Intelligent Design, the best explanation of Origins
Would you like to react to this message? Create an account in a few clicks or log in to continue.
Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


You are not connected. Please login or register

Intelligent Design, the best explanation of Origins » Origin of life » The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated

The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated

Go down  Message [Page 1 of 1]

Otangelo


Admin
The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated

https://reasonandscience.catsboard.com/t2997-the-problem-of-the-origin-of-the-hardware-and-software-in-the-cell-is-far-greater-than-commonly-appreciated

- Getting the basic elements to make the building blocks of life
- RNA world
- RNA and DNA synthesis
- Polymerization through catalysts on clay
- The Eigen threshold
- The transition from the RNA world, to the DNA world
- Obtaining the genetic Code
- The genetic code is optimal amongst 1 million
- The second, overlapping code in DNA
- The amazing information storage capacity of DNA
- Getting the information in the genome
- Getting the gene expression machinery to make proteins
- Origin of the 37 gene codes: Did they evolve? 

It is known, that explaining where the information stored in DNA comes from, in special to make the first organism, is a problem not explained by science, and unsolved. This has been traditionally, a major argument used by IDists to make their case for design. Not rarely, proponents of materialism resort to the so-called RNA world, but it is plagued with problems. The foremost are two: The hardware, and the software problem: How to get RNA and DNA on the Hadean Earth, and the second is how to get information to give life a first go. Prebiotic synthesis of RNA and DNA has never been solved. The hurdles are truly formidable. I have listed 37 different unsolved issues 1 Adherents of evolution usually start their narrative when life already started. While it is true, that mutations provoke change, it is by far not substantiated, that such changes, either single point mutations, or lateral gene transfer, or larger sections like exons, nor genetic shift or gene flow could bring forward the millions of different species on earth. But when we look to the root, the enormity of the problem faced by science to solve the riddle of how information-rich life started, becomes clear. No naturalistic explanations exist, despite decades of attempts to solve the riddle. The problem is formidable, and manyfold. First of all, there is no evidence that the atoms in the usable form required to make RNA and DNA were extant on the early earth. 19  Secondly, even IF we presuppose that this problem has a viable solution, catalysis on clay to form polymerization of RNA strands is just wishful thinking. 3  But even, let's suppose, that was the way it went, there is the next problem:

The primary incentive behind the theory of self-replicating systems that Manfred Eigen outlined was to develop a simple model explaining the origin of biological information and, hence, of life itself. Eigen’s theory revealed the existence of the fundamental limit on the fidelity of replication (the Eigen threshold): If the product of the error (mutation) rate and the information capacity (genome size) is below the Eigen threshold, there will be stable inheritance and hence evolution; however if it is above the threshold, the mutational meltdown and extinction become inevitable (Eigen, 1971). The Eigen threshold lies somewhere between 1 and 10 mutations per round of replication

The very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded.  The crucial question is how the Darwin-Eigen cycle could have started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses, replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could emerge is a  puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. The origin of life—or, to be more precise, the origin of the first replicator systems and the origin of translation—remains a huge enigma, and progress in solving these problems has been very modest—in the case of translation, nearly negligible.4

Now let us suppose that this problem would be overcome by RNA catalysis. The next huge step would be to go from short polypeptide RNA to long, stable DNA chains. The transition from RNA to DNA is the next overwhelmingly huge problem. Highly complex nanomachines are required to synthesize DNA from RNA: At least hypercomplex enzymes like RNR proteins are required 6 Of course, to make those, DNA is required, which turns the riddle a catch22 problem: 


What came first, DNA or the machines that make DNA? 

Now let's suppose, that problem would have been solved, and we have the raw materials, RNA, and DNA, and some working prebiotic polymerization mechanism. Lets even suppose that RNA on clay would work. 
The next problem would be to form the genetic code, of 64 codons, and the assignment of the meaning of each codon to one of the 20 amino acids used to make proteins. 8 That is the genetic cipher, or the translation code. Assigning the meaning of one symbol to something else is ALWAYS based on mind. 7 There is NO viable alternative explanation. One science paper has called the origin of the genetic code the universal enigma 10 On top of that, the genetic code is near-optimal amongst 1 million alternative codes, which are less robust. How to explain that feat?   9 Furthermore, an “overlapping language” has been found in the genetic code. How to explain THAT marvel of ingeniosity? Now, let's suppose we had RNA, DNA, polymerization, and the genetic code. We can equate it to an information storing hard disk but of far higher sophistication than anything devised by man. 12 Even Richard Dawkins had to admit in 

The Blind Watchmaker, pp. 116–117.... 
there is enough information capacity in a single human cell to store the Encyclopaedia Britannica, all 30 volumes of it, three or four times over. 

Now, let's suppose, we have a fully operational raw material, and the genetic language upon which to store genetic information. Only now, we can ask: Where did the information come from to make the first living organism? Various attempts have been made to lower the minimal information content to produce a fully working operational cell. Often, Mycoplasma is mentioned as a reference to the threshold of the living from the non-living. Mycoplasma genitalium is held as the smallest possible living self-replicating cell. It is, however, a pathogen, an endosymbiont that only lives and survives within the body or cells of another organism ( humans ).  As such, it IMPORTS many nutrients from the host organism. The host provides most of the nutrients such bacteria require, hence the bacteria do not need the genes for producing such compounds themselves. As such, it does not require the same complexity of biosynthesis pathways to manufacturing all nutrients as a free-living bacterium. 

Better candidates are the simplest free-living bacteria such as Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  14  They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help. 

Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55. 

Now, after several chemical evolutionary miraculous events, we have eventually a functional genome, with complex instructional codified information stored to make a hypothetical minimal self-replicating cell. But we have not yet dealt with the origin of the transcription and translation machinery, necessary to express the genetic information, to make proteins.  Where did that machinery come from? Of course, genetic information is required to specify the amino acid chains that make these machines. The problem is nothing short of monumental. The macro-molecular machinery belongs to the most complex known.  To make proteins, and direct and insert them to the right place where they are needed, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps are required. Each step requires extremely complex molecular machines composed of numerous subunits and co-factors, which require the very own processing procedure described below, which makes its origin an irreducible  catch22 problem 16
 
To exemplify this, lets take the Ribosome 17
The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. 
The design of the translation system in even the simplest modern cells ( such as CarsonellaMycoplasma,) is extremely complex. At the heart of the system is the ribosome, a large complex of at least three RNA molecules and 60–80 proteins arranged in precise spatial architecture and interacting with other components of the translation system in the most finely choreographed fashion. These other essential components include the complete set of tRNAs for the 20 amino acids (~40 tRNA species considering the presence of isoacceptor tRNAs in all species), the set of 18–20 cognate aminoacyl-tRNA synthetases, and a complement of at least 7–8 translation factors.. Together with the universal conservation of ~30 RNA species [three rRNAs, the signal recognition particle (SRP) RNA, and tRNAs of at least 18 specificities]  5

To end the story: Science has catalogized, so far, besides the standard genetic code, other 37 different codes, specially employed in mitochondria.  Invertebrates use a different mitochondrial genetic code than in vertebrates, and both of those codes are different from the “universal” genetic code. That means that the eukaryotic cells that eventually evolved into invertebrates must have formed when a cell that used the “universal” code engulfed a cell that used a different code. Of course, that raises the question, if originally, two different codes emerged. However, the eukaryotic cells that eventually evolved into vertebrates must have formed when a cell that used the “universal” code engulfed a cell that used yet another different code. As a result, invertebrates must have evolved from one line of eukaryotic cells, while vertebrates must have evolved from a completely separate line of eukaryotic cells. But this isn’t possible, since evolution depends on vertebrates evolving from invertebrates.

Now, of course, this serious problem can be solved by assuming that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. But how that would be possible? After all, the invertebrates spent supposedly millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At a minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work. Along with explaining how nuclear DNA can evolve to produce the new structures needed to change invertebrates into vertebrates, proponents of evolution must also explain how, at the same time, mitochondria can evolve to use a different genetic code!

There would be much more to say, as to ask: Where did the gene regulatory network, that orchestrates gene expression come from, and how is that regulated, and how are proteins directed to their end destination. But i leave that to another article. So, the end question: How is all this better explained? By chance, or intelligent design? I go with the latter. 


1. https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759
2. https://reasonandscience.catsboard.com/t2437-essential-elements-and-building-blocks-for-the-origin-of-life#7789
3. https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible#7307
4. https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world
5. https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world#4442
6. https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible#7650
7. https://reasonandscience.catsboard.com/t2057-origin-of-translation-of-the-4-nucleic-acid-bases-and-the-20-amino-acids-and-the-universal-assignment-of-codons-to-amino-acids
8. https://reasonandscience.catsboard.com/t2001-origin-and-evolution-of-the-genetic-code-the-universal-enigma
9. https://reasonandscience.catsboard.com/t1404-the-genetic-code-is-nearly-optimal-for-allowing-additional-information-within-protein-coding-sequences
10. https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin
11. https://reasonandscience.catsboard.com/t2185-the-second-code-of-dna
12. https://reasonandscience.catsboard.com/t2052-the-amazing-dna-information-storage-capacity
13. https://microbewiki.kenyon.edu/index.php/Pelagibacter_ubique#:~:text=Description%20and%20significance,of%20all%20microbial%20plankton%20cells.
14. https://www.uniprot.org/proteomes/UP000002528
15. https://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events#7792
16. https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins
17. https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines
18. http://blog.drwile.com/?p=14280
19. https://reasonandscience.catsboard.com/t2437-essential-elements-and-building-blocks-for-the-origin-of-life#7789

The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated Dna-go10



Last edited by Admin on Sat Oct 03, 2020 4:30 pm; edited 1 time in total

https://reasonandscience.catsboard.com

Otangelo


Admin
In the Origin of life community, there are two hypotheses of how life came to be. The metabolism first, and the RNA world hypothesis. Both are plagued with problems. Let's give a closer look at the RNA world. How to get RNA and DNA on the early Earth, and how to get information to give life the first go are major unsolved problems. Prebiotic synthesis of RNA and DNA has never been demonstrated in the laboratory.  I have listed 37 different unsolved issues in regards of RNA synthesis. No naturalistic explanations exist, despite decades of attempts to solve the riddle. There is no evidence that the elements, in special carbon, and nitrogen in the usable form were extant on the early earth to make the basic building blocks of life, including RNA and DNA. Catalysis on clay to form polymerization of RNA strands is just wishful thinking. 

The primary incentive behind the theory of self-replicating systems that Manfred Eigen outlined was to develop a simple model explaining the origin of biological information and, hence, of life itself. Eigen’s theory revealed the existence of the fundamental limit on the fidelity of replication, called the Eigen threshold:  The very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded. Hence, the dramatic paradox of the origin of life is that to attain the minimum complexity required for a biological system to start, a system of a far greater complexity appears to be required. How such a system could emerge is an unsolved puzzle. The origin of life—or, to be more precise, the origin of the first replicator systems and the origin of translation—remains a huge enigma, and progress in solving these problems has been very modest—in the case of translation, nearly negligible.

The next huge step would be to go from short polypeptide RNA to long, stable DNA chains. The transition from RNA to DNA is the next overwhelmingly huge problem. Highly complex nanomachines are required to synthesize DNA from RNA: Amongst them, hypercomplex enzymes like Ribonucleotide reductase proteins. Of course, to make those, DNA is required, which turns the riddle a catch22 problem: 

What came first, DNA or the machines that make DNA? The next problem would be to form the genetic code, consistent of 64 triplet codons, and the assignment of the meaning of each codon to one of the 20 amino acids used to make proteins. That is the genetic cipher or the translation code. Assigning the meaning of one symbol to something else is ALWAYS based on the mind. There is NO viable alternative explanation. One science paper has called the origin of the genetic code the universal enigma  On top of that, the genetic code is near-optimal amongst 1 million alternative codes, which are less robust. How to explain that feat?  Furthermore, an “overlapping language” has been found in the genetic code. Now, let's suppose we had RNA, DNA, polymerization, and the genetic code. We can equate it to an information storing hard disk but of far higher sophistication than anything devised by man. Even Richard Dawkins had to admit in  The Blind Watchmaker: there is enough information capacity in a single human cell to store the Encyclopaedia Britannica, all 30 volumes of it, three or four times over. 

Next: Where did the information come from to make the first living organism? One of the simplest free-living bacteria is Pelagibacter ubique. It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,3 million base pairs and code for about 1,300 proteins.   If a chain could link up, what is the probability that the code letters would line up to confer instructional, complex, codified information to make this bacteria? The chances to get the sequence randomly would be 4^1,200,000 or 10^722,000 There are 10^80 of atoms in the whole universe. Consider that we cannot explain its origin through evolution, because evolution depends on DNA replication, which origin we try to elucidate. 

But we have not yet dealt with the origin of the machines that encode, send, and decode the information, that is the transcription and translation machinery, necessary to express the genetic information, to make proteins.  Where did that machinery come from? Of course, genetic information is required to specify the amino acid chains that make these proteins. To make proteins, and direct and insert them to the right place where they are needed, at least 25  extremely complex biosyntheses and production-line like manufacturing steps are required. Each step requires molecular machines composed of numerous subunits and co-factors, which require the very own processing procedure described to make them, which makes its origin an irreducible  catch22 problem 
 
To exemplify this, lets take one of those macromolecules:  the Ribosome 
The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. 
The design of the translation system in even the simplest modern cells is extremely complex. At the heart of the system is the ribosome, a large complex of at least three RNA molecules and 60–80 proteins arranged in precise spatial architecture and interacting with other components of the translation system in the most finely choreographed fashion. These other essential components include the complete set of tRNAs for the 20 amino acids, the set of 20  aminoacyl-tRNA synthetases. Furthermore, about 200 scaffold and assembly proteins, and 75 co-factors are required, to synthesize the Ribosome. How could that have occurred, in special considering, that there was no evolution at this stage?

Once all this emerged, DNA replication errors had to be reduced ten billion times by error check and repair mechanisms. All the machinery described required a protective envelope, which had to create a homeostatic environment, diminishing the calcium concentration in the cell ten thousand 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 the 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 the 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. 


So, the end question: How is all this better explained? By chance, or intelligent design? I go with the latter. 

https://reasonandscience.catsboard.com

Back to top  Message [Page 1 of 1]

Permissions in this forum:
You cannot reply to topics in this forum