tag:blogger.com,1999:blog-37148773.post6419634035059432360..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: "The Soul of the Matter"Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger200125tag:blogger.com,1999:blog-37148773.post-60172146767498819632016-09-24T03:50:28.966-04:002016-09-24T03:50:28.966-04:00Hey Otangelo, when my kids decide to act the muppe...Hey Otangelo, when my kids decide to act the muppet and think they can act stupid when I've explained multiple times what they're doing wrong, I try to explain it in Chinese. Would that perhaps help you understand?<br />Or Spanish? Grasso sounds Italian, would Italian help you comprehend?<br /><br />"What you need to point out is, what i ignore in regard of the scientific evidence that you think favours your views."<br /><br />No, I show you the flaw in your reasoning. Perhaps you this will help you understand:<br />這是很清楚的給我,你讀科學文獻你讀天書一樣。<br /><br />Zhè shì hěn qīngchǔ de gěi wǒ, nǐ dú kēxué wénxiàn nǐ dú tiān shū yīyàng.Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29779193876261125552016-09-23T21:00:14.178-04:002016-09-23T21:00:14.178-04:00I guess Bill thinks if his cousin has different pa...I guess Bill thinks if his cousin has different parents than he has, then this strengthens the hypothesis that babies are delivered by the stork.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35907804857501714142016-09-23T20:55:40.958-04:002016-09-23T20:55:40.958-04:00Bill,
"If they are not monophyletic do you t...Bill,<br /><br /><i>"If they are not monophyletic do you think that this may weaken the common descent hypothesis?"</i><br /><br />No. It only weakens the idea that those flightless birds are more direct relatives to each other than to other members of the larger group called paleognaths. They're still relatives, only they're "cousins," rather than "sisters."Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38172101618698042312016-09-23T20:48:41.044-04:002016-09-23T20:48:41.044-04:00Bill Cole, I have to ask: Do you even understand ...Bill Cole, I have to ask: Do you even understand what common descent is? The type of questions you are asking is not what would be expected from someone who does.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5543069566362320472016-09-23T15:46:46.768-04:002016-09-23T15:46:46.768-04:00Is there any evidence from this paper that weakens...<i>Is there any evidence from this paper that weakens the common descent hypothesis in your opinion?</i><br /><br />I suppose that every instance of homoplasy is a slight weakening of the common descent hypothesis, if you really want to think of it that way. Mind you, we expect to see homoplasy under common descent, so it can't really be used as evidence. The question for you to ask is what we would expect to see under whatever you want to present as an alternative — separate creation? — that we don't expect to see under common descent. I'd say we would expect to see no consistent relationships between "kinds" in the data. The paper falsifies that expectation, therefore no separate creation within Palaeognathae.<br /><br />Ostrich DNA doesn't have both paleognath and neognath type sequences, and I don't think even you know what you mean by that.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66444230097990673642016-09-23T13:43:47.442-04:002016-09-23T13:43:47.442-04:00Ed,
Please point out what i ignore. Davies infere...Ed, <br />Please point out what i ignore. Davies inference imho is irrelevant. What you need to point out is, what i ignore in regard of the scientific evidence that you think favours your views.ElShamah777https://www.blogger.com/profile/12608626398803379702noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28170548536072301472016-09-23T13:24:01.048-04:002016-09-23T13:24:01.048-04:00John,
"What makes this evidence of common des...John,<br />"What makes this evidence of common descent is that multiple genes all tell the same story. The story is in the paper, and just staring at the raw sequence won't tell you much of interest."<br /><br />I will re read the paper tonight with your clarifications in mind. <br /><br />Is there any evidence from this paper that weakens the common descent hypothesis in your opinion? i.e. multiple loss of flightlessness or the ostriches DNA that has both paleognath and neognath type sequences. <br />Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4466012483067570272016-09-23T12:48:08.404-04:002016-09-23T12:48:08.404-04:00If they are not monophyletic do you think that thi...<i>If they are not monophyletic do you think that this may weaken the common descent hypothesis?</i><br /><br />Holy shit. It beggars belief that someone ignorant and stupid enough to even ask this question thinks he knows better than John Harshman and every other competent researcher in the field how the diversity of species inhabiting the earth arose. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60542000915884087492016-09-23T12:21:43.227-04:002016-09-23T12:21:43.227-04:00Bill,
Yes, ostriches are paleognaths. Are you sur...Bill,<br /><br />Yes, ostriches are paleognaths. Are you sure you read the paper? To pick one statement of several: "Analyses of this dataset support a phylogeny in which paleognaths are monophyletic but ratites are not."<br /><br />If you actually want to see all the genetic information behind the paper, look at <a href="https://treebase.org/treebase-web/search/study/summary.html?id=2134" rel="nofollow">this</a>. You can get it in two formats, Nexus and NeXML, in links at the bottom. Neither is all that user-friendly. What makes this evidence of common descent is that multiple genes all tell the same story. The story is in the paper, and just staring at the raw sequence won't tell you much of interest.<br /><br />So, to repeat: if you can't understand the evidence for common descent, what makes you think you understand the supposed evidence against common descent, whatever it may be?John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36125548279189374902016-09-23T11:39:31.620-04:002016-09-23T11:39:31.620-04:00Photosynthesis
"From what I read between you...Photosynthesis<br /><br />"From what I read between you and John right here, you are mistaking common ancestry and monophyletic origins of some group. Here the group of flightless birds. The issue is not whether these flightless birds share common ancestry, but whether they form a monophyletic group."<br /><br />If they are not monophyletic do you think that this may weaken the common descent hypothesis?Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84094254739933748072016-09-23T11:34:53.542-04:002016-09-23T11:34:53.542-04:00John
"Bill, what this shows is that you don&#...John<br />"Bill, what this shows is that you don't understand what you read. You should probably take this as an indication that you shouldn't be so quick to reject the claims of standard biology. And you should probably begin to doubt your ability to understand what you think is the evidence against common descent (which you have never managed to present or reference)"<br /><br />Yes, this subject is new to me. Asking a question in not rejecting your hypothesis, it is trying to understand it. You asked me to agree that there is strong evidence supporting common descent of paleognaths and I don't know how unless I understand your work.<br /><br />Is the Ostrich classified under paleognaths? Based on the limited genetic information published in your paper this seemed to be the biggest outlier.Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42173623804423599052016-09-23T10:39:42.147-04:002016-09-23T10:39:42.147-04:00Ed,
Please point out what i ignore. Davies infere...Ed, <br />Please point out what i ignore. Davies inference imho is irrelevant. What you need to point out is, what i ignore in regard of the scientific evidence that you think favours your views.ElShamah777https://www.blogger.com/profile/12608626398803379702noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60025345834137055992016-09-23T09:05:21.160-04:002016-09-23T09:05:21.160-04:00Thanks Otangelo, you have proven my point. You rea...Thanks Otangelo, you have proven my point. You read science papers/ literature/ books the same way you read the bible, you only cherry pick and quote mine what you like and ignore everything else.Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40978849662136000762016-09-23T08:22:23.153-04:002016-09-23T08:22:23.153-04:00"namely that the genetic cipher could have em...<i>"namely that the genetic cipher could have emerged naturally. Obviously it couln't"</i><br /><br />Gods-of-the-gaps all over again. Sure Otangelo, sure, gods-did-it.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90351369486925757812016-09-23T06:41:14.072-04:002016-09-23T06:41:14.072-04:00Finally, what is going to motivate the addition of...Finally, what is going to motivate the addition of new amino acids to the genetic code? They would have little if any utility until incorporated into proteins - but that will not happen until they are included in the genetic code. So the new amino acids must be synthesised and somehow incorporated into useful proteins (by enzymes that lack them), and all of the necessary machinery for including them in the code (dedicated tRNAs and activating enzymes) put in place – and all done opportunistically! Totally incredible!<br /><br />Why do you think , did Larry conveniently not answer my question, why the 3 additional unusual amino acids that he mentioned and that a few organisms use, would prove evolution of the genetic code ? Because that proves NOTHING. The conceptual problem is much deeper, and cannot be solved without relying to intelligence. <br /><br />I have two topics at my library, where i extensively analyse and elucidate this remarkable situation, and why its EXTRAORDINARY evidence for design:<br /><br />The origin of the genetic cipher, the most perplexing problem in biology<br /><br />Origin of translation of the 4 nucleic acid bases and the 20 amino acids, and the universal assignment of codons to amino acidsAnonymoushttps://www.blogger.com/profile/05265343573323745994noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38544497369136766022016-09-23T06:41:01.639-04:002016-09-23T06:41:01.639-04:00Ed,
read Davies whole book. The fifth miracle. Y...Ed, <br /><br />read Davies whole book. The fifth miracle. Yes, this books tops probaly any other book written about the OOL in regard of making the problems clear that OOL researchers face. The ONLY rational inference is design. But, as Davies writes, in his and the opinion of 99,999% of practicing scientists: it is the job of science to solve mysteries without recourse to divine intervention. ( Only Larry appears here like a messias in the picture, and like a hero oposes this view, and graciously thinks the supernatural should be investigated by science... LOL ). <br /><br />And Calis list of scientific papers is diarrheal attempt of these trying to prove the impossible, namely that the genetic cipher could have emerged naturally. Obviously it couln't. For example, just picking the first paper, we read:<br /><br />http://www.pnas.org/content/102/12/4442.full.pdf<br /><br />The emergence of translation was obviously associated with expansion to a triplet code and selective pressures that led to codon assignments usingthe third position that minimize susceptibility to adverse effects of mutation and errors in translation.<br /><br />Now THINK about the hogwash of this pseudo-scientific claim:<br /><br />In the topic : Origin and evolution of the genetic code: the universal enigma at my virtual library, i quote:<br /><br />Progressive development of the genetic code is not realistic<br /><br />In view of the many components involved in implementing the genetic code, origin-of-life researchers have tried to see how it might have arisen in a gradual, evolutionary, manner. For example, it is usually suggested that to begin with the code applied to only a few amino acids, which then gradually increased in number. But this sort of scenario encounters all sorts of difficulties with something as fundamental as the genetic code.<br /><br />First, it would seem that the early codons need have used only two bases (which could code for up to 16 amino acids); but a subsequent change to three bases (to accommodate 20) would seriously disrupt the code. Recognising this difficulty, most researchers assume that the code used 3-base codons from the outset; which was remarkably fortuitous or implies some measure of foresight on the part of evolution (which, of course, is not allowed).<br /><br /><br />Much more serious are the implications for proteins based on a severely limited set of amino acids. In particular, if the code was limited to only a few amino acids, then it must be presumed that early activating enzymes comprised only that limited set of amino acids, and yet had the necessary level of specificity for reliable implementation of the code. There is no evidence of this; and subsequent reorganization of the enzymes as they made use of newly available amino acids would require highly improbable changes in their configuration. Similar limitations would apply to the protein components of the ribosomes which have an equally essential role in translation.<br /><br /><br />Further, tRNAs tend to have atypical bases which are synthesized in the usual way but subsequently modified. These modifications are carried out by enzymes, so these enzymes too would need to have started life based on a limited number of amino acids; or it has to be assumed that these modifications are later refinements - even though they appear to be necessary for reliable implementation of the code.<br /><br /><br /><br /><br /><br />Anonymoushttps://www.blogger.com/profile/05265343573323745994noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58208881388384985252016-09-23T02:40:10.194-04:002016-09-23T02:40:10.194-04:00Oops, I've added the wrong link. This one is b...Oops, I've added the wrong link. <a href="http://www.rationalskepticism.org/general-debunking/bizarre-article-claims-genetic-code-is-result-of-design-t38328-40.html#p1874534" rel="nofollow">This one is better.</a>Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35868155520781820512016-09-23T02:32:48.661-04:002016-09-23T02:32:48.661-04:00Otangelo:
It's pretty clear to me, you read s...Otangelo:<br /><br />It's pretty clear to me, you read science literature the same way you read the bible. You only read the stuff which give you a warm feeling inside, but you ignore the stuff which contradicts your beliefs/ you can't incorporate into your beliefs. All of a sudden you call these personal inference/ personal beliefs/ what ever.<br /><br />I expect you will most likely ignore things like:<br />Samuel 15:3: "This is what the Lord Almighty says ... 'Now go and strike Amalek and devote to destruction all that they have. Do not spare them, but kill both man and woman, child and infant, ox and sheep, camel and donkey.' " <br /><br />and <br /><br />“I do not permit a woman to teach or to have authority over a man; she must be silent.” (1 Timothy 2:12) .<br /><br />Unlike religious beliefs, science doesn't work this way. You can't cherry pick the results from experiments which confirm your model/ theory and ignore the results which contradict the model you're experimenting on. Scientists have tried this at times, but the end result is like the scientists presenting the cold fusion experiments, 5 minutes of fame and the remainder of your life in shame.<br /><br />If I were you, and you're really interested in cutting edge science on OOL, you should go to page 3 of the thread Luitsuite posted above and check out the papers quoted there. I've made it easy for you, <a href="http://www.rationalskepticism.org/general-debunking/bizarre-article-claims-genetic-code-is-result-of-design-t38328-45.html" rel="nofollow">just click the link</a>. It's fascinating stuff.Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60451459096084413692016-09-22T23:26:55.890-04:002016-09-22T23:26:55.890-04:00John, can you explain to me how this conclusion in...<i>John, can you explain to me how this conclusion in your paper is consistent with a hypothesis of common descent among paleognath birds.</i><br /><br />Bill, what this shows is that you don't understand what you read. You should probably take this as an indication that you shouldn't be so quick to reject the claims of standard biology. And you should probably begin to doubt your ability to understand what you think is the evidence against common descent (which you have never managed to present or reference). <br /><br />bwilson has explained, but I'll repeat: ratites are polyphyletic but paleognaths are monophyletic. This is quite clearly stated in the paper.<br />John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78246257693165289132016-09-22T21:39:52.380-04:002016-09-22T21:39:52.380-04:00Bill,
"My circular argument comment is on Un...Bill,<br /><br /><i>"My circular argument comment is on Universal Common Descent."</i><br /><br />I know. This is how we started the conversation. I disagree that there's any circularity about it. Only, again, it's a huge hypothesis still under scrutiny. (A lot of people accept it, but I think that it's still an open question.<br /><br /><i>"I think there is certainly common descent among species the question is how much.</i><br /><br />Agreed. But I suspect that we both draw the line at very different depths.<br /><br /><i>"I have gone into this discussion with John Harshman and read a few papers he wrote on flightless birds"</i><br /><br />From what I read between you and John right here, you are mistaking common ancestry and monophyletic origins of some group. Here the group of flightless birds. The issue is not whether these flightless birds share common ancestry, but whether they form a monophyletic group.<br /><br />John's analyses suggest, quite convincingly, that these birds evolved their flightless-associated characteristics independently, rather than all the flightless species being derived from a single species of flightless birds. I told you, independent evolution of some characteristics can be quite a hard sell, but John's phylogenetic studies, combined with the biogeography of those birds, etc, make for a good case. So, as a group, flightless birds would be polyphyletic. In other words, they did not inherit their flightless-associated characteristics from a common ancestor. However, they ultimately share common ancestry since all of them come from the same subgroup of birds. Namely the paleognath birds.<br /><br />Clear enough?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67825434373791875902016-09-22T21:24:19.621-04:002016-09-22T21:24:19.621-04:00Allan Jones,
What makes you think I disagree that...Allan Jones,<br /><br />What makes you think I disagree that there's common ancestry there? Did you see that I mentioned vertebrates?<br /><br />The issue with creationists is that they don't see things the same way we do. This is why I start by explaining that there's obvious, "no excuses are possible," ones. Once those are understood, and their irrefutability. I mean organisms sharing even parasitic DNA elements in the very same positions, or the same "disabling" mutations in pseudogenes, the biogeography of the living species and of the fossils that put them even better together, the fossils themselves, their anatomies, plus their timing. Those make cases strong beyond any reasonable doubt (unreasonable is always possible). After those, the rest, like your flying mammal (why did you write "avian mammal"?) and primate, get much easier to accept given that independent evolution of everything from bone structure to organs to etc, etc, is a rather hard sell.<br /><br />The issue is that for creationists similar anatomy, no matter how hard to evolve independently, is not enough to establish common ancestry because, to them, gods are out there making similar life forms like engineers make similar cars. But if they already understand that common ancestry between at least some species can be established beyond reasonable doubt, then our reasons to accept common ancestry based on similarities-that-cannot-be-explained-by-independent-evolution become understandable (even if they don't accept them). Understanding would be quite an accomplishment, right?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19177699033777824322016-09-22T19:29:17.425-04:002016-09-22T19:29:17.425-04:00BC, ratites are paleognaths, but not all paleognat...BC, ratites are paleognaths, but not all paleognaths are ratites. Your quote says that ratites (ostriches, kiwis, cassowaries, etc.) are a polyphyletic group. They are not necessarily each other's closest relatives. The quote goes on about this because the article is refuting a particular hypothesis about ratite evolution. <br /><br />The quote does not in any way contradict the idea that all paleognaths share a common ancestor. It just indicates that ratites (flightless) have ancestors and cousins (different paleognaths, including tinamous) that could fly.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35931877689336285512016-09-22T19:22:34.320-04:002016-09-22T19:22:34.320-04:00@photosynthesis "Common descent can be quite ...@photosynthesis "Common descent can be quite convincingly demonstrated for closely related species ". How about two very different species. A 100kg bipedal primate and a 5g avian mammal. There's an almost perfect mapping of the bones of the skeleton between the two species. This looks very much like the two species must be derived from a common ancestor.<br />http://imgur.com/58ntmQhAnonymoushttps://www.blogger.com/profile/18245824732239901064noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91924267563109699542016-09-22T18:07:39.906-04:002016-09-22T18:07:39.906-04:00Isn't that amazing, John Harshman? Here you h...Isn't that amazing, John Harshman? Here you had disproven common ancestry and proven the existence of God, both in one paper. And you didn't even realize it! How lucky that you have Bill Cole to interpret your research and tell you what it really means. You'd be lost without him, wouldn't you?Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16052773623106440772016-09-22T17:50:47.013-04:002016-09-22T17:50:47.013-04:00I think there is certainly common descent among sp...<i>I think there is certainly common descent among species the question is how much.</i><br /><br />I'm having a hard time understanding this statement. How can there be just a little bit of common descent? Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.com