tag:blogger.com,1999:blog-3855268335402896473.post8796608959877355282..comments2024-01-23T02:32:28.567-08:00Comments on Darwin's God: Here’s That Protein-Protein Interaction ProblemUnknownnoreply@blogger.comBlogger216125tag:blogger.com,1999:blog-3855268335402896473.post-961122297209266682014-07-30T17:46:53.283-07:002014-07-30T17:46:53.283-07:00When I say it's "an open question," ...When I say it's "an open question," I mean neither teleological SA nor naturalistic UCA has ANY inductive evidence for them when the data set being used is that being used natural scientists. Thus, there is no inductive criteria that favors the one over the other in that sense.Jeffhttps://www.blogger.com/profile/16852362499722076519noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-55385552485719045042014-07-30T17:37:59.547-07:002014-07-30T17:37:59.547-07:00ME: But that still leaves SA standing per the only...ME: But that still leaves SA standing per the only hypothesis rejection criteria that is rational--i.e., INDUCTIVE criteria.<br /><br />There is no inductive evidence for an SA history. That's not what I mean by SA left "standing." I mean that since there is no EXPLANATION for either a UCA history or an SA history, there is no inductive evidence for either kind of history. Hence, neither is rejectable via induction applied to the same data set.<br /><br />Pedant: What data set?<br /><br />Jeff: Data that doesn't include personal claims relevant to the question at hand.<br /><br /> Pedant: Do you mean the fossil succession in geologic time? Do mean the enormous data set showing that "life comes from life.?<br />Are you claiming that such data have NO BEARING WHATSOEVER on the hypotheses of separate or continuous ancestry? <br />Jeff: They don't provide, to date, a way to explain or imply the posited lineages and posited transitional forms. Consequently, they have no role in grounding inductive evidence yet. They may yet as we learn more, but currently they don't.<br /><br />Pedant: That they are not suggestive of any testable hypothesis?<br /><br />Jeff: It doesn't matter whether they are suggestive; there are no testable hypotheses relevant to what CH is discussing TO DATE. Thus, nothing CH is saying until now is even controversial from a rational point of view.<br />ME: I'll hunt down one of my logic books.<br /><br />Pedant: Are you saying that you can't remember how you derived the claim:<br />Jeff: No, that's not what I'm saying. The inductive chapters in logic books deal with evidence in a particular sense. If a set of statements implies or models events, that hypothetical statements or modeling heuristic that is considered "best" is that which satisfies criteria such as parsimony, predictive/explanatory breadth, etc. But there is no explanation nor predictive heuristic that implies or models the events in question in terms of a UCA history, etc.<br />What's going on is this: Scientists choose to explain as much as possible naturalistically. Some are even confused enough to believe that "warranted belief" and "evidence" can be distinguished from false beliefs if even humans aren't free to regulate their own discursive thought. <br />But wanting to explain something naturally doesn't mean that it IS explicable naturalistically. Since at least human minds must be free to think discursively (as opposed to all their beliefs being mere groundless "intuitions"), the goal of explaining all things naturalistically is not even possible for humans. So it's an OPEN question as to whether there was free-will involved in the origin of the first oraganism(s) and the lineages, for no one has a clue how to explain abiogenesis or lineages in terms of what is known about the causes of variation.Jeffhttps://www.blogger.com/profile/16852362499722076519noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-19408402793384589272014-07-18T14:30:55.793-07:002014-07-18T14:30:55.793-07:00natschuster: So we need pretty precise conditions ...<b>natschuster</b>: <i>So we need pretty precise conditions for it to happen? </i><br /><br />It seems more a case of lots of possibilities are available. Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-78918455507065398742014-07-18T14:28:11.992-07:002014-07-18T14:28:11.992-07:00natschuster: Doesn't hybridization only take p...<b>natschuster</b>: <i>Doesn't hybridization only take place between closely related species? </i><br /><br />Generally. <br /><br /><b>natschuster</b>: <i>Doesn't the horizontal gene transfer take place all over the place? </i><br /><br />There are many mechanisms of horizontal gene transfer. Viruses are very prolific at inserting their genes into alien genomes, while bacteria sometimes trade genes with distant cousins. Presumably, there was less stringent barriers in the distant past. <br /><br /><b>natschuster</b>: <i>I still think I have less in common with a chimp than the diatoms in question with each other. </i><br /><br />Can you justify that? <br /><br /><b>natschuster</b>: <i>Anyway, if every single species that ever lived is the result of incremental mutation how come are so few even possible examples in the fossil record? </i><br /><br />Simple mutation is just one of many mechanisms of variation. <br /><br /><b>natschuster</b>: <i>Maybe we should take the fossil record at face value, and assume it shows what really happened? </i><br /><br />Then you have a clear record of evolution, from primitive single-celled organisms to colonial life to multicellular life to metazoa to deuterostomes to chordates to vertebrates to gnathostomes to lobe-fined to tetrapods to amniotes (to pick a single lineage). <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-40893915027107060582014-07-18T14:08:20.644-07:002014-07-18T14:08:20.644-07:00So we need pretty precise conditions for it to hap...So we need pretty precise conditions for it to happen? We need to get really lucky?natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-80572854880772469432014-07-18T14:06:06.286-07:002014-07-18T14:06:06.286-07:00Just found this:
? http://darwins-god.blogspot.co...Just found this:<br /><br />? http://darwins-god.blogspot.com/2014/07/here-are-three-important-take-aways.html?showComment=1405717445079#c6428153314073268928natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-47399973909876033792014-07-18T13:54:21.134-07:002014-07-18T13:54:21.134-07:00Who criticized him? Evolutionists? Anyway, so how ...Who criticized him? Evolutionists? Anyway, so how strong is the case?<br /><br />Doesn't hybridization only take place between closely related species? Doesn't the horizontal gene transfer take place all over the place?<br /><br />I still think I have less in common with a chimp than the diatoms in question with each other. Anyway, if every single species that ever lived is the result of incremental mutation how come are so few even possible examples in the fossil record? I know, I know, Darwin said the fossil record ins incomplete. Maybe we should take the fossil record at face value, and assume it shows what really happened? That's the empirical, evidence base science. thing to do.natschusterhttps://www.blogger.com/profile/05312526400131321079noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-62970956863827870732014-07-18T03:26:24.853-07:002014-07-18T03:26:24.853-07:00"It demonstrates how molecular evolution can ..."It demonstrates how molecular evolution can convert one complex molecular machine into a second, equally complex machine by successive deletions, innovations, and recruitment from other molecular systems."<br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-79404079877735292972014-07-18T03:25:39.623-07:002014-07-18T03:25:39.623-07:00Also from the paper: "We show that NF-T3SSs e...Also from the paper: "We show that NF-T3SSs evolved from the flagellum by a series of genetic deletions, innovations, and recruitments of components from other cellular structures. Our evolutionary analysis suggests that NF-T3SSs then quickly adapted to different eukaryotic cells while maintaining a core structure that remains highly similar to the flagellum. This is an example of evolutionary tinkering where a complex structure arises by exaptation, the recruitment of elements that evolved initially for other functions in other cellular structures."<br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-27587773391797914712014-07-18T03:20:53.049-07:002014-07-18T03:20:53.049-07:00John: you are still talking about a multi protein ...<b>John</b>: <i>you are still talking about a multi protein complex which already assumes the existence of the proteins. </i><br /><br />That was the question raised. natschuster: So how did something like the flagellum evolve.<br /><br /><b>John</b>: <i>If you examine the genes, the opposite picture is more plausible, even to evolutionists;<br />http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002983 </i><br /><br />Let's look! "The T3SS was initially adapted to the transport of flagellar components through the membrane and was probably exapted on multiple occasions to transport other proteins." <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-73526460013898395202014-07-17T23:54:48.578-07:002014-07-17T23:54:48.578-07:00you are still talking about a multi protein comple...you are still talking about a multi protein complex which already assumes the existence of the proteins.<br /><br />Also, the paper you cited is from Nick Matzke's imagination. It provides no details whatsoever and goes back to the dark ages of treating proteins as blobs. If you examine the genes, the opposite picture is more plausible, even to evolutionists;<br />http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002983<br /><br />Another clue might have been their next 100 word essay, "The Emergence of Consciousness"<br /><br />Where can I gain more knowledge like this?!Johnhttps://www.blogger.com/profile/17904230581828301988noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-78973205820376800232014-07-17T17:33:03.784-07:002014-07-17T17:33:03.784-07:00Blas: Then successfull reproduction replaces lower...<b>Blas</b>: <i>Then successfull reproduction replaces lower energy level in the river example. </i><br /><br />That seems reasonable. It's not a perfect analogy. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-40306386777274180102014-07-17T17:31:42.529-07:002014-07-17T17:31:42.529-07:00Depends what you mean by smooth. There's no co...Depends what you mean by smooth. There's no complex fossil series, but that's not necessarily expected as the ancestor was free-living, and the events occurred half a billion years ago. Barnacles were preceded by more primitive crustaceans, and molecular evidence supports the phylogeny. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-23674839034838590192014-07-17T17:04:54.986-07:002014-07-17T17:04:54.986-07:00Zachriel said
"Life is optimized for succes...Zachriel said <br /><br />"Life is optimized for successful reproduction"<br /><br /><br />Then successfull reproduction replaces lower energy level in the river example.<br /><br /><br /><br />Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-54662208782432019172014-07-17T16:54:12.527-07:002014-07-17T16:54:12.527-07:00This comment has been removed by the author.Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-74029485115730127112014-07-17T15:19:36.532-07:002014-07-17T15:19:36.532-07:00Blas: I´ll take your not answer as a yes.
You se...<b>Blas</b>: <i>I´ll take your not answer as a yes. </i><br /><br />You seemed to be agreeing with our position. Were you not? <br /><br /><b>Blas</b>: <i>But then life is the opposite to optimization </i><br /><br />Life is optimized for successful reproduction. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-40212260673843677892014-07-17T15:10:09.368-07:002014-07-17T15:10:09.368-07:00natschuster: I found this in the article
The quo...<b>natschuster</b>: <i>I found this in the article </i><br /><br />The quote is from Graham Lawton, a journalist with New Scientist, and the magazine was roundly criticized for overstating the case.<br /><br /><b>Graham Lawton</b>: <i>Darwin assumed that descent was exclusively "vertical" </i><br /><br />Darwin devotes an entire chapter of <i>Origin of Species</i> to hybridization which is a primary horizontal mechanism. <br /><br /><b>natschuster</b>: <i>Anyway, the differences in the diatoms do seem much more trivial, just one part of the test was a little biiger or smaller, than that between chimps and monkeys. </i><br /><br />To a diatom, you're just a bigger monkey. <br /><br /><b>natschuster</b>: <i>Anyway, if there are so many problems that require so much apologetics with the nested hierarchy, then maybe evolution is not the best explanation. </i><br /><br />Sorry that biology is complicated, but there many mechanism involved. <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-90580808714951349752014-07-17T15:09:40.395-07:002014-07-17T15:09:40.395-07:00I´ll take your not answer as a yes.
But then life ...I´ll take your not answer as a yes.<br />But then life is the opposite to optimization, because life works to avoid to reach the lower potential energy status. Improve protein to protein interaction is like river building walls to increase the like level.Blashttps://www.blogger.com/profile/13205610477389739651noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-89724647762158970872014-07-17T15:00:08.561-07:002014-07-17T15:00:08.561-07:00I found this in the article:
"The problems b...I found this in the article:<br /><br />"The problems began in the early 1990s when it became possible to<br />sequence actual bacterial and archaeal genes rather than just RNA.<br />Everybody expected these DNA sequences to confirm the RNA tree, and<br />sometimes they did but, crucially, sometimes they did not. RNA, for<br />example, might suggest that species A was more closely related to<br />species B than species C, but a tree made from DNA would suggest the<br />reverse.<br /><br />Which was correct? Paradoxically, both--but only if the main<br />premise underpinning Darwin's tree was incorrect. Darwin assumed<br />that descent was exclusively "vertical", with organisms passing<br />traits down to their offspring. But what if species also routinely<br />swapped genetic material with other species, or hybridised with<br />them? Then that neat branching pattern would quickly degenerate into<br />an impenetrable thicket of interrelatedness, with species being<br />closely related in some respects but not others."<br /><br />I understand that diatoms have a great deal of intraspecies variation. So the examples may be just that. There isn't that much overlap between humans and chimps. Anyway, the differences in the diatoms do seem much more trivial, just one part of the test was a little biiger or smaller, than that between chimps and monkeys.<br /><br />Anyway, if there are so many problems that require so much apologetics with the nested hierarchy, then maybe evolution is not the best explanation.natschusterhttps://www.blogger.com/profile/05312526400131321079noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-41376007778724472982014-07-17T09:57:26.770-07:002014-07-17T09:57:26.770-07:00So? The study strongly supports speciation. It'...So? The study strongly supports speciation. It'sfo just not the smooth pattern of the canonical ring species. <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-7337069084921850732014-07-17T09:55:25.000-07:002014-07-17T09:55:25.000-07:00natschuster: Graham Lawton, "Why Darwin was w...<b>natschuster</b>: <i>Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009) </i><br />Not sure where the article indicates a discrepancy between morphology and genetics. <br /><br /><b>natschuster</b>: <i>Then there's the hyraxes and aardvarks mentioned above mentioned above. </i><br /><br />Well, let's agree that they nest within eukaryotes, metazoa, chordates, vertebrates, tetradpods, amniotes, mammals, eutheria, afrotheria. <br /><br /><b>natschuster</b>: <i>There's the fact that some of our DNA is closer to that of the gorilla than the chimp. </i><br /><br />Incomplete lineage sorting. That's straight arithmetic, given population genetics. <br /><br /><b>natschuster</b>: <i>There's those seaslugs that have plant DNA for making chlorophyll. </i><br /><br />The sea slugs incorporate the organelles into their cells. It's not a mystery. Some of the genes have even been incorporated into sea slug genorme, but we can clearly determine their origin. <br /><br />What is your point exactly? That the nested hierarchy isn't perfect? That's been known since Darwin. <br /><br /><b>natschustser</b>: <i>And the changes that I did see in the diatoms and such may very well just have been intra-species variety., they were so tirvial </i><br /><br />The difference between humans and chimpanzees is also rather trivial really. Same basic body plan. <br /> Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-26196423884805922602014-07-17T08:52:01.757-07:002014-07-17T08:52:01.757-07:00natschuster: So while a protein is developing, say...<b>natschuster</b>: <i>So while a protein is developing, say ten mutations to create a new binding site, each still has some function? </i><br /><br />If it takes ten independent mutations to form a new binding site, it may not be plausible. However, many proteins have weak secondary functions, so if selection for the primary function is relaxed (such as after a gene duplication), the secondary function may evolve more precisely. <br /><br />Furthermore, point mutations are not the only mechanism of new protein evolution. Proteins are made up of motifs, and changing these motifs allows the rapid evolution of new functions. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-42669445115816218882014-07-17T08:47:49.022-07:002014-07-17T08:47:49.022-07:00I found this in the article you linked in the part...I found this in the article you linked in the part about terrestrial mammals:<br /><br />"However, detailed records of gradual<br />speciation events do not exist, suggesting that<br />ALLOPATRIC SPECIATIONmight be the norm"<br /><br />I admit I didn't read the article thoroughly. I do have a life outside of blogging.<br /><br /><br />And the changes that I did see in the diatoms and such may very well just have been intra-species variety., they were so tirvialnatschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-61646146302976452432014-07-17T08:32:03.677-07:002014-07-17T08:32:03.677-07:00"Do you have specifics in mind? "
There&..."Do you have specifics in mind? "<br />There's this:<br /><br /> Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009)<br /><br />Then there's the hyraxes and aardvarks mentioned above mentioned above. There's the fact that some of our DNA is closer to that of the gorilla than the chimp. There's those seaslugs that have plant DNA for making chlorophyll. <br /><br /> <br />natschusterhttps://www.blogger.com/profile/05312526400131321079noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-73005913246715406212014-07-17T08:11:28.387-07:002014-07-17T08:11:28.387-07:00Here's a review that you might find informativ...Here's a review that you might find informative. <br />http://www.somosbacteriasyvirus.com/speciation.pdf<br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.com