tag:blogger.com,1999:blog-1090883723146476626.post7969130511891383916..comments2023-11-03T06:35:51.218-06:00Comments on Evolution Engineered: The Design Matrix RevealedJJS P.Eng.http://www.blogger.com/profile/05029579563816207022noreply@blogger.comBlogger36125tag:blogger.com,1999:blog-1090883723146476626.post-87113698003111969652008-09-03T11:49:00.000-06:002008-09-03T11:49:00.000-06:00Hi Art, I didn't know you had been "disinvited" fr...Hi Art, <BR/><BR/>I didn't know you had been "disinvited" from TT. That's problematic for me, since I consider you one of the best critics around. Without good critics, what's the point of discussing ID? And what's the fun of it? <BR/><BR/>You write, <BR/><B>I hope you will take note of the inconsistency on Mike Gene's part when it comes to Yarus et al. He is willing to look at data that pertains to some issues. But not in this case.</B><BR/><BR/>Ummm, let's see. He probably lowered his Discontinuity score because of it. Not low enough for you, but then he's working from a Rabbit perspective, and you're working from a Duck perspective, so I think that explains it. And did Yarus's work also cover amino acids' affinity with <B>all</B> their tRNAs? Because Mike wrote: <BR/><BR/>"...there is no law of nature which determines that the codon UCU must represent the amino acid serine, because other codons can also represent this amino acid, for example, AGC." (p.71 of the <I>DM</I>Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-15097655649695550152008-08-19T17:23:00.000-06:002008-08-19T17:23:00.000-06:00Hi Bilbo,I'll be gone for a few days as well, duri...Hi Bilbo,<BR/><BR/>I'll be gone for a few days as well, during which time this thread will possibly wander off the front page, and thus into history (or perhaps oblivion). If you wish to keep this back and forth going, you should start a discussion on your own blog (TT doesn't work as I've long ago been disinvited from there).<BR/><BR/>I hope you will take note of the inconsistency on Mike Gene's part when it comes to Yarus et al. He is willing to look at data that pertains to some issues. But not in this case. IMO, this betrays a bias that takes precedence over other arguments, a prejudice grounded in the proposition that the origins of life cannot ever be allowed to come into the field of scientific play. The stereochemical basis for the genetic code is threatening to our telic thinkers because it is a chink in their "OOL NO NO NEVER!!" facade, a "fortress" in which ID seems more and more entrenched. They will not be able to think clearly and objectively about research like this - it crosses a line that must not be crossed.<BR/><BR/>Whatever the reason for your hiatus, best of luck.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-76173980466326286512008-08-19T11:51:00.000-06:002008-08-19T11:51:00.000-06:00I'll be gone for a few days, Art. After finally u...I'll be gone for a few days, Art. After finally understanding that Yarus found that 11 out of 12 amino acids have affinity for their (anti)codons, I understand your frustration with Mike Gene for not talking about more specifically in his book. However, given that he scored pseudogenes as a -4, PCP pathway as -2, the vertebrate eye as 0, and the genetic code a whopping (notice the sarcasm) +3, I don't think we're dealing with a guy who ignores the scientific evidence. I think he deserves better from you. <BR/><BR/>I'll be gone until next week.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-3182232832127399692008-08-18T08:20:00.000-06:002008-08-18T08:20:00.000-06:00Does Matty ever show up at ARN? I haven't been th...Does Matty ever show up at ARN? I haven't been there for a while.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-65872187723709875692008-08-18T08:19:00.000-06:002008-08-18T08:19:00.000-06:0011 out of 12 amino acids? I guess I counted wrong...11 out of 12 amino acids? I guess I counted wrong at iscid (not surprising, if you know me). That's much more impressive and I would definitely give you a -2 on Discontinuity. <BR/><BR/>However, the question remains, could this be explained from a design perspective? Would a knowledgeable designer (by hypothesis), realizing that the amino acids have an affinity for specific codons have a good design reason for designing the appropriate synthetases, that would bind those amino acids to the tRNAs having those codons? For example, if the designer used synthetases that bound those amino acids to different tRNAs, would the affinity with the other codons interfere with the binding between the synthetases and the tRNAs? That doesn't sound clear. Let's use a single example: Say amino acid x has an affinity for the anticodon of tRNA-x. However, its synthetase binds it to tRNA-y. Would amino acid x's affinity to tRNA-x interfere with its binding to tRNA-y? If so, then a knowledgeable designer would have designed it so the synthetase would bind amino acid x to tRNA-x, instead of to tRNA-y. <BR/><BR/>So the experiment I propose would be to change the synthetase so that an amino acid binds to a different tRNA, one that it doesn't have an affinity with; put it in with it's old tRNA and its new tRNA, and see what happens. Would we notice a difference in binding time or tendencies? Would it bind to the new tRNA, only slower? If so, then we would have a design explanation for why the 11 of 12 amino acids bind to tRNAs that have anticodons with which they have affinity. <BR/><BR/>Would this disprove the non-teleological explanation? No. We would have ambiguous results, unsurprisingly. Which is why the "facts" don't always give us the clear conclusions we think they do. And that's why Mike Gene's use of the duck/rabbit picture. <BR/><BR/>Yeah, on re-reading the article on C-T deamination and the stop codons, I'm not sure it explains the 3 codons. However, I'm curious what the author was getting at about most of the codons in prokaryotes being a certain type.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-38065775553868841512008-08-17T08:24:00.000-06:002008-08-17T08:24:00.000-06:00Yeah, I miss Matty. So does Arp of Jockstrappe.Yeah, I miss Matty. So does Arp of Jockstrappe.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-48623219532411699262008-08-17T08:20:00.000-06:002008-08-17T08:20:00.000-06:00Hi Bilbo,Returning to this discussion:You said: ” ...Hi Bilbo,<BR/>Returning to this discussion:<BR/><BR/>You said: ” I found another library. Data for discontinuity: Apparently 12 amino acids show no affinity for the (anti)codons. No remnants of an earlier code found. At best, highly speculative scenarios of how the code could have evolved from an RNA world.”<BR/><BR/>I don’t know where you got this from, but its wrong. The facts are that 11/12 of the amino acids that were tested showed a decided and significant affinity for RNAs that possess codon and/or anticodon. The other amino acids have not been tested – not for philosophical or theological reasons, but because the method cannot be used with these amino acids. I discuss this in more detail at http://fluorescentflicker.wordpress.com/2007/12/30/bradfords-hammer/#comments . <BR/><BR/>Quoting Mike Gene: <BR/>"When it comes to Discontinuity, we must pay tribute to the fact that there are dozens, perhaps hundreds, of papers where scientists have speculated about the evolutionary origin of the code and gathered circumstancial evidence to support their respective cases. Neverthelss, the various explanations remain largely in the realm of speculation....the code is universal, lacking any trace of simpler precursors or permutations spawned from such ancient precursor states....if the code was indeed spawned from non-teleological forces acting over great spans of time, we would predict the existence of such permutations someplace in the biological world. That they do not exist argues against such an origin. As a result of the above considerations, I give the code a Discontinuity score of 2." <BR/><BR/>If it hadn't been for the hundreds of papers by scientists speculating on a non-teleological origin, Mike probably would have given it a higher score.”<BR/><BR/>This is pretty lame. Basically, Mike Gene is saying, because the scientific community hasn’t come to a clear and unequivocal model for each and every step in the OOL, then the positive results of Yarus and coworkers may be ignored. As I have been saying in this discussion here, this fairly screams “don’t try to confuse the issue with facts”. This is, in a nutshell, the DM. An attempt to substitute vague and unfounded suspicion for hard experimental data.<BR/><BR/>You said: ”I think I've explained why I wouldn't. But I understand why you do, and I don't think you are entirely unjustified. I do suggest a -1, instead of a -2.”<BR/><BR/>Thanks. This would bring us to an examination of the scale of the DM. But I have better things to do with my blogging time than quibble thusly. So I’m happy to leave things at this significant point of agreement. (It’s significant in that we can see what the other is saying, and comment about the specific issue.)<BR/><BR/>Incidentally, as most of us have found, the ARN search tool is really bad. I’ll keep trying to find the specific reference I alluded to before, but will mention as an aside that I have found more recent studies that also fill in the “gap” between Yarus and the genetic code as we know it. Maybe someday when I get caught up on my <A HREF="http://aghunt.wordpress.com" REL="nofollow">blog</A>, I’ll put something together on this.<BR/><BR/>“I've only read Franklin Harold's book, The Way of the Cell, and I doubt he was familiar with Yarus's work. It could be that Harold would have changed his mind. There's also Maynard Smith and Stuart Kaufmann. Again, they might not have known about Yarus, but Kaufmann makes the point that the arbitrariness is apparent from the fact that the amino acids bind to the stem of the tRNAs, and not the anticodons.”<BR/><BR/>Obviously, Kaufmann was speaking without the knowledge of Yarus et al. <BR/><BR/>“Art said...<BR/>Mike Gene's blog entry has nothing to do with the matter I mentioned.<BR/><BR/>Well, if I recall, you thought the 3 stop codons were sub-optimal. Mike offers an explanation of why they aren't, and it ties in with his thoughts on C-T deamination.”<BR/><BR/>My point is that, from a purely conceptual and hypothetical point of view, one stop codon works as well as three. My point has nothing to do with the base content of the stop codon, and is as applicable to the stop codon as UAA as CCC (or whatever…).<BR/><BR/><BR/>“I'm working with the hypothesis that a knowledgeable designer did choose to design our kind of life, and tried to come up with an explanation as to why she would choose to have the tRNA synthetases bind those amino acids that showed affinity with certain tRNAs to those tRNAs. Is is testable? Can we change the synthetases in vitro and see what happens?”<BR/><BR/>Yes. But what this has to do with your hypothesis is a bit unclear.<BR/><BR/>“I'm not sure I agree. Let's say on closer inspection the face on Mars still looks designed. We land and explore, and find no other designed-looking objects. We have high scores for Analogy and Discontinuity, but low for Rationality and Foresight. I don't think our conclusion of design will be as strong, and doubters will be tolerated.”<BR/><BR/>I think I see your point. I remain skeptical that a similar scenario has, or will, play out when it comes to life as we know it.<BR/><BR/>“”Seeing as Mike Gene thinks I accused him of child abuse and poor parenting...I sort of suspect that people are confusing me with someone else.”<BR/><BR/>Did you?”<BR/><BR/>No.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-26566632380656279142008-08-16T14:47:00.000-06:002008-08-16T14:47:00.000-06:00Oops, forgot to sign in as Bilbo, again, but that'...Oops, forgot to sign in as Bilbo, again, but that's who this is. <BR/><BR/>Art: <B>Seriously, Bilbo. How can you assert a positive value for discontinuity in the case of the genetic code when the only data - I repeat, the ONLY data - point to continuity.</B><BR/><BR/>I found another library. Data for discontinuity: Apparently 12 amino acids show no affinity for the (anti)codons. No remnants of an earlier code found. At best, highly speculative scenarios of how the code could have evolved from an RNA world. <BR/><BR/><B>You show us quite clearly how IDists care nary an iota for data.</B><BR/> <BR/>Once again, ouch. I'm hurt that you have such a low opinion of me. I think I've earned better. As to Mike Gene, from his book, p. 281: <BR/>"<B>When it comes to Discontinuity, we must pay tribute to the fact that there are dozens, perhaps hundreds, of papers where scientists have speculated about the evolutionary origin of the code and gathered circumstancial evidence to support their respective cases. Neverthelss, the various explanations remain largely in the realm of speculation....the code is universal, lacking any trace of simpler precursors or permutations spawned from such ancient precursor states....if the code was indeed spawned from non-teleological forces acting over great spans of time, we would predict the existence of such permutations someplace in the biological world. That they do not exist argues against such an origin. As a result of the above considerations, I give the code a Discontinuity score of 2.</B>" If it hadn't been for the hundreds of papers by scientists speculating ona non-teleological origin, Mike probably would have given it a higher score. <BR/><BR/> <B>If you were to go where the experiments lead, you would have to assign a negative value.</B><BR/><BR/>I think I've explained why I wouldn't. But I understand why you do, and I don't think you are entirely unjustified. I do suggest a -1, instead of a -2.<BR/><BR/><B>I would be interested in the list of "informed commenters" who have reviewed the work of Yarus et al. and offered positive experimental evidence that is not in agreement with his work.</B> <BR/><BR/>I've only read Franklin Harold's book, <I>The Way of the Cell</I>, and I doubt he was familiar with Yarus's work. It could be that Harold would have changed his mind. There's also Maynard Smith and Stuart Kaufmann. Again, they might not have known about Yarus, but Kaufmann makes the point that the arbitrariness is apparent from the fact that the amino acids bind to the stem of the tRNAs, and not the anticodons. <BR/><BR/> Art said... <BR/><B>Mike Gene's blog entry has nothing to do with the matter I mentioned.</B><BR/><BR/>Well, if I recall, you thought the 3 stop codons were sub-optimal. Mike offers an explanation of why they aren't, and it ties in with his thoughts on C-T deamination.<BR/><BR/>Bilbo: <BR/><B>"True, but I was just trying to understand the data at that time. Let me offer an ID perspective, now. A knowledgeable designer, realizing that there was an affinity between some of the amino acids and their codons or anti-codons, designed the tRNA synthases so that the amino acids would bind to tRNAs with those codons, thus avoiding potential problems of interference by binding to the wrong tRNAs."</B><BR/><BR/><B>That's just an unsupported and untestable assertion. I can as easily and as justifiably claim that a knowledgeable designer would have nothing to do with any of this, and thus that life as we know cannot be designed.</B><BR/><BR/>I'm working with the hypothesis that a knowledgeable designer <I>did</I> choose to design our kind of life, and tried to come up with an explanation as to why she would choose to have the tRNA synthetases bind those amino acids that showed affinity with certain tRNAs <B>to</B> those tRNAs. Is is testable? Can we change the synthetases <I>in vitro</I> and see what happens? <BR/><BR/><B>My main problem with the DM (as I'm reading it here) is that it seems to be a needless multiplier. If one is going to see an analogy, then rationality and foresight, at the very least, are going to be foregone conclusions. The same will usually be true for discontinuity (a property that is folded integrally into most analogies in the first place).</B><BR/><BR/>I'm not sure I agree. Let's say on closer inspection the face on Mars still looks designed. We land and explore, and find no other designed-looking objects. We have high scores for Analogy and Discontinuity, but low for Rationality and Foresight. I don't think our conclusion of design will be as strong, and doubters will be tolerated. <BR/><BR/><B>Seeing as Mike Gene thinks I accused him of child abuse and poor parenting...I sort of suspect that people are confusing me with someone else.</B><BR/><BR/>Did you?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-16406158050492717782008-08-16T12:42:00.000-06:002008-08-16T12:42:00.000-06:00Art: Seriously, Bilbo. How can you assert a positi...Art: <B>Seriously, Bilbo. How can you assert a positive value for discontinuity in the case of the genetic code when the only data - I repeat, the ONLY data - point to continuity.</B><BR/><BR/>Are we still talking about only 8 (out of 20) amino acids? And the catalyzing activity of tRNA that your going to reference? I'll agree that it supports continuity. The question is, how much does it support it? And it looks to me like the answer is, not a lot. But I'm out of time. Libraries closed on Sundays. Be back Monday.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-78679289275303104002008-08-16T12:37:00.000-06:002008-08-16T12:37:00.000-06:00From The Design Matrix, p.xiv, : "The Internet can...From <I>The Design Matrix</I>, p.xiv, : <B>"The Internet can be an extremely hostile environment and their support with stimulating questions, commentary, and/or kind words has been greatly appreciated. These people include...Art..."</B>.<BR/><BR/>There, now don't you feel ashamed of yourself?Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-30135432120173980982008-08-16T12:30:00.000-06:002008-08-16T12:30:00.000-06:00Hi Art, I'm running out of time (so many blogs, so...Hi Art, I'm running out of time (so many blogs, so little time). But I really miss Matty. Don't you?Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-91157915452178175792008-08-16T11:35:00.000-06:002008-08-16T11:35:00.000-06:00"And I don't think you're giving Mike Gene enough ..."And I don't think you're giving Mike Gene enough credit* for expanding "it looks designed," into the four categories of Analogy, Discontinuity, Rationality, and Foresight. Even high scores in Analogy and Discontinutiy do not guarantee an overall high score for Design."<BR/><BR/>My main problem with the DM (as I'm reading it here) is that it seems to be a needless multiplier. If one is going to see an analogy, then rationality and foresight, at the very least, are going to be foregone conclusions. The same will usually be true for discontinuity (a property that is folded integrally into most analogies in the first place).<BR/><BR/>"*You of all people, the only ID critic included in his list of acknowledgements. Oh just thinking about it causes so much heartache. Take your football and begone!"<BR/><BR/>Football? You been talkin' to Matty somewhere?<BR/><BR/>In any case, this is the second mention I've seen made of this. Seeing as Mike Gene thinks I accused him of child abuse and poor parenting, and that I'm some terrible bullying ogre, I sort of suspect that people are confusing me with someone else. I'm pretty sure he would not mention such a monster in any positive sense.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-56890791502069097752008-08-15T20:38:00.000-06:002008-08-15T20:38:00.000-06:00"True, but I was just trying to understand the dat..."True, but I was just trying to understand the data at that time. Let me offer an ID perspective, now. A knowledgeable designer, realizing that there was an affinity between some of the amino acids and their codons or anti-codons, designed the tRNA synthases so that the amino acids would bind to tRNAs with those codons, thus avoiding potential problems of interference by binding to the wrong tRNAs."<BR/><BR/>That's just an unsupported and untestable assertion. I can as easily and as justifiably claim that a knowledgeable designer would have nothing to do with any of this, and thus that life as we know cannot be designed.<BR/><BR/>I will need some time to dig up the reference I cryptically refrred to above - the second item of positive support for continuity. The study I have mentioned elsewhere showed how a part of the tRNA actually participated in the reaction catalyzed by tRNA synthetases. That's a bang-up piece of data that supports a very interesting hypothesis that flows from the RNA World scenario.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-5988322188709016132008-08-15T19:50:00.000-06:002008-08-15T19:50:00.000-06:00Mike Gene's blog entry has nothing to do with the ...Mike Gene's blog entry has nothing to do with the matter I mentioned.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-92232476625276086292008-08-15T19:49:00.000-06:002008-08-15T19:49:00.000-06:00Seriously, Bilbo. How can you assert a positive v...Seriously, Bilbo. How can you assert a positive value for discontinuity in the case of the genetic code when the only data - I repeat, the ONLY data - point to continuity. <BR/><BR/>You show us quite clearly how IDists care nary an iota for data. If you were to go where the experiments lead, you would have to assign a negative value.<BR/><BR/>I would be interested in the list of "informed commenters" who have reviewed the work of Yarus et al. and offered positive experimental evidence that is not in agreement with his work. <BR/><BR/>(I know I'm asking a lot, but I am not inclined to equate the off-the-cuff comments of some IDists with the solid and compelling experimental results I am discussing. I want names and pointers, so I can see the specifics as far as commentary about the stereochemical basis of the genetic code.)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-25688336319564716802008-08-15T14:28:00.000-06:002008-08-15T14:28:00.000-06:00Mike Gene just wrote up something on the advantage...Mike Gene just wrote up something on the advantages of 3 stop codons:<BR/><BR/>http://www.thedesignmatrix.com/content/complementing-the-cytosine-deamination-story/#more-168Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-77487283673612210612008-08-15T14:04:00.000-06:002008-08-15T14:04:00.000-06:00Art wrote: Thanks for the pointers. FYI, Mike Gene...Art wrote: <B>Thanks for the pointers. FYI, Mike Gene’s C deamination pt2 avoids the matter of additional mutational mechanisms. It also avoids some other issues that were brought up on the ARN boards. All in all, his case is pretty slim.</B><BR/><BR/>Could you "point" me in the right direction for specific objections?<BR/><BR/><B>As for Jules’ contributions, I think your statements call into serious question the application of the DM for discovery and understanding. On the ISCID boards, we learned of two solid, incontrovertible, and as yet un-refuted pieces of data that link the genetic code with the RNA World.</B><BR/> <BR/>I re-read the thread, and I think I saw <I>one</I> solid piece of data: 8 amino acids display affinity for their codons or anti-codons. I missed the second piece of data. <BR/><BR/> <B>(Jules never offered anything to counter the facts and their implications, and neither I daresay has any other ID proponent.)</B><BR/><BR/>True, but I was just trying to understand the data at that time. Let me offer an ID perspective, now. A knowledgeable designer, realizing that there was an affinity between some of the amino acids and their codons or anti-codons, designed the tRNA synthases so that the amino acids would bind to tRNAs with those codons, thus avoiding potential problems of interference by binding to the wrong tRNAs. <BR/> <BR/><B>You remain unmoved, and I suspect that you would support jjs’ assignment of a value of +2 for the “discontinuity” of the genetic code.</B><BR/><BR/>Yeah, showing that 8 amino acids bind to their codons or anti-codons didn't "move" me much, since I wanted to know why they would bind to the stems instead. Speculation that in an RNA world things were different and would explain all of that didn't "move" me much either. Have any of those details been filled in? What I score for Discontinuity doesn't matter much, since I'm just part of the peanut gallery. But so far, looking from the sidelines, +2 looks about right. <BR/><BR/><BR/> <B>IMO, this really renders the DM as pointless. Here’s why:<BR/><BR/>I would think that the default value for any of the DM categories would be 0, and I would think that any movement away from 0 would require some sort of experimental evidence. I have pointed out two as yet unchallenged studies that support the idea of continuity. As of the moment, we don’t have a “singularity to the human genome” demonstration in the lab, but we still have solid data that is not consistent with discontinuity. This is why I gave a value of -2.</B><BR/><BR/>I agree that a default value of 0 is a good place to start. I think the data that shows some sort of continuity is weak, but should be included in our score. That's why +2 instead of higher. But I'll go down to +1 if you go up to -1. Deal? <BR/><BR/><B>jjs (and all other ID proponents) offer no experimental data to support the notion of discontinuity – none whatsoever. So, from the perspective of experiment, the case is crystal clear, and as I have stated.</B><BR/><BR/>Since most informed commenters (regardless of their views on ID) on the genetic code seem to think that it is arbitrary, I'm guessing that it was based on some sort of experimental data. And showing that 8 amino acids have an affinity for their codons doesn't make the case crystal clear. <BR/><BR/><B>In this light, and given that I am rather sure that you and jjs will argue for a positive value here, it seems to me that the use of the DM is quite apart from empirical study. Y’all don’t seem to be interested in actual data. What this leaves us is evidence-free suspicion. But that’s where we were before the DM – unsupported suspicion, wishful thinking, and the like. The DM doesn’t add anything to the toolkit, and indeed seems more than ever to be an artificial multiplier of “it looks that way to me, thus design”.</B><BR/><BR/>The part about not being interested in actual data is what really hurts, Art. And I don't think you're giving Mike Gene enough credit* for expanding "it looks designed," into the four categories of Analogy, Discontinuity, Rationality, and Foresight. Even high scores in Analogy and Discontinutiy do not guarantee an overall high score for Design. <BR/><BR/> *You of all people, the <I>only</I> ID critic included in his list of acknowledgements. Oh just thinking about it causes so much heartache. Take your football and begone!Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-1642098770550036042008-08-13T20:33:00.000-06:002008-08-13T20:33:00.000-06:00Hi Bilbo,Thanks for the pointers. FYI, Mike Gene’...Hi Bilbo,<BR/><BR/>Thanks for the pointers. FYI, Mike Gene’s C deamination pt2 avoids the matter of additional mutational mechanisms. It also avoids some other issues that were brought up on the ARN boards. All in all, his case is pretty slim.<BR/><BR/>As for Jules’ contributions, I think your statements call into serious question the application of the DM for discovery and understanding. On the ISCID boards, we learned of two solid, incontrovertible, and as yet un-refuted pieces of data that link the genetic code with the RNA World. (Jules never offered anything to counter the facts and their implications, and neither I daresay has any other ID proponent.) You remain unmoved, and I suspect that you would support jjs’ assignment of a value of +2 for the “discontinuity” of the genetic code. IMO, this really renders the DM as pointless. Here’s why:<BR/><BR/>I would think that the default value for any of the DM categories would be 0, and I would think that any movement away from 0 would require some sort of experimental evidence. I have pointed out two as yet unchallenged studies that support the idea of continuity. As of the moment, we don’t have a “singularity to the human genome” demonstration in the lab, but we still have solid data that is not consistent with discontinuity. This is why I gave a value of -2.<BR/><BR/>jjs (and all other ID proponents) offer no experimental data to support the notion of discontinuity – none whatsoever. So, from the perspective of experiment, the case is crystal clear, and as I have stated.<BR/><BR/>In this light, and given that I am rather sure that you and jjs will argue for a positive value here, it seems to me that the use of the DM is quite apart from empirical study. Y’all don’t seem to be interested in actual data. What this leaves us is evidence-free suspicion. But that’s where we were before the DM – unsupported suspicion, wishful thinking, and the like. The DM doesn’t add anything to the toolkit, and indeed seems more than ever to be an artificial multiplier of “it looks that way to me, thus design”.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-67092542347089232982008-08-12T12:09:00.000-06:002008-08-12T12:09:00.000-06:00Mike Gene's second essay on C deamination: http://...Mike Gene's second essay on C deamination: <BR/><BR/>http://idthink.net/biot/deam2/index.htmlBilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-23660237284202215692008-08-12T12:07:00.000-06:002008-08-12T12:07:00.000-06:00Art said: Um, what I meant was that codes and lang...Art said: <B>Um, what I meant was that codes and languages are arbitrary constructs. There is no physical connection between the letters "cat" and a feline. The same is not true for the genetic code. Triplets code for amino acids because they are connected (historically) with those amino acids. Thus, when it comes to analogy, the genetic code is a solid negative.</B><BR/><BR/>Which is why I mentioned computer codes. We come up with a code, then all the instructions that determine how the computer "interprets" the code. There is no conscious mind in the computer that connects the code to what to do with it, in contrast to our minds that connect "cat" to a certain animal. These instructions in the computer are the same sort of thing like the enzymes (proteins) that connect the proper tRNA to the proper amino acid. <BR/><BR/>So, yes, the genetic code is very much like the kind of codes we create for non-conscious machines.<BR/><BR/>Art: <B>I need only point out that one stop codon is all that is needed. Three stop codons = much more "opportunity" for nonsense mutation.</B><BR/><BR/>Ah, interesting. So here is where an ID researcher would have an opportunity to do research: Why would a designer use 3 stop codons, instead of 1? Or do we already know the advantage of redundant stop codons?<BR/><BR/>Art: <B>The genetic code is optimal only to the extent that evolution optimized it. It actually has not preserved the designs in which it first appeared.</B><BR/><BR/>Or has it not preserved them because they were never there? In his book, Mike Gene argues that we have found organisms where the code has evolved, even though it is not as optimal. Yet organisms that use it manage to survive in their own little niches. If there were previous codes, it seems logical to think that there would be little niches where they were preserved.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-70724612362353030592008-08-12T11:54:00.000-06:002008-08-12T11:54:00.000-06:00Art, here is the link to the discussion you had wi...Art, here is the link to the discussion you had with Jules (me, of course) at iscid(don't know how to do that blue thingy without help): http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000606#000001<BR/><BR/>It seemed to involve Yarus's findings.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-45925563432744097262008-08-10T21:43:00.000-06:002008-08-10T21:43:00.000-06:00Hi Bilbo,Some very brief comments for this evening...Hi Bilbo,<BR/><BR/>Some very brief comments for this evening.<BR/><BR/>"As to Analogy, I know next to nothing about computers, but aren't the codes used basically ones where "the meaning of words is determined by (and only by) the medium on which the language is conveyed"?"<BR/><BR/>Um, what I meant was that codes and languages are arbitrary constructs. There is no physical connection between the letters "cat" and a feline. The same is not true for the genetic code. Triplets code for amino acids because they are connected (historically) with those amino acids. Thus, when it comes to analogy, the genetic code is a solid negative.<BR/><BR/>"As to the Discontinuity of the genetic code, Jules had a go around with Art at ISCID, and I don't think Art demonstrated continuity nearly as well as he seems to think."<BR/><BR/>I don't recall Jules ever having commented on the work of Yarus and coworkers. Care to help me refresh my memory?<BR/><BR/>"As to Rationality, Art needs to show that there is a way to avoid nonsense mutations, without destroying the ability to mutate at all."<BR/><BR/>Not at all. I need only point out that one stop codon is all that is needed. Three stop codons = much more "opportunity" for nonsense mutation.<BR/><BR/>" Further, Mike Gene has already written an essay on the question of how other mutations would affect C deamination."<BR/><BR/>I missed this as well. Got a pointer?<BR/><BR/>"As to Foresight, if computer simulations are correct, then our genetic code is one of the most optimal there is, able to preserve design far into the future."<BR/><BR/>The genetic code is optimal only to the extent that evolution optimized it. It actually has not preserved the designs in which it first appeared.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-5954905447251701262008-08-09T16:16:00.000-06:002008-08-09T16:16:00.000-06:00Welcome to EE, Bilbo."It looks like I got you some...Welcome to EE, Bilbo.<BR/><BR/><I>"It looks like I got you some free advertising at TT."</I><BR/><BR/>You mean I went to the bank machine for nothing??? ;)<BR/><BR/>As for being <A HREF="http://telicthoughts.com/great-review-of-mike-genes-take-on-ic/#comment-199525" REL="nofollow">"Mike Gene's interpreter"</A>, how much does that pay? ;)<BR/><BR/>Thanks for posting my review at TT. It's been the high-point of my very short blogging "career" :)JJS P.Eng.https://www.blogger.com/profile/05029579563816207022noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-51030463494795970622008-08-09T16:13:00.000-06:002008-08-09T16:13:00.000-06:00Art, I never put the Design Matrix forward as a "f...Art, I never put the Design Matrix forward as a "foolproof" way of finding design in nature, and neither did Mike Gene:<BR/><BR/><I>"While the DM is not an objective measure of design in natural object, it can be a useful tool, helping to provide direction to those who wish to “follow the Rabbit**”<BR/>JJS P.Eng. Last Paragraph. This post.<BR/><BR/>“If you ... still find yourself wanting independent evidence of a designer and needing some part of evolution to be disproved, you will have been disappointed."<BR/>Mike Gene, Chapter 10, Design Matrix</I>JJS P.Eng.https://www.blogger.com/profile/05029579563816207022noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-80327537823065575752008-08-09T09:41:00.000-06:002008-08-09T09:41:00.000-06:00Hi JJS, I forgot to sign in as Bilbo, but that's w...Hi JJS, I forgot to sign in as Bilbo, but that's who this is writing. <BR/><BR/>It looks like I got you some free advertising at TT. I joined ARN in 2001. From what I remember, Mike Gene usually had the last word in his debates with Art. But perhaps my perspective is prejudiced. <BR/><BR/>As to Analogy, I know next to nothing about computers, but aren't the codes used basically ones where "the meaning of words is determined by (and only by) the medium on which the language is conveyed"?<BR/><BR/>As to the Discontinuity of the genetic code, Jules had a go around with Art at ISCID, and I don't think Art demonstrated continuity nearly as well as he seems to think. <BR/><BR/>As to Rationality, Art needs to show that there is a way to avoid nonsense mutations, without destroying the ability to mutate at all. Further, Mike Gene has already written an essay on the question of how other mutations would affect C deamination. <BR/><BR/>As to Foresight, if computer simulations are correct, then our genetic code is one of the most optimal there is, able to preserve design far into the future.Anonymousnoreply@blogger.com