tag:blogger.com,1999:blog-3855268335402896473.post8351883762740814403..comments2024-01-23T02:32:28.567-08:00Comments on Darwin's God: The Naked Ape: An Open Letter to BioLogos on the Genetic EvidenceUnknownnoreply@blogger.comBlogger75125tag:blogger.com,1999:blog-3855268335402896473.post-17192520836384880532016-06-03T05:19:11.322-07:002016-06-03T05:19:11.322-07:00Excellent article. Decades of trying to align part...Excellent article. Decades of trying to align parts of genomes have not produced the hierarchical tree predicted by common ancestry, in spite of selective massaging the available data. A fresh conceptual start is needed, based on understanding the various codes involved and the informational outcomes deliberately Designed. Only then will facts such as lineage-specific mi-RNAs and cis-regulatory patterns start to make sense.Anonymoushttps://www.blogger.com/profile/04397061685310863492noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-40125756397722531332016-06-01T11:46:28.145-07:002016-06-01T11:46:28.145-07:00Blas: Natural selection able to make the populatio...<b>Blas</b>: <i>Natural selection able to make the population oscillate between to extremes not leading it to a new capability. </i><br /><br />One example of a selectable pathway is the evolution of the mammalian middle ear. <br /><br /><b>Blas</b>: <i>As we can observe you need more than oscillations to perform that change. </i><br /><br />Sure. For instance, we would expect intermediates with reduced hind limbs. If we were to look at strata from 50 to 35 million year ago, do you think we might find such organisms? <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-48220677179153757822016-06-01T09:24:24.211-07:002016-06-01T09:24:24.211-07:00Zachriel said
While there is some oscillation, t...<b>Zachriel said</b> <br /><i> While there is some oscillation, they never return to their previous condition. In either case, that's called natural selection</i><br /><br />Natural selection able to make the population oscillate between to extremes not leading it to a new capability.<br /><br /><b>Zachriel said</b> <br /><i> Pigs did not evolve into dolphins. They do share a common ancestor, though.</i> <br /><br />A pig like common ancestor. As we can observe you need more than oscillations to perform that change. <br /><br /><b>Zachriel said</b> <br /><i> You're saying Newton's Universal Law of Gravitation isn't scientific? </i> <br /><br />No I´m saying that stating that that law is universal (valid at any place and any time of the Universe) is a not scientific claim. You do not have evidence for that. May be you have evidence on the contrary unless dark matter exists.<br /><br /><b>Zachriel said</b> <br /><i>That is simply false. The central notion of Newton's Theory of Gravitation is that the force of gravity affects both the moon and the apple, the motion of planets in their orbits, as well as the rate of falling of the apple. .</i><br /><br />And is strong supported because we can “explain” that the orbits of the planets are not perfect ellipses?<br />Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-23166262438366780782016-06-01T08:13:57.457-07:002016-06-01T08:13:57.457-07:00Blas: Exactly, but we do not see actual heritable ...<b>Blas</b>: <i>Exactly, but we do not see actual heritable changes, adaptations changes like the changes in Darwin´s finches beaks goes for and back with changing environmental conditions. </i><br /><br />While there is some oscillation, they never return to their previous condition. In either case, that's called natural selection. <br /><br /><b>Blas</b>: <i>To make a dolphin with a pig you need more than what we see in the Galapagos. </i><br /><br />Pigs did not evolve into dolphins. They do share a common ancestor, though. <br /><br /><b>Blas</b>: <i>No, calling “universal” gravitation is not scientific. </i><br /><br />You're saying Newton's Universal Law of Gravitation isn't scientific? <br /><br /><b>Blas</b>: <i>The point is that the strong support for gravitation comes from de experiments we make here on earth not from the explanation of the disagreement for what we see in the space. </i><br /><br />That is simply false. The central notion of Newton's Theory of Gravitation is that the force of gravity affects both the moon and the apple, the motion of planets in their orbits, as well as the rate of falling of the apple. <br /><br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-55946040806726995392016-06-01T04:56:18.019-07:002016-06-01T04:56:18.019-07:00Zachriel said
When it leads to a heritable change...<b>Zachriel said</b> <br /><i>When it leads to a heritable change, it's called evolution.</i><br /><br />Exactly, but we do not see actual heritable changes, adaptations changes like the changes in Darwin´s finches beaks goes for and back with changing environmental conditions. To make a dolphin with a pig you need more than what we see in the Galapagos.<br /><br /><b>Zachriel said</b> <br /><i>That's clearly wrong. It's called universal gravitation because it unifies the fall of the apple and the movements of the planets.</i> <br /><br />No, calling “universal” gravitation is not scientific. We can only suppose that is universal hopping the dark matter exists. And that is not the point. The point is that the strong support for gravitation comes from de experiments we make here on earth not from the explanation of the disagreement for what we see in the space. Dark matter is not support for the “universal” gravitation is an hypothesis to keep gravitation universal.<br /><br /><b>Zachriel said</b> <br /><i>See Li et al.,</i> <br /><br />I need some time to read that papers. See you later.<br />Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-67058327228778267362016-05-31T13:20:32.132-07:002016-05-31T13:20:32.132-07:00Li et al., The hearing gene Prestin unites echoloc...Li et al., The hearing gene Prestin unites echolocating bats and whales, Curreny Biology 2010Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-75757828608105627482016-05-31T13:19:21.734-07:002016-05-31T13:19:21.734-07:00This comment has been removed by the author.Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-81751543301109451622016-05-31T12:47:35.397-07:002016-05-31T12:47:35.397-07:00Blas: Yes, we observe adaptive changes, not evolut...<b>Blas</b>: <i>Yes, we observe adaptive changes, not evolutive change.</i><br /><br />When it leads to a heritable change, it's called evolution.<br /><br /><b>Blas</b>: <i>The support of the theory of gravity do ot come from the explanations of the difference between the actual orbits and the ellipses but from the scientific experiments of gravity.</i><br /><br />That's clearly wrong. It's called universal gravitation because it unifies the fall of the apple and the movements of the planets. <br /><br /><b>Blas</b>: <i>How many exceptions we have in the fitting of the synonymous differences to the standard phylogeny? </i><br /><br />See Li et al., Echolocation is a sensory mechanism for locating, ranging and identifying objects which involves the emission of calls into the environment and listening to the echoes returning from objects [1]. Only microbats and toothed whales have acquired sophisticated echolocation, indispensable for their orientation and foraging [1]. Although the bat and whale biosonars originated independently and differ substantially in many aspects [2], we here report the surprising finding that the bottlenose dolphin, a toothed whale, is clustered with microbats in the gene tree constructed using protein sequences encoded by the hearing gene Prestin, Current Biology 2010.<br /><br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-26902262395695665962016-05-31T11:30:16.704-07:002016-05-31T11:30:16.704-07:00Zachriel said:
That's right. When combined w...<b>Zachriel said:</b> <br /><i> That's right. When combined with sources of variation, it can lead to adaptive change, such as is observed with Darwin's finches. .</i><br /><br />Yes, we observe <b>adaptive</b> changes, not evolutive change.<br /><br /><b>Zachriel said:</b> <br /><i> That's right. There are multiple influences on the orbit of a planet, so we don't expect perfect ellipses. Instead, we have complex, and possibly chaotic, orbits.</i><br /><br />And so? It is almost impossible to calculate the gravitational resultants of three bodies imagine a star system. The support of the theory of gravity do ot come from the explanations of the difference between the actual orbits and the ellipses but from the scientific experiments of gravity.<br /><br /><b>Zachriel said:</b> <br /><i> Synonymous differences fit the nested hierarchy expected from the standard phylogeny. Non-synonymous differences support the standard phylogeny, except when the organisms are under selection for high-frequency hearing.</i><br /><br />How many exceptions we have in the fitting of the synonymous differences to the standard phylogeny? <br /><br />Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-92035525086679233792016-05-31T10:59:36.287-07:002016-05-31T10:59:36.287-07:00Blas: The natural selection testable is the one th...<b>Blas</b>: <i>The natural selection testable is the one that eliminates the less reproductive members of a population. </i><br /><br />That's right. When combined with sources of variation, it can lead to adaptive change, such as is observed with Darwin's finches. <br /><br /><b>Blas</b>: <i>No. And? </i><br /><br />That's right. There are multiple influences on the orbit of a planet, so we don't expect perfect ellipses. Instead, we have complex, and possibly chaotic, orbits. <br /><br /><b>Blas</b>: <i>Please explain how Non synonymus differences supports standard phylogeny and Non-synonymous differences support natural selection. </i><br /><br />Synonymous differences fit the nested hierarchy expected from the standard phylogeny. Non-synonymous differences support the standard phylogeny, except when the organisms are under selection for high-frequency hearing. <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-16166152248974333372016-05-31T08:39:19.167-07:002016-05-31T08:39:19.167-07:00Zachriel said:
He proposed specific and testable ...<b>Zachriel said:</b> <br /><i>He proposed specific and testable mechanisms to explain the variations of the basic pattern, including natural selection and hybridization.</i><br /><br />The natural selection testable is the one that eliminates the less reproductive members of a population. If you want to test NS as the mechanism by why dolphin and a fish are similar you need to test the selection of a Labrador with “fishy” traits. <br />hybridization is a possible explanation for some of the imperfections, but a posible explanation do not give strong support.<br /><br /><b>Zachriel said:</b> <br /><i>Is the Earth's orbit a perfect ellipse?</i> <br /><br />No. And?<br /><br /><b>Zachriel said:</b> <br /><i>Gee whiz, Blas. We can define substitutions without reference to theory. Call them "differences" if it makes you feel better. Synonymous difference support the standard phylogeny. Non-synonymous differences support natural selection. </i><br /><br />Please explain how Non synonymus differences supports standard phylogeny and Non-synonymous differences support natural selection. <br />Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-39318513194953201942016-05-31T05:32:32.355-07:002016-05-31T05:32:32.355-07:00Blas: A perfect nested hierarchy would be a strong...<b>Blas</b>: <i>A perfect nested hierarchy would be a strong support to common descent, as Darwin knew the nested hierarchy is not perfect proposed that an imperfect nested hierarchy would still support CD. </i><br /><br />He proposed specific and testable mechanisms to explain the variations of the basic pattern, including natural selection and hybridization. <br /><br /><b>Blas</b>: <i>There is any objective measure of the imperfections of the nested hirarchy that establish there is still support for CD? </i><br /><br />Is the Earth's orbit a perfect ellipse? <br /><br /><b>Blas</b>: <i>The concept of “susbstitutions” is a derivation of ToE, then it cannot be support of ToE is circular reasoning. </i><br /><br />Gee whiz, Blas. We can define substitutions without reference to theory. Call them "differences" if it makes you feel better. Synonymous difference support the standard phylogeny. Non-synonymous differences support natural selection. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-73099487003956580062016-05-30T21:55:34.037-07:002016-05-30T21:55:34.037-07:00Thank you also for the polite reply, Ghostrider. T...Thank you also for the polite reply, Ghostrider. Thank you very much. Sorry that I reply so late but I did not seen this before. I wish you a nice day.Anonymoushttps://www.blogger.com/profile/03615166809736365065noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-2194047040242243412016-05-30T16:36:55.261-07:002016-05-30T16:36:55.261-07:00Zachriel said
The nested hierarchy and fossil su...<b>Zachriel said </b> <br /><i>The nested hierarchy and fossil succession support common descent. </i> <br /><br />A perfect nested hierarchy would be a strong support to common descent, as Darwin knew the nested hierarchy is not perfect proposed that an imperfect nested hierarchy would still support CD. The point is how much imperfections still support CD? There is any objective measure of the imperfections of the nested hirarchy that establish there is still support for CD?<br />As everybody agrees the fossil record is incomplete it cannot be strong support for nothing.<br /><br /><b>Zachriel said </b> <br /><i>What we observe is that synonymous substitutions support the standard phylogeny, while the non-synonymous substitutions support adaptation to similar situations. </i> <br />The concept of “susbstitutions” is a derivation of ToE, then it cannot be support of ToE is circular reasoning. <br />Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-68960836740268606092016-05-30T12:55:48.209-07:002016-05-30T12:55:48.209-07:00Blas: Why this explanation would support common de...<b>Blas</b>: <i>Why this explanation would support common descent? </i><br /><br />The nested hierarchy and fossil succession support common descent. <br /><br /><b>Blas</b>: <i>This NS it is not testable. </i><br /><br />We can directly observe natural selection, and its relationship to population genetics. <br /><br /><b>Blas</b>: <i>We do not observe actual mutations mutations of the prestin that led actual mammals to achieve high frequency hearing. </i><br /><br />What we observe is that synonymous substitutions support the standard phylogeny, while the non-synonymous substitutions support adaptation to similar situations. <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-84986145856521006822016-05-30T10:33:16.722-07:002016-05-30T10:33:16.722-07:00Then you are explaining part of the imperfections ...Then you are explaining part of the imperfections by saying that a blind ramdom process found the same solutions for the same problems. An intelligent mind can also do that. Why this explanation would support common descent?<br />This NS it is not testable. We do not observe actual mutations mutations of the prestin that led actual mammals to achieve high frequency hearing. Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-46837372704723122622016-05-30T09:50:05.006-07:002016-05-30T09:50:05.006-07:00Blas: How can NS explain the imperfections of the ...<b>Blas</b>: <i>How can NS explain the imperfections of the nested hierarchy?</i><br /><br />Natural selection means that certain trait will appear in distantly related organisms; for instance, both a fish and a dolphin have hydrodynamic shapes. This is due, not to their shared common ancestry, but to selection for life in the water. Another example is prestin, which is a protein involved in high-frequency hearing. While prestin is largely conserved in mammals, and synonymous substitutions support the standard phylogeny, non-synonymous substitutions in whales and bats show a closer relationship than would otherwise be expected. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-51900188473571879832016-05-30T06:09:36.908-07:002016-05-30T06:09:36.908-07:00Cornelius Hunter: If empirical contradictions are ...<b>Cornelius Hunter</b>: <i>If empirical contradictions are simply transformed into virtues, then there is no hope for informed, meaningful discourse. </i><br /><br />They're not "empirical contradictions", but rather countervailing influences. Branching descent leads to a nested hierarchy, while natural selection sometimes confounds the nested hierarchy. Other mechanisms also counter the pattern expected of branching descent, including hybridization, saturation, and horizontal gene transfer. <br /><br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-51733499031361723322016-05-30T05:19:53.834-07:002016-05-30T05:19:53.834-07:00How can NS explain the imperfections of the nested...How can NS explain the imperfections of the nested hierarchy?Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-7226684208789328992016-05-29T06:46:29.067-07:002016-05-29T06:46:29.067-07:00Blas: Then we are back to philosophy defining what...<b>Blas</b>: <i>Then we are back to philosophy defining what is science and what is not. </i><br /><br />It's not a close situation. Natural selection is a testable mechanism, indeed, can be directly observed. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-47379899399552501892016-05-28T11:55:04.209-07:002016-05-28T11:55:04.209-07:00Then we are back to philosophy defining what is sc...Then we are back to philosophy defining what is science and what is not.Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-48247572437578714942016-05-28T11:25:18.257-07:002016-05-28T11:25:18.257-07:00Zach:
The consilience of the evidence strongly su...Zach:<br /><br /><i>The consilience of the evidence strongly supports common descent, and many of the conflicts to the nested hierarchy are evidence of specific and testable mechanisms, such as natural selection.</i><br /><br />This claim illustrates the problem that the OP is trying to resolve. If empirical contradictions are simply transformed into virtues, then there is no hope for informed, meaningful discourse. If we continue with these claims that are not vulnerable to the empirical data, then evolution has no empirical content and the discussion simply is incommensurate, as philosophers put it.<br /><br />What we are trying to establish here is a reasoned, intelligent discourse. The prerequisite is a common understanding of the scientific evidence.Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-39135865994780780212016-05-28T11:04:03.366-07:002016-05-28T11:04:03.366-07:00Blas: That is not a scientific claim ...
Of cour...<b>Blas</b>: <i>That is not a scientific claim ... </i><br /><br />Of course it's a scientific claim, and we even provided an example. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-69697549771014394882016-05-28T08:53:41.745-07:002016-05-28T08:53:41.745-07:00Zachriel said:
The consilience of the evidence str...<b>Zachriel said:</b><br /><i>The consilience of the evidence strongly supports common descent, and many of the conflicts to the nested hierarchy are evidence of specific and testable mechanisms, such as natural selection.</i> <br /><br />That is not a scientific claim and do not answer tobthe question how much imperfections in the nested hierarchy still support ToE? Consilience and acutal testable mechanisms are not strong evidence for common descent are just possible explanations for the imperfections of the nested hierarchy.<br />Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-55738256332277553232016-05-28T08:21:40.272-07:002016-05-28T08:21:40.272-07:00Great post as usual Cornelius. I was just watching...Great post as usual Cornelius. I was just watching a new youtube video that contained these same problems of phylogenetic incongruency acknowledged by Richard Goldstein.<br /><br />Video Title:Phyloseminar #58: Richard Goldstein (University College London)<br /><br />Video Link: https://www.youtube.com/watch?v=_GFYMZz_qII<br /><br />If even he and others mentioned in your article recognize how scientifically intractable these models have become, then why not step back and rethink the approach instead of adding epicycles.Julian Bajenahttps://www.blogger.com/profile/01000400566604420282noreply@blogger.com