Who had the "good idea" to exchange Thymine to Uracil?
https://reasonandscience.catsboard.com/t2258-who-had-the-good-idea-to-exchange-thymine-to-uracil
https://www.widbook.com/ebook/chapters/life-and-the-universe-by-intelligent-design
Figure 1. The "mystery" of the exchange of uracil ( RNA for thymine (T) in the DNA. Who would have had such foresight, and such a chemical genius?
One of the nitrogen bases used in RNA (Figure 1) is uracil (U), but this DNA base "appears" exchanged for thymine (T). But why? That question shows to be even more intriguing when we see that thymine and uracil differ only by a methyl more or less, and apparently, this change takes place in a "harmless" position in terms of interactions between bases that are primarily established through hydrogen bonds. Several explanations have been offered, 2 and today we know that this exchange U/T has an amazing logic. It was apparently a planned strategy with full mastery for any storage system and transmission of information, right from the beginning, accurately and efficiently. The importance of exchanging U/T can also be recognized by the great effort that the cell makes to process it. Such an exchange is made by the cell through the machinery of the cell, and uses a methylation reaction catalyzed by folic acid, which occurs before incorporation of T, and requires one of the nucleotides in DNA.
But why this exchange U/T so " tenue"? Everything indicates today that this exchange has two crucial and specific purposes: The first purpose is to increase the specificity pairing in DNA, because it trades U of T, and Thymine is much more selective in its pairing with adenine (A) in the duo Adenine-Thymine, The base uracil (U) would also make a preferential pairing with Adenine, but not as selectively, since uracil can pair also efficiently with all other bases, including itself. This selectivity is best explained if we remember that DNA is made of nucleic acids, phosphates, and sugar molecules which are hydrophilic and - water-soluble - and the addition of a hydrophobic methyl causes it to be repelled from the rest of the DNA, moving it to a specific position on the helice that makes thymine bind exclusively with adenine, increasing the efficiency of DNA to store and transmit information. Methylation which exchanges uracil with thymine is therefore a strategy of increasing the integrity of the information that needs to be maximized in DNA. Being an immense and fundamental nanomolecular software, DNA can't do any wrong, and everything in it seems that was planned to minimize pairing and reading errors. Another reason for methylation and exchange of U/T also seems to relate to the integrity of information. It is known that cytosine (C) in DNA suffers over time, a reaction of deamination, thereby turning slowly into Uracil (Figure 1).
This deamination C generates a "foreign" U base in DNA. In RNA, this deamination is not worrisome because RNA is quickly used and recycled, and there is not enough time to accumulate this "error". But DNA has a lifetime much longer and so this "damage", via natural degradation, becomes critical. And without proper repair, the deamination of C in U would be catastrophic. Who or what designed DNA, then - blind unguided evolutionary processes or chance ( since there was no evolution prior DNA replication ), or a intelligent mind - realizing and considering this deadly obstacle, that would cause a point mutation, deleterious, random and frequently, which used his foresight capacity, and solved the problem in two ingenious ways ? If U would not have been swapped into T in DNA, the cell would not know and recognize what would be a "legitimate", or an "illegitimate" U, and that U "alien" formed by the degradation of C. But just changing the U of T, DNA would only be able to recognize each and every U as" alien ", but how to eliminate it? For this, another ingenious solution was found to create a machinery and a repair enzyme - the "uracil DNA glycosylase" 1 - that is used specifically to correct this natural, seemingly "inevitable" defect. The exchange of U/T appears well be a spectacle of irreducible complexity associated with brilliant foresight that, according to scientific design detection methods proposed by the TDI, provides seemingly irrefutable evidence of intelligence that created life. Well, there is another hypothesis, that evolution has created such a process via a 'frozen accident "[frozen accident] or simply chance. Something that would have happened slow, gradual and successively by unguided natural processes. Do you believe in miracles without a saint that synchronized these miracles? You decide and choose.
The Dilemma of exchanging U/T. Notice here a huge dilemma for evolution. Assume now that life started by an "RNA Eve" in an event known as "RNA world". Lets put aside for a moment the enormous difficulties encountered to justify the synthesis, catalysis, and transformation in DNA of this "primordial RNA", and imagine - since only imagination seems to work here - that in fact, RNA gave rise to DNA. But one that uses the same DNA bases of RNA, U and C together, and not T and C as "intelligent DNA" today, it would be "fatal" to Life. As seen, the use of the T in the DNA would cause a catastrophic confusion because the natural deamination of C to T in the DNA-RNA processing would be feasible, evolution would have, before the DNA-based Life existed, have the foresight of a brilliant providing, a priori, all the U T methylation machinery before replacing such "primordial RNA" into the primordial DNA, and at the same time and in the same "miraculous" place, provide to the "newborn" DNA an efficient mechanism of enzymatic repair replacing U by C. Two chemistry "miracles", and simultaneously would have to occur synchronically. Incidentally, three miracles, because the machinery removed from the hydroxyl of RNA ribose would have to be there too, but running the DNA was degraded too fast, 100 times too fast. And life could not wait for the chance to regain viability. Chance or design?
Figure 1. Natural DNA degradation via deamidation of cytosine (C) which is transformed into uracil (U). If DNA would use uracil, bye bye, there would be no life.
Who or what would then, in a single chemical trick like this, be able to solve "a priori", that is, with foresight, and in an ingenious way this "mortal" problem? At the same time, with this already brilliant solution, optimize selectivity - and everything indicates stability too - the software of life, DNA? The three options we have are either unguided natural processes, or a genius that knew bioinformatics and chemistry with a masters degree, and not to forget the "other areas of knowledge" of genetics as well; or none of the 3 alternatives, not forgetting the agnostics. What is the best inference? The facts are there, for he who has eyes and an intelligent mind, see, think and respond. But the decision to see, think and respond, of course, is yours alone.
https://reasonandscience.catsboard.com/t2258-who-had-the-good-idea-to-exchange-thymine-to-uracil
https://www.widbook.com/ebook/chapters/life-and-the-universe-by-intelligent-design
Figure 1. The "mystery" of the exchange of uracil ( RNA for thymine (T) in the DNA. Who would have had such foresight, and such a chemical genius?
One of the nitrogen bases used in RNA (Figure 1) is uracil (U), but this DNA base "appears" exchanged for thymine (T). But why? That question shows to be even more intriguing when we see that thymine and uracil differ only by a methyl more or less, and apparently, this change takes place in a "harmless" position in terms of interactions between bases that are primarily established through hydrogen bonds. Several explanations have been offered, 2 and today we know that this exchange U/T has an amazing logic. It was apparently a planned strategy with full mastery for any storage system and transmission of information, right from the beginning, accurately and efficiently. The importance of exchanging U/T can also be recognized by the great effort that the cell makes to process it. Such an exchange is made by the cell through the machinery of the cell, and uses a methylation reaction catalyzed by folic acid, which occurs before incorporation of T, and requires one of the nucleotides in DNA.
But why this exchange U/T so " tenue"? Everything indicates today that this exchange has two crucial and specific purposes: The first purpose is to increase the specificity pairing in DNA, because it trades U of T, and Thymine is much more selective in its pairing with adenine (A) in the duo Adenine-Thymine, The base uracil (U) would also make a preferential pairing with Adenine, but not as selectively, since uracil can pair also efficiently with all other bases, including itself. This selectivity is best explained if we remember that DNA is made of nucleic acids, phosphates, and sugar molecules which are hydrophilic and - water-soluble - and the addition of a hydrophobic methyl causes it to be repelled from the rest of the DNA, moving it to a specific position on the helice that makes thymine bind exclusively with adenine, increasing the efficiency of DNA to store and transmit information. Methylation which exchanges uracil with thymine is therefore a strategy of increasing the integrity of the information that needs to be maximized in DNA. Being an immense and fundamental nanomolecular software, DNA can't do any wrong, and everything in it seems that was planned to minimize pairing and reading errors. Another reason for methylation and exchange of U/T also seems to relate to the integrity of information. It is known that cytosine (C) in DNA suffers over time, a reaction of deamination, thereby turning slowly into Uracil (Figure 1).
This deamination C generates a "foreign" U base in DNA. In RNA, this deamination is not worrisome because RNA is quickly used and recycled, and there is not enough time to accumulate this "error". But DNA has a lifetime much longer and so this "damage", via natural degradation, becomes critical. And without proper repair, the deamination of C in U would be catastrophic. Who or what designed DNA, then - blind unguided evolutionary processes or chance ( since there was no evolution prior DNA replication ), or a intelligent mind - realizing and considering this deadly obstacle, that would cause a point mutation, deleterious, random and frequently, which used his foresight capacity, and solved the problem in two ingenious ways ? If U would not have been swapped into T in DNA, the cell would not know and recognize what would be a "legitimate", or an "illegitimate" U, and that U "alien" formed by the degradation of C. But just changing the U of T, DNA would only be able to recognize each and every U as" alien ", but how to eliminate it? For this, another ingenious solution was found to create a machinery and a repair enzyme - the "uracil DNA glycosylase" 1 - that is used specifically to correct this natural, seemingly "inevitable" defect. The exchange of U/T appears well be a spectacle of irreducible complexity associated with brilliant foresight that, according to scientific design detection methods proposed by the TDI, provides seemingly irrefutable evidence of intelligence that created life. Well, there is another hypothesis, that evolution has created such a process via a 'frozen accident "[frozen accident] or simply chance. Something that would have happened slow, gradual and successively by unguided natural processes. Do you believe in miracles without a saint that synchronized these miracles? You decide and choose.
The Dilemma of exchanging U/T. Notice here a huge dilemma for evolution. Assume now that life started by an "RNA Eve" in an event known as "RNA world". Lets put aside for a moment the enormous difficulties encountered to justify the synthesis, catalysis, and transformation in DNA of this "primordial RNA", and imagine - since only imagination seems to work here - that in fact, RNA gave rise to DNA. But one that uses the same DNA bases of RNA, U and C together, and not T and C as "intelligent DNA" today, it would be "fatal" to Life. As seen, the use of the T in the DNA would cause a catastrophic confusion because the natural deamination of C to T in the DNA-RNA processing would be feasible, evolution would have, before the DNA-based Life existed, have the foresight of a brilliant providing, a priori, all the U T methylation machinery before replacing such "primordial RNA" into the primordial DNA, and at the same time and in the same "miraculous" place, provide to the "newborn" DNA an efficient mechanism of enzymatic repair replacing U by C. Two chemistry "miracles", and simultaneously would have to occur synchronically. Incidentally, three miracles, because the machinery removed from the hydroxyl of RNA ribose would have to be there too, but running the DNA was degraded too fast, 100 times too fast. And life could not wait for the chance to regain viability. Chance or design?
Figure 1. Natural DNA degradation via deamidation of cytosine (C) which is transformed into uracil (U). If DNA would use uracil, bye bye, there would be no life.
Who or what would then, in a single chemical trick like this, be able to solve "a priori", that is, with foresight, and in an ingenious way this "mortal" problem? At the same time, with this already brilliant solution, optimize selectivity - and everything indicates stability too - the software of life, DNA? The three options we have are either unguided natural processes, or a genius that knew bioinformatics and chemistry with a masters degree, and not to forget the "other areas of knowledge" of genetics as well; or none of the 3 alternatives, not forgetting the agnostics. What is the best inference? The facts are there, for he who has eyes and an intelligent mind, see, think and respond. But the decision to see, think and respond, of course, is yours alone.
