A Simple Gene Origination Calculation

_{July 27, 2008

Intelligent Design}

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In this month’s Nature Genetics, there is an article by Zhou, et. al., dealing with the generation of new genes in Drosophila melanogaster—the fruit fly. While only having access to the abstract, I nonetheless was struck by one of their findings: the rate of new functional gene generation. As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

Here’s the link to the abstract.

Comments

Addendum to my #157: Contradicting Lehninger is not my aim. Understanding what he wrote in the context of this discussion is my aim.Daniel King_{August 8, 2008
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Paul Giem (155) I will try to defend my position further:
Otherwise, if he has no arguing room, he simply drops the subject, as he did with the question of whether DNA code was information (or language), or just an analogy which was therefore not “evidence” (see his comments 81 and 82 and my comment 114, then his further silence on the matter instead of conceding the point, or else contesting it, which he probably knew better than to do).
I am satisfied that arguments from analogy are inadequate as proofs, and as an acolyte of Dr Beardsley, whose work I quoted in #82, I await evidence that the analogy in question has been subject to empirical test and has produced new findings of scientific value. What more is there to discuss?
Note the complete lack of any sense of responsibility to find any data that contradicts Lehninger, or even any sense that Lehninger carries any weight whatsoever.
How can I find data that contradicts Lehninger, when I don't know what he said? You haven't provided a direct quote or any further information beyond your claim. You have only pointed me to an ancient textbook which is out of print and not readily available to me. Bear in mind that you made the claim that this reference is a refutation of the feasibility of exploring abiogenesis scientifically. In scientific circles, it is the responsibility of the person making a claim to support it. It is inappropriate to wave hands and say "refute me!"
Further evidence of this argumentative nature is that. after all his claims that naturalistic OOL scenarios are based on “evidence” and ID is based on “speculation”, and after all the discussion of the shrinkage of RNA strands to the size of the Spiegelman monster, and his attempting to play ‘gotcha” over the fact that Q-beta replicase has produced up to Spiegelman monsters, rather than demonstrating that larger strings of RNA could reasonably be created from Spiegelman monsters, he finally acknowledges what could have ended the discussion early, namely, knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issues of abiogenetic RNA syntheses. * * * Since the Haruna/Spiegelman work on this highly specialized system is irrelevant to abiogenesis, I wonder why Shapiro even considered it. Perhaps he included it because it was a landmark in RNA biochemistry.
You made a claim that the Spiegelman devolution work was an example of the futility of studying abiogenesis. I presented evidence from the scientific literature that this work is irrelevant to abiogenesis and that your claim is therefore wrong. You call that playing "gotcha." But you have not admitted your error.
One might think that this is a concession, but actually it is not. He now sees that the evidence is against RNA elongating beyond Spiegelman monsters using nucleotides and Q-beta replicase. But rather than saying so, he chooses to try to take the whole subject off the table by declaring it irrelevant...
I knew all along that there was no extension beyond the viral genomic template in the QBeta case and I don't recall saying otherwise. In no way did I want to take the whole subject of RNA synthesis and elongation off the table. I claimed only that the QBeta example was irrelevant to abiogenesis. Much relevant work on RNA has been done more recently. I would be pleased to cite some for you.
...it was there precisely because some had used the Spiegelman experiments to “prove” that the abioltic synthesis of long strings of RNA was reasonably feasible, and that Shapiro was honestly critiquing them.
That I agree completely with Shapiro's position on the Spiegelman experiments is evident from the analysis of the QBeta system that I have posted above.
Until such time as he has enough gumption to go to the library (isn’t that how we all did research before the advent of the Internet?), or to explain why he can’t and be willing to abide by the results without further information to the contrary, I see no reason why I should give him exact quotes from Lehninger.
You see no reason to give me exact quotes from Lehninger. I had hoped for a more collegial and scholarly attitude. You assert that I lack gumption. Do you believe that I am afraid of what I might find in those books? In fact, I have searched every public library in my region and have found no copies of Shapiro or Lehninger 2nd Edition (I hope you had the edition right). I have requested interlibrary loan of both books, and am awaiting the results of those requests. While those processes wend their way, I am taking my family to the Finger Lakes region of New York next week. So if you don't hear from me for a while, it's because I (hopefully) will have other fish to fry!Daniel King_{August 8, 2008
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Hi Paul G: I hear you loud and clear. It does rather look -- unless Mr King can show serious progress -- like argumentative, closed-minded objectionism, as a manifestation of selective hyperskepticism. I have commented latterly above correctively, but with a serious eye to the interested onlooker, who might lack enough context to see that this is a side-track off a side-track. It is in that context that I have put the central problem with the OOL models above: they are dealing with the construction of an energetically massively unfavourable system. That is why in the observed cases life chemistry uses enzymes to push reactions that would not occur at appreciable rates in the absence of such constraints. Enzymes, of course, are a principal and highly complex product of the D/RNA coding scheme. (Just think of the ATP synthesis for the required energy flow to keep such energy absorbing reactions going in vivo. Here too, Wiki's evo mat bias shows: if "ATP is the common "energy currency" of cells," and is claimed to have evolved from prior functional units, why and how do we get the required "energy currency" before ATP Synthase, and if such existed, why the evolution to a vastly more complex entity, and apparently before life architectures branched out [thus, the info generation challenge and the encoding in D/RNA challenge too . . .]? Currency conversion is of course a major change! And, what has been the in-vivo observed -- as opposed to speculative -- prior currency regime?) RNA world of course, further, was introduced because it was found that sometimes RNA can have a catalytic effect, so there was a hope to cut through the chicken-egg dilemma just noted. But, that gets us to RNA synthesis, which falls under the rebuke from Shapiro cited at 72 above. In short, there is a problem with the syntheses, precisely because of unfavourable energetics so that one has to set up rather special circumstances to get to the RNA strands -- and note that one of the key issues of chirality [handedness] is that, energetically, L- and R- forms are equivalent; so apart from in life, chemical synthesis gets us racemic, 50-50 products, which would then interfere mutually on polymerisation and shapes. All this, in a context where specific key-lock fit of functional groups of atoms is a crucial part of the chemistry of observed life. F2XL summarises the synthesis part of this in 61 [and cf the 1996 creationist summary and critique by Aw Swee-Eng as already linked at 150, and again here; which does address the implications of chirality -- of course two years before the date of final changes in Musgrave's shoddy TO hit piece]:
Regarding the RNA world: A chief problem with it is that for RNA strands to form IN THE FIRST PLACE, you need sufficient amounts of concentrated carbon-5 sugars, phosphates, and also nucleotides bases (adenine, thymine, guanine, and cytosine). The catch is that these three constituents can only be artificially synthesized in completely different circumstances for each of those things listed. A phosphate group cannot develop in the same mix as a carbon sugar, and so on. That wouldn’t even begin to explain how the information in the RNA got there in the first place.
This is typical of OOL dilemmas, as was summarised in 72. Back on the original topic as put by PaV, once we have functioning life forms, evolutionary materialist models have the problem of getting to rather large increments of information required for new body plans and adaptations, without the routinely known source of FSCI -- intelligence. And, even when such models appeal (circularly!) to inferred evolutionary pathways as Zhou and co do, we then get to implausible rates of evolution even in families of animals notorious for wide variation, here Diptera and Drosophila: 5 - 11 new genes per mn yrs, to account for the variation in the Dibtera in some 225 mn yrs is simply impalusible. So, PaV is right to observe:
As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.” Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.
Onlookers should note that over the course of two weeks and over 150 comments, this has never been cogently addressed from the evo mat side. The OOL challenge compounds the matter of course, and the observed repeated resort to personalities and rabbit-trail diversions and objectionism underscores that ther eis no solid case on the merits. The TO rebuttal page is amply illustrative of how poor the Evo mat case is on the said merits. In turn, that easily explains just why it is that the Darwinista Establishment takes such pains to make sure those who try to challenge in the academy are expelled, and seek to monopolise the education and media environments so that the public and kids coming up are indoctrinated, not educated. That is sadly shameful, and deeply revealing. Thanks again PG GEM of TKIkairosfocus_{August 7, 2008
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Kairosfocus, Daniel King is arguing in a no concession one concession, maximum objection, you do all the work manner here. If you want to sharpen your arguments against his position, it may be worth arguing with him; otherwise, you are wasting your time. That's a pretty big charge, so here's the evidence. The one concession I found was in (75), where he said to you,
Thanks for the readings. I bow to your scholarship. * * * I agree. There are daunting challenges in that field. I’m happy to be merely an occasional student and spectator of those proceedings.
Otherwise, if he has no arguing room, he simply drops the subject, as he did with the question of whether DNA code was information (or language), or just an analogy which was therefore not "evidence" (see his comments 81 and 82 and my comment 114, then his further silence on the matter instead of conceding the point, or else contesting it, which he probably knew better than to do). If a concession is mandatory, the next step, if possible, is to minimize the point as much as possible. See, for example, when he requested references (115, [with a history], and 123), and then, when I provided them (135), argued against Lehninger because (a.) the reference is not "to the primary scientific literature", being a textbook (142), (b.) it was not readily accessible to him (142), and (c.) the reference was old (149). Note the complete lack of any sense of responsibility to find any data that contradicts Lehninger, or even any sense that Lehninger carries any weight whatsoever. This is classic advocacy not based in fact. Further evidence of this argumentative nature is that. after all his claims that naturalistic OOL scenarios are based on "evidence" and ID is based on "speculation", and after all the discussion of the shrinkage of RNA strands to the size of the Spiegelman monster, and his attempting to play 'gotcha" over the fact that Q-beta replicase has produced up to Spiegelman monsters, rather than demonstrating that larger strings of RNA could reasonably be created from Spiegelman monsters, he finally acknowledges what could have ended the discussion early, namely,
knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issues of abiogenetic RNA syntheses. * * * Since the Haruna/Spiegelman work on this highly specialized system is irrelevant to abiogenesis, I wonder why Shapiro even considered it. Perhaps he included it because it was a landmark in RNA biochemistry.
One might think that this is a concession, but actually it is not. He now sees that the evidence is against RNA elongating beyond Spiegelman monsters using nucleotides and Q-beta replicase. But rather than saying so, he chooses to try to take the whole subject off the table by declaring it irrelevant. He probably at least suspects that his postulated reason why Shapiro included it in Origins, that " it was a landmark in RNA biochemistry", was incorrect, and that it was there precisely because some had used the Spiegelman experiments to "prove" that the abioltic synthesis of long strings of RNA was reasonably feasible, and that Shapiro was honestly critiquing them. If Daniel really believes what he says, I expect him to criticize anyone who uses the Spiegelman in this way. I'm not holding my breath, but who knows? Until such time as he has enough gumption to go to the library (isn't that how we all did research before the advent of the Internet?), or to explain why he can't and be willing to abide by the results without further information to the contrary, I see no reason why I should give him exact quotes from Lehninger. It would appear that all he wants to do is to carp and in the meantime send us on ever-widening errands, sucking up our time but never (well, almost never) admitting to being satisfied, even temporarily. Frankly, I am tired of this game. As you have commented frequently, most recently in (154), and I pointed out in (53), the main point in this thread has yet to be answered, let alone the vastly more difficult (for believers in naturalism) problem of OOL.Paul Giem_{August 7, 2008
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DK: Cf above. Given the context, it is you as objector who has something to show. I have already pointed to the key thermodynamics pattern for the chemistry of life, namely that there is an undelrying reason why life chemistry is so heavily enzyme dependent: life chemistry is largely based on energetically unfavourable reactions, that require the sort of constraints provided by the enzymes. In turn such enzymes are highly complex, rather long-chain proteins coded for in the relevant D/RNA, i.e. we have a circle of cause at work; it works for propagating life forms but not for originating same. That is the general context for hte issue of 2-5 and 3-5 bonds, and even if PG is wrong on this point, or if Lehninger is wrong, the basic issue is still unanswered: OOL per the usual models is so vastly thermodynamically improbable that it is for all practical purposes impossible. Which brings us back to the underlying point in PaV's original post. And so, we need to come back from the rabbit trail to the main issue, unless you can show us credible evidence that PG and/or Lehninger are wrong on the specific point. Even if you can, that still does not affect the material issue. So, if there is just a string of objections without substantive evidence, we know enough to decide the main case on the real merits -- and the prudent verdict (provisional though it currently is) is plainly not in your favour. GEM of TKIkairosfocus_{August 7, 2008
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kairosfocus,
Now, PG has repeatedly cited — most recently in 135 supra — a statement circa 1970 on the observed tendency of reactions in the monomers for R/DNA. namely that in vitro, they tend to form 2-5 bonds not the 3-5 ones found in life. If that was true in 1970, it is true today, as that is a fact of observation.
My respect for Lehninger knows no bounds. However, without knowing anything more than Paul Giem's bald statement, I can't evaluate its significance. What did Lehninger actually say? What was the context? What were the conditions employed in the experiments? From what source did Lehninger get his information? I have tried to find more information by searching The National Library of Medicine's PubMed data base and Internet search engines, but have not been successful. Any help you care to give on the merits? I would be grateful.Daniel King_{August 7, 2008
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Mr King Mr Lehninger was a noted expert on biochemistry, whose main textbook was a longstanding classic. Wiki:
Albert Lester Lehninger (February 17, 1917 – March 4, 1986) was an American biochemist, and is widely regarded as a pioneer in the field of bioenergetics. He made fundamental contributions to the current understanding of metabolism at a molecular level. In 1948, he discovered, with Eugene Kennedy, that mitochondria are the site of oxidative phosphorylation in eukaryotes, which ushered in the modern study of energy transduction. He is the author of a number of classic texts, including: Biochemistry, The Mitochondrion, Bioenergetics and, most notably, his quintessential series Principles of Biochemistry. The latter being a widely used text for introductory biochemistry courses at the college and university levels. As a dedicated educator, it was Lehninger's argument that a knowledge of biochemistry is useful for all well-informed citizens, no matter their callings--let alone the very real intellectual excitement it can offer
Now, PG has repeatedly cited -- most recently in 135 supra -- a statement circa 1970 on the observed tendency of reactions in the monomers for R/DNA. namely that in vitro, they tend to form 2-5 bonds not the 3-5 ones found in life. If that was true in 1970, it is true today, as that is a fact of observation. Moreover, as he has said, the statement is by an acknowledged expert [in a context of a standard College textbook; which means his peers would be expected to read it, so there is a further incentive to get the statement right], and it is an admission in the teeth of interests. Such statements have a high intrinsic probability of accuracy. That means the burden of proof is on the objector. You have not met that burden, but instead have tried to dismiss the claim because it is not from a research document, and now on grounds that it is "old." Neither of these are likely to be even relevant to the material question of accuracy. For, if a fact claim is true, its age is immaterial. (Indeed, even if subsequently there has been found a way to induce D/RNA in vitro to take up more life-like bonds [through say a suitable catalyst or enzyme], the older tendency is probably indicative of the balance of the thermodynamics. And, in general it is notorious that the molecules and structures of life are inherently energetically unfavourable. That's why catalysts and especially enzymes play key roles in life. Enzymes, in turn, are characteristically highly complex proteins coded for by D/RNA. This in turn brings us right back to the complexity of observed life systems and the difficulty of accounting for their FSCI per OOL models and empirical evidence.) In short, sadly, your arguments appear to be a case of selective hyperskepticism. In fact, properly, we have good reason to accept Mr Lehninger's observation as PG cites, unless you or others can show good reason to reject it. GEM of TKIkairosfocus_{August 7, 2008
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PPS: It is worth separating out the publication date on the AiG article: CEN Tech. J., vol. 10, no. 3, 1996. That is, BEFORE Musgrave's hit piece.kairosfocus_{August 7, 2008
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PS: Here is an AiG more or less semitechnical page on OOL issues. It will further underscore just how strawmannish the Musgrave page at TO is.kairosfocus_{August 7, 2008
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Paul Giem (146), You have made a case that RNA synthesis studies have been futile as approaches to understanding abiogenesis. You chose to rest that case on secondary references (books) rather than the primary scientific literature, and you have eloquently defended that choice. I respect your decision, but I offer the following in rebuttal: In addition to their other deficiencies, the references you gave are antique. The Shapiro book was published in 1986, twenty-two years ago, and has long been out of print. It was not a scholarly, peer-reviewed publication, but a general-audience work. The Lehninger text dates to 1970. Are we to believe that nothing has been done in this field in the interim? Moreover, with respect to Shapiro, you said,
One would have to read most of the book...to understand the precise context...
so one is at a disadvantage in evaluating the basis of his "negative remark" about the Spiegelman devolution experiment. Nevertheless, knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issues of abiogenetic RNA syntheses. QBeta is a small, icosahedral virus (bacteriophage) that infects E. coli. Its genome is a single-strand of RNA about 4,000 nucleotides in length, encoding three structural proteins and a replicase (RNA-copying enzyme). [see, for example, Klovins, J, Berzins, V and van Duin, J RNA 1998 4: 948-957] In earlier work, [Haruna and Spiegelman Proc Natl Acad Sci U S A. 1966 Jun;55(6): 1539-54] had discovered an exquisite specificity of the phage replicase: it only works when provided with its own genomic RNA as a template for copying. This makes sense biologically, for if the replicase recognized and were bound as well as its own genome by the far more abundant messenger RNA molecules in infected cells, replication of the viral genome couldn't get off the ground to generate new phage genomes. Another biological point: the phage is a highly evolved organism that replicates with maximum efficiency. It contains no genetic sequences that are not essential to its survival. There is no reason (no survival advantage) why its replicase should synthesize any additional information either in vivo or in vitro. That's why I say that Shapiro's statement, "The RNA did not acquire a new capacity, nor could it do so.” is understandable. Since the Haruna/Spiegelman work on this highly specialized system is irrelevant to abiogenesis, I wonder why Shapiro even considered it. Perhaps he included it because it was a landmark in RNA biochemistry. Since you have Shapiro's book, perhaps you would kindly shed light on that issue. Regarding the Lehninger reference, you have presented nothing for me to work with. Perhaps Lehninger was in a similar position to Shapiro, citing work available up to that time. Neither of those good gentlemen had a crystal ball.Daniel King_{August 7, 2008
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Paul Giem, First, and most important, I wanted to say my appreciation for your refreshingly original thought on several issues, including your structuring of issues on ages and dating of life and cosmos. Well worth a thought or two. Having taken a couple of days' timeout [to allow the personalities games above to cool down], I must note too, sadly, on how the above shows which side is focused on substantial issues and which is reverting to personalities in the noticeable absence of dealing with the material matters substantially. Third, it is astonishing to me that after a week and a half, not one truly substantial response has been made in the thread from the evo mat side to PaV's main point in the original post:
As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.” Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.
Similarly, once the personalities were out of the way, there was no substantial answer to the implications of want of search resources to achieve genomes by chance + necessity, starting from the origin of life question. [And note, we didn't even touch on the chirality issue!] The pattern above, which is all too familiar from all too many cases in point, must be telling astute onlookers something on the true balance of the case on the merits. And, not to the merit of the evo mat advocates. Finally, of course 43 above responds to the Ian Musgrave Talk Origins page [linked at "claims" in 20 above from you] which tries to brush aside the force of the issue. I am especially astonished at the strawman argument set up by Mr Musgrave's third diagram on "creationist" and "real" views of abioogenesis. In fact, not only is it the case that any number of creationist sources [not even counting design theory sources] do make a serious address on OOL issues in light of the typical models used, but it is the OOL researchers who are openly admitting that their frameworks lack empirical warrant! (The cited exchange between Shapiro and Orgel at 72 above, underscores the point.) On a further look at the TO page, I find Musgrave's bland assertion:
"this [Mycoplasm] is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems" --> This is a particularly slick glide-by of the requisite for real-world science that it must rest on observation! --> We also have observed life forms, with a genome that has observed minimal fucntional length 300 - 500 k, and that is -- with M. g. as the key case in point -- for organisms dependent on others for key nutrients; which leads to the inference that the real required DNA length for full independent life function is of order 1 mn. --> So, we need to look askance at Musgrave's dismissal that "The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins . . ." --> For, in fact M.g. plainly has too few proteins already to be an independent life form! --> This is debate tactics, not serious science -- as the dismissive and profane title of Mr Musgrave's piece warns the astute reader. --> Indeed, the level of tactics used underscores why so many UD participants view references to To with disdain!
The want of a serious rebuttal, here or from a Darwinist resource sites such as TO -- and let us note how the Musgrave page's serious problems have not been fixed in ten years! -- simply underscores the force of the search resources issue, on OOL and OO body plan level biodiversity. Let us take note of this. GEM of TKIkairosfocus_{August 7, 2008
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bFast, (145) I don't have a single source that comprehensively presents the evidence for young life. I can tell you of a few sources I would recommend as introductions. Origins: Linking Science and Scripture by Ariel Roth is a good general introduction, as is Faith, Reason, and Earth History by Leonard Brand. For radiometric dating, I recommend Radioisotopes and the Age of the Earth, Vol. II, edited by Larry Vardiman, Andrew Snelling, and Eugene Chaffin. The interpretation of their data is not always completely clear, but the data themselves are fascinating. An earlier version of the carbon-14 data is available at http://www.globalflood.org/papers/2003ICCc14.html Finally, there is my own stuff, available by clicking on my name. Chapter 5 of Scientific Theology, my article "Carbon-14 in Fossil Carbon", and my article "Carbon-14 Dating Models and Experimental Implications", would all be good reads. There are probably other resources that would be useful that I don't recall at present. I hope that helps.Paul Giem_{August 5, 2008
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Daniel (142), Sorry that the references were not all that you had hoped they would be. I agree that references come in a scale of reliability, and that textbooks are not as high on that scale as reports of original research in peer-reviewed journals. However, the latter are not infallible. The fact is that there is nothing infallible in science. And the fact is that nobody has the time to read only journal articles on every point of interest. So some rules of thumb have to be utilized to get through the maze in reasonable time. One of the rules of thumb is, the more the primary data are emphasized, and clearly separated from interpretation, the more reliable the source is. A second is, the more experienced and knowledgeable the source is, the more reliable the conclusion is (peer review is simply the concurrence of two or more experts, or at least the view of one expert pre-criticized). A third is, admissions against interest, as the lawyers would say, are more reliable than comments on neutral matters, which are still more reliable than claims that one's theory is correct, all other things being equal. Both the Origins reference and the Biochemistry reference were by knowledgeable experts, and were admissions against interest. Therefore it would seem that they should be accepted as accurate unless and until direct references from original experiments contradicts them. Since I took the trouble to find the nearest copy of Origins, and then drive to the library and back (some 30 miles), I find it hard to be too sympathetic to your plea that "I don’t have either of these books at hand". If you are located in somewhere like Palau, I will be more sympathetic, but otherwise do a little work. I find it fascinating that, after stating that you do not have access to Shapiro's Origins, you go on to state,
I believe I know the reasons for Shapiro’s remark, based on my understanding of the biology underlying the Spiegelman experiments.
You then go on to ask,
Do you understand that biology?
AFAICT, the Spiegelman experiments were biochemistry, not biology, although I will admit that the lines between biochemistry and molecular biology have become somewhat blurred. But since you think you know why Shapiro said what he did without reading more than the sentence I quoted, perhaps you could state your understanding, then read him and find out whether you were correct. Then perhaps we can discuss "the biology underlying the Spiegelman experiments" and we'll find out whether I "understand that biology".
The synthesis of long strands of RNA under laboratory conditions is a major issue for you.
It seems to be an important issue for Shapiro, and even for Spiegelman. Is it not important for you?
Perhaps you could help me narrow down the field, so I can check further. Would you like strand elongation catalyzed by an enzyme, or not? Elongation on a template (as in the Spiegelman QBeta case) or not? Primer, or not?
I already know that one can get mini-Spiegelman monsters, and even apparently Spiegelman monsters, from enzyme catalysts plus trinucleotides. What I would like to see is systematic elongation of the chain well beyond the Spiegelman monster, either without an enzyme catalyst, or with an enzyme catalyst that could reasonably have been formed in a prebiotic earth. (Plus I'd like to see a reasonable prebiotic synthesis of trinucleotides, and some way of showing that the elongated strings can develop a code and turn into actual living organisms, but first things first.)
Surely your faith does not rest on such a slender reed
Why not? Did not the apostle Paul (1 Cor. 15) stake his entire belief system on the historicity of a miracle? Besides, I thought that a religion that was falsifiable would be superior to one that was not. A religion that is not falsifiable cannot, and for that reason, tell us anything about nature. It would seem to be an advantage for a religion to guide us when dealing with nature.
Apparently the work of naturalists, which does not bear in any way on considerations of the existence of deities, upsets you.
Right now it doesn't upset me at all; I'm actually kind of pleased by the way things are going. But if it did, that wouldn't matter. Just as it doesn't matter if naturalists become upset because there is evidence in nature for God's activity. Being upset doesn't change the truth. The nature of reality is not susceptible to political correctness.
That’s it? That’s your entire comment?
Nice catch. I accidentally hit the "Submit Comment" icon before I was quite ready, and ran out of time to correct the comment, so let it stand. I agree with "Kepler, Newton," "Einstein", and "Pasteur" that there is not "an inherent incompatibility between science and religious belief." My comments in (143) might be helpful in this regard. You ask, "Does Scripture define the limits of science?" I don't think so. On the other hand, as I read it, this text seems to indicate that some things can be found out by us, and I presume that science can be one way of finding out some of those things, but that others things cannot be found out, and that it is futile to try to do so. I agree with the sentiment of the text. What those secret things are is not clear from Scripture, even assuming that Scripture is accurate on this issue, but we have no right to assume that someday science will find the answer to every question. There may very well be questions to which the answer will always be above the reach of empirical study, and maybe even answers that we cannot grasp at all. It is simply not appropriate to say, for example, that the origin of life must someday yield to scientific inquiry. Maybe, maybe not (even secular OOL researchers acknowledge this possibility). If science can't tell us how life originated, and God doesn't deign to give us a mechanism, (which is how it looks right now), then we are out of luck. We'll just have to live with it. But hey, if you want to try, be my guest.Paul Giem_{August 5, 2008
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Paul, thanks for the calculation. As you can see in my discussion #124, point #3, I agree that non-coding DNA is not expected to be truly random withing the neo-Darwinian paradyme. I was intrigued by your YLC position. You seem to be able, as many are not, to separate your scientific exploration from your religious perspective. I have met a few others, like yourself, who are not religion-first, yet hold to a belief in young life. I have seen evidence that I find irrefutable, that indicates that life is old. My primary source of evidence, other than the commom reading, is my brother, a working geologist. That said, it seems clear to me that your knowlege base in this field is greater than my own. Do you have a good single source that presents your evidence for young life? It would be intriguing if you could convince me that life really is young.bFast_{August 5, 2008
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bFast, (68) Sorry for the delay in replying. The statistic you are looking for is an exponential distribution, where the probability of any given codon being a stop codon is 3/64 and thus for a non-stop codon being 61/64. The probability of finding a string of at least n codons is 61/64ths to the n power. That calculates out to about 0.3649 at 21 codons, which is fairly close to 1/e (0.3678...). At 100 codons, that works out to about 0.00822, which is small, but not astronomically so. All this assumes that the genome is random, which, regardless of which side of the ID argument one takes, it is not. Daniel, (142) I'll get back to you later.Paul Giem_{August 5, 2008
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Ritafairclough, (137) Your initial "Why?" appears to be based on a common misunderstanding, articulated by Thomas Kuhn, that it is impossible for the same person to work within two different paradigms at will. It also, less excusably, misunderstands the basis for my position. Your misunderstanding is made explicit in the following:
I find it, to be perfectly honest, dishonest that your primary objection to the whole thing has not been made clear to all, namely that as you believe the earth is not very many years old none of it could have happened that way in any case.
Here, IIUC, you are stating that the young age of the earth is my starting point, and that since a variant of ID is implicit in YEC, ID is simply a freebie. My arguments for ID would therefore be somehow dishonest because I don't constantly remind people of my opinion on the timescale. There are a couple of areas where you have badly misunderstood. If it is an honest mistunderstanding, I suppose an apology will be forthcoming. First, I do not have a webpage at AIG. What AIG did was to reprint my contribution to a book, In Six Days, edited by John Ashton, with an editorial comment interspersed. They did so without asking my permission first, although when I asked them to change their editorial comment and correct a misprint of theirs, they did so. I am not in fact affiliated with AIG, as your comment would imply. Secondly, I do not march in lockstep with AIG, and did so even less at the time my contribution was written. I currently am a YEC, although not a YUC (young universe creationist), as is AFAICT their position. At the time I wrote the piece, I was a YLEC (young life on earth creationist) but not a YEC. Note one of the passages you quoted: "It basically forces one into accepting a short chronology for life on earth." It does not say "for the earth." And even now, I am not dogmatic either about YUC being wrong or YEC being right. I base my opinions primarily on my perception of the scientific evidence (which can change, and has changed), as I view the Biblical evidence as inconclusive on both those questions. But perhaps the most profound misunderstanding is that you apparently think that my primary argument is for short age, and (I am guessing here but your use of the word "know" in your last sentence suggests that I am right), I am really dependent on a literal reading of an "inerrant" Bible for my opinion. Let me put it to you bluntly. I don't believe in an inerrant Bible. The reasons are outlined in chapter 3 of Scientific Theology (a free online copy is available by clicking on my name). (In fact, there are inerrantists who argue that Genesis 1 describes long periods of time, and even TE's who claim to be inerrantists. Inerrancy turns out to be a plastic concept.) Nor do I start my personal philosophy with the Bible. Other than prejudice, it is inexcusable that you should have read my material on the AIG website and concluded that. Rather, I realized early on that the Bible was only one (or perhaps two, or 66, or something) book competing for the title of divine revelation. My number one datum was that the origin of life could not be explained currently, and it appeared unlikely that it would ever be explained, by naturalistic processes. (Actually, that was my number 4 datum, after the facts that science could explain most of the universe, that science was impotent to explain the origin of the universe, and the at mechanism was impotent to explain quantum mechanics. See chapter 2 in my book. But the origin of life was the first and most important area I researched.) If one accepts that datum as accurate, then ID becomes a live option as an answer for other questions, and the question of age needs to be revisited without the weight of scientific opinion being essentially determinative, as the substantial majority of scientists have been wrong in one area already. Then it makes sense to look at such areas as carbon-14 dating with a fresh perspective. Then it makes sense to accept the results of carbon-14 dating if they appear to conflict with the standard "scientific" interpretation of age. Then it makes sense to consider afresh the possibility that the Biblical record is substantially correct. Then it makes sense to ask whether the Biblical record might be substantially correct in other ways. Given your accusation, it is ironic that I get criticism from YLEC (to use the broadest term) colleagues who want me to start from the Bible. They understand where I am coming from very well. I suspect that you do not because you don't want to believe that my position can exist. As to my not reacting negatively every time I hear long ages being discussed, I think that those who have read this blog for some time are well aware, from my comments, of my belief in a short age for life on earth. I have not tried to hide it. (see the last paragraph of comment 59 above). But to refuse time to those who are trying to construct a naturalistic theory for the origin of life, or for that matter, for the diversity of life, would be to force naturalism into a strawman position. Sure, it would be easy to knock down, but it wouldn't prove that the real theory is wrong. That is, when I discuss naturalistic theories, I try to take them on their own terms. This is partly for argumentative fairness, and partly because, in a sense, I am in this game for keeps also. If someone were to, for example, show that if one just added vanadium, or platinum, or clay, or something else, or all of the above, to a Miller-Urey apparatus, within a year or so some primitive bug would emerge from the soup, my entire inferential chain would essentially collapse. Then I would either have to find a new chain, or give up on YLEC. (I guess that makes my theory falsifiable.) In addition, this is not my blog, and I do not have the right, let alone the obligation, to correct every comment to my own way of thinking on age. That is especially true when the majority view of the moderators is long-age. I need to deal respectfully with their views, and one of the ways to do that is to refrain from constantly yapping about short age whenever an age-related question comes up. Paul Nelson doesn't do that, so why should I? If there should be a discussion of age-related issues on this blog, I might say more. But obviously, most of the discussion is on ID, and so that's where my comments will be directed. Hopefully you now understand where I am coming from a little better.Paul Giem_{August 5, 2008
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Paul Giem #135:
I found the references. The first is Robert Shapiro, Origins, A Skeptic’s Guide to the Creation of Life on Earth, p. 162. One would have to read most of the book (which I highly recommend) to understand the precise context, but suffice it to say that when, discussing the Spiegelman experiments, when he says, “The RNA did not acquire a new capacity, nor could it do so.” (p. 161), it was a negative remark. The reference for RNA naturally forming 2?-5? rather than 3?-5? linkages is found in Albert Lehninger, Biochemistry: The Molecular Basis of Cell Structure and Function, 1970, p. 779. I think I actually used the second edition, and it was in that book, but I don’t happen to have a copy of that edition.
Thanks for your good efforts, but I hope you understand that references to books are not as helpful or as scholarly as references to the primary scientific literature. One reason is accessibility. I don't have either of these books at hand, but I have good access, mainly through the Internet, to the primary literature. The other is reliability. Book citations are secondary sources, necessarily selective, and possibly inaccurate. For example, the "negative remark" by Shapiro has to be taken in context. I believe I know the reasons for Shapiro's remark, based on my understanding of the biology underlying the Spiegelman experiments. Do you understand that biology?
I found out that nucleotides can be joined to yield strings that could theoretically code for a protein up to 81 amino acids long, although the sequence was not, as far as I know, for an actual protein. The size RNA was apparently about that of the Spiegelman monster. Apparently according to Shapiro, there have also been experiments where ribose has been joined to a base, probably adenine, and others where phosphates have been added to nucleosides, although Shapiro did not give references, so I am unable at present to evaluate how important those reactions were. Shapiro didn’t seem too impressed with them...
And from your #114:
Now ask yourself, have you ever read of experiments that actually resulted in longer RNA strands from shorter initial ones? Why would that be?
The synthesis of long strands of RNA under laboratory conditions is a major issue for you. In fact, I believe that I have read of experiments that resulted in longer RNA strands from shorter initial ones. I may even have read of experiments in which RNA strands were synthesized without a primer. Perhaps you could help me narrow down the field, so I can check further. Would you like strand elongation catalyzed by an enzyme, or not? Elongation on a template (as in the Spiegelman QBeta case) or not? Primer, or not?
I am not sure how to interpret one of your comments. “The idea that an unsolved problem in science is an argument for the existence of a deity is attractive to many.” Do you see that as good, or as bad?
How I see it is irrelevant. I was simply acknowledging your perspective as a premise for what I said next.
I am not sure that there is any other way to detect the existence of a deity than otherwise unexplained events in nature or history (which is claimed as a part of nature by believers in naturalism).
Surely your faith does not rest on such a slender reed.
If there is to be any evidence for the existence of God, it must upset naturalists. Then naturalists will just have to be upset if God really exists and can be detected, as Romans 1 and Hebrews 11 seem to indicate.
Apparently the work of naturalists, which does not bear in any way on considerations of the existence of deities, upsets you.
You say, “Given that a deity created life on this planet, would it not be an act of devotion in the tradition of Kepler, Newton, and Einstin to continue efforts to discover how the deity brought that marvel about?” Deuteronomy 29:29
That's it? That's your entire comment? First, let me correct the spelling of Einstein, and then let me add the name of Louis Pasteur to those good theists who understood the scientific method and employed it so effectively, contradicting the notion that there is an inherent incompatibility between science and religious belief. Regarding Deuteronomy 29:29. King James version:
The secret things belong unto the LORD our God: but those things which are revealed belong unto us and to our children for ever, that we may do all the words of this law.
Does Scripture define the limits of science?Daniel King_{August 5, 2008
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Rita Again, this shows that human languages (and indeed comptuer languages) can express rigid structure, syntax, and semantics but none of those things are absolutly required, whereas in DNA they are. They are as required in DNA as in any machine language I'm familiar with and I've used a lot of machine languages. I'll agree that DNA, as far as we know, isn't a high level structured language like Pascal or English but when we learn more about it we may indeed find out that it is. We only understand a small fraction of it at this point in time. In the nonce, coding DNA, which we understand fairly well, is quite like low-level machine languages (typically called "assembly langauge") with messages encoded in a serial stream of base-4 digits. Ribosomes read copies of these serial streams sequentially, executing the instructions as they go along, exactly like paper tape going through old computers. I'd love someone to describe to me how an abstraction layer like the genetic code can arise without being planned. There is nothing else in nature that utilizes abstraction layers except for living things and manmade machines.DaveScot_{August 5, 2008
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-----Paul Giem: "It appears that sparc knew exactly what he was doing." I agree. The fiasco with DK would have been hard to miss. While I agree with Dave's final decision, I note that sparc covered his anatomy very well. That conflict was no accident---it was "designed." That would explain why he didn't apologize for the violation.StephenB_{August 5, 2008
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Now, on more substantial matters: 1] Islands and archipelagos of function Cf 43 above. This will show that it almost does not matter, once we see that functionality is sensitive to perturbation, i.e. the islands are relatively isolated in a vastly larger sea of non-functional configs. In particular, we should realise that 500 - 1,000 bits of increment in information capacity is enough to easily exhaust not just planetary scale resources, but those of the observed cosmos. And, that 300 - 500 k bases is actually an underestimate for life functionality, as the organisms with such short genomes are dependent on others to provide key nutrients that they cannot make for themselves. 1 mn bases is more like the real lower limit. 4^1 mn ~ 6.4 *10^602,059. 10^1,000 islands of 10^1,500 functional configs each -- each of these vastly more than the observed universe can access across its lifetime, would bring that down to searching for 1 in about 10^ 598,500. It here were 10^500 sub-universes of scale similar to ours, that would hardly make a practical difference. In other words, we have excellent reason to see that functionality is truly isolated in the config spaces for DNA of adequate chain length to sustain life. 2] Translation DNA is a digital CODE, with connexion to a defined artificial programming language, and is used in physically executing algorithms through molecular machinery. Kindly show a single instance where such FSCI has originated -- per directly known cause -- through chance + mechanical necessity without intelligent intervention. (By contrast we routinely know that such are produced by intelligent agents.) Not only is this a matter of direct observation, but also, the requisite search to produce such a complex, would easily exhaust the search resources of the cosmos. But we know also that intelligent agents use insight, knowledge, imagination and skill to narrow down the search zone to manageable proportions. That is why intelligence outperforms chance-based search. Whether or no poems can be translated from French to German and back again is utterly irrelevant to this. 3] Quantification I have given [1] a simple framework in which quantification may be presented as a vector, [2] a link to which the quantification of the wider CSI concept is defined, [3] above, real world discussions on the decisive quantification issue -- configuration space and isolation of biofunctional states therein. That is more than enough to answer to the real issue: we have a filter for identifying that certain phenomena show objective, empirically identifiable, credibly reliable signs of intelligence as the decisively important causal factor. ____________ That's all folks. GEM of TKIkairosfocus_{August 5, 2008
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Dave and Sparc: I must first thank you Dave for being sufficiently concerned to try to stop abusive use of my name in a context where I have specifically requested its non-use, because of the spamming effects. [Sparc, your use of my name here cannot get me "expelled," but it can cause me problems and headaches. I ask you to respect that. Also, I think you should be very careful of how you decide to use personal information online, in general; especially in this context. And, above when I noted on a second unauthorised use of my name here in this thread, I had no intent6 that it be taken as by the same person.] As I have stated all along, I have left my contact information accessible enough through my personal site for accountability and responsible communication. That is a point where I think I can balance the spamming issue and the need for a measure of accountability and responsible communication. As to the issue of irresponsible use, I note that the always linked page lists at its very head:
A Kairosfocus Briefing Note . . .
And it states in the note at its foot:
This briefing note was originally created by GEM of TKI . . . [NB: Because of abuse of my given name in blog commentary threads, I have deleted my given name from this page, and invite serious and responsible interlocutors to use my email contact below to communicate with me.] . . .
I think that should be clear enough. GEM of TKIkairosfocus_{August 5, 2008
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Paul Giem The OP says
14,000 genes/8 new functional genes per million years
I'm surprised that you have not mentioned some disagreement with that figure. From what I've read at the AIG website you appear to believe that the earth is literally less then 100,000 years old, or thereabouts. While your points are interesting I find it more interesting that you don't make plain your meta-ojection to the whole idea in the first place, I.E that a million years cannot have passed in any case. Why? Earlier you said
It is true that standard evolutionary theory assumes that chimpanzees and humans (or monkeys and humans, for that matter) descended from a common ancestor which was not a modern chimpanzee. However, until the ancestor is found, it remains hypothetical, and the ancestor could be essentially a modern chimpanzee, or the ancestor, the modern chimpanzee, and the modern human could be genetically equidistant.
Yes, the ancestor is yet to be found but I find it, to be perfectly honest, dishonest that your primary objection to the whole thing has not been made clear to all, namely that as you believe the earth is not very many years old none of it could have happened that way in any case. Your AIG webpage, presumably written by you says
It basically forces one into accepting a short chronology for life on earth. Thus, if one accepts a designer intelligent enough to produce life, and a short timescale, it becomes very difficult to avoid the claims of the Bible.
Why do you even pretend to consider things and construct arguments against events that require a long chronology when you already know they are not possible?RitaFairclough_{August 5, 2008
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bFast
Rita, I am a bit lost. Why the comparison between translating french to german and back with transcribing DNA?
I'm just making the point that perhaps "language" is the wrong word to use when talking about DNA. Languages, as I have pointed out, have features that DNA does not have and so perhaps a different word would be more accurate when talking about language. Earlier you said
Now, DNA is a language — it is not “like” a language. When we speak of the “machine language” of a computer’s central processor, it is a language as DNA is a language, as english is a language.
Except one of those things is different to the other. If DNA is a language, can it be translated into French? If not then it's not "like" english, at least in that specific way, which can be so translated (and back again if desired). DaveScot
Like computer languages it has rigid structure, syntax, and semantics associated with it.
And I believe this is another significant difference. New languages can evolve in surprisingly little time, taking their roots from whatever is available. For example, groups of deaf children left to their own devices and neglected have be found to invent their own sign language. Again, this shows that human languages (and indeed comptuer languages) can express rigid structure, syntax, and semantics but none of those things are absolutly required, whereas in DNA they are. So, another way in which DNA needs a better word then "language". There are too many differences.RitaFairclough_{August 5, 2008
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Daniel King, (115 and 123) I found the references. The first is Robert Shapiro, Origins, A Skeptic’s Guide to the Creation of Life on Earth, p. 162. One would have to read most of the book (which I highly recommend) to understand the precise context, but suffice it to say that when, discussing the Spiegelman experiments, when he says, "The RNA did not acquire a new capacity, nor could it do so." (p. 161), it was a negative remark. The reference for RNA naturally forming 2'-5' rather than 3'-5' linkages is found in Albert Lehninger, Biochemistry: The Molecular Basis of Cell Structure and Function, 1970, p. 779. I think I actually used the second edition, and it was in that book, but I don't happen to have a copy of that edition. I found out that nucleotides can be joined to yield strings that could theoretically code for a protein up to 81 amino acids long, although the sequence was not, as far as I know, for an actual protein. The size RNA was apparently about that of the Spiegelman monster. Apparently according to Shapiro, there have also been experiments where ribose has been joined to a base, probably adenine, and others where phosphates have been added to nucleosides, although Shapiro did not give references, so I am unable at present to evaluate how important those reactions were. Shapiro didn't seem too impressed with them, which raises the question of whether they were similar to the very artificial synthesis of pyrimidines. But I though that in fairness I should include this information. I am not sure how to interpret one of your comments. "The idea that an unsolved problem in science is an argument for the existence of a deity is attractive to many." Do you see that as good, or as bad? I am not sure that there is any other way to detect the existence of a deity than otherwise unexplained events in nature or history (which is claimed as a part of nature by believers in naturalism). If there is to be any evidence for the existence of God, it must upset naturalists. Then naturalists will just have to be upset if God really exists and can be detected, as Romans 1 and Hebrews 11 seem to indicate. You say, "Given that a deity created life on this planet, would it not be an act of devotion in the tradition of Kepler, Newton, and Einstin to continue efforts to discover how the deity brought that marvel about?" Deuteronomy 29:29Paul Giem_{August 4, 2008
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Sorry Sparc. You’re back. KairosFocus: Stop complaining about people using your real name here. You link to your website constantly and your real name appears on it. Fix it yourself one way or the other but don’t expect us to waste our time on it anymore.
Thank you Dave.sparc_{August 4, 2008
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Rita, I am a bit lost. Why the comparison between translating french to german and back with transcribing DNA? BTW, there actually is a very tight parallel to the French-German thing. Consider that a coding gene will translate from DNA to protein. However, it is totally possible to reverse this translation back to DNA. The results, however, will not be identical to the original DNA, the results will produce the identical protein, but will involve different DNA sequence. This because there are multiple DNA sequences that transcribe to the same amino acid in the protein.bFast_{August 4, 2008
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Rita DNA is a code structured very much like morse code. Coding DNA performs essentially the same task as computer code in that it consists of abstract instructions which control a machine. Like computer languages it has rigid structure, syntax, and semantics associated with it. We're very far from being able to "speak" it fluently but it is indeed a machine language. I'm fluent in several machine languages so this is very familiar ground for me. DaveScot_{August 4, 2008
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Sorry Sparc. You're back. KairosFocus: Stop complaining about people using your real name here. You link to your website constantly and your real name appears on it. Fix it yourself one way or the other but don't expect us to waste our time on it anymore. DaveScot_{August 4, 2008
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It appears that sparc knew exactly what he was doing. He said,
It would be interesting if [name deleted] shows up here to discuss the differences between FSCI and [name omitted by me] with Kairosfocus.
That would appear to be a deliberate tweak. Granted that it was his first time, but he appears to have known better. Whoever is doing the editing (DaveScot?) should also remove the link, and possibly the permutation, to make it harder to make the objectionable connection.Paul Giem_{August 4, 2008
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Sorry for the mutiple posts! I wrote:
My point (and Hofstaders) is that a poem can be in one language, say French, then translated into German by somebody and then translated into French again by somebody else. Hofstader actually did this, in various ways.
And my point was that the french to german back to french gives a poem (chances are good) that is different to the original poem. It might be about the same thing and have similar language and concepts but chances are it's expressed in different ways. Very different from the "translation into a different symbolic representation" represented by sequencing DNA and talking about it on a blog, for example. The code has the same values whatever the representation, on the screen or in the testtube.RitaFairclough_{August 4, 2008
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