossible on Sat Feb 04, 2017 6:53 pm
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.
53 Re: Abiogenesis is impossible on Wed Feb 08, 2017 2:33 pm
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.
55 What can we know about how life began ? on Tue Apr 11, 2017 8:20 pm
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 development 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 irreducible complex and interdependent. At the paper :
How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept , the author writes :
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 cars 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:
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 ajusted 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. Thats a hudge problem for natural mechanisms, where no intelligence is in place.
A minimal metabolic set was also required:
a proeminent proposal, the so often mentioned RNA world, has also unbridgeable flaws, and cannot explain the origin of life adequately:
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. Thats a classic catch22 problem:
amongst many other catch22 situations that plague OOL researchers:
Furthermore, you need homeostatsis and a functional signaling network right from the start:
the hability 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 ?
Then you need a set of proteins that use in their action centers metal clusters. To make them, is a enormous feat and requires whole production lines and irreducible multistep biosynthesis processes:
Another hudge task is to create various cell codes, amongst them proeminently 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:
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.
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:
Abiogensis is a hudge 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 computers 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 inumerous 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 by a lucky accident.
Abiogenesis is impossible
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