All cellular functions are  irreducibly complex
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04-09-2015, 04:04 AM
RE: All cellular functions are  irreducibly complex
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04-09-2015, 06:43 AM
RE: All cellular functions are  irreducibly complex
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13-09-2015, 07:12 AM
RE: All cellular functions are  irreducibly complex
The awe inspiring spliceosome, the most complex macromolecular machines known, and pre-mRNA processing in eukaryotic cells

http://reasonandscience.heavenforum.org/...otic-cells

Along the way to make proteins in eukaryotic cells,  there is a whole chain of subsequent events that must all be fully operational, and the machinery in place, in order to get the functional product, that is  proteins. At the beginning of the process, DNA is transcribed in the RNA polymerase molecular machine, to yield messenger RNA ( mRNA ) , which afterwards must go through post transcriptional modifications. That is CAPPING,  ELONGATION,  SPLICING, CLEAVAGE,POLYADENYLATION AND TERMINATION , before it can be EXPORTED FROM THE NUCLEUS TO THE CYTOSOL,  and PROTEIN SYNTHESIS INITIATED, (TRANSLATION), and  COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING.

Bacterial mRNAs are synthesized by the RNA polymerase starting and stopping at specific spots on the genome. The situation in eukaryotes is substantially different. In particular, transcription is only the first of several steps needed to produce a mature mRNA molecule. The mature transcript for many genes is encoded in a discontinuous manner in a series of discrete exons, which are separated from each other along the DNA strand by non-coding introns. mRNAs, rRNAs, and tRNAs can all contain introns that must be removed from precursor RNAs to produce functional molecules.The formidable task of identifying and splicing together exons among all the intronic RNA is performed by a large ribonucleoprotein machine, the spliceosome, which is composed of several individual small nuclear ribonucleoproteins,  five snRNPs,  pronounced ‘snurps’, (U1, U2, U4, U5, and U6) each containing an RNA molecule called an snRNA that is usually 100–300 nucleotides long, plus additional protein factors that recognize specific sequences in the mRNA or promote conformational rearrangements in the spliceosome required for the splicing reaction to progress, and many more additional proteins that come and go during the splicing reaction.  It has been described as one of "the most complex macromolecular machines known," "composed of as many as 300 distinct proteins and five RNAs".

The snRNAs perform many of the spliceosome’s mRNA recognition events. Splice site consensus sequences are recognized by non-snRNP factors; the branch-point sequence is recognized by the branch-point-binding protein (BBP), and the polypyrimidine tract and 3′ splice site are bound by two specific protein components of a splicing complex referred to as U2AF (U2 auxiliary factor), U2AF65 and U2AF35, respectively.

This is one more great example of a amazingly complex molecular machine, that will operate and exercise its precise orchestrated function properly ONLY with ALL components fully developed and formed and able to interact in a highly complex, ordered , precise manner. Both, the software, and the hardware, must be in place fully developed, or the mechanism will not work. No intermediate stage will do the job. And neither would  snRNPs (U1, U2, U4, U5, and U6) have any function if not fully developed. And even if they were there, without the branch-point-binding protein (BBP) in place, nothing done, either, since the correct splice site could not be recognized. Had the introns and exons not have to emerge simultaneously with the Spliceosome ? No wonder, does the paper : " Origin and evolution of spliceosomal introns " admit:  Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. 1 and it  concludes that : The elucidation of the general scenario of evolution of eukaryote gene architecture by no account implies that the main problems in the study of intron evolution and function have been solved. Quite the contrary, fundamental questions remains wide open. If the first evolutionary step would have been the arise of  self-splicing Group II introns, then the question would follow : Why would evolution not have stopped there, since that method works just fine ? 


There is no credible road map, how introns and exons, and  the splice function could have emerged gradually. What good would the spliceosome be good for, if the essential sequence elements to recognise where to slice would not be in place ? What would happen, if the pre mRNA with exons and introns were in place, but no spliceosome ready in place to do the post transcriptional modification, and neither the splicing code, which directs the way where to splice ?  In the article : ‘JUNK’ DNA HIDES ASSEMBLY INSTRUCTIONS, the author,  Wang,  observes that splicing "is a tightly regulated process, and a great number of  diseases are caused by the 'misregulation' of splicing in which the gene was not cut and pasted correctly." Missplicing in the cell can have dire consequences as the desired product is not produced, and often the wrong products can be toxic for the cell. For this reason, it  has been proposed that  ATPases are important for ‘proofreading’ mechanisms that promote fidelity in splice site selection. In his textbook Essentials of Molecular Biology, George Malacinski points out why proper polypeptide production is critical:

"A cell cannot, of course, afford to miss any of the splice junctions by even a single nucleotide, because this could result in an interruption of the correct reading frame, leading to a truncated protein." 


The required precision is quite amazing, and even more astounding is the fact that these incredibly complex molecular machines are able and capable to do the Job in the precise manner as needed. 

Following the binding of these initial components, the remainder of the splicing apparatus assembles around them, in some cases displacing some of the previously bound components.

Question: How could the information to assemble the splicing apparatus correctly have emerged gradually ? In order to do so, had the assembly parts not have to be there, at the assembly site, fully developed, and ready for recruitment?  Had the availability of these parts not have  to be synchronized so that at some point, either individually or in combination, they were all available at the same time ? Had the assembly not have to be coordinated in the right way right from the start ? Had the parts not have to be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’ ? even if sub systems or parts are put together in the right order, they also need to interface correctly.


Is it feasable that this complex machine were the result of a progressive evolutionary development, in which simple molecules are the start of the biosynthesis chain and are then progressively developed in sequencial steps, if the end goal is not known by the process and mechanism promoting the development ?  How could  each intermediate in the pathway be a end point in the pathway, if that end point had no function ? Did not  each intermediate have to be usable in the past as an end product ? And how could the be usable, if the amino acid sequence chain had only a fraction of the fully developed sequence ? How could successive steps be added to improve the efficiency of a product where there was no use for it at this stage ?  Despite the fact that proponents of naturalism embrace this kind of scenario, it seems obvious that is extremely unlikely to be possible that way.

Martin and Koonin admit in their paper  “Hypothesis: Introns and the origin of nucleus-cytosol compartmentalization,”:  The transition to spliceosome-dependent splicing will also impose an unforgiving demand for inventions in addition to the spliceosome. And furthermore: More recent are the insights that there is virtually no evolutionary grade detectable in the origin of the spliceosome, which apparently was present in its (almost) fully fledged state in the common ancestor of eukaryotic lineages studied so far. Thats a surprising admittance.

This means that  the spliceosome  appeared fully formed almost abruptly, and that the intron invasion took place over a short time and has not changed for supposedly hundreds of millions of years.

In another interesting paper : Breaking the second genetic code, the authors write 2 :  The genetic instructions of complex organisms exhibit a counter-intuitive feature not shared by simpler genomes: nucleotide sequences coding for a protein (exons) are interrupted by other nucleotide regions that seem to hold no information (introns). This bizarre organization of genetic messages forces cells to remove introns from the precursor mRNA (pre-mRNA) and then splice together the exons to generate translatable instructions. An advantage of this mechanism is that it allows different cells to choose alternative means of pre-mRNA splicing and thus generates diverse messages from a single gene. The variant mRNAs can then encode different proteins
with distinct functions. One difficulty with understanding alternative pre-mRNA splicing is that the selection of particular exons in mature mRNAs is determined not only by intron sequences adjacent to the exon boundaries, but also by a multitude of other sequence elements present in both exons and introns. These auxiliary sequences are recognized by regulatory factors that assist or prevent the function of the spliceosome — the molecular machinery in charge of intron removal.

Moreover, coupling between RNA processing and gene transcription influences alternative splicing, and recent data implicate the packing of DNA with histone proteins and histone covalent modifications — the epigenetic code — in the regulation of splicing. The interplay between the histone and the splicing codes will therefore need to be accurately formulated in future approaches. 

Question: How could natural mechanisms have provided  the tuning, synchronization and coordination  between the histone and the splicing codes ? First, these two codes and the carrier proteins and molecules ( the hardware and software ) would have to emerge by themself, and in a second step orchestrate  their coordination. Why is it reasonable to believe, that unguided, random chemical reactions would be capable of emerging with  the immensly complex organismal functions ? 

Fazale Rana puts it nicely :  Astounding is the fact that other codes, such as the histone binding code, transcription factor binding code, the splicing code, and the RNA secondary structure code, overlap the genetic code. Each of these codes plays a special role in gene expression, but they also must work together in a coherent integrated fashion.
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13-09-2015, 07:22 AM
RE: All cellular functions are  irreducibly complex
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13-09-2015, 08:59 AM
RE: All cellular functions are  irreducibly complex
(13-09-2015 07:12 AM)Godexists Wrote:  The awe inspiring spliceosome, the most complex macromolecular machines known, and pre-mRNA processing in eukaryotic cells

http://reasonandscience.heavenforum.org/...otic-cells

Along the way to make proteins in eukaryotic cells,  there is a whole chain of subsequent events that must all be fully operational, and the machinery in place, in order to get the functional product, that is  proteins. At the beginning of the process, DNA is transcribed in the RNA polymerase molecular machine, to yield messenger RNA ( mRNA ) , which afterwards must go through post transcriptional modifications. That is CAPPING,  ELONGATION,  SPLICING, CLEAVAGE,POLYADENYLATION AND TERMINATION , before it can be EXPORTED FROM THE NUCLEUS TO THE CYTOSOL,  and PROTEIN SYNTHESIS INITIATED, (TRANSLATION), and  COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING.

Bacterial mRNAs are synthesized by the RNA polymerase starting and stopping at specific spots on the genome. The situation in eukaryotes is substantially different. In particular, transcription is only the first of several steps needed to produce a mature mRNA molecule. The mature transcript for many genes is encoded in a discontinuous manner in a series of discrete exons, which are separated from each other along the DNA strand by non-coding introns. mRNAs, rRNAs, and tRNAs can all contain introns that must be removed from precursor RNAs to produce functional molecules.The formidable task of identifying and splicing together exons among all the intronic RNA is performed by a large ribonucleoprotein machine, the spliceosome, which is composed of several individual small nuclear ribonucleoproteins,  five snRNPs,  pronounced ‘snurps’, (U1, U2, U4, U5, and U6) each containing an RNA molecule called an snRNA that is usually 100–300 nucleotides long, plus additional protein factors that recognize specific sequences in the mRNA or promote conformational rearrangements in the spliceosome required for the splicing reaction to progress, and many more additional proteins that come and go during the splicing reaction.  It has been described as one of "the most complex macromolecular machines known," "composed of as many as 300 distinct proteins and five RNAs".

The snRNAs perform many of the spliceosome’s mRNA recognition events. Splice site consensus sequences are recognized by non-snRNP factors; the branch-point sequence is recognized by the branch-point-binding protein (BBP), and the polypyrimidine tract and 3′ splice site are bound by two specific protein components of a splicing complex referred to as U2AF (U2 auxiliary factor), U2AF65 and U2AF35, respectively.

This is one more great example of a amazingly complex molecular machine, that will operate and exercise its precise orchestrated function properly ONLY with ALL components fully developed and formed and able to interact in a highly complex, ordered , precise manner. Both, the software, and the hardware, must be in place fully developed, or the mechanism will not work. No intermediate stage will do the job. And neither would  snRNPs (U1, U2, U4, U5, and U6) have any function if not fully developed. And even if they were there, without the branch-point-binding protein (BBP) in place, nothing done, either, since the correct splice site could not be recognized. Had the introns and exons not have to emerge simultaneously with the Spliceosome ? No wonder, does the paper : " Origin and evolution of spliceosomal introns " admit:  Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. 1 and it  concludes that : The elucidation of the general scenario of evolution of eukaryote gene architecture by no account implies that the main problems in the study of intron evolution and function have been solved. Quite the contrary, fundamental questions remains wide open. If the first evolutionary step would have been the arise of  self-splicing Group II introns, then the question would follow : Why would evolution not have stopped there, since that method works just fine ? 


There is no credible road map, how introns and exons, and  the splice function could have emerged gradually. What good would the spliceosome be good for, if the essential sequence elements to recognise where to slice would not be in place ? What would happen, if the pre mRNA with exons and introns were in place, but no spliceosome ready in place to do the post transcriptional modification, and neither the splicing code, which directs the way where to splice ?  In the article : ‘JUNK’ DNA HIDES ASSEMBLY INSTRUCTIONS, the author,  Wang,  observes that splicing "is a tightly regulated process, and a great number of  diseases are caused by the 'misregulation' of splicing in which the gene was not cut and pasted correctly." Missplicing in the cell can have dire consequences as the desired product is not produced, and often the wrong products can be toxic for the cell. For this reason, it  has been proposed that  ATPases are important for ‘proofreading’ mechanisms that promote fidelity in splice site selection. In his textbook Essentials of Molecular Biology, George Malacinski points out why proper polypeptide production is critical:

"A cell cannot, of course, afford to miss any of the splice junctions by even a single nucleotide, because this could result in an interruption of the correct reading frame, leading to a truncated protein." 


The required precision is quite amazing, and even more astounding is the fact that these incredibly complex molecular machines are able and capable to do the Job in the precise manner as needed. 

Following the binding of these initial components, the remainder of the splicing apparatus assembles around them, in some cases displacing some of the previously bound components.

Question: How could the information to assemble the splicing apparatus correctly have emerged gradually ? In order to do so, had the assembly parts not have to be there, at the assembly site, fully developed, and ready for recruitment?  Had the availability of these parts not have  to be synchronized so that at some point, either individually or in combination, they were all available at the same time ? Had the assembly not have to be coordinated in the right way right from the start ? Had the parts not have to be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’ ? even if sub systems or parts are put together in the right order, they also need to interface correctly.


Is it feasable that this complex machine were the result of a progressive evolutionary development, in which simple molecules are the start of the biosynthesis chain and are then progressively developed in sequencial steps, if the end goal is not known by the process and mechanism promoting the development ?  How could  each intermediate in the pathway be a end point in the pathway, if that end point had no function ? Did not  each intermediate have to be usable in the past as an end product ? And how could the be usable, if the amino acid sequence chain had only a fraction of the fully developed sequence ? How could successive steps be added to improve the efficiency of a product where there was no use for it at this stage ?  Despite the fact that proponents of naturalism embrace this kind of scenario, it seems obvious that is extremely unlikely to be possible that way.

Martin and Koonin admit in their paper  “Hypothesis: Introns and the origin of nucleus-cytosol compartmentalization,”:  The transition to spliceosome-dependent splicing will also impose an unforgiving demand for inventions in addition to the spliceosome. And furthermore: More recent are the insights that there is virtually no evolutionary grade detectable in the origin of the spliceosome, which apparently was present in its (almost) fully fledged state in the common ancestor of eukaryotic lineages studied so far. Thats a surprising admittance.

This means that  the spliceosome  appeared fully formed almost abruptly, and that the intron invasion took place over a short time and has not changed for supposedly hundreds of millions of years.

In another interesting paper : Breaking the second genetic code, the authors write 2 :  The genetic instructions of complex organisms exhibit a counter-intuitive feature not shared by simpler genomes: nucleotide sequences coding for a protein (exons) are interrupted by other nucleotide regions that seem to hold no information (introns). This bizarre organization of genetic messages forces cells to remove introns from the precursor mRNA (pre-mRNA) and then splice together the exons to generate translatable instructions. An advantage of this mechanism is that it allows different cells to choose alternative means of pre-mRNA splicing and thus generates diverse messages from a single gene. The variant mRNAs can then encode different proteins
with distinct functions. One difficulty with understanding alternative pre-mRNA splicing is that the selection of particular exons in mature mRNAs is determined not only by intron sequences adjacent to the exon boundaries, but also by a multitude of other sequence elements present in both exons and introns. These auxiliary sequences are recognized by regulatory factors that assist or prevent the function of the spliceosome — the molecular machinery in charge of intron removal.

Moreover, coupling between RNA processing and gene transcription influences alternative splicing, and recent data implicate the packing of DNA with histone proteins and histone covalent modifications — the epigenetic code — in the regulation of splicing. The interplay between the histone and the splicing codes will therefore need to be accurately formulated in future approaches. 

Question: How could natural mechanisms have provided  the tuning, synchronization and coordination  between the histone and the splicing codes ? First, these two codes and the carrier proteins and molecules ( the hardware and software ) would have to emerge by themself, and in a second step orchestrate  their coordination. Why is it reasonable to believe, that unguided, random chemical reactions would be capable of emerging with  the immensly complex organismal functions ? 

Fazale Rana puts it nicely :  Astounding is the fact that other codes, such as the histone binding code, transcription factor binding code, the splicing code, and the RNA secondary structure code, overlap the genetic code. Each of these codes plays a special role in gene expression, but they also must work together in a coherent integrated fashion.

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13-09-2015, 09:41 AM (This post was last modified: 13-09-2015 09:45 AM by Bucky Ball.)
RE: All cellular functions are  irreducibly complex
(13-09-2015 07:12 AM)Godexists Wrote:  The awe inspiring spliceosome, the most complex macromolecular machines known, and pre-mRNA processing in eukaryotic cells

http://reasonandscience.heavenforum.org/...otic-cells

Along the way to make proteins in eukaryotic cells,  there is a whole chain of subsequent events that must all be fully operational, and the machinery in place, in order to get the functional product, that is  proteins. At the beginning of the process, DNA is transcribed in the RNA polymerase molecular machine, to yield messenger RNA ( mRNA ) , which afterwards must go through post transcriptional modifications. That is CAPPING,  ELONGATION,  SPLICING, CLEAVAGE,POLYADENYLATION AND TERMINATION , before it can be EXPORTED FROM THE NUCLEUS TO THE CYTOSOL,  and PROTEIN SYNTHESIS INITIATED, (TRANSLATION), and  COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING.

Bacterial mRNAs are synthesized by the RNA polymerase starting and stopping at specific spots on the genome. The situation in eukaryotes is substantially different. In particular, transcription is only the first of several steps needed to produce a mature mRNA molecule. The mature transcript for many genes is encoded in a discontinuous manner in a series of discrete exons, which are separated from each other along the DNA strand by non-coding introns. mRNAs, rRNAs, and tRNAs can all contain introns that must be removed from precursor RNAs to produce functional molecules.The formidable task of identifying and splicing together exons among all the intronic RNA is performed by a large ribonucleoprotein machine, the spliceosome, which is composed of several individual small nuclear ribonucleoproteins,  five snRNPs,  pronounced ‘snurps’, (U1, U2, U4, U5, and U6) each containing an RNA molecule called an snRNA that is usually 100–300 nucleotides long, plus additional protein factors that recognize specific sequences in the mRNA or promote conformational rearrangements in the spliceosome required for the splicing reaction to progress, and many more additional proteins that come and go during the splicing reaction.  It has been described as one of "the most complex macromolecular machines known," "composed of as many as 300 distinct proteins and five RNAs".

The snRNAs perform many of the spliceosome’s mRNA recognition events. Splice site consensus sequences are recognized by non-snRNP factors; the branch-point sequence is recognized by the branch-point-binding protein (BBP), and the polypyrimidine tract and 3′ splice site are bound by two specific protein components of a splicing complex referred to as U2AF (U2 auxiliary factor), U2AF65 and U2AF35, respectively.

This is one more great example of a amazingly complex molecular machine, that will operate and exercise its precise orchestrated function properly ONLY with ALL components fully developed and formed and able to interact in a highly complex, ordered , precise manner. Both, the software, and the hardware, must be in place fully developed, or the mechanism will not work. No intermediate stage will do the job. And neither would  snRNPs (U1, U2, U4, U5, and U6) have any function if not fully developed. And even if they were there, without the branch-point-binding protein (BBP) in place, nothing done, either, since the correct splice site could not be recognized. Had the introns and exons not have to emerge simultaneously with the Spliceosome ? No wonder, does the paper : " Origin and evolution of spliceosomal introns " admit:  Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. 1 and it  concludes that : The elucidation of the general scenario of evolution of eukaryote gene architecture by no account implies that the main problems in the study of intron evolution and function have been solved. Quite the contrary, fundamental questions remains wide open. If the first evolutionary step would have been the arise of  self-splicing Group II introns, then the question would follow : Why would evolution not have stopped there, since that method works just fine ? 


There is no credible road map, how introns and exons, and  the splice function could have emerged gradually. What good would the spliceosome be good for, if the essential sequence elements to recognise where to slice would not be in place ? What would happen, if the pre mRNA with exons and introns were in place, but no spliceosome ready in place to do the post transcriptional modification, and neither the splicing code, which directs the way where to splice ?  In the article : ‘JUNK’ DNA HIDES ASSEMBLY INSTRUCTIONS, the author,  Wang,  observes that splicing "is a tightly regulated process, and a great number of  diseases are caused by the 'misregulation' of splicing in which the gene was not cut and pasted correctly." Missplicing in the cell can have dire consequences as the desired product is not produced, and often the wrong products can be toxic for the cell. For this reason, it  has been proposed that  ATPases are important for ‘proofreading’ mechanisms that promote fidelity in splice site selection. In his textbook Essentials of Molecular Biology, George Malacinski points out why proper polypeptide production is critical:

"A cell cannot, of course, afford to miss any of the splice junctions by even a single nucleotide, because this could result in an interruption of the correct reading frame, leading to a truncated protein." 


The required precision is quite amazing, and even more astounding is the fact that these incredibly complex molecular machines are able and capable to do the Job in the precise manner as needed. 

Following the binding of these initial components, the remainder of the splicing apparatus assembles around them, in some cases displacing some of the previously bound components.

Question: How could the information to assemble the splicing apparatus correctly have emerged gradually ? In order to do so, had the assembly parts not have to be there, at the assembly site, fully developed, and ready for recruitment?  Had the availability of these parts not have  to be synchronized so that at some point, either individually or in combination, they were all available at the same time ? Had the assembly not have to be coordinated in the right way right from the start ? Had the parts not have to be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’ ? even if sub systems or parts are put together in the right order, they also need to interface correctly.


Is it feasable that this complex machine were the result of a progressive evolutionary development, in which simple molecules are the start of the biosynthesis chain and are then progressively developed in sequencial steps, if the end goal is not known by the process and mechanism promoting the development ?  How could  each intermediate in the pathway be a end point in the pathway, if that end point had no function ? Did not  each intermediate have to be usable in the past as an end product ? And how could the be usable, if the amino acid sequence chain had only a fraction of the fully developed sequence ? How could successive steps be added to improve the efficiency of a product where there was no use for it at this stage ?  Despite the fact that proponents of naturalism embrace this kind of scenario, it seems obvious that is extremely unlikely to be possible that way.

Martin and Koonin admit in their paper  “Hypothesis: Introns and the origin of nucleus-cytosol compartmentalization,”:  The transition to spliceosome-dependent splicing will also impose an unforgiving demand for inventions in addition to the spliceosome. And furthermore: More recent are the insights that there is virtually no evolutionary grade detectable in the origin of the spliceosome, which apparently was present in its (almost) fully fledged state in the common ancestor of eukaryotic lineages studied so far. Thats a surprising admittance.

This means that  the spliceosome  appeared fully formed almost abruptly, and that the intron invasion took place over a short time and has not changed for supposedly hundreds of millions of years.

In another interesting paper : Breaking the second genetic code, the authors write 2 :  The genetic instructions of complex organisms exhibit a counter-intuitive feature not shared by simpler genomes: nucleotide sequences coding for a protein (exons) are interrupted by other nucleotide regions that seem to hold no information (introns). This bizarre organization of genetic messages forces cells to remove introns from the precursor mRNA (pre-mRNA) and then splice together the exons to generate translatable instructions. An advantage of this mechanism is that it allows different cells to choose alternative means of pre-mRNA splicing and thus generates diverse messages from a single gene. The variant mRNAs can then encode different proteins
with distinct functions. One difficulty with understanding alternative pre-mRNA splicing is that the selection of particular exons in mature mRNAs is determined not only by intron sequences adjacent to the exon boundaries, but also by a multitude of other sequence elements present in both exons and introns. These auxiliary sequences are recognized by regulatory factors that assist or prevent the function of the spliceosome — the molecular machinery in charge of intron removal.

Moreover, coupling between RNA processing and gene transcription influences alternative splicing, and recent data implicate the packing of DNA with histone proteins and histone covalent modifications — the epigenetic code — in the regulation of splicing. The interplay between the histone and the splicing codes will therefore need to be accurately formulated in future approaches. 

Question: How could natural mechanisms have provided  the tuning, synchronization and coordination  between the histone and the splicing codes ? First, these two codes and the carrier proteins and molecules ( the hardware and software ) would have to emerge by themself, and in a second step orchestrate  their coordination. Why is it reasonable to believe, that unguided, random chemical reactions would be capable of emerging with  the immensly complex organismal functions ? 

Fazale Rana puts it nicely :  Astounding is the fact that other codes, such as the histone binding code, transcription factor binding code, the splicing code, and the RNA secondary structure code, overlap the genetic code. Each of these codes plays a special role in gene expression, but they also must work together in a coherent integrated fashion.

Tell us, GE, how does it feel to have spent so many hours of your life, ... perhaps your whole life, involved with and promoting a bullshit fallacy ? No one here buys this crap. You have no converts. You're a failure. Science does not buy this nonsense. IF what you say did make sense, you would be asked to lecture and you would receive awards for this nonsense. In fact you are reduced to misrepresenting the positions of a few scientists, most of whom do not buy into your crap. You are as intellectually dishonest as they come.

Insufferable know-it-all.Einstein God has a plan for us. Please stop screwing it up with your prayers.
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13-09-2015, 11:20 AM
RE: All cellular functions are  irreducibly complex
This is what actual scientists comment about my op.

Dale Dickinson: Loved this post when I read it. I have a PhD in genetics and molecular biology and did two postdocs on cell signaling. The more I got into complex molecular and signaling cascades the more I came to believe that evolution was an absolute farce. Almost any change in DNA sequence (assuming at a locus that effects functional RNA production in some fashion) has a deleterious impact. While a positive impacts do come along, they are very, very rare, and given simple probability theory, could not account for irreducibly complex structures such as the spliceosome or signaling pathways with multiple levels of control and cross-talk.
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13-09-2015, 12:12 PM
RE: All cellular functions are  irreducibly complex
(13-09-2015 11:20 AM)Godexists Wrote:  This is what one actual scientists commented about my op.

Corrected for you.
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13-09-2015, 12:26 PM
RE: All cellular functions are  irreducibly complex
(13-09-2015 11:20 AM)Godexists Wrote:  This is what actual scientists comment about my op.

Dale Dickinson: Loved this post when I read it. I have a PhD in genetics and molecular biology and did two postdocs on cell signaling. The more I got into complex molecular and signaling cascades the more I came to believe that evolution was an absolute farce. Almost any change in DNA sequence (assuming at a locus that effects functional RNA production in some fashion) has a deleterious impact. While a positive impacts do come along, they are very, very rare, and given simple probability theory, could not account for irreducibly complex structures such as the spliceosome or signaling pathways with multiple levels of control and cross-talk.

Citation needed.

And rather unconvincing regardless. One person being irrational - even if that person is trained in biology - does not constitute actual evidence against evolution.

"Owl," said Rabbit shortly, "you and I have brains. The others have fluff. If there is any thinking to be done in this Forest - and when I say thinking I mean thinking - you and I must do it."
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13-09-2015, 12:52 PM (This post was last modified: 13-09-2015 01:04 PM by Bucky Ball.)
RE: All cellular functions are  irreducibly complex
(13-09-2015 11:20 AM)Godexists Wrote:  This is what actual scientists comment about my op.

Dale Dickinson: Loved this post when I read it. I have a PhD in genetics and molecular biology and did two postdocs on cell signaling. The more I got into complex molecular and signaling cascades the more I came to believe that evolution was an absolute farce. Almost any change in DNA sequence (assuming at a locus that effects functional RNA production in some fashion) has a deleterious impact. While a positive impacts do come along, they are very, very rare, and given simple probability theory, could not account for irreducibly complex structures such as the spliceosome or signaling pathways with multiple levels of control and cross-talk.

There is no evidence against the Theory of Evolution. Every major university in the world teaches it. ANY ONE scientist who could demonstrate it's unviability would be showered with fame and a Nobel prize. Evolution is seen operating every day in hospital labs and medical clinics, thousands of times every day, as pathogens EVOLVE resistance to the medications used to defeat them. These ARE "beneficial" to them. The "sequence" doesn't have to change, just the make-up of the DNA itself. More proof this fool knows nothing about the subject he pretends to go on about. He is an utter failure. The overwhelming consensus of science is that Evolution is the best theory we have that explains what we observe. Science is very competitive. Any scientist that could prove it was not true, (and it has been proven true by DNA), would have instant fame and recognition. These sorts of lame attempts by religious nuts just prove their desperation.

Where did Dale Dickinson say that ?
Prove it.

The fact is, GE is a damn liar.

We have seen the nonsense that science would not accept any alteration of, or tolerate and change to the theory of Evolution utterly debunked by the rise of Epigenetics. This was a surprise to genetics, but proven true. The idea that science holds it's present views of the mechanisms of Evolution sacrosanct and inviolable is false, and has been proven false by the rise abnd acceptance of Epigenetics.

Quote:Almost any change in DNA sequence (assuming at a locus that effects functional RNA production in some fashion) has a deleterious impact. While a positive impacts do come along, they are very, very rare, and given simple probability theory, could not account for irreducibly complex structures such as the spliceosome or signaling pathways with multiple levels of control and cross-talk.

... is a string of meaningless, (and incorrect) and in fact self-contradictory English words. The fact is these structures, building upon each other, HAVE been explained by multiple papers, by multiple scientists.

Insufferable know-it-all.Einstein God has a plan for us. Please stop screwing it up with your prayers.
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