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Resonate your identity with Naseeb journals. Express your opinions, share your thoughts, post your writings and connect with like minded people through the power of expression.
Poetry of the Genetic Code
Genetic code: A ?poetry,? ?optimal? and ?efficient? for ?parallel codes? that store not only ?protein-coding information? but also ?binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure.? Now let?s anticipate ad hoc evolutionary formulations explaining away the newly discovered features of the genetic code in an attempt to fit data to theory, let alone whether Darwinism predicted such intricacies. ?Nadeem
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Silent No Longer pubs.acs.org)
Ivan Amato
Chemical and Engineering News 85 (4), 38-40 (Jan 22, 2007)
Researchers unearth another stratum of meaning in the genetic code
The more scientists study the genetic code, the more it reads like poetry. In a poem, every word, every line break, even every syllable can carry more than a literal meaning. So too can the molecular letters, syllables, and words of the genetic code carry more biologically relevant meanings than they appear to at first.
Now, a cadre of researchers is discovering intriguing depths of meaning in "synonyms" in the genetic code?very short wordlike sequences, or codons, that translate into exactly the same amino acids during the construction of a protein. Scientists are finding that synonymous codons influence the temporal pattern by which a messenger RNA (mRNA) molecule bearing genetic specifications from a cell's nucleus is translated by machinelike ribosomes into protein molecules.
These punctuations in the RNA-to-protein translation process have unexpected consequences: They can change the timing by which nascent proteins fold as they elongate and peel away from ribosomes. This means that two stretches of mRNA that differ only in synonymous codons can translate into two proteins that have identical amino acid sequences but different three-dimensional shapes. Such differences can convey important, even grave, biological and medical meanings. It's akin to the way the same hand can fold into an affirming thumbs-up gesture or into a shape involving the middle finger that conveys another sentiment altogether.
"We know that one individual given drug A will have to sleep for three days, but another taking the same drug will suffer no such effect," notes Michael M. Gottesman, chief of the Laboratory of Cell Biology at the National Cancer Institute (NCI) in Bethesda, Md. He now thinks that such individual differences in response to drug treatments and in susceptibility to diseases could correspond to different synonymous codons that lead to differently folded protein products. Most researchers have assumed that this type of genetic variation is too subtle to matter much. In fact, an often-used moniker for the variation is "silent polymorphism." Nonsilent polymorphisms are those variations in a gene's code that do lead to amino acid changes.
Last month, Gottesman and coworkers reported results of their investigation of a silent polymorphism that isn't so silent (Science, DOI: 10.1126/science.1135308). They found it in the gene that codes for P-glycoprotein (P-gp), a protein that takes residence in cell membranes, where it pumps drug molecules out of the cell. By purging the cell of drugs, this protein renders about half of human cancers resistant to a diversity of drugs.
Gottesman's group discovered that a silent polymorphism sometimes found in this gene gives rise to a version of P-gp that is less effective at expelling drugs from cells than the "wild type" of the protein. The researchers conjecture that the altered protein function derives from a synonymous codon's effects on the timing of translation and folding as the P-gp protein is being made and as it insinuates itself into a cell's membrane. In their studies, the researchers expressed the gene with and without the silent polymorphism in cultured human carcinoma cells, an AIDS-related human cell line, and two lines of cells derived from monkey kidney.
"The beauty of the paper is that it is based on natural examples," that is, living cells, comments Anton Komar of Cleveland State University. He was one of the first scientists to suggest, in the late 1980s, that silent polymorphisms in genes might have important biological consequences. Previously, Komar and others had found evidence that synonymous codons might affect protein folding, but those studies were done in cell-free test-tube preparations. "Nobody paid attention," Komar recalls. The consensus view, he points out, has long been that only those polymorphisms that translate into amino acid substitutions in the associated proteins were biologically or medically significant. To Komar, Gottesman's findings ought to change that view.
"Looking closely at silent polymorphisms could become a vast project now," Komar says. "We have the whole genome in hand."
Gottesman was attracted to research into silent polymorphisms three years ago during a discussion with Randall Kincaid, a former immunology lab head at the National Institutes of Health in Bethesda, who now runs Veritas, a biotech company in nearby Rockville. Kincaid mentioned a malaria vaccine project that required him to produce loads of a human protein in a microbial host. The protein, however, kept folding up and aggregating into unusable clumps. Kincaid told Gottesman that to circumvent this protein-folding headache, his team used a genetic engineering technique that involves exchanging some of the codons in the human gene with synonymous codons that are more prevalent in the microbial host used to manufacture the protein in bulk.
During that 2003 discussion, Gottesman says, "a light bulb went off in my head." For Gottesman, Kincaid's protein-folding headache sounded like a potential answer to a mystery he and his colleagues had been encountering in their research on P-gp. Listening to Kincaid, Gottesman wondered if the differences in folding that his team had observed stemmed from the silent polymorphisms found in the gene for P-gp.
Silent polymorphisms are among a more general class known as single-nucleotide polymorphisms, or SNPs (pronounced "snips"). SNPs consist of one nucleotide letter substituting for another. In the mRNA transcribed from a gene, every string of three nucleotides constitutes a codon that corresponds to and is ultimately translated into one of 20 amino acids.
For example, the mRNA codon designated UUU (uracil-uracil-uracil) encodes the amino acid phenylalanine, whereas the codon UUA (uracil-uracil-adenine) encodes leucine. Because a leucine replaces a phenylalanine, the polymorphism is nonsilent in this case, and the codons are nonsynonymous. On the other hand, the mRNA codons GGU, GGC, GGA, and GGG all encode glycine. That makes them synonymous codons, and their protein constructs all have the same amino acid sequence.
Gottesman's group traced one particular silent SNP in the gene for P-gp?in which a GGC codon changes into GGT?to altered protein activity. Both codons correspond to glycine. Using several analytical methods, the researchers concluded that the folding, final shape, and function of P-gp indeed are influenced by silent SNPs.
"These results may not only change our thinking about mechanisms of drug resistance, but may also cause us to reassess our whole understanding of SNPs in general and what role they play in disease," states NCI Director John E. Niederhuber in a press release.
Komar conjectures that synonymous codons might affect protein folding by tweaking the timing of that folding. In cells, he notes, the concentrations of amino acid-toting transfer RNA (tRNA) molecules, each of which corresponds to a specific mRNA codon, roughly mirror the overall frequencies at which the codons appear.
During protein translation, the mRNA codons sequentially specify which tRNA must come into the ribosome complex to deliver the next amino acid to be stitched onto the growing protein. A polymorphism that substitutes an infrequent codon for a relatively common but synonymous codon ought to result in a delay in translation because there is less of the corresponding amino acid-bearing tRNA around, Komar says. Because of the momentary pause, the growing protein could fold in a different way than if the pause were absent.
The details of the altered folding kinetics remain largely unknown, but recent work by Luda Diatchenko of the University of North Carolina and her colleagues has opened up one route of investigation into those matters (Science 2006, 314, 1930). Like Gottesman's group, they found that different synonymous codons in a gene can lead to changes in the production of its protein product. The gene Diatchenko's team studied encodes a neurotransmitter-degrading enzyme called human catechol-O-methyltransferase, or COMT. This enzyme is central to the regulation of pain perception. The COMT gene exists in three common variants, each one consisting of both silent and nonsilent codon changes.
Depending on which variant a person has, he or she is likely to have low, average, or high pain sensitivity. The researchers found that differences in COMT production derive far more from differences in synonymous codons in the COMT gene than in nonsynonymous ones that lead to amino acid changes.
Moreover, Diatchenko and her colleagues were able to relate those codon and clinical differences to the presence or absence of a specific stabilizing loop structure in the mRNA molecules encoding the enzyme. The mRNAs that were more stable yielded COMT activities up to 25 times higher than that associated with the least stable mRNA. The researchers surmise that these stability differences influence either the rate at which the mRNA molecules are degraded or at which they can be translated into protein. Because the more stable mRNAs produce more of the neurotransmitter-degrading enzyme, they ultimately correspond to less pain sensitivity.
"We need to give much more weight to synonymous changes," Diatchenko concludes. "Now that we know that the difference in COMT expression depends on the secondary structure of mRNA, we can think of targeting this mechanism" to alleviate such conditions as persistent pain, she says.
Confirming that the genetic code has built into it "colons or commas" that influence the kinetics of protein synthesis and folding, Komar notes, is a reminder that the code has yet to be fully decrypted. It's a molecular poem whose deconstruction must continue. The question now for Komar and others is whether they've identified a previously hidden stratum of meaning in the genetic code that will significantly help account for the differences that make individuals unique, in illness and in health.
-----------------
The genetic code is nearly optimal for allowing additional information within protein-coding sequences www.genome.org)
Shalev Itzkovitz and Uri Alon
Genome Research 17, 405-412 (2007)
Abstract: DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These "parallel codes" include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code?minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
-----------------
The code of codes: Scientists discover parallel codes in genes www.eurekalert.org)
Public news of Itzkovitz/Alon article, Cold Spring Harbor Laboratory (Feb 8, 2007)
The genetic code is nearly optimal for harboring information
REHOVOT, Israel (Fri., Feb. 9, 2007) -- Today, researchers from The Weizmann Institute of Science report the discovery of two new properties of the genetic code. Their work, which appears online in Genome Research, shows that the genetic code?used by organisms as diverse as reef coral, termites, and humans?is nearly optimal for encoding signals of any length in parallel to sequences that code for proteins. In addition, they report that the genetic code is organized so efficiently that when the cellular machinery misses a beat during protein synthesis, the process is promptly halted before energy and resources are wasted.
"Our findings open the possibility that genes can carry additional, currently unknown codes," explains Dr. Uri Alon, principal investigator on the project. "These findings point at possible selection forces that may have shaped the universal genetic code."
The genetic code consists of 61 codons?tri-nucleotide sequences of DNA?that encode 20 amino acids, the building blocks of proteins. In addition, three codons signal the cellular machinery to stop protein synthesis after a full-length protein is built.
While the best-known function of genes is to code for proteins, the DNA sequences of genes also harbor signals for folding, organization, regulation, and splicing. These DNA sequences are typically a bit longer: from four to 150 or more nucleotides in length.
Alon and his doctoral student Shalev Itzkovitz compared the real genetic code to alternative, hypothetical genetic codes with equivalent codon-amino acid assignment characteristics. Remarkably, Itzkovitz and Alon showed that the real genetic code was superior to the vast majority of alternative genetic codes in terms of its ability to encode other information in protein-coding genes?such as splice sites, mRNA secondary structure, or regulatory signals.
Itzkovitz and Alon also demonstrated that the real genetic code provides for the quickest incorporation of a stop signal?compared to most of the alternative genetic codes?in cases where protein synthesis has gone amiss (situations that scientists call "frameshift errors"). This helps the cell to conserve its energy and resources.
"We think that the ability to carry parallel codes?or information beyond the amino acid code?may be a side effect of selection for avoiding aberrant protein synthesis," says Itzkovitz. "These parallel codes were probably exploited during evolution to allow genes to support a wide range of signals to regulate and modify biological processes in cells."
The results of this study will be useful for researchers seeking to identify DNA sequences that regulate the expression and function of the genome. Many currently known regulatory sequences reside in non-protein-coding regions, but this may give scientists incentive to delve deeper into the protein-coding genes in order to solve life's mysteries.
About Genome Research: Genome Research genome.org) is an international, continuously published, peer-reviewed journal published by Cold Spring Harbor Laboratory Press. Launched in 1995, it is one of the five most highly cited primary research journals in genetics and genomics.
About Cold Spring Harbor Laboratory Press: Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit cshlpress.com.
-----------------
Silent No Longer pubs.acs.org)
Ivan Amato
Chemical and Engineering News 85 (4), 38-40 (Jan 22, 2007)
Researchers unearth another stratum of meaning in the genetic code
The more scientists study the genetic code, the more it reads like poetry. In a poem, every word, every line break, even every syllable can carry more than a literal meaning. So too can the molecular letters, syllables, and words of the genetic code carry more biologically relevant meanings than they appear to at first.
Now, a cadre of researchers is discovering intriguing depths of meaning in "synonyms" in the genetic code?very short wordlike sequences, or codons, that translate into exactly the same amino acids during the construction of a protein. Scientists are finding that synonymous codons influence the temporal pattern by which a messenger RNA (mRNA) molecule bearing genetic specifications from a cell's nucleus is translated by machinelike ribosomes into protein molecules.
These punctuations in the RNA-to-protein translation process have unexpected consequences: They can change the timing by which nascent proteins fold as they elongate and peel away from ribosomes. This means that two stretches of mRNA that differ only in synonymous codons can translate into two proteins that have identical amino acid sequences but different three-dimensional shapes. Such differences can convey important, even grave, biological and medical meanings. It's akin to the way the same hand can fold into an affirming thumbs-up gesture or into a shape involving the middle finger that conveys another sentiment altogether.
"We know that one individual given drug A will have to sleep for three days, but another taking the same drug will suffer no such effect," notes Michael M. Gottesman, chief of the Laboratory of Cell Biology at the National Cancer Institute (NCI) in Bethesda, Md. He now thinks that such individual differences in response to drug treatments and in susceptibility to diseases could correspond to different synonymous codons that lead to differently folded protein products. Most researchers have assumed that this type of genetic variation is too subtle to matter much. In fact, an often-used moniker for the variation is "silent polymorphism." Nonsilent polymorphisms are those variations in a gene's code that do lead to amino acid changes.
Last month, Gottesman and coworkers reported results of their investigation of a silent polymorphism that isn't so silent (Science, DOI: 10.1126/science.1135308). They found it in the gene that codes for P-glycoprotein (P-gp), a protein that takes residence in cell membranes, where it pumps drug molecules out of the cell. By purging the cell of drugs, this protein renders about half of human cancers resistant to a diversity of drugs.
Gottesman's group discovered that a silent polymorphism sometimes found in this gene gives rise to a version of P-gp that is less effective at expelling drugs from cells than the "wild type" of the protein. The researchers conjecture that the altered protein function derives from a synonymous codon's effects on the timing of translation and folding as the P-gp protein is being made and as it insinuates itself into a cell's membrane. In their studies, the researchers expressed the gene with and without the silent polymorphism in cultured human carcinoma cells, an AIDS-related human cell line, and two lines of cells derived from monkey kidney.
"The beauty of the paper is that it is based on natural examples," that is, living cells, comments Anton Komar of Cleveland State University. He was one of the first scientists to suggest, in the late 1980s, that silent polymorphisms in genes might have important biological consequences. Previously, Komar and others had found evidence that synonymous codons might affect protein folding, but those studies were done in cell-free test-tube preparations. "Nobody paid attention," Komar recalls. The consensus view, he points out, has long been that only those polymorphisms that translate into amino acid substitutions in the associated proteins were biologically or medically significant. To Komar, Gottesman's findings ought to change that view.
"Looking closely at silent polymorphisms could become a vast project now," Komar says. "We have the whole genome in hand."
Gottesman was attracted to research into silent polymorphisms three years ago during a discussion with Randall Kincaid, a former immunology lab head at the National Institutes of Health in Bethesda, who now runs Veritas, a biotech company in nearby Rockville. Kincaid mentioned a malaria vaccine project that required him to produce loads of a human protein in a microbial host. The protein, however, kept folding up and aggregating into unusable clumps. Kincaid told Gottesman that to circumvent this protein-folding headache, his team used a genetic engineering technique that involves exchanging some of the codons in the human gene with synonymous codons that are more prevalent in the microbial host used to manufacture the protein in bulk.
During that 2003 discussion, Gottesman says, "a light bulb went off in my head." For Gottesman, Kincaid's protein-folding headache sounded like a potential answer to a mystery he and his colleagues had been encountering in their research on P-gp. Listening to Kincaid, Gottesman wondered if the differences in folding that his team had observed stemmed from the silent polymorphisms found in the gene for P-gp.
Silent polymorphisms are among a more general class known as single-nucleotide polymorphisms, or SNPs (pronounced "snips"). SNPs consist of one nucleotide letter substituting for another. In the mRNA transcribed from a gene, every string of three nucleotides constitutes a codon that corresponds to and is ultimately translated into one of 20 amino acids.
For example, the mRNA codon designated UUU (uracil-uracil-uracil) encodes the amino acid phenylalanine, whereas the codon UUA (uracil-uracil-adenine) encodes leucine. Because a leucine replaces a phenylalanine, the polymorphism is nonsilent in this case, and the codons are nonsynonymous. On the other hand, the mRNA codons GGU, GGC, GGA, and GGG all encode glycine. That makes them synonymous codons, and their protein constructs all have the same amino acid sequence.
Gottesman's group traced one particular silent SNP in the gene for P-gp?in which a GGC codon changes into GGT?to altered protein activity. Both codons correspond to glycine. Using several analytical methods, the researchers concluded that the folding, final shape, and function of P-gp indeed are influenced by silent SNPs.
"These results may not only change our thinking about mechanisms of drug resistance, but may also cause us to reassess our whole understanding of SNPs in general and what role they play in disease," states NCI Director John E. Niederhuber in a press release.
Komar conjectures that synonymous codons might affect protein folding by tweaking the timing of that folding. In cells, he notes, the concentrations of amino acid-toting transfer RNA (tRNA) molecules, each of which corresponds to a specific mRNA codon, roughly mirror the overall frequencies at which the codons appear.
During protein translation, the mRNA codons sequentially specify which tRNA must come into the ribosome complex to deliver the next amino acid to be stitched onto the growing protein. A polymorphism that substitutes an infrequent codon for a relatively common but synonymous codon ought to result in a delay in translation because there is less of the corresponding amino acid-bearing tRNA around, Komar says. Because of the momentary pause, the growing protein could fold in a different way than if the pause were absent.
The details of the altered folding kinetics remain largely unknown, but recent work by Luda Diatchenko of the University of North Carolina and her colleagues has opened up one route of investigation into those matters (Science 2006, 314, 1930). Like Gottesman's group, they found that different synonymous codons in a gene can lead to changes in the production of its protein product. The gene Diatchenko's team studied encodes a neurotransmitter-degrading enzyme called human catechol-O-methyltransferase, or COMT. This enzyme is central to the regulation of pain perception. The COMT gene exists in three common variants, each one consisting of both silent and nonsilent codon changes.
Depending on which variant a person has, he or she is likely to have low, average, or high pain sensitivity. The researchers found that differences in COMT production derive far more from differences in synonymous codons in the COMT gene than in nonsynonymous ones that lead to amino acid changes.
Moreover, Diatchenko and her colleagues were able to relate those codon and clinical differences to the presence or absence of a specific stabilizing loop structure in the mRNA molecules encoding the enzyme. The mRNAs that were more stable yielded COMT activities up to 25 times higher than that associated with the least stable mRNA. The researchers surmise that these stability differences influence either the rate at which the mRNA molecules are degraded or at which they can be translated into protein. Because the more stable mRNAs produce more of the neurotransmitter-degrading enzyme, they ultimately correspond to less pain sensitivity.
"We need to give much more weight to synonymous changes," Diatchenko concludes. "Now that we know that the difference in COMT expression depends on the secondary structure of mRNA, we can think of targeting this mechanism" to alleviate such conditions as persistent pain, she says.
Confirming that the genetic code has built into it "colons or commas" that influence the kinetics of protein synthesis and folding, Komar notes, is a reminder that the code has yet to be fully decrypted. It's a molecular poem whose deconstruction must continue. The question now for Komar and others is whether they've identified a previously hidden stratum of meaning in the genetic code that will significantly help account for the differences that make individuals unique, in illness and in health.
-----------------
The genetic code is nearly optimal for allowing additional information within protein-coding sequences www.genome.org)
Shalev Itzkovitz and Uri Alon
Genome Research 17, 405-412 (2007)
Abstract: DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These "parallel codes" include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code?minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
-----------------
The code of codes: Scientists discover parallel codes in genes www.eurekalert.org)
Public news of Itzkovitz/Alon article, Cold Spring Harbor Laboratory (Feb 8, 2007)
The genetic code is nearly optimal for harboring information
REHOVOT, Israel (Fri., Feb. 9, 2007) -- Today, researchers from The Weizmann Institute of Science report the discovery of two new properties of the genetic code. Their work, which appears online in Genome Research, shows that the genetic code?used by organisms as diverse as reef coral, termites, and humans?is nearly optimal for encoding signals of any length in parallel to sequences that code for proteins. In addition, they report that the genetic code is organized so efficiently that when the cellular machinery misses a beat during protein synthesis, the process is promptly halted before energy and resources are wasted.
"Our findings open the possibility that genes can carry additional, currently unknown codes," explains Dr. Uri Alon, principal investigator on the project. "These findings point at possible selection forces that may have shaped the universal genetic code."
The genetic code consists of 61 codons?tri-nucleotide sequences of DNA?that encode 20 amino acids, the building blocks of proteins. In addition, three codons signal the cellular machinery to stop protein synthesis after a full-length protein is built.
While the best-known function of genes is to code for proteins, the DNA sequences of genes also harbor signals for folding, organization, regulation, and splicing. These DNA sequences are typically a bit longer: from four to 150 or more nucleotides in length.
Alon and his doctoral student Shalev Itzkovitz compared the real genetic code to alternative, hypothetical genetic codes with equivalent codon-amino acid assignment characteristics. Remarkably, Itzkovitz and Alon showed that the real genetic code was superior to the vast majority of alternative genetic codes in terms of its ability to encode other information in protein-coding genes?such as splice sites, mRNA secondary structure, or regulatory signals.
Itzkovitz and Alon also demonstrated that the real genetic code provides for the quickest incorporation of a stop signal?compared to most of the alternative genetic codes?in cases where protein synthesis has gone amiss (situations that scientists call "frameshift errors"). This helps the cell to conserve its energy and resources.
"We think that the ability to carry parallel codes?or information beyond the amino acid code?may be a side effect of selection for avoiding aberrant protein synthesis," says Itzkovitz. "These parallel codes were probably exploited during evolution to allow genes to support a wide range of signals to regulate and modify biological processes in cells."
The results of this study will be useful for researchers seeking to identify DNA sequences that regulate the expression and function of the genome. Many currently known regulatory sequences reside in non-protein-coding regions, but this may give scientists incentive to delve deeper into the protein-coding genes in order to solve life's mysteries.
About Genome Research: Genome Research genome.org) is an international, continuously published, peer-reviewed journal published by Cold Spring Harbor Laboratory Press. Launched in 1995, it is one of the five most highly cited primary research journals in genetics and genomics.
About Cold Spring Harbor Laboratory Press: Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit cshlpress.com.
Comments on this journal
"Many investigators now consider nucleic acids to be much more plausible candidates for the first self-replicating molecules. The work of Watson and Crick and others has shown that proteins are formed according to the instructions coded in DNA. But there is a hitch. DNA cannot do its work, including forming more DNA, without the help of catalytic proteins, or enzymes. In short, proteins cannot form without DNA, but neither can DNA form without proteins. To those pondering the origin of life, it is a classic chicken-and-egg problem: Which came first, proteins or DNA?" 1
"The development of the metabolic system, which, as the primordial soup thinned, must have "learned" to mobilize chemical potential and to synthesize the cellular components, poses Herculean problems. So also does the emergence of the selectively permeable membrane without which there can be no viable cell. But the major problem is the origin of the genetic code and of its translation mechanism. Indeed, instead of a problem it ought rather to be called a riddle. The code is meaningless unless translated. The modern cell's translating machinery consists of at least fifty macromolecular components which are themselves coded in DNA: the code cannot be translated otherwise than by products of translation. It is the modern expression of omne vivum ex ovo. When and how did this circle become closed? It is exceedingly difficult to imagine." 2 (emphasis in original)
"Anyone trying to solve this puzzle immediately encounters a paradox. Nowadays nucleic acids are synthesized only with the help of proteins, and proteins are synthesized only if their corresponding nucleotide sequence is present. It is extremely improbable that proteins and nucleic acids, both of which are structurally complex, arose spontaneously in the same place at the same time. Yet it also seems impossible to have one without the other. And so, at first glance, one might have to conclude that life could never, in fact, have originated by chemical means." 3
The RNA world hypothesis has attempted to evade the ?hitch? in the DNA-protein chicken-and-egg chase, only to get knocked down by newfangled quandaries. Now the typical criticism is doomed to strike, ?Foolhardy it is to give up looking for a natural cause. Argument from ignorance it is to regress to design and to hold back scientific progress.? At first, the criticism seems fairly reasonable, but deeper psychoanalysis of such an outlook, which refuses to embrace the scientific spirit in embarking toward wherever positive evidence leads, shows that the objection affords the latitude to indefinitely retain human ego in the comfort zone of the naturalist?s preconceived philosophical commitment to materialism. It is quite obvious then why it is in the best personal interest of the naturalist to remain faithfully committed to such an objection, critical to fortifying, despite opposing scientific evidence, the gospel of materialistic philosophy from the slightest possibility of collapse. And by the way, censuring design on religious or on supernatural grounds is also an effective strategy to sustain materialistic totalitarianism in the sciences.
1. John Horgan (Science Writer), ?In the Beginning ?,? Scientific American 264 (2), 100-109 (February 1991).
2. Jaques Monod (Biochemist and Physiology/Medicine Nobel Prize Laureate), Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology (London: Penguin, 1997) 143.
3. Leslie Orgel (Biochemist, Salk Institute for Biological Studies), "The Origin of Life on the Earth," Scientific American, 271 (4), 54 (October 1994).
Nature recognized certain protein syntheses as aberrant and avoided them. Nature produced and detected parallel codes. Nature exploited the codes and allowed genes to support a wide range of signals to regulate and modify cellular processes. How do natural processes produce from scratch complex and specified actions that ?recognize, produce, detect, exploit, allow, support, regulate, and modify? certain operations in order to actualize the final specified outcome (life-support) and that ?avoid? other operations in the probabilistic phase space of all possibilities? The speculation conceals multitude of devastating molecular and mathematical hurdles that are so effortlessly overlooked with anthropomorphic action verbs that otherwise characterize causal actions of intelligent agency.
>> Their work, which appears online in Genome Research, shows that the genetic code?used by organisms as diverse as reef coral, termites, and humans?is nearly optimal for encoding signals of any length in parallel to sequences that code for proteins.
>> Itzkovitz and Alon also demonstrated that the real genetic code provides for the quickest incorporation of a stop signal?compared to most of the alternative genetic codes?in cases where protein synthesis has gone amiss (situations that scientists call "frameshift errors"). This helps the cell to conserve its energy and resources.
>> Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons.
The observations, consistent with the ID paradigm, appear to have been unforeseen for evolutionary theory, however. For instance, under the Darwinist paradigm, how did the genetic code, ?used by organisms as diverse as reef coral, termites, and humans? and yet purportedly suffused with evolutionary scrap (?junk DNA?) accumulated over geological eons, turn out to be ?nearly optimal for encoding signals of any length in parallel to sequences that code for proteins?? Did some portions of the genome deteriorate into scrap, and other portions evolve optimality, energy efficiency, parallel encoding, and ?poetry?? If so, how did that happen? Under the Darwinist paradigm, I would imagine that the fact that the genetic code is a universal feature of living things means that (1) the newly discovered features of the code evolved by chance or by natural law early in the history of life on Earth, or (2) the features evolved several times in diverse evolutionary lineages. In the past, punctuated equilibrium was invented ad hoc when the fossil record (rapid wave of novel morphology, long stasis of unchanged morphology, and sudden extinction) did not bear out the Darwinist prediction of many gradually evolving transitional forms. I expect that evolutionists will likewise justify ad hoc (1) or (2) or amalgamation thereof to fit data to theory.
>> Confirming that the genetic code has built into it "colons or commas" that influence the kinetics of protein synthesis and folding, Komar notes, is a reminder that the code has yet to be fully decrypted. It's a molecular poem whose deconstruction must continue.
If the genetic code is ?yet to be fully decrypted? and if it is ?a molecular poem whose deconstruction must continue,? then why is so much of the DNA considered ?non-coding junk? (a misnomer)? ID theory had stated long before these findings that ?junk? DNA is not an unessential, evolutionary relic and that there is a lot we do not yet know about genomics. While ID encourages scientific inquiry from a design or an engineering perspective, evolutionary theory declares things inexplicable remnants of blind, natural processes. Anyone who does not concede the evolutionary perspective in biological research is considered to have stepped outside the bounds of science and is accorded little hearing and indeed no employment or research funding in the scientific enterprise.
The geneticist Theodosius Dobzhansky wrote in 1973 an essay titled ?Nothing in Biology Makes Sense Except in the Light of Evolution.? So how do these latest findings make sense in the light of evolution? Or, should we force evolution to make sense in the light of these findings, by adding more auxiliary fixes like punctuated equilibrium?