At Sci News: New Interactive Phylogenetic Map Shows Full Diversity of Life on Earth

Pnyikos, in response to post 2, and in response to this quote from Dr. Cornelius Hunter, “We have known for a long time that common descent has failed hard”, replies that,

"Common descent is fully compatible with ID, the theistic version being that God intervened many times in the evolution of life to guide it along the desired path. It’s much more satisfying intellectually than God “poofing” whole animals into existence ex nihilo, to replace others which have an awful lot in common with them."

Well, I don't care about what is 'much more intellectually satisfying'. I care about what the empirical evidence itself actually says. Shoot, Darwinists are Darwinists precisely because it is personally 'much more intellectually satisfying' for them to believe in Darwinism, not because of what the empirical evidence actually says, but because they don't want to be accountable to the God Who created them.

"Although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist." - Richard Dawkins - The Blind Watchmaker - 1986 "I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers. It isn’t just that I don’t believe in God and, naturally, hope that I’m right in my belief. It’s that I hope there is no God! I don’t want there to be a God; I don’t want the universe to be like that.” - Thomas Nagel - The Last Word - Oxford University Press: 1997

The full quote from Dr. Cornelius Hunter went as such, "We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data." Thus it is the 'quantitive results' from the genetic evidence itself that is showing common descent to have 'failed hard'. Pnyikos did not find these quantitive results ''intellectually satisfying' and thus appealed to lateral gene transfer to try to get around Ewert's findings. Yet, first off, lateral, and/or horizontal, gene transfer does not get him out of his jam with what the empirical evidence is actually saying,

Common Ancestry: Wikipedia vs. the Data - Casey Luskin - October 5, 2012 Excerpt: In fact, the largest category of genes here is eukaryotic (cells with a nucleus) genes that have no homolog among prokaryotes (cells without a nucleus) -- they don't even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. All this is the opposite of "a direct correlation with common descent.",,, ,,, if two phylogenetic trees aren't congruent, the problem isn't that common descent is wrong, but rather the conflict is simply evidence of HGT.,,, Syvanen, (in "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, Vol. 46:339-356 (2012), invokes widespread HGT (Horizontal Gene Transfer), but he's uncommonly honest about the data and its implications, offering the radical suggestion that "life might indeed have multiple origins.",,, let's now look within eukaryotes.,,, The biochemical organization of the innate immune systems of plants and animals is strikingly similar -- but this is a direct non-correlation with common descent. Thus, evolutionary scientists are forced to call them "unexpectedly similar," postulating that the similarities were "independently derived." This data is not explained by Darwinian evolution and common descent. It is explained by common design. Somehow, something tells me not to expect any corrections over at Wikipedia. http://www.evolutionnews.org/2012/10/common_ancestry_1065001.html

Secondly, in his paper showing common descent to have 'failed hard', "Ewert specifically chose Metazoan species because “horizontal gene transfer is held to be rare amongst this clade.”

Response to a Critic: But What About Undirected Graphs? - Andrew Jones - July 24, 2018 Excerpt: The thing is, Ewert specifically chose Metazoan species because “horizontal gene transfer is held to be rare amongst this clade.” Likewise, in Metazoa, hybridization is generally restricted to the lower taxonomic groupings such as species and genera — the twigs and leaves of the tree of life. In a realistic evolutionary model for Metazoa, we can expect to get lots of “reticulation” at lower twigs and branches, but the main trunk and branches ought to have a pretty clear tree-like form. In other words, a realistic undirected graph of Metazoa should look mostly like a regular tree. https://evolutionnews.org/2018/07/response-to-a-critic-but-what-about-undirected-graphs/

Pnyikos also appealed to "endosymbiosis, which joins two or more organisms into one, like the mitochondria that were originally bacteria fusing with a cell that was one of the archae", in order to try to counter Ewert's findings showing common descent to have 'failed hard'. Yet "endosymbiosis", as far as empirical science itself is concerned, is not nearly as 'intellectually satisfying' as Pnyikos would have hoped it to be, and certainly does not get him out of his jam with what the empirical evidence is actually saying.

Endosymbiosis: A Theory in Crisis by Jeffrey P. Tomkins, Ph.D. * - Oct. 30, 2015 Excerpt: However, now that genome sequencing is inexpensive and widespread, the evolutionary story of endosymbiosis has become increasingly clouded and controversial. As new bacterial and eukaryotic genomes are sequenced and the proteins they encode are deduced, the whole evolutionary idea of endosymbiosis has been thrown into utter confusion. One of the most unexpected discoveries has been the utter lack of identified genes that would support the evolutionary tale. As stated in a recent paper, "What was not anticipated was how relatively few mitochondrial proteins with bacterial homologs [sequence similarity] would group specifically with -Proteobacteria in phylogenetic [evolutionary tree] reconstructions: At most, only 10–20% of any of the mitochondrial proteomes examined so far display a robust -proteobacterial signal.4" This lack of evidence for mitochondrial genes derived from bacterial origin in both the mitochondrial DNA and the genome contained in the cell’s nucleus, where most mitochondrial genes are located, is a serious problem for the evolutionary story.,,, http://www.icr.org/article/endosymbiosis-theory-crisis Information Processing Differences Between Archaea and Eukarya—Implications for Homologs and the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 18, 2015 Abstract In the grand schema of evolution, a mythical prokaryote to eukaryote cellular transition allegedly gave rise to the diversity of eukaryotic life (eukaryogenesis). One of the key problems with this idea is the fact that the prokaryotic world itself is divided into two apparent domains (bacteria and archaea) and eukarya share similarities to both domains of prokaryotes while also exhibiting many major innovative features found in neither. In this article, we briefly review the current landscape of the controversy and show how the key molecular features surrounding DNA replication, transcription, and translation are fundamentally distinct in eukarya despite superficial similarities to prokaryotes, particularly archaea. These selected discontinuous molecular chasms highlight the impossibility for eukarya having evolved from archaea. In a separate paper, we will address alleged similarities between eukarya and bacteria. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-archaea-and-eukarya/ Information Processing Differences Between Bacteria and Eukarya—Implications for the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 25, 2015 Excerpt: In a previous report, we showed that a vast chasm exists between archaea and eukarya in regard to basic molecular machines involved in DNA replication, RNA transcription, and protein translation. The differences in information processing mechanisms and systems are even greater between bacteria and eukarya, which we elaborate upon in this report. Based on differences in lineage-specific essential gene sets and in the vital molecular machines between bacteria and eukarya, we continue to demonstrate that the same unbridgeable evolutionary chasms exist—further invalidating the myth of eukaryogenesis. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/

Moreover, although Pnyikos finds God “poofing” whole animals into existence ex nihilo" to be intellectually dissatisfying, the fossil record itself could care less what Pnyikos finds to be 'intellectually satisfying' or not. Simply put, from the Cambrian explosion onward, the fossil record is severely discordant with Darwinian expectations of common descent.

Günter Bechly video: Fossil Discontinuities: A Refutation of Darwinism and Confirmation of Intelligent Design - 2018 https://www.youtube.com/watch?v=M7w5QGqcnNs The fossil record is dominated by abrupt appearances of new body plans and new groups of organisms. This conflicts with the gradualistic prediction of Darwinian Evolution. Here 18 explosive origins in the history of life are described, demonstrating that the famous Cambrian Explosion is far from being the exception to the rule. Also the fossil record establishes only very brief windows of time for the origin of complex new features, which creates an ubiquitous waiting time problem for the origin and fixation of the required coordinated mutations. This refutes the viability of the Neo-Darwinian evolutionary process as the single conceivable naturalistic or mechanistic explanation for biological origins, and thus confirms Intelligent Design as the only reasonable alternative. Gunter Bechly Explains What The Fossil Evidence Really Says - video (2021) 16:49 minute mark - Dr. Bechly quotes many leading Darwinian paleontologists who also agree that the fossil record is severely discordant with Darwin's theory. https://youtu.be/V15sjy7gtVM?t=1009 Scientific study turns understanding about evolution on its head - July 30, 2013 Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form. Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories. ,,,Dr Matthew Wills said: "This pattern, known as 'early high disparity', turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn't a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.",,, Author Martin Hughes, continued: "Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on. Co-author Dr Sylvain Gerber, added: "A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,” http://phys.org/news/2013-07-scientific-evolution.html

Verse:

Genesis 1:21 So God created the great creatures of the sea and every living thing with which the water teems and that moves about in it, according to their kinds, and every winged bird according to its kind. And God saw that it was good.

bornagain77

Bornagain77, you wrote: "We have known for a long time that common descent has failed hard." Common descent is fully compatible with ID, the theistic version being that God intervened many times in the evolution of life to guide it along the desired path. It's much more satisfying intellectually than God "poofing" whole animals into existence ex nihilo, to replace others which have an awful lot in common with them. That said, I should add that common descent does not mean a traditional tree structure. As one gets into the early steps in the evolution of life, there is so much lateral transfer that one has a web rather than a tree. Then individual trees of life for the three domains are like trees from a common underground root system that keeps penetrating itself like the mycelium of a mushroom. Further complicating the process is endosymbiosis, which joins two or more organisms into one, like the mitochondria that were originally bacteria fusing with a cell that was one of the archae. [Query: how does one produce the vertical bars in the left hand margin to accompany quotes from a single post? Unlike on Usenet, I see no way to directly reply to posts like the one by Bornagain77.] pnyikos

The map is lovely, and a joy to navigate once one catches on to a few tricks. One is to pick a genus you know and love, and then to zoom out by clicking on "family" or some higher taxon to get a bird's eye view of the surrounding terrain. I used the genus Zaglossus, the long beaked echidna that is critically endangered in all three species and is not nearly as well known as Tachyglossus, the short beaked echidna that has been successfully bred by zoos. But when I zoomed out, I discovered a weakness: it does not do a good job of enabling one to reconstruct the Tree of Life. Juxtaposed with Monotremata are Lepidosauria (lizards and snakes -- so far so good) and Marsupilia. Still OK, but the colored dividing lines between marsupials and placentals are thicker than the ones between marsupials and monotremes. This suggests the discredited Marsupionta hypothesis that marsupials are more closely related to monotremes than to placentals. Even if all such mistakes can be eliminated, the "map" depiction is much harder to grasp than the phylogenetic tree depiction of phylogeny. Could someone modify the software used to generate the map to produce a comprehensive tree of life to replace the pitifully sketchy Tolweb tree of life? This tree had languished for a decade when I last looked at it, after having been drastically reduced from the University of Phoenix Tree of Life which it somehow replaced. pnyikos

The ability to answer questions of descent become easier and easier. Somehow I doubt the pattern actually discerned will not come close to supporting any form of naturalized Evolution. Where did all those proteins come from? How do they actually work together? Begging the question, the current logical fallacy, will just provide more excuses for nonsense. jerry

Unfortunately, mechanisms produce patterns. And evolution by means of blind and mindless processes wouldn't produce a tree. Heck, given starting populations of prokaryotes, blind and mindless processes can only produce variations of more prokaryotes. Universal common descent can't even get started. ET

Much better on a bigger screen. Alan Fox

played around with it for about an hour–pretty cool………

Not much good on an Android phone, unfortunately. Alan Fox

A few notes:

"The lay-person reading this, or watching the (Richard Dawkins) video above, is given the clear impression that every gene or pseudogene in every living organism gives essentially the same phylogenetic tree, when analysed with its homologs from other species. This is simply not true. If this were true, then phylogeny building in the genomic era would be a walk in the park. But, as many of my readers will know from personal experience, it is not. If this were true, terms like horizontal gene transfer, incomplete lineage sorting, introgression, and molecular convergence would be rare curiosities in the genomic literature. But they are common (click on the links in the previous sentence to see searched for these terms on Google Scholar). If this were true, commonly-used phylogenetic software like ASTRAL, ASTRID and BUCKy, designed to deal with gene tree incongruence, would be seldom used. But they are used often. I hardly need to labour my point to the present audience. Dawkins’ statements are simply wrong. Gloriously and utterly wrong." Richard Buggs, “Obsolete Dawkinsian evidence for evolution” at Nature: Ecology & Evolution https://uncommondesc.wpengine.com/intelligent-design/dawkinss-claim-every-gene-delivers-approximately-the-same-tree-of-life-contested-at-nature-journal/ Molecular Data Wreak Havoc on the Tree of Life - Casey Luskin - February 7, 2014 Excerpt: during the 1990s, early into the revolution in molecular genetics, many studies began to show that phylogenetic trees derived from anatomy and those derived from molecules often contradicted each other. Stephen Meyer - Darwin's Doubt - (pp. 122-123) ,,,Moreover, when complex parts that are shared by different animals aren't distributed in a treelike pattern, that wreaks havoc on the assumption of homology that's used to build phylogenetic trees. In other words, this kind of extreme convergent evolution refutes the standard assumption that shared biological similarity (especially complex biological similarity like a brain and nervous system) implies inheritance from a common ancestor. If brains and nervous systems evolved multiple times, this undermines the main assumptions used in constructing phylogenetic trees, calling into question the very basis for inferring common ancestry.,,, http://www.evolutionnews.org/2014/02/the_ghost_of_te081981.html Forbidden Question: Common Descent or Common Design? - Jonathan Witt - October 22, 2021 Excerpt: “In 1965 one of the most important scientists of the last century, Linus Pauling, and biologist Emil Zuckerkandl, considered by some as the father of molecular biology, suggested a way that macroevolution could be tested and proved; If the comparison of anatomical and DNA sequences led to the same family tree of organisms, this would be strong evidence for macroevolution. According to them, only evolution would explain the convergence of these two independent chains of evidence. By implication, the opposite finding would count against macroevolution. So what were the results? Over the past 28 years, experimental evidence has revealed that family trees based on anatomical features contradict family trees based on molecular similarities, and at many points. They do not converge. Just as troubling for the idea of macroevolution. family trees based on different molecules yield conflicting and contradictory family trees. As a 2012 paper published in Biological Reviews of the Cambridge philosophical Society reported, "Incongruence between phylogenies derived from morphological versus molecular analysis, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species". Another paper published the following year in the journal Nature, highlighted the extent of the problem. The authors compared 1,070 genes in twenty different yeasts and got 1,070 different trees. https://evolutionnews.org/2021/10/forbidden-question-common-descent-or-common-design/ Logged Out - Scientists Can't Find Darwin's "Tree of Life" Anywhere in Nature by Casey Luskin - Winter 2013 Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors. Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,, Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance: • A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."6 • A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."7 • A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."8 Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded.",,, Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?" ,,, "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."10,,, A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."12,,, http://www.salvomag.com/new/articles/salvo27/logged-out.php "These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes. Instead, we need to turn our attention to the role of genomic novelty in the evolution of phenotypic diversity and innovation.,,, We can now sequence de novo the genomes and transcriptomes (the genes expressed at any one time/place) of any organism. We have sequence data for algae, pythons, green sea turtles, puffer fish, pied flycatchers, platypus, koala, bonobos, giant pandas, bottle-nosed dolphins, leafcutter ants, monarch butterfly, pacific oysters, leeches…the list is growing exponentially. And each new genome brings with it a suit of unique genes. Twenty percent of genes in nematodes are unique. Each lineage of ants contains about 4000 novel genes, but only 64 of these are conserved across all seven ant genomes sequenced so far." - WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? - Life Evolves Via A Shared Genetic Toolkit Seirian Sumner https://www.edge.org/response-detail/25533 - Matti Leisola, Heretic (2018), pages 83-84 and 118-119 New Paper by Winston Ewert Demonstrates Superiority of Design Model - Cornelius Hunter - July 20, 2018 Excerpt: Ewert’s three types of data are: (i) sample computer software, (ii) simulated species data generated from evolutionary/common descent computer algorithms, and (iii) actual, real species data. Ewert’s three models are: (i) a null model which entails no relationships between any species, (ii) an evolutionary/common descent model, and (iii) a dependency graph model. Ewert’s results are a Copernican Revolution moment. First, for the sample computer software data, not surprisingly the null model performed poorly. Computer software is highly organized, and there are relationships between different computer programs, and how they draw from foundational software libraries. But comparing the common descent and dependency graph models, the latter performs far better at modeling the software “species.” In other words, the design and development of computer software is far better described and modeled by a dependency graph than by a common descent tree. Second, for the simulated species data generated with a common descent algorithm, it is not surprising that the common descent model was far superior to the dependency graph. That would be true by definition, and serves to validate Ewert’s approach. Common descent is the best model for the data generated by a common descent process. Third, for the actual, real species data, the dependency graph model is astronomically superior compared to the common descent model. Where It Counts Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered — the actual, real, biological species data — the results were unambiguous. Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent. Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other. We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand. Ten thousand is a big number. But it gets worse, much worse. Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division. The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set, given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division. Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth? Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros. That’s the ratio of how probable the data are on these two models! By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage over that of common descent. 10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence. This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits. But It Gets Worse The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450. In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450. We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data. https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/

bornagain77

played around with it for about an hour--pretty cool......... chuckdarwin