Theory of Intelligent Design, the best explanation of Origins

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Abiogenesis is impossible

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51 Re: Abiogenesis is impossible on Mon Jan 30, 2017 10:06 am



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52 Re: Abiogenesis is impossible on Sat Feb 04, 2017 6:53 pm


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.

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53 Re: Abiogenesis is impossible on Wed Feb 08, 2017 2:33 pm


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.

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54 Re: Abiogenesis is impossible on Thu Mar 23, 2017 8:53 am


plausible prebiotic synthesis

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55 What can we know about how life began ? on Tue Apr 11, 2017 8:20 pm


What can we know about how life began ?

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 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

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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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.

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