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Post by Al Moritz on Feb 10, 2010 22:22:43 GMT
In other words: "because the non-coding regions show little similarity to chimp sequences and because I don't know the precise function of the RNA transcripts, they must do absolutely nothing". It is precisely this Darwinian mentality that Sternberg said inhibited research in this topic. For under a Darwinian premise, human beings just can't be that different from chimps. And, as would (or should) be expected, the claim is untrue: we have found functions for many of them. See, e.g., these articles: Non-coding-RNA regulators of RNA polymerase II transcription, 2006 www.nature.com/nrm/journal/v7/n8/abs/nrm1946.html and Small dsRNAs induce transcriptional activation in human cells, 2006 www.pnas.org/content/103/46/17337.abstract . These non-coding RNA (i.e. those that are not translated into protein) have important regulatory functions. There are some misunderstandings here. It is a strawman to claim that scientists who consider a lot of DNA 'junk' deny the importance of non-coding regions. In fact, it is consensus among biochemists and biologists that gene regulation is a deciding factor in the differences between species, including the differences between humans and chimpanzees. After all, our cells 'only' express about 20,000 proteins, and we have this in common not just with chimpanzees, but with many other species, down to mice and probably further. And gene-regulation is driven by non-coding regions. So when you say: "For under a Darwinian premise, human beings just can't be that different from chimps", this is patently false. The fact that many non-coding regions are important, however, does not take away the likelihood that a lot of DNA is in fact 'junk'. Scientists have deleted up to 1.5 megabase (mb) regions of genes and found no deleterious effect. See: Nobrega MA et al. 2004. Megabase deletions of gene deserts result in viable mice. Nature 431: 988-993. A comment is found here: www.jgi.doe.gov/science/highlights/nobrega1004.htmlGiven the ludicrous differences in gene sizes between the Viscacha rat and the Brown Norway rat it is belief-defying to uphold the view that all of the extra Viscacha gene is essential.
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Post by zameel on Feb 10, 2010 23:44:00 GMT
It is a strawman to claim that scientists who consider a lot of DNA 'junk' deny the importance of non-coding regions. In fact, it is consensus among biochemists and biologists that gene regulation is a deciding factor in the differences between species, including the differences between humans and chimpanzees This is not consensus at all. Many Darwinians literally thought and still think the 2% or 5% difference (depending on whether indels are included) in coding regions between chimps and humans is the deciding factor in the differences. The gene regulatory elements in non-coding regions, the introns in this case, which include "promotors", "enhancers" and the like, were only disovered in the mid-90s, so this supposed consensus came relatively late. "Junk DNA" goes back to the 70s I think - because of the "central dogma" in biology it was thought anything that does not code proteins was junk, and the "selfish gene" model helped explain why they tagged along - both which according to Sternberg inhibited research on this topic. The fact that many non-coding regions are important, however, does not take away the likelihood that a lot of DNA is in fact 'junk'. "Junk" means nonfunctional i.e. useless, not merely that we can do without them. As Shapiro and Sternberg said the non-coding regions will be thought of as expert cellular control regimes. But the view that most of the DNA is "junk" persists only because of a Darwinian framework, not because of the evidence. See above where Ayala claimed Alu sequences were useless, but which in fact have functions in post transcription RNA splicing. Scientists have deleted up to 1.5 megabase (mb) regions of genes and found no deleterious effect. See: Nobrega MA et al. 2004. Megabase deletions of gene deserts result in viable mice. Nature 431: 988-993. A comment is found here: www.jgi.doe.gov/science/highlights/nobrega1004.html This is a straw man - there is equivocation first with nonessential and nonfunctional, and second, men are not mice: the above project and discussion is about the human genome. Further, Darwinian evolution would certainly not predict that "some noncoding sequences, even those that persist through the pressures of evolution, may indeed be disposable". By Darwinian logic, a logic with which I would agree, conserved elements most likely have a function, for otherwise they should be subject to neutral evolution.
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Post by Al Moritz on Feb 11, 2010 11:34:08 GMT
This is not consensus at all. Many Darwinians literally thought and still think the 2% or 5% difference (depending on whether indels are included) in coding regions between chimps and humans is the deciding factor in the differences. The gene regulatory elements in non-coding regions, the introns in this case, which include "promotors", "enhancers" and the like, were only disovered in the mid-90s, so this supposed consensus came relatively late. "Junk DNA" goes back to the 70s I think - because of the "central dogma" in biology it was thought anything that does not code proteins was junk, and the "selfish gene" model helped explain why they tagged along - both which according to Sternberg inhibited research on this topic. Fact check: the knowledge of promotors, and thus the importance of non-coding regions, dates back to the discovery of the lac operon, consisting of promotor, terminator and operator: en.wikipedia.org/wiki/Lac_operonIt was discovered on 1961 by Jacob and Monod (see ref. 4 in the article), who received the Nobel Prize for the discovery in 1965.
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Post by zameel on Feb 11, 2010 17:21:32 GMT
This is not consensus at all. Many Darwinians literally thought and still think the 2% or 5% difference (depending on whether indels are included) in coding regions between chimps and humans is the deciding factor in the differences. The gene regulatory elements in non-coding regions, the introns in this case, which include "promotors", "enhancers" and the like, were only disovered in the mid-90s, so this supposed consensus came relatively late. "Junk DNA" goes back to the 70s I think - because of the "central dogma" in biology it was thought anything that does not code proteins was junk, and the "selfish gene" model helped explain why they tagged along - both which according to Sternberg inhibited research on this topic. Fact check: the knowledge of promotors, and thus the importance of non-coding regions, dates back to the discovery of the lac operon, consisting of promotor, terminator and operator: en.wikipedia.org/wiki/Lac_operonIt was discovered on 1961 by Jacob and Monod (see ref. 4 in the article), who received the Nobel Prize for the discovery in 1965. The idea of "junk DNA" was in fact designed to rescue the "central dogma" from Monod-Jacob's gene regulation view (that proteins do indeed feedback information to DNA), so the latter's importance went into obscurity for over a generation until the late 90s, and even then the "central dogma" and "junk DNA" persisted. There is a good historical review here: www.springerlink.com/content/83t71g3355185l25/fulltext.pdf (reproduced here: junkdna.com/pellionisz_principle/ ): A Historical Recount: Specific Review of the Nascence and Demise of the Central Dogma and Junk DNA ConjecturesThe central dogma in its various renderings held that transfer of information from proteins and RNA back to DNA never happens. The central dogma of molecular biology was put forward in Crick's talks from 1956 (Fig. 4, c.f. recollection of Jacob, [14], p. 286), and published two years later [61]. This concept might be called "don't look back" or "no feedback permitted" postulate. Further, proponents of junk DNA [20] claimed that, even if a process could be found, a recursion from proteins and/or RNA to DNA could not retrieve information from functionless junk DNA (that is 98.7% of the human DNA). This conjecture may be called "even if you look back, you find only junk" postulate. Recursion for information was not only forbidden but in addition was pre-judged as useless because of an assumed void of information. It may be Watson's reduced version of the central dogma [62], wherein he emphasized what was surely found in genomic function and avoided needless and unsupported prohibitions, that helped the central dogma receive common acceptance from 1965 to 1969-1970, skirting sharp personal criticisms that were already present at its conception (e.g., questions as to its dogmatic stance; see Jacob's Memoirs, [14] pp. 288). A factor in the prevalence of the central dogma during this period might be that, since the 1965 Nobel Prize for Jacob and Monod's work on operon regulation [13], it had to be evident to Watson that, given the operon regulation of gene expression (as a function of the level of produced proteins), the prohibition of a protein-to-DNA information channel need not be in Watson's textbooks. His simplified and convenient view (avoiding controversial prohibitions and their refutation by data) is called here the concept of forward growth - which is, without recursion, only half the loop. This view, backed by Watson, prevailed so strongly that even the 50th anniversary issue of Scientific American, celebrating the discovery of the structure of DNA by Watson and Crick (1953) depicted as the general understanding that gene expression of DNA results, through RNA, in the construction of protein structures (see Fig.3, a composite illustration of the modified cover page figure of Scientific American of April, 2003, where on the right side the model of a Purkinje brain cell is pictured, from [5]) Reality was, as might be expected, much more complicated than any simplification. As early as 1969, in the Britten and Davidson theory of gene regulation [15], and by 1970 (cf. philosophical reflection by Darden [63]), the central dogma was squarely confronted by the discovery of reverse transcription, later called retroviruses, from RNA to DNA [16, 64]. Both Watson and Crick responded promptly but separately to the challenge posed by the discovery of the new enzyme that flagrantly violated their views. In the June 27, 1970 issue of Nature, the reverse transcriptase discovery was announced, and an anonymous "News and Views" article claimed: "Central Dogma Reversed". (Quote from Darden [63]): "Watson, in the 1970 second edition of his Molecular Biology of the Gene [18], said: 'The concept of a DNA provirus for an RNA virus is clearly a radical proposal. It overturns the belief that flow of genetic information always goes in the direction of DNA to RNA and never RNA to DNA. [Emphasis added, AJP] On the other hand, it offers an even greater variety of ways for cells to exchange genetic information. Considering the enormous complexity of biological systems, it would not be surprising if this device were uniquely advantageous in some situations.'" ([18], pp. 621-622) Crick (1970) also responded immediately to the challenge [17] but in a different way. (Unfortunately, the dogma wasn't allowed to gracefully expire.) Crick published a paper in Nature. His version of the central dogma, he contended, had not been reversed, as the anonymous Nature article had claimed. Crick stated, correctly, that in 1958 he had framed the central dogma in terms of the general transfer of information from nucleic acids to protein - but not the reverse (Crick 1958). That abstract claim had not yet been challenged. "If it were shown that information could flow from proteins to nucleic acids, he said, then such a finding would "shake the whole intellectual basis of molecular biology" ([17], p. 563). (Quote from Darden [63], emphasis added, Pellionisz). Thus, by 1970 the intellectual split between Crick, the originator of "The Central Dogma" (1956, [61]) and its promoter Watson (1965, [62]), threatened the collapse of the genomics establishment. The shaky ground of "The Central Dogma" was not really firmed up by the confession; "Dogma was just a catch phrase" (Crick, quoted in [65]). In the same year of the split, Ohno's junk DNA idea came to the rescue. Ohno first referred to garbage DNA in the human genome ([19], p. 62). Meaning that, even if there was recursive information access to DNA from proteins or from RNA, e.g. there was supposedly no information in the intronic and intergenic regions to be found and retrieved. Although the term "garbage DNA" floated in 1970, it did not take hold, but by 1972, in his presentation he began using the more suitable term "junk DNA", which did stick [20]. One should appreciate that, immediately after his presentation, the first person to rise in the discussion vehemently objected to the basis of the junk DNA conjecture (see "Discussion" by Boyer, in [20]): "It thus seems to me that the permissible number of structural loci is - as yet - a somewhat suspect way to arrive at figures of 1% structural utility to 99% junk." Why is it that Nobel Prize-winning experimental work (c.f. [66], Jacob's Nobel Lecture on his Prize with Monod, 1965) was available as early as within five years after Crick's conception of his dogma - yet no theoretical confrontation developed? Their operon regulation [13] clearly demonstrated that the protein-level, viewed as a result of genetic activity, did have an information-feedback mechanism on the genes in the DNA, such that down- or up-regulated DNA-RNA activity resulted, in accordance with the amount of protein already generated: "Experiments on genetic transfer by conjugation not only led to a revision of the concepts on the mechanisms of information transfer which occur in protein synthesis; they also made it possible to analyze the regulation of this synthesis. ... the operator is not transcribed into messenger and repression can be exerted only at the level of DNA. ... Gene expression was then usually believed to consist in the accumulation of stable structures in the cytoplasm, probably the RNA of ribosomes, which were assumed to serve as templates specifying protein structures... Such a scheme, which can be summarized by the aphorism 'one gene-one ribosome-one enzyme', was hardly compatible with an immediate protein synthesis at maximal rate." [13] In retrospect, and judging from Jacob's Memoirs [14] it seems evident that Jacob was fully aware of the intellectual conflict between the Jacob-Monod finding and Crick's central dogma, even at its birth (not shying away from direct criticism of the label "dogma", however): "In an acute sense of publicity, to baptize Central Dogma - that is to say, incontestable truth - a hypothesis that was unsupported by any serious argument." ([14], pp. 288) However, it appears that Jacob did not directly confront Crick on the latter's conception of the dogma [61], since that was prior to the publication of the Jacob-Monod operon concept. Jacob and Monod (1961) published their "operon regulation" work soon after, but did not receive their Prize until 1965; whereas in the following year, Watson and Crick (1962) received their award. Thus it was arguably more politic to avoid a direct conflict among the foursome. Almost simultaneously, however, in 1965 Watson [62] distanced himself from the central notion by putting forward his "simplified version" emphasizing what was undeniably true, although he did not dwell upon issues already controversial; see Fig. 2.) The point of this paper, however, is neither iconoclastic (discarding pragmatic doctrines while simply leaving a theoretical void in their place), nor to merely cite evidence for the widely reported means of feedback processes from proteins to DNA (and RNA to DNA). The point is to fill the void. PRGF is proposed to break through the "double ceiling" of the central dogma and junk DNA that impeded theoretical advances for half a century. Theoretical and Factual Breakdown of the Central Dogma and Junk DNAFurther flogging of two dead horses is avoided as much as possible. This abbreviated section merely supplies evidence, gives credit where most needed and points to the most powerful reviews. From the theoretical viewpoint of informatics, the "double lock" on recursive information has long been suspect. First, there is no more information for hereditary material than that present in the DNA. In humans, if 98.7% of the DNA is arbitrarily closed to access and in addition its information voided, the remaining information that 1.3% of the (human) genome harbors is deemed simply insufficient to govern development of such advanced organisms as vertebrates. It was painfully experienced, for instance, that when constructing a computer model of 1.68 million brain cells of the frog cerebellum, algorithmic approaches had to be invoked, rather than pretending that an impossible amount of information was available to specify the vast neural network in its every detail [67]. As for factual contradictions, the array of evidence - against both the central dogma and junk DNA conjectures - is staggering; see respective reviews [52, 53, 56]. Beyond the early factual evidence belying the validity of the central dogma ("Operonic Regulation by Feedback from Proteins to DNA"), another large assortment of facts is available, as follows. For an account of the (forbidden) information-transfer from RNA back to the DNA, see the very recent review by Mattick [59]; with background about the RNA world [68, 69, 70, 71, 72]. Major issues are gene silencing (or "turning genes on and off", e.g., by so-called LINE way stations, and switching via SINE-s). It is noteworthy that the PRGF is fully consistent with the currently vague notion of "turning genes on and off" - but goes further by invoking recursion not only the sign(s) of the "parallel feedback" are meaningful, but much more important information is the set of algorithmic values of recursive signals. [73, 74, 75, 76]. For the "orbidden" protein-to-DNA interaction, see the work on protein binding with the DNA, and methylation of the DNA by proteins - rendering DNA transcription reversibly or permanently impossible [77, 78, 79, 80, 81, 82]. For the (also forbidden) protein-protein interactions see Prions [83] and a detailed and philosophical review [52]. --------------------------------------------------------- Notice that Pellionisz says according to the "central dogma" and "junk DNA" models (which James Shapiro and others in the field strongly contest to a degree that it must be considered mainstream scientific, if not public, opinion) it was (and is) assumed the 2% divergence in human and chimp genomes was sufficient to account for the difference between the two. So your view that "it is consensus among biochemists and biologists that gene regulation is a deciding factor in the differences between species, including the differences between humans and chimpanzees" is incorrect; the "deciding factor" for many is the divergence in coding regions. Instead of addressing this substantial error, you pick on a technical error on my part that is, at least historically, negligible.
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Post by Al Moritz on Feb 11, 2010 20:09:13 GMT
The idea of "junk DNA" was in fact designed to rescue the "central dogma" from Monod-Jacob's gene regulation view (that proteins do indeed feedback information to DNA), so the latter's importance went into obscurity for over a generation until the late 90s, and even then the "central dogma" and "junk DNA" persisted. There is a good historical review here: www.springerlink.com/content/83t71g3355185l25/fulltext.pdf (reproduced here: junkdna.com/pellionisz_principle/ ): A Historical Recount: Specific Review of the Nascence and Demise of the Central Dogma and Junk DNA ConjecturesThe central dogma in its various renderings held that transfer of information from proteins and RNA back to DNA never happens. The central dogma of molecular biology was put forward in Crick's talks from 1956 (Fig. 4, c.f. recollection of Jacob, [14], p. 286), and published two years later [61]. This concept might be called "don't look back" or "no feedback permitted" postulate. Further, proponents of junk DNA [20] claimed that, even if a process could be found, a recursion from proteins and/or RNA to DNA could not retrieve information from functionless junk DNA (that is 98.7% of the human DNA). This conjecture may be called "even if you look back, you find only junk" postulate. Recursion for information was not only forbidden but in addition was pre-judged as useless because of an assumed void of information. It may be Watson's reduced version of the central dogma [62], wherein he emphasized what was surely found in genomic function and avoided needless and unsupported prohibitions, that helped the central dogma receive common acceptance from 1965 to 1969-1970, skirting sharp personal criticisms that were already present at its conception (e.g., questions as to its dogmatic stance; see Jacob's Memoirs, [14] pp. 288). A factor in the prevalence of the central dogma during this period might be that, since the 1965 Nobel Prize for Jacob and Monod's work on operon regulation [13], it had to be evident to Watson that, given the operon regulation of gene expression (as a function of the level of produced proteins), the prohibition of a protein-to-DNA information channel need not be in Watson's textbooks. His simplified and convenient view (avoiding controversial prohibitions and their refutation by data) is called here the concept of forward growth - which is, without recursion, only half the loop. This view, backed by Watson, prevailed so strongly that even the 50th anniversary issue of Scientific American, celebrating the discovery of the structure of DNA by Watson and Crick (1953) depicted as the general understanding that gene expression of DNA results, through RNA, in the construction of protein structures (see Fig.3, a composite illustration of the modified cover page figure of Scientific American of April, 2003, where on the right side the model of a Purkinje brain cell is pictured, from [5]) Reality was, as might be expected, much more complicated than any simplification. As early as 1969, in the Britten and Davidson theory of gene regulation [15], and by 1970 (cf. philosophical reflection by Darden [63]), the central dogma was squarely confronted by the discovery of reverse transcription, later called retroviruses, from RNA to DNA [16, 64]. Both Watson and Crick responded promptly but separately to the challenge posed by the discovery of the new enzyme that flagrantly violated their views. In the June 27, 1970 issue of Nature, the reverse transcriptase discovery was announced, and an anonymous "News and Views" article claimed: "Central Dogma Reversed". (Quote from Darden [63]): "Watson, in the 1970 second edition of his Molecular Biology of the Gene [18], said: 'The concept of a DNA provirus for an RNA virus is clearly a radical proposal. It overturns the belief that flow of genetic information always goes in the direction of DNA to RNA and never RNA to DNA. [Emphasis added, AJP] On the other hand, it offers an even greater variety of ways for cells to exchange genetic information. Considering the enormous complexity of biological systems, it would not be surprising if this device were uniquely advantageous in some situations.'" ([18], pp. 621-622) Crick (1970) also responded immediately to the challenge [17] but in a different way. (Unfortunately, the dogma wasn't allowed to gracefully expire.) Crick published a paper in Nature. His version of the central dogma, he contended, had not been reversed, as the anonymous Nature article had claimed. Crick stated, correctly, that in 1958 he had framed the central dogma in terms of the general transfer of information from nucleic acids to protein - but not the reverse (Crick 1958). That abstract claim had not yet been challenged. "If it were shown that information could flow from proteins to nucleic acids, he said, then such a finding would "shake the whole intellectual basis of molecular biology" ([17], p. 563). (Quote from Darden [63], emphasis added, Pellionisz). Thus, by 1970 the intellectual split between Crick, the originator of "The Central Dogma" (1956, [61]) and its promoter Watson (1965, [62]), threatened the collapse of the genomics establishment. The shaky ground of "The Central Dogma" was not really firmed up by the confession; "Dogma was just a catch phrase" (Crick, quoted in [65]). In the same year of the split, Ohno's junk DNA idea came to the rescue. Ohno first referred to garbage DNA in the human genome ([19], p. 62). Meaning that, even if there was recursive information access to DNA from proteins or from RNA, e.g. there was supposedly no information in the intronic and intergenic regions to be found and retrieved. Although the term "garbage DNA" floated in 1970, it did not take hold, but by 1972, in his presentation he began using the more suitable term "junk DNA", which did stick [20]. One should appreciate that, immediately after his presentation, the first person to rise in the discussion vehemently objected to the basis of the junk DNA conjecture (see "Discussion" by Boyer, in [20]): "It thus seems to me that the permissible number of structural loci is - as yet - a somewhat suspect way to arrive at figures of 1% structural utility to 99% junk." Why is it that Nobel Prize-winning experimental work (c.f. [66], Jacob's Nobel Lecture on his Prize with Monod, 1965) was available as early as within five years after Crick's conception of his dogma - yet no theoretical confrontation developed? Their operon regulation [13] clearly demonstrated that the protein-level, viewed as a result of genetic activity, did have an information-feedback mechanism on the genes in the DNA, such that down- or up-regulated DNA-RNA activity resulted, in accordance with the amount of protein already generated: "Experiments on genetic transfer by conjugation not only led to a revision of the concepts on the mechanisms of information transfer which occur in protein synthesis; they also made it possible to analyze the regulation of this synthesis. ... the operator is not transcribed into messenger and repression can be exerted only at the level of DNA. ... Gene expression was then usually believed to consist in the accumulation of stable structures in the cytoplasm, probably the RNA of ribosomes, which were assumed to serve as templates specifying protein structures... Such a scheme, which can be summarized by the aphorism 'one gene-one ribosome-one enzyme', was hardly compatible with an immediate protein synthesis at maximal rate." [13] In retrospect, and judging from Jacob's Memoirs [14] it seems evident that Jacob was fully aware of the intellectual conflict between the Jacob-Monod finding and Crick's central dogma, even at its birth (not shying away from direct criticism of the label "dogma", however): "In an acute sense of publicity, to baptize Central Dogma - that is to say, incontestable truth - a hypothesis that was unsupported by any serious argument." ([14], pp. 288) However, it appears that Jacob did not directly confront Crick on the latter's conception of the dogma [61], since that was prior to the publication of the Jacob-Monod operon concept. Jacob and Monod (1961) published their "operon regulation" work soon after, but did not receive their Prize until 1965; whereas in the following year, Watson and Crick (1962) received their award. Thus it was arguably more politic to avoid a direct conflict among the foursome. Almost simultaneously, however, in 1965 Watson [62] distanced himself from the central notion by putting forward his "simplified version" emphasizing what was undeniably true, although he did not dwell upon issues already controversial; see Fig. 2.) The point of this paper, however, is neither iconoclastic (discarding pragmatic doctrines while simply leaving a theoretical void in their place), nor to merely cite evidence for the widely reported means of feedback processes from proteins to DNA (and RNA to DNA). The point is to fill the void. PRGF is proposed to break through the "double ceiling" of the central dogma and junk DNA that impeded theoretical advances for half a century. Theoretical and Factual Breakdown of the Central Dogma and Junk DNAFurther flogging of two dead horses is avoided as much as possible. This abbreviated section merely supplies evidence, gives credit where most needed and points to the most powerful reviews. From the theoretical viewpoint of informatics, the "double lock" on recursive information has long been suspect. First, there is no more information for hereditary material than that present in the DNA. In humans, if 98.7% of the DNA is arbitrarily closed to access and in addition its information voided, the remaining information that 1.3% of the (human) genome harbors is deemed simply insufficient to govern development of such advanced organisms as vertebrates. It was painfully experienced, for instance, that when constructing a computer model of 1.68 million brain cells of the frog cerebellum, algorithmic approaches had to be invoked, rather than pretending that an impossible amount of information was available to specify the vast neural network in its every detail [67]. As for factual contradictions, the array of evidence - against both the central dogma and junk DNA conjectures - is staggering; see respective reviews [52, 53, 56]. Beyond the early factual evidence belying the validity of the central dogma ("Operonic Regulation by Feedback from Proteins to DNA"), another large assortment of facts is available, as follows. For an account of the (forbidden) information-transfer from RNA back to the DNA, see the very recent review by Mattick [59]; with background about the RNA world [68, 69, 70, 71, 72]. Major issues are gene silencing (or "turning genes on and off", e.g., by so-called LINE way stations, and switching via SINE-s). It is noteworthy that the PRGF is fully consistent with the currently vague notion of "turning genes on and off" - but goes further by invoking recursion not only the sign(s) of the "parallel feedback" are meaningful, but much more important information is the set of algorithmic values of recursive signals. [73, 74, 75, 76]. For the "orbidden" protein-to-DNA interaction, see the work on protein binding with the DNA, and methylation of the DNA by proteins - rendering DNA transcription reversibly or permanently impossible [77, 78, 79, 80, 81, 82]. For the (also forbidden) protein-protein interactions see Prions [83] and a detailed and philosophical review [52]. Very strange and in my view highly selective interpretation of the history of genetic science. So your view that "it is consensus among biochemists and biologists that gene regulation is a deciding factor in the differences between species, including the differences between humans and chimpanzees" is incorrect.Nonsense. Throughout my education as a biochemist and molecular biologist it was always clear that this is the consensus. I have an insider view, being a scientist in the relevant disciplines myself. You may, of course, believe what you want. from Monod-Jacob's gene regulation view (that proteins do indeed feedback information to DNA), so the latter's importance went into obscurity for over a generation until the late 90s,Incorrect. My education in molecular biology started in the mid-Eighties, and the importance of promotors was at least from that time on never in doubt. Late 90s? No kidding.
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Post by himself on Feb 12, 2010 0:08:44 GMT
[quote author=zameel As I've said repeatedly, quoting Behe, ID does not necessitate tweaking: it can happen by the one single act of creation. But the question is exactly what was "specified" in that act of creation? According to the fine-tuning view, the laws were specified. But as IDers have shown, the laws themselves are not adequate as explanations for the origin and diversification of life. [/quote]
We may safely assume that we have not yet discovered nor understood all the laws to be found in nature. And it would be a great surprise if a Victorian naturalist stumbled on the complete explanation of it all. Not even Newton did that, and gravity is a whole lot better understood.
Of course, to say that everything was "specified" in an act of creation necessarily implies that natural mechanisms exist by which those specifications have been realized. After all, a design department usually comes with a manufacturing department.
Natural science deals only with transformations of matter -- with the "manufacturing." I.e., how matter in one form is altered to another form. Coils of aluminum are transformed into beverage cans. Sodium and chlorine, a flammable metal and a poisonous gas, are transformed into table salt, a delicious condiment. Species of one form are transformed insensibly over time and by circumstance into an altered form. An embryo is transformed by stages into an adult. This has nothing to do with creation.
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Post by zameel on Feb 12, 2010 8:06:34 GMT
Throughout my education as a biochemist and molecular biologist it was always clear that this is the consensus. I have an insider view, being a scientist in the relevant disciplines myself. According to you the consensus is/was that mutations in regulatory regions determined our divergence from chimps, and not the 2% difference in coding regions? Do you have proof for that? There was a notion of gene regulation, but that this was a "deciding factor" in species evolution as consensus, needs to be proven. Pellionisz summarises (in his peer-reviewed article): "By 1969, the field of gene regulation was growing at a healthy rate, to result in the work of Britten and Davidson [15]. However, in 1970 a wound opened up in genomics that has not yet healed. On one hand, the first major failure on Crick's doctrine was revealed [16]. Both Crick and Watson responded, but in different ways [17, 18]. To keep the establishment together, Ohno declared the same year that all but the genetic DNA was garbage DNA [19], along with the slightly modified term of junk DNA [20] - a notion which prevailed for a generation." In the same article, Pellionisz shows a feature from Scientific American 2003 which illustrates the view that the "1.3%" difference in coding regions determined our different brain size, as the intergenic regions were thought to be junk. What exactly in your view was the consensus? My education in molecular biology started in the mid-Eighties, and the importance of promotors was at least from that time on never in doubt By "importance" I meant its challenge to the central dogma and junk DNA, and its contribution to species divergence, not merely that the idea was around. I would have thought that was clear from the article.
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Post by Al Moritz on Feb 13, 2010 1:26:45 GMT
According to you the consensus is/was that mutations in regulatory regions determined our divergence from chimps, and not the 2% difference in coding regions? Do you have proof for that? There was a notion of gene regulation, but that this was a "deciding factor" in species evolution as consensus, needs to be proven. Ok, you may have a point here, Zameel. I may have confused the fact that there was an overwhelming consensus that gene regulation is important with the idea that there was a consensus regarding its importance in determining the difference between species -- although it would surprise me if there was not, your peer-reviewed article notwithstanding. Guess from where I knew that there was an overwhelming consensus that gene regulation is important? From the differentiation of organs. I was always taught (by different sources throughout my career), and it really is bloody obvious, that what makes a heart cell a heart cell, a muscle cell a muscle cell, a brain cell a brain cell, and a skin cell a skin cell, is differential gene expression, which is based on gene regulation by non-coding regions. Of course, all these cells have one and the same identical genome in terms of the A, C, G, T base sequences. So if cells in different organs are different, which they evidently are, there must be differential gene expression. This is bloody glaringly obvious to everyone in the field. Your peer-reviewed article may not agree, but the facts are what they are. So my major point still stands: There was always a consensus that non-coding regions are important, and that fact does not contradict the idea that there is indeed junk DNA. Again see my post above with the ludicrously different mouse genome sizes (and no, that this is mice and not humans is completely irrelevant for the more general scientific point here). Saying that "none of it is junk" cannot be maintained does not equate to saying that "all of it is junk". *** With this, I consider the discussion about gene regulation closed from my end, and this is my last response. If not you, the other readers here will accept the obviousness of my points, and I have said enough.
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Post by zameel on Feb 13, 2010 2:39:10 GMT
Guess from where I knew that there was an overwhelming consensus that gene regulation is important? From the differentiation of organs. I was always taught (by different sources throughout my career), and it really is bloody obvious, that what makes a heart cell a heart cell, a muscle cell a muscle cell, a brain cell a brain cell, and a skin cell a skin cell, is differential gene expression, which is based on gene regulation by non-coding regions. Of course, all these cells have one and the same identical genome in terms of the A, C, G, T base sequences. So if cells in different organs are different, which they evidently are, there must be differential gene expression. This is bloody glaringly obvious to everyone in the field. Your peer-reviewed article may not agree, but the facts are what they are. The peer-reviewed article says nothing about cellular differentiation, which is not the topic we are discussing, but it seems you have again misunderstood scientific opinions about this issue to give an obvious importance to non-coding regions of the genome. You know what else is glaringly obvious? Not only do all cells have the same coding regions, they have the same non-coding regions in the DNA too. So this supposedly obvious importance of non-coding regions in the differentiation of cells is wanting. Cellular differentiation during development remains a large mystery but we know it has a lot to do with extrinsically regulated spatiotemporal coordination and intrinsically monitored chromatin modification to allow access to specific genes and no access to others (transcription factors are obviously important in this regard). For a brief review article see: www.nature.com/scitable/topicpage/Gene-Expression-Regulates-Cell-Differentiation-931So my major point still stands: There was always a consensus that non-coding regions are important, and that fact does not contradict the idea that there is indeed junk DNA. Just so readers can understand the background to this question: after discovering the double helix, Crick proposed the "sequence hypothesis": that DNA transmits information to RNA which is translated into protein. This became known as the "central dogma" in biology, that is, the forward direction of information from DNA to RNA to protein, i.e. there is little or no "feedback" - the genetic material itself would be sufficient to produce proteins in question. This was challenged by gene regulation (where proteins feedback to DNA) and discovery of "reverse transcriptase" in viruses (that convert RNA back into DNA). The most important response that managed to rescue the central dogma was the idea of junk DNA, that all intergenic DNA are useless; only coding regions have importance, and unless proteins feedback to coding regions they are feeding back to "junk". For this reason Richard Sternberg and Andras Pellionisz have said these frameworks (the latter calls the "central dogma" and "junk DNA" a "double ceiling") have inhibited research in the field of gene regulation. Again see my post above with the ludicrously different mouse genome sizes (and no, that this is mice and not humans is completely irrelevant for the more general scientific point here). The mutagenesis experiment you allude to was done after David Haussler found about 500 segments each 1000 bp were ultraconserved in mice and men, which in fact challenged the idea of "junk DNA". "Trash became treasure" according to this discovery: www.sciencentral.com/articles/view.php3?type=article&article_id=218392305 . "There were about five hundred stretches of DNA in the human genome that hadn't changed at all in the millions and millions of years that separated the human from the mouse and the rat," says Haussler. "I about fell off my chair. It's very unusual to have such an amount of conservation continually over such a long stretch of DNA." These regions are intergenic i.e. they are non-coding, and Haussler "confirmed that negative selection is three times stronger in these regions than it is for nonsynonymous changes in coding regions." As far as Haussler is concerned, "It is a mystery what molecular mechanisms would place virtually every base in a segment of size up to 1 kilobase [i.e., 1000 bp] under this level of negative selection" www.hhmi.org/research/investigators/haussler.html . These regions also matched with chicken, dog and fish sequences which makes the chances of a coincidence for the absence of neutral selection prohibitive: "From what we know about the rate at which DNA changes from generation to generation, the chance of finding even one stretch of DNA in the human genome that is unchanged between humans and mice and rats over these hundred million years is less than one divided by ten followed by 22 zeros. It's a tiny, tiny fraction. It's virtually impossible that this would happen by chance." The Nobrega et al experiment does not account for this fact, which means the question of function is still open. Haussler's later work shows that these regions may indeed have function: Junk DNA Now Look Like Powerful Regulators, 2007 www.sciencedaily.com/releases/2007/04/070423185538.htm - Haussler and Bjerano found 10,402 sequences or tansposons that showed signs of function. "We used to think they were mostly messing things up. Here is a case where they are actually useful," Bejerano said Saying that "none of it is junk" cannot be maintained does not equate to saying that "all of it is junk". But the same article you linked itself says "Personally, I fall into the "it's all junk" end of the spectrum". I assumed the links posted would have been read, especially by the one linking them.
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Post by zameel on Feb 13, 2010 21:30:54 GMT
"Natural selection" does not predict transitional forms, common descent does. Unfortunately, various themes are conflated to give the impression of the confirmation of ideas that are associated with but are not what certain findings show. Not all IDers deny common descent (Behe doesn't), and common descent is not the subject-matter of ID. It is also untrue that "transitional forms" have been found in most cases - this is only the case if universal common descent is assumed from the outset. What the fossil record in fact shows is abrupt changes, with species coming in and out of the fossil record without much change. The Cambrian explosion (in which all major animal phyla emerged in about 5 my, which geologically speaking, is very "sudden") is a remarkable example of this. Although soft-bodied fauna are found in the pre-Cambrian, none of them have ancestry to the Cambrian fauna. There are also many problems with Darwinian interpretations of the sequences; for instance, the recent "tiktalik" which was thought to be a transitional between fish and tetrapod (and inspired Neil Shubin's eager book Your Inner Fish) has been shown to be nonsense, as tetrapods existed long before tiktalik: www.nature.com/nature/journal/v463/n7277/full/463040a.htmlAnother example of a so-called transition that has recently been overturned is the dinasour-bird transition, which shows how flimsy such reconstructions actually are: Bird-from-Dinosaur Theory of Evolution Challenged www.sciencedaily.com/releases/2010/02/100209183335.htm
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Post by zameel on Mar 12, 2010 14:45:16 GMT
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Post by zameel on Mar 14, 2010 4:05:47 GMT
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jonkon
Master of the Arts
Posts: 111
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Post by jonkon on Mar 17, 2010 23:27:10 GMT
- In their cavalier dismissal of miracles to address their abuse by the Roman Catholic Church, the Puritan founders of the Royal Society inadvertently undermined their own scientific endeavors and historic Christianity. Since anomalous observations are the basis for scientific progress, the question is not whether miracles are scientifically possible, but rather the historical question of whether the event in question actually occurred. However, just because the event has been deemed a miracle, it does not necessarily follow that the miracle is a work of God. If the Bible is assumed to be true, then there is at work another being, Satan, who has the power to also influence natural phenomena so as to lead people into false doctrines. The criterion of truth in such matters should be “philosophical coherence,” expounded in the website: Carmine, James D., “Bad Religions and Good Religions,” 14 December 2005, www.intellectualconservative.com/article4806.html- It is presumptuous for a Christian to attempt to prove that which the Creator has clearly stated is a self-evident. It merely remains to point out the obvious, i.e. we know that God exists because atheists exist. The issue is not the existence of God, per se, but rather that fact that the existence of God is even an issue. It is a readily observed fact that dogs and other animals do not engage in theological discussions. They merely go about their business of eating, sleeping, and raising babies. Only a being created in the image of God, with free will, for the purpose of fellowship with God is capable of rejecting that fellowship. - Whether science and religion conflict depends upon what you mean by “science”? While what is being taught in the schools clearly appears to conflict with the existence of God, an entirely different picture emerges once you actually try to apply what is taught in school to the design of commercially successful products. Among other things, the “scientific method” taught is incapable of distinguishing between causal connections and coincidence, a major issue in the safety and reliability of products. My professional interests in the design of safe, reliable, and producible products led to a systematic study of the intellectual biographies of the leading figures of science. What I found was that experimental science emerged as a product of the systematic, rational defense of historic Christianity and that it can only be understood and applied within that context. In particular, the fundamental issues of applied science – Configuration, Control, and Reliability – are intimately linked with and lead into the classical proofs of God's existence – Ontological, Teleological, and Cosmological – respectively. WRT the discussions in this thread on ID, both ID and “Scientific Creationism” are unnecessary and undesirable compromises of Biblical Creationism – the Genesis account is a historical fact and any “scientific evidence” to the contrary is a misinterpretation of the raw data. As a product designer I find it ironic that Creationists and Evolutionists blindly talk about “design in nature” without any real understanding of what a designer actually does and what would constitute evidence of “design.” A “scientific” theory of origins falls out as a special case of a broader theory of applied science. “Reverse-engineering” of nature is a widely accepted practice in product design. What is not appreciated is the reverse process is also possible in that evidence of good design practice is found in nature and is commonly misinterpreted as evidence of naturalistic evolution, eg. A hierarchical classification of species, leading to the misinterpretation of common descent, and so-called “vestigial” organs.
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Post by eastshore4 on Apr 16, 2010 20:39:55 GMT
I hope you guys don't mind if I fire off a few more questions:
-I'm going to start going to Church here. I wanted to get my own bible, but from what I understand there's a few different "versions" out there, King James version, etc. Do they more or less have the same content despite perhaps differences in certain translations? Is there any particular one you can recommend?
-Is there any good books on a sort of "middle-of-the-road" interpretation of the bible? Right now I'm still kind of stuck in this whole "either/or" mindset. Reading some of the dialogue between Evangelists and Episcopalians has got me into this mindset that the Bible's gotta be either entirely literal or entirely rhetorical, and those who try to strike a balance are only well-wishers. I've always been drawn to walking the line between the two extremes, but I want to make sure it's a coherent stance to believe the bible is "inspired" instead of divine dictation or a human-constructed self help book.
-One argument I've come across lately has been the argument of how God and Theology evolve. Just reading about the transition from OT to NT shows many "theological upgrades" going on, then there's the whole "trimming" of many gods down to one. I guess a theist can argue that it's a sort of progressive revelation, but it also seems to give credence to the idea of God as a human construct, i.e. us influencing God instead of the other way around. What's the general impression of this?
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Post by jamierobertson on Apr 16, 2010 21:12:20 GMT
Hi ho,
Bibles - Well, they're the same content but English now is hugely different to English in the early 17th century. The New International Version is widely used and is a decent balance between readability and fidelity to the text, I believe. EDIT - my own Bible is a NIV Study Bible, which has a lot of footnotes and cross-references, which I thoroughly enjoy using!
Inspiration - I exactly agree with your point - inspiration doesn't have to mean dictation! - but I don't have a lot of commentaries. Tekton Apologetics (www.tektonics.org), whilst having something of a split reputation on the web, has a lot of material and holds to a similar sort of position on inspiration.
Evolving Theology - I must say, I personally think the change of God from OT to NT is overstated. It was Jesus who called the Pharisees a brood of poisonous snakes and cleared the temple, and it was Jehova whom Jonah accused of being too lenient with evildoers who repented. I can accept the concept of a "progressive revelation" of God, but I'm not convinced it's necessary. And reading the NT, there are several odd features (use of women, breaking down of cultural barriers) which aren't what you'd expect from someone at that time and place just making it up.
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