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Biochemical fine-tuning - essential for life

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Biochemical fine-tuning - essential for life

http://reasonandscience.heavenforum.org/t2591-biochemical-fine-tuning-essential-for-life

Today, it is particularly striking to many scientists that cosmic constants, physical laws, biochemical pathways, and terrestrial conditions are just right for the emergence and flourishing of life. 1 It now seems that only a very restricted set of physical conditions operative at several major junctures of emergence could have opened the gateways to life.

Fine-tuning in biochemistry is represented by the strength of the chemical bonds that makes the universal genetic code possible. Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen. 2

Fine-tuning in biochemistry is represented in molecular biological terms by the strength of chemical bonds that make the universal genetic code possible. The messages coded in RNA and DNA would not be possible if the strengths of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

As it happens, the average bond energy of a carbon–oxygen double bond is about 30 kcal per mol higher than that of a carbon–carbon or carbon–nitrogen double bond, a difference that reflects the fact that ketones normally exist as ketones and not as their enol-tautomers. If (in the sense of a “counterfactual variation”) the difference between the average bond energy of a carbon–oxygen double bond and that of a carbon–carbon and carbon–nitrogen double bond were smaller by a few kcal per mol, then the nucleobases guanine, cytosine, and thymine would exist as “enols” and not as “ketones,” and Watson–Crick base-pairing would not exist – nor would the kind of life we know.

It looks as though this is providing a glimpse of what might appear (to those inclined) as biochemical fine-tuning of life.




AmazingWatson–Crick base-pairing
The existence of Watson–Crick base-pairing in DNA and RNA is crucially dependent on the position of the chemical equilibria between tautomeric forms of the nucleobases.1 These equilibria in both purines and pyrimidines lie sharply on the side of amide- and imide-forms containing the (exocyclic) oxygen atoms in the form of carbonyl groups (C=O) and (exocyclic) nitrogen in the form of amino groups (NH2). The positions of these equilibria in a given environment are an intrinsic property of these molecules, determined by their physico-chemical parameters (and thus, ultimately, by the fundamental physical constants of this universe). The chemist masters the Herculean task of grasping and classifying the boundless diversity of the constitution of organic molecules by using the concept of the “chemical bond.” He pragmatically deals with the differences in the thermodynamic stability of molecules by using individual energy parameters, which he empirically assigns to the various types of bonds in such a way that he can simply add up the number and kind of bonds present in the chemical formula of a molecule and use their associated average bond energies to estimate the relative energy content of essentially any given organic molecule.

Now comes the striking interpretation of the Darwinism-inclined and indoctrinated mind :

Whatever biological phenomena appear fine-tuned can be interpreted in principle as the result of life having finetuned itself to the properties of matter through natural selection. Indeed, to interpret in this way what we observe in the living world is mainstream thinking within contemporary biology and biological chemistry.

Sometimes it strikes me how un-imaginative these folks are. They cannot imagine anything else beside NATURAL SELECTION. So the hero on the block strikes again. The multi-versatile mechanism propagated by Darwin explains and solves practically any issue and arising question of origins. Can't explain a phenomena in question ? NS did it.....  huh....

Conceive (through chemical reasoning) potentially natural alternatives to the structure of RNA; synthesize such alternatives by chemical methods; compare them with RNA with respect to those chemical properties that are fundamental to its biological function. Fortunately for this special case of the nucleic acids, it is not at all problematic to decide what the most important of these properties has to be: it must be the capability to undergo informational Watson–Crick base-pairing. The relevance of the perspective created in such a project will strongly depend on the specific choice of the alternatives’ chemical structures. The quest is to focus on systems deemed to
be potentially natural in the sense that they could have formed, according to chemical reasoning, by the very same type of chemistry that (under unknown circumstances) must have been operating on earth (or elsewhere) at the time when and at the place where the structure type of RNA was born. Candidates that lend themselves to this choice are oligonucleotide systems, the structures of which are derivable from (CH2O)n sugars (n = 4, 5, 6) by the type of chemistry that allows the structure of natural RNA to be derived from the C5-sugar ribose (see Figure 16.2).



This approach is based on the supposition that RNA structure originated through a process that was combinatorial in nature with respect to the assembly and functional selection of an informational system within the domain of sugar-based oligonucleotides. In a way, the investigation is an attempt to mimic the selection filter of such a natural process by chemical means, irrespective of whether RNA first appeared in an abiotic or a biotic environment.
In retrospect, the results of systematic experimental investigations carried out along these lines justify the effort (see Figure 16.3).



It is found that hexopyranosyl analogs of RNA (with backbones containing six carbons per sugar unit instead of five carbons and six-membered pyranose rings instead of five-membered furanose rings) do not possess the capability of efficient informational Watson–Crick base-pairing. Therefore, these systems could not have acted as functional competitors of RNA in nature’s the intelligent designers ( makes much more sense, doesnt't it ? Nature has no conscience nor mind to make choices ) choice of a genetic system, even though these sixcarbon alternatives of RNA should have had a comparable chance of being formed under the conditions that formed RNA. The reason for their failure revealed itself in chemical model studies: six-carbon-six-membered-ring sugars are found to be too bulky to adapt to the steric requirements of Watson–Crick base-pairing within oligonucleotide duplexes. In sharp contrast, an entire family of nucleic acid alternatives in which each member comprises repeating units of one of the four possible five-carbon sugars (ribose being one of them) turned out to be highly efficient informational base-pairing systems. 


1. Barrow, FITNESS OF THE COSMOS FOR LIFE,  Biochemistry and Fine-Tuning, page 56
2. Barrow, FITNESS OF THE COSMOS FOR LIFE,  Biochemistry and Fine-Tuning, page 154

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Perfect Timing 1
Exact fine-tuning is not limited to the structure of biomolecules. Sometimes the rate of biochemical processes is also meticulously refined. Recent studies indicate that the rate of messenger RNA and protein breakdown, two processes central to the cell's activity, are exquisitely regulated by the cell's machinery.

Shutting Down Production
Messenger RNA (mRNA) plays a central role in protein production. These molecules mediate the transfer of information from the nucleotide sequences of DNA to the amino acid sequences of proteins. The cell's machinery copies mRNA from DNA only when the cell needs the protein encoded by a particular gene housed in the DNA. When that protein is not needed, the cell shuts down production. This practice is a matter of efficiency. In this way, the cell makes only the mRNAs and consequently the proteins it needs.  Once produced, mRNAs continue to direct the production of proteins at the ribosome. Fortunately, mRNA molecules have limited stability and only exist intact for a brief period of time before they break down. This short life- time benefits the cell. If mRNA molecules unduly persisted, then they would direct the production of proteins at the ribosome beyond the point the cell needs. Overproduction would not only be wasteful, it would also lead to the coexistence of proteins that carry out opposed functions within the cell. The careful control of mRNA levels is necessary for the cell to have the right amounts of proteins at the right time. Unregulated protein levels would compromise life.  Until recently, biochemists thought regulation of mRNA levels (and hence protein levels) occurred when the cell's transcriptional machinery carefully controlled mRNA production. New research, however, indicates that mRNA breakdown also helps regulate its level.  Prior to this work, biochemists thought that the degradation of mRNA was influenced only by abundance, size, nucleotide sequence, and so forth. However, this perspective was incorrect. The breakdown of mRNA molecules is not random but precisely orchestrated. Remarkably, messenger RNA molecules, which correspond to proteins that  are part of the same metabolic pathways, have virtually identical decay rates. The researchers also found that mRNA molecules, which specify proteins involved in the cell's central activities, have relatively slow breakdown rates. Proteins only needed for transient cell processes are encoded by mRNAs with rapid rates of degradation. The decay of mRNA molecules is not only fine-tuned but also displays an elegant biochemical logic that bespeaks of intelligence.

Tagged for Destruction
Proteins, which play a role in virtually every cell structure and activity, are constantly made—and destroyed—by the cell. Those that take part in highly specialized activities within the cell are manufactured only when needed. Once these proteins have outlived their usefulness, the cell breaks them down into their constitutive amino acids. The removal of unnecessary proteins helps keep the cell's interior free of clutter.  On the other hand, proteins that play a central role in the cell's operation are produced on a continual basis. After a period of time, however, these proteins inevitably suffer damage from wear and tear and must be destroyed and replaced with newly made proteins. It's dangerous for the cell to let dam- aged proteins linger.  Once a protein is damaged, it's prone to aggregate with other proteins. These aggregates disrupt cellular activities. Protein degradation and turnover, in many respects, are just as vital to the cell's operation as protein production. And, as is the case for mRNAs, protein degradation is an exacting, delicately balanced process.  This complex undertaking begins with ubiquitination. When damaged, proteins misfold, adopting an unnatural three-dimensional shape. Misfolding exposes amino acids in the damaged protein's interior. These exposed amino acids are recognized by E3 ubiquitin ligase, an enzyme that attaches a small protein molecule (ubiquitin) to the damaged protein. Ubiquitin functions as a molecular tag, informing the cell's machinery that the damaged protein is to be destroyed. Severely damaged proteins receive multiple tags.

To the Rescue
Ubiquitination is a reversible process with de-ubiquitinating enzyme removing inappropriate ubiquitin labels. This activity prevents the cell's  machinery from breaking down fully functional proteins that may have been accidentally tagged for destruction because E3 ubiquitin ligase occasionally makes mistakes.  A massive protein complex, a proteasome, destroys damaged ubiquitinated proteins, functioning like the cell's garbage can. The overall molecular architecture of the proteasome consists of a hollow cylinder topped with a lid that can exist in either an opened or closed conformation. Protein breakdown takes place within the cylinder's interior. The lid portion of the proteasome controls the entry of ubiquitinated proteins into the cylinder.  The proteasome lid contains de-ubiquitinating activity. If a protein has only one or two ubiquitin tags, it's likely not damaged and the lid will remove the tags rescuing the protein from destruction. The cell's machinery then recycles the rescued protein. If, on the other hand, the protein has several ubiquitin tags, the lid cannot remove them all and shuttles the damaged protein entry into the proteasome cylinder.  The proteasome lid regulates a delicate balance between destruction and rescue, ensuring that truly damaged proteins are destroyed and proteins that can be salvaged escape unnecessary degradation. The cell's protein degradation system, like messenger RNA breakdown, displays fine-tuning and elegant biochemical logic that points to a Creator's handiwork.

Must regulation, delicate balance and fine-tuning when a protein needs to be expressed, and when degraded, not be preprogrammed, and is it not a mechanism life-essential, and required to be fully functional right from the start when life began? The paradigm of Darwinism leads to the conclusion and belief that gradual, stepwise evolutionary change can give rise to all molecular functions, but evidence shows that life in ALL its forms is interdependent, functions depend on the "joint-venture" of various different cell types, or organs, and had to emerge together, as a whole, not individually.  The regulation of protein expression had to emerge together with the capacity of protein degradation when required, and the recognition and regulation mechanism of both functions.  This is strong evidence of intelligent design.

1. Cell's design, F.Rana, page 119

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Fine-tuning, which traditionally was an argument of design from cosmology, extends to biochemistry

Today, it is particularly striking to many scientists that cosmic constants, physical laws, biochemical pathways, and terrestrial conditions are just right for the emergence and flourishing of life. 1 It now seems that only a very restricted set of physical conditions operative at several major junctures of emergence could have opened the gateways to life.

Fine-tuning in biochemistry is represented by the strength of the chemical bonds that makes the universal genetic code possible. Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen. 2

Fine-tuning in biochemistry is represented in molecular biological terms by the strength of chemical bonds that make the universal genetic code possible. The messages coded in RNA and DNA would not be possible if the strengths of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

As it happens, the average bond energy of a carbon–oxygen double bond is about 30 kcal per mol higher than that of a carbon–carbon or carbon–nitrogen double bond, a difference that reflects the fact that ketones normally exist as ketones and not as their enol-tautomers. If (in the sense of a “counterfactual variation”) the difference between the average bond energy of a carbon–oxygen double bond and that of a carbon–carbon and carbon–nitrogen double bond were smaller by a few kcal per mol, then the nucleobases guanine, cytosine, and thymine would exist as “enols” and not as “ketones,” and Watson–Crick base-pairing would not exist – nor would the kind of life we know.

It looks as though this is providing a glimpse of what might appear (to those inclined) as biochemical fine-tuning of life.

AmazingWatson–Crick base-pairing
The existence of Watson–Crick base-pairing in DNA and RNA is crucially dependent on the position of the chemical equilibria between tautomeric forms of the nucleobases.1 These equilibria in both purines and pyrimidines lie sharply on the side of amide- and imide-forms containing the (exocyclic) oxygen atoms in the form of carbonyl groups (C=O) and (exocyclic) nitrogen in the form of amino groups (NH2). The positions of these equilibria in a given environment are an intrinsic property of these molecules, determined by their physico-chemical parameters (and thus, ultimately, by the fundamental physical constants of this universe). The chemist masters the Herculean task of grasping and classifying the boundless diversity of the constitution of organic molecules by using the concept of the “chemical bond.” He pragmatically deals with the differences in the thermodynamic stability of molecules by using individual energy parameters, which he empirically assigns to the various types of bonds in such a way that he can simply add up the number and kind of bonds present in the chemical formula of a molecule and use their associated average bond energies to estimate the relative energy content of essentially any given organic molecule.

Now comes the striking interpretation of the Darwinism-inclined and indoctrinated mind :

Whatever biological phenomena appear fine-tuned can be interpreted in principle as the result of life having finetuned itself to the properties of matter through natural selection. Indeed, to interpret in this way what we observe in the living world is mainstream thinking within contemporary biology and biological chemistry.

Sometimes it strikes me how un-imaginative these folks are. They cannot imagine anything else beside NATURAL SELECTION. So the hero on the block strikes again. The multi-versatile mechanism propagated by Darwin explains and solves practically any issue and arising question of origins. Can't explain a phenomena in question ? NS did it..... huh....

Conceive (through chemical reasoning) potentially natural alternatives to the structure of RNA; synthesize such alternatives by chemical methods; compare them with RNA with respect to those chemical properties that are fundamental to its biological function. Fortunately for this special case of the nucleic acids, it is not at all problematic to decide what the most important of these properties has to be: it must be the capability to undergo informational Watson–Crick base-pairing. The relevance of the perspective created in such a project will strongly depend on the specific choice of the alternatives’ chemical structures. The quest is to focus on systems deemed to
be potentially natural in the sense that they could have formed, according to chemical reasoning, by the very same type of chemistry that (under unknown circumstances) must have been operating on earth (or elsewhere) at the time when and at the place where the structure type of RNA was born. Candidates that lend themselves to this choice are oligonucleotide systems, the structures of which are derivable from (CH2O)n sugars (n = 4, 5, 6) by the type of chemistry that allows the structure of natural RNA to be derived from the C5-sugar ribose .

This approach is based on the supposition that RNA structure originated through a process that was combinatorial in nature with respect to the assembly and functional selection of an informational system within the domain of sugar-based oligonucleotides. In a way, the investigation is an attempt to mimic the selection filter of such a natural process by chemical means, irrespective of whether RNA first appeared in an abiotic or a biotic environment. In retrospect, the results of systematic experimental investigations carried out along these lines justify the effort

It is found that hexopyranosyl analogs of RNA (with backbones containing six carbons per sugar unit instead of five carbons and six-membered pyranose rings instead of five-membered furanose rings) do not possess the capability of efficient informational Watson–Crick base-pairing. Therefore, these systems could not have acted as functional competitors of RNA in nature’s the intelligent designers ( makes much more sense, doesnt't it ? Nature has no conscience nor mind to make choices ) choice of a genetic system, even though these sixcarbon alternatives of RNA should have had a comparable chance of being formed under the conditions that formed RNA. The reason for their failure revealed itself in chemical model studies: six-carbon-six-membered-ring sugars are found to be too bulky to adapt to the steric requirements of Watson–Crick base-pairing within oligonucleotide duplexes. In sharp contrast, an entire family of nucleic acid alternatives in which each member comprises repeating units of one of the four possible five-carbon sugars (ribose being one of them) turned out to be highly efficient informational base-pairing systems.

1. Barrow, FITNESS OF THE COSMOS FOR LIFE, Biochemistry and Fine-Tuning, page 56
2. Barrow, FITNESS OF THE COSMOS FOR LIFE, Biochemistry and Fine-Tuning, page 154

Biochemical fine-tuning - essential for life
http://reasonandscience.heavenforum.org/t2591-biochemical-fine-tuning-essential-for-life

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