Evolution Intelligent Design

Researchers: Whales took to water by LOSING genes

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Eighty-five genes:

Abstract: The transition from land to water in whales and dolphins (cetaceans) was accompanied by remarkable adaptations. To reveal genomic changes that occurred during this transition, we screened for protein-coding genes that were inactivated in the ancestral cetacean lineage. We found 85 gene losses. Some of these were likely beneficial for cetaceans, for example, by reducing the risk of thrombus formation during diving (F12 and KLKB1), erroneous DNA damage repair (POLM), and oxidative stress–induced lung inflammation (MAP3K19). Additional gene losses may reflect other diving-related adaptations, such as enhanced vasoconstriction during the diving response (mediated by SLC6A18) and altered pulmonary surfactant composition (SEC14L3), while loss of SLC4A9 relates to a reduced need for saliva. Last, loss of melatonin synthesis and receptor genes (AANAT, ASMT, and MTNR1A/B) may have been a precondition for adopting unihemispheric sleep. Our findings suggest that some genes lost in ancestral cetaceans were likely involved in adapting to a fully aquatic lifestyle. – Matthias Huelsmann, Nikolai Hecker, Mark S. Springer John Gatesy, Virag Sharma1,| and Michael Hiller, Science Advances 25 Sep 2019: Vol. 5, no. 9, eaaw6671 DOI: 10.1126/sciadv.aaw6671

Paper (open access).

But isn’t that the kind of thing the villain Michael Behe argues in Darwin Devolves?

If much evolution occurs by the loss of information. we need a theory other than Darwinism (natural selection acting on random mutations allegedly creates information) to help us understand the history of life.

See also: A Review Of Behe’s Darwin Devolves That Looks At What Behe Actually Says

and

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16 Replies to “Researchers: Whales took to water by LOSING genes

  1. 1
    bornagain77 says:

    Aside from the obvious fact that losing genes does NOT come close to explaining how it is even remotely possible to evolve from a small terrestrial deerlike organism into a modern whale in just 4.5 million years,,,

    Right of Reply: Our Response to Jerry Coyne – September 29, 2019
    written by Günter Bechly, Brian Miller and David Berlinski
    Excerpt: The available window of time for the transition from the terrestrial pakicetids to fully marine basilosaurids (Pelagiceti) is only 4.5 million years.
    https://quillette.com/2019/09/29/right-of-reply-our-response-to-jerry-coyne/

    Whale Evolution vs. Population Genetics – Richard Sternberg and Paul Nelson – video
    https://www.youtube.com/watch?v=0csd3M4bc0Q

    Evolution And Probabilities: A Response to Jason Rosenhouse – August 2011
    Excerpt: The equations of population genetics predict that – assuming an effective population size of 100,000 individuals per generation, and a generation turnover time of 5 years – according to Richard Sternberg’s calculations and based on equations of population genetics applied in the Durrett and Schmidt paper, that one may reasonably expect two specific co-ordinated mutations to achieve fixation in the timeframe of around 43.3 million years. When one considers the magnitude of the engineering fete, such a scenario is found to be devoid of credibility.
    http://www.uncommondescent.com.....osenhouse/

    Aside from the obvious fact that losing genes does NOT come close to explaining how it is even remotely possible to evolve from a small terrestrial deerlike organism into a modern whale in just 4.5 million years, they are also falsely presupposing that it is possible to change one organism into a radically new organism by simply ‘tinkering’ with genes,, (amazingly by ‘losing genes’ in this case).

    Yet, directly contrary to the reductive materialistic presupposition that undergirds Darwinian evolution, body plans are NOT reducible to genes, nor to mutations to genes, (nor are the body plans of organisms reducible to any other material particulars within molecular biology that Darwinian materialists may wish to invoke),,,

    Darwinism vs Biological Form – video
    https://www.youtube.com/watch?v=JyNzNPgjM4w

    The failure of the reductive materialism of Darwinian evolution to be able to explain the basic form and/or body plan of any particular organism occurs at a very low level. Much lower than DNA itself.
    In the following article entitled ‘Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics’, which studied the derivation of macroscopic properties from a complete microscopic description, the researchers remark that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, The researchers further commented that their findings challenge the reductionists’ point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description.”

    Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics – December 9, 2015
    Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,,
    It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,,
    “We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s,” added Co-author Professor Michael Wolf from Technical University of Munich. “So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists’ point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description.”
    http://phys.org/news/2015-12-q.....godel.html

    i.e. Darwinists literally have no foundation within physics to stand upon for their foundational presupposition of reductive materialism.

    Supplemental note, the supposed transitional series for whale evolution is not nearly as clear cut as Darwinists have falsely portrayed it to be.

    Real Science vs. Bill Nye the “Science” Guy – Casey Luskin – March 20, 2015
    Excerpt: Annual Review of Ecology and Systematics,, found that Ambulocetus had “large feet” and called its mode of swimming “inefficient” — very different from whales. Another paper found that unlike whales, Ambulocetus was tied to freshwater environments and lived near “the mouths of rivers, lunging out at terrestrial prey — analogous to the hunting process of crocodilians.” This mammal had nothing like “whalelike flippers.”
    http://www.evolutionnews.org/2.....94591.html

    In the following video, Philip Gingerich, the paleontologist who discovered and reconstructed Rhohocetus, which has been called by evolutionists, ‘the most spectacular intermediary fossil in whale evolution’, states this about that “most spectacular intermediary fossil”,,,

    “Well, I told you we don’t have the tail in Rodhocetus. We don’t know for sure whether it had a ball vertebrate indicating a (tail) fluke or not. So I speculated (that) it might have had a (tail) fluke.,,, Since then we found the forelimbs, the hands, and the front arms, the arms in other words of Rodhocetus, and we understand that it doesn’t have the kind of arms that can be spread out like flippers are on a whale.,, If you don’t have flippers, I don’t think you can have a fluke tail and really powered swimming. And so I now doubt that Rodhocetus would have had a fluke tail.”
    Philip Gingerich paleontologist –
    Whale Evolution vs. The Actual Evidence – video – fraudulent fossils revealed (11:40 minute mark)
    https://youtu.be/VSmO4nQ717U?t=699

    I suggest watching the entire video to see how crucial Rodhocetus was for the Darwinian ‘just so’ story of whale evolution to see just how devastating that admission by Dr. Gingerich is to the ‘just so’ story of whale evolution.

    Making up missing links with plaster and body parts from other creatures – April 2014
    Excerpt: The two scientists who found the lion’s share of walking whale fossils essentially created the best fossil proof of evolution using plaster models and drawings and supplied these to museums and science magazines. In each case, they started with incomplete fossils of a land mammal. Whenever a fossil part was missing, they substituted a whale body part (blowholes, fins and flukes) on the skeletal model or skull that they distributed to museums. When these same scientists later found fossils negating their original interpretations, they did not recall the plaster models or drawings. Now museums are full of skulls and skeletons of ‘walking whales’ that are simply false.” Dr. Werner went on to say, “I suspect some curators are not aware of the significance of these substitutions nor are they aware of the updated fossils. Museums should now remove all of the altered skeletons, skulls and drawings since the most important parts of these ‘walking whales’ are admittedly made up. Museums will also have to delete these images from their websites as they are misleading the public.” –
    http://www.thegrandexperiment......ution.html

    Also of interest:

    An Email Exchange Regarding “Vestigial Legs” Pelvic Bones in Whales by Jim Pamplin
    Excerpt: The pelvic bones (supposed Vestigial Legs) of whales serve as attachments for the musculature associated with the penis in males and its homologue, the clitoris, in females. The muscle involved is known as the ischiocavernosus and is quite a powerful muscle in males. It serves as a retractor muscle for the penis in copulation and probably provides the base for lateral movements of the penis. The mechanisms of penile motion are not well understood in whales. The penis seems to be capable of a lot of independent motion, much like the trunk of an elephant. How much of this is mediated by the ischiocavernosus is not known.
    In females the anatomical parts are smaller and more diffuse. I would imagine that there is something homologous to the perineal muscles in man and tetrapods, which affect the entire pelvic area – the clitoris, vagina and anus.
    The pelvic rudiments also serve as origins for the ischiocaudalis muscle, which is a ventral muscle that inserts on the tips of the chevron bones of the spinal column and acts to flex the tail in normal locomotion.
    James G. Mead, Ph.D. – Curator of Marine Mammals – National Museum of Natural History – Smithsonian Institution

    Whale sex: It’s all in the hips – Sept. 8, 2014
    Excerpt: Both whales and dolphins have pelvic (hip) bones, (supposed) evolutionary remnants from when their ancestors walked on land more than 40 million years ago. Common wisdom has long held that those bones are simply vestigial, slowly withering away,,,
    New research from USC and the Natural History Museum of Los Angeles County (NHM) flies directly in the face of that assumption, finding that,, pelvic bones serve a purpose,,,
    “Everyone’s always assumed that if you gave whales and dolphins a few more million years of evolution, the pelvic bones would disappear. But it appears that’s not the case,”,,,
    Dean collaborated with fellow co-corresponding author Jim Dines,,, on a painstaking four-year project to analyze cetacean (whale and dolphin) pelvic bones.
    The muscles that control a cetacean’s penis – which has a high degree of mobility – attach directly to its pelvic bones.,,,
    http://phys.org/news/2014-09-whale-sex-hips.html

  2. 2
    Bob O'H says:

    Researchers: Whales took to water by LOSING genes

    No. That’s not what they’re saying – they look at losses associated with moving to an aquatic environment, but don’t say that losing genes (or, more precisely, gene inactivation) is what allowed them to become aquatic.

    This is what they write:

    Comparative analysis of cetacean genomes has provided important insights into the genomic determinants of cetacean traits and aquatic specializations. Several studies revealed patterns of positive selection in genes with roles in the nervous system, osmoregulation, oxygen transport, blood circulation, or bone microstructure (5–7). An adaptive increase in myoglobin surface charge likely permitted a high concentration of this oxygen transport and storage protein in cetacean muscles (8). In addition to patterns of positive selection, the loss (inactivation) of protein-coding genes is associated with derived cetacean traits. For example, cetaceans have lost a large number of olfactory receptors, taste receptors, and hair keratin genes (9–12).

    So there is evidence for positive selection too. What the authors did in this study was to specifically look for inactivation:

    To investigate the contribution of gene inactivation to the evolution of adaptations to a fully aquatic environment in cetaceans, we systematically searched for protein-coding genes that were inactivated in the cetacean stem lineage (a flowchart of the screen is shown in fig. S1). Briefly, we considered 19,769 genes annotated in the human genome and searched for gene-inactivating mutations throughout a phylogeny of 62 mammalian species, comprising four cetaceans, two pinnipeds, a manatee, and 55 terrestrial mammals (table S1)

  3. 3
    bornagain77 says:

    as to:

    Bob O’Hara: “So there is evidence for positive selection too.”

    correction

    Bob O’Hara: “So (ignoring timescales) there is evidence for positive selection too.”

    There all better:

    Of Whales and Timescales – 05/27/19
    Excerpt: . For example, analysis by Durrett and Schmidt calculated that the time required for just two specific coordinated mutations to co-occur in our human ancestors (assuming neither is harmful on its own) would have been over 200 million years. Mike Behe then found a factor of 30 they missed, implying it would take more like 6 billion years.*,,,
    ,,, the larger problem is that the changes involved in adapting a generic mammalian template into a whale are certainly not all simple, independent, single-letter changes. It seems obvious that multiple coordinated changes would be needed, and it turns out that would require a lot longer than mere millions of years.
    https://evolutionnews.org/2018/03/of-whales-and-timescales/

  4. 4
    ET says:

    Bob O’H- There still isn’t a mechanism capable of producing a fully aquatic cetacean starting with populations of land mammals. There definitely isn’t enough time in the universe for blind and mindless processes to do the job.

    Naturalistic science says that no one knows how whales became aquatic

  5. 5
    Bob O'H says:

    ba77 – As. you’ve read Durrett and Schmidt, you’ll be able to tell me how it is relevant, i.e. go through the examples of positive selection and show that the Durrett and Schmidt model is appropriate.

  6. 6
    bornagain77 says:

    Bob (and weave) O’Hara wants to know how the waiting time problem is even ‘relevant’ to his claims that there is evidence for positive selection for gradual Darwinian. That is an interesting question coming from a professor/statistician who admits on his ‘linked in’ page that “I torture data until it confesses. Sometimes I have to resort to Bayesianism”

    Bob O’Hara
    Professor at NTNU
    “I torture data until it confesses. Sometimes I have to resort to Bayesianism” – 2016
    “I tortured data, mainly in ecology and evolutionary biology.” – 2009
    https://de.linkedin.com/in/bob-o-hara-93b0a210

    Of course the problem with Bob (and weave) O’Hara’s admitting that he statistically ‘tortures data until it confesses’ is that data, like people, will confess to anything you want if you torture it/them long enough.

    “If you torture the data long enough, it will confess to anything.”
    – Ronald Harry Coase (/?ko?s/; 29 December 1910 – 2 September 2013) was a British economist. Coase believed economists should study real markets and not theoretical ones,

    And like economists should study real markets and not theoretical ones, I suggest that Bob (and weave) O’Hara should study the real world of the fossil record, mutations, and genetics and not his theoretical world based on his self admitted ‘tortured’ version of population genetics.

    Right of Reply: Our Response to Jerry Coyne
    written by Günter Bechly, Brian Miller and David Berlinski – Sept. 2019
    Excerpt: The whales? And in twelve million years? Not likely. The available window of time for the transition from the terrestrial pakicetids to fully marine basilosaurids (Pelagiceti) is only 4.5 million years. This corresponds to the lifespan of a single larger mammal species, as Donald Prothero correctly notes. Prothero is Coyne’s ideological ally. They should be better friends. Short time spans give rise to a generic waiting time problem—a much-discussed issue in mainstream population genetics. It is easy to see why. The time required for even a single pair of coordinated mutations to originate and spread in a population is, at least, an order of magnitude longer than the window of time established by the fossil record. Either the fossil record must go, or the waiting time must go, but they cannot go on together. The whales are the least of it. The emergence of a single pair of coordinated mutations in the human lineage required a waiting time of 216 million years. The separation of the chimpanzee and human lineages took place only six or seven million years ago. These figures are clearly in conflict. This is the standard view, the one held by mainstream evolutionary biologists. (Rick Durrett and Deena Schmidt GENETICS November 1, 2008)
    https://quillette.com/2019/09/29/right-of-reply-our-response-to-jerry-coyne/

    Also of note to the waiting time problem:

    The waiting time problem in a model hominin population – 2015 Sep 17
    John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner
    Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,,
    Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information.
    While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man.
    It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years.
    http://www.ncbi.nlm.nih.gov/pm.....MC4573302/

    The real world simply is not kind to Bob (and weave) O’Hara’s statistically tortured theoretical one in the least. For instance, when the ‘real world’ effects of mutations were added to ‘Fisher’s ‘fundamental’ proof for Darwinian evolution’ then Fisher’s supposed theoretical proof for Darwinian evolution was falsified by real world data.

    Fisher’s proof of Darwinian evolution has been flipped?
    – December 27, 2017
    Excerpt: we re-examine Fisher’s Theorem, showing that because it disregards mutations, and because it is invalid beyond one instant in time, it has limited biological relevance. We build a differential equations model from Fisher’s first principles with mutations added, and prove a revised theorem showing the rate of change in mean fitness is equal to genetic variance plus a mutational effects term. We refer to our revised theorem as the fundamental theorem of natural selection with mutations. Our expanded theorem, and our associated analyses (analytic computation, numerical simulation, and visualization), provide a clearer understanding of the mutation–selection process, and allow application of biologically realistic parameters such as mutational effects. The expanded theorem has biological implications significantly different from what Fisher had envisioned.
    https://uncommondescent.com/intelligent-design/fishers-proof-of-darwinian-evolution-has-been-flipped/

    The fundamental theorem of natural selection with mutations – June 2018
    Excerpt: Because the premise underlying Fisher’s corollary is now recognized to be entirely wrong, Fisher’s corollary is falsified. Consequently, Fisher’s belief that he had developed a mathematical proof that fitness must always increase is also falsified.
    https://link.springer.com/article/10.1007/s00285-017-1190-x

    As well, it is now found that “Promising efforts at disentangling the effects of genes and the environment on complicated traits may have been confounded by statistical problems.”

    New Turmoil Over Predicting the Effects of Genes – April 2019
    Promising efforts at disentangling the effects of genes and the environment on complicated traits may have been confounded by statistical problems.
    Excerpt:,,, But now, two results published last month have cast doubt on those findings, and have illustrated that problems with interpretations of GWAS, (genome-wide association studies), results are far more pervasive than anyone realized. The work has implications for how scientists think about the interactions between genetic and environmental effects. It also “raise[s] the ghosts of the possibility that we overestimate … how important genetics is in contributing to differences between people,”
    ,,, “The new studies are really quite disconcerting,” Barton said, because they demonstrated that scientists had been mistaking biases in the polygenic score calculations for something biologically interesting.,,,
    ,,, Though it was always understood to be a problem, “no one realized how big of a problem it was,”,,,
    “It was just that sort of feeling where the world shifts under your feet slightly,”,,, “It’s fairly humbling to see all of that work go away.”,,,
    That’s not to say that genome-wide association studies do not have incredible power.,,,
    It’s when they’re accumulated to make inferences about differences between populations, both in evolutionary and medical contexts, that things can go wrong.
    “We have to go back to the thinking box,” Nielsen said. “This is a major wake-up call … a game changer.”
    https://www.quantamagazine.org/new-turmoil-over-predicting-the-effects-of-genes-20190423/

    i.e. the ‘real world’ was not kind to the ‘tortured’ statistical one that Darwinists had constructed!

    Of course the real world is never kind to those who prefer to live in their own imagined version of reality. But it is simply insulting, especially in science, that Darwinists such as Bob (and weave) insist that we accept their imagined/tortured statistical version of reality as representative of the real world.

    Here is a song you may enjoy Bob (and weave)

    “I wish the real world, would just stop hassling me
    I wish the real world, would just stop hassling me
    I wish the real world, would just stop hassling me
    And you, and me”
    – Matchbox Twenty – Real World (Official Video)
    https://www.youtube.com/watch?v=fwJazZIWNgg

  7. 7
    bornagain77 says:

    Of note to the preceding comment,,, that is not for me to say that statistics, when properly used, is not very useful. What I am trying to say is that statistics, especially in the hands of Darwinists, is very much ripe for abuse:

    Scientific method: Statistical errors – P values, the ‘gold standard’ of statistical validity, are not as reliable as many scientists assume. – Regina Nuzzo – 12 February 2014
    Excerpt: “P values are not doing their job, because they can’t,” says Stephen Ziliak, an economist at Roosevelt University in Chicago, Illinois, and a frequent critic of the way statistics are used.,,,
    “Change your statistical philosophy and all of a sudden different things become important,” says Steven Goodman, a physician and statistician at Stanford. “Then ‘laws’ handed down from God are no longer handed down from God. They’re actually handed down to us by ourselves, through the methodology we adopt.”,,
    One researcher suggested rechristening the methodology “statistical hypothesis inference testing”3, presumably for the acronym it would yield.,,
    The irony is that when UK statistician Ronald Fisher introduced the P value in the 1920s, he did not mean it to be a definitive test. He intended it simply as an informal way to judge whether evidence was significant in the old-fashioned sense: worthy of a second look. The idea was to run an experiment, then see if the results were consistent with what random chance might produce.,,,
    Neyman called some of Fisher’s work mathematically “worse than useless”,,,
    “The P value was never meant to be used the way it’s used today,” says Goodman.,,,
    The more implausible the hypothesis — telepathy, aliens, homeopathy — the greater the chance that an exciting finding is a false alarm, no matter what the P value is.,,,
    “It is almost impossible to drag authors away from their p-values, and the more zeroes after the decimal point, the harder people cling to them”11,,
    http://www.nature.com/news/sci.....E-20140213

    Yet to repeat, statistics, when properly used, (i.e. letting the data speak for itself instead of trying to ‘torture’ the data into saying what you want it to say), then statistics can indeed be very useful,

    This Could Be One of the Most Important Scientific Papers of the Decade – July 23, 2018
    Excerpt: Now we come to Dr. Ewert’s main test. He looked at nine different databases that group genes into families and then indicate which animals in the database have which gene families. For example, one of the nine databases (Uni-Ref-50) contains more than 1.8 million gene families and 242 animal species that each possess some of those gene families. In each case, a dependency graph fit the data better than an evolutionary tree.
    This is a very significant result. Using simulated genetic datasets, a comparison between dependency graphs and evolutionary trees was able to distinguish between multiple evolutionary scenarios and a design scenario. When that comparison was done with nine different real genetic datasets, the result in each case indicated design, not evolution. Please understand that the decision as to which model fit each scenario wasn’t based on any kind of subjective judgement call. Dr. Ewert used Bayesian model selection, which is an unbiased, mathematical interpretation of the quality of a model’s fit to the data. In all cases Dr. Ewert analyzed, Bayesian model selection indicated that the fit was decisive. An evolutionary tree decisively fit the simulated evolutionary scenarios, and a dependency graph decisively fit the computer programs as well as the nine real biological datasets.
    http://blog.drwile.com/this-co.....he-decade/

    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/

    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/

  8. 8
    ET says:

    LoL! @ Bob O’H- Durrett and Schmidt is relevant to any scenario in which specific mutations are required to produce a result. In “Human Errors” Nathan Lents makes the claim that once mutations happen it is then highly, highly improbable that the same site will experience another change. That is nothing more than two specific mutations occurring.

    Positive selection? That is just evo double-talk as nature does not select.

  9. 9
    Bob O'H says:

    bs77 – you have utterly failed to answer my question. It can’t have been that difficult to grasp the issue – even ET understood it. Yes, waiting time is important, but waiting time for what? And is the situation examined by Durrett and Schmidt relevant to positive selection in whale evolution?

  10. 10
    ET says:

    Earth to Bob O’H- “Positive selection” does NOT and cannot make the right mutations happen.

  11. 11
    bornagain77 says:

    Bob (and weave) O’Hara, I’ll take the honest admission from you that you ‘torture’ data to make it confess to what you want it to say to be more than enough evidence to refute any claim that you, or any other Darwinists, may make in regards to any sequence comparisons.

    You guys simply are NOT credible!

    In regards to ‘positive selection’, again, the real world of empirical science is not kind to your imaginary Darwinian world in the least.

    The Strength of Natural Selection in the Wild – David Berlinski – April 25, 2005
    Excerpt: Natural selection disappears as a biological force and reappears as a statistical artifact. The change is not trivial. It is one thing to say that nothing in biology makes sense except in the light of evolution; it is quite another thing to say that nothing in biology makes sense except in the light of various regression correlations between quantitative characteristics. It hardly appears obvious that if natural selection is simply a matter of correlations established between quantitative traits, that Darwin’s theory has any content beyond the phenomenological, and in the most obvious sense, is no theory at all.
    – Berlinski
    http://www.discovery.org/a/2531/

    Genome-wide analysis of a long-term evolution experiment with Drosophila – 2010
    Excerpt of concluding paragraph: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments.”
    http://www.homepages.ed.ac.uk/.....202010.pdf

    “The Third Way” – James Shapiro, Denis Noble, and etc.. etc..,,,
    excerpt: “some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
    http://www.thethirdwayofevolution.com/

    “the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer”
    Michael Lynch – The Origins of Genome Architecture, p 368

    No Controversies About Darwinism? Try This One – May 30, 2017
    Excerpt: “Natural selection functions in the realm of philosophy, not science.” For support, he quotes none other than staunch Darwinian Richard Lewontin of Harvard, who at least had the intellectual rigor to critically examine the meaning of natural selection:
    “For what good is a theory that is guaranteed by its internal logical structure to agree with all conceivable observations, irrespective of the real structure of the world? If scientists are going to use logically unbeatable theories about the world, they might as well give up natural science and take up religion. Yet is that not exactly the situation with Darwinism?”
    (Lewontin, “Testing the Theory of Natural Selection,” Nature 236, no. 543 (1972): 181-182, cited by Bethell, p. 65).,,,
    E.O. Wilson claims that kin selection is unscientific. His opponents will counter that group selection is unscientific. Perhaps it’s all unscientific. Its definitions are fuzzy, its units are unspecified, and it predicts opposite outcomes with equal ease. It cannot be falsified. Students, and thoughtful adults, deserve to know such things.
    https://www.evolutionnews.org/2017/05/no-controversies-about-darwinism-try-this-one/

    (August 2018) Natural Selection is not an actual ’cause’ of anything but is defined as an after the fact ‘effect’. Yet in the literature, Darwinists continue to talk of natural selection as if it had some sort of ‘before the fact’ causal power of an intelligent agent.
    As Adam Sedgwick originally pointed out to Charles Darwin himself about his theory of natural selection, “what is it but a secondary consequence of supposed, or known, primary facts. Development is a better word because more close to the cause of the fact.”,,, and yet,,, “You write of “natural selection” as if it were done consciously by the selecting agent.”
    https://uncommondescent.com/intelligent-design/is-darwinism-completely-worthless-to-science/#comment-663106

  12. 12
    Bob O'H says:

    bs77 – I guess the concepts like humour & hyperbole have escaped you.

  13. 13
    bornagain77 says:

    Bob (and weave): “I guess the concepts like humour & hyperbole have escaped you.”

    Well actually, since ‘humour & hyperbole’, (like mathematics, beauty, persons, etc.. etc..), are both immaterial abstract concepts that are irreducible to the materialistic explanations of Darwinian evolution, (and therefore are to be considered ‘illusory’ on a Darwinian worldview), it turns out that both ‘humour & hyperbole’ have in fact escaped you. And I find that turn of events for you to be extremely humorous.

    And as M. Anthony Mills states in the following article, even ‘persons’ become ‘unreal’ in the Darwinist’s materialistic worldview. In fact he goes on to state, “Not just you, but tables, chairs, countries, countrymen, symphonies, jokes, legal contracts, moral judgments, and acts of courage or cowardice — all of these must be fully explicable in terms of those more fundamental, material constituents.
    In fact, more problematic for the materialist than the non-existence of persons is the existence of mathematics.”
    https://uncommondescent.com/intelligent-design/is-beauty-for-its-own-sake-an-argument-against-darwinism/#comment-685251

  14. 14
    Bob O'H says:

    I rest my case.

  15. 15
    ET says:

    It looks like concepts like science, reality and honesty have escaped Bob O’H…

  16. 16
    bornagain77 says:

    definition:

    case
    b. (1): the evidence supporting a conclusion or judgment
    (2): ARGUMENT
    especially : a convincing argument
    makes a good case for adopting the proposal
    https://www.merriam-webster.com/dictionary/case

    Since ‘making a case’ requires making irrefutably sound logical arguments as well as presenting solid empirical evidence for your position, and since you have neither (and since you refuse to accept sound logical and empirical falsification of your ‘case’), Bob (and weave) you never had, and never will have, ‘a case to rest’. You have a dogmatic belief system that is very much akin to a fundmentalists religion based purely on blind faith.

    Indeed logic itself, which is indispensable for you in supposedly ‘making your case’, cannot even be grounded within the reductive materialism of your Darwinian worldview. So again, Bob (and weave) you never had, and never will have, ‘a case to rest’.

    This following site is an easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic cannot be accounted for unless we believe in God who guarantees our perceptions and reasoning are trustworthy in the first place.

    Presuppositional Apologetics – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    Is God Real? Evidence from the Laws of Logic – J. Warner Wallace
    Excerpt: All rational discussions (even those about the existence or non-existence of God) require the prior foundation of logical absolutes. You’d have a hard time making sense of any conversation if the Laws of Logic weren’t available to guide the discussion and provide rational boundaries. Here are three of the most important Laws of Logic you and I use every day:
    The Law of Identity
    Things “are” what they “are”. “A” is “A”. Each thing is the same with itself and different from another. By this it is meant that each thing (be it a universal or a particular) is composed of its own unique set of characteristic qualities or features.
    The Law of Non-Contradiction
    “A” cannot be both “A” and “Non-A” at the same time, in the same way and in the same sense. Contradictory statements cannot both be true in the same sense at the same time.
    The Law of Excluded Middle
    A statement is either true or false. For any proposition, either that proposition is true, or its negation is true. There is no middle position. For example, the claim that “A statement is either true or false” is either true or false.
    These logical rules are necessary in order for us to examine truth statements. We also need them to point out when someone is reasoning illogically. We use the Laws of Logic all the time; you couldn’t even begin to read or reason through this blog post if you didn’t employ these laws. In fact, you’ve never had an intelligent, rational conversation without using these laws. They’re not a matter of subjective opinion; they are, instead, objectively true. So, here’s an important question: “From where do the transcendent, objective laws of logic come?”
    As an atheist, I would have been the first to describe myself as rational. In fact, I saw myself as far more reasonable than many of the Christians I knew. But, I was basing my rationality on my ability to understand and employ the Laws of Logic. How could I account for these transcendent laws without the existence of a transcendent Law Giver?
    (1) The Objective Laws of Logic Exist
    We cannot deny the Laws of Logic exist. In fact, any reasonable or logical argument against the existence of these laws requires their existence in the first place.
    The Objective Laws of Logic Are Conceptual Laws
    These laws are not physical; they are conceptual. They cannot be seen under a microscope or weighed on a scale. They are abstract laws guiding logical, immaterial thought processes.
    The Objective Laws of Logic Are Transcendent
    The laws transcend location, culture and time. If we go forward or backward a million years, the laws of logic would still exist and apply, regardless of culture or geographic location.
    The Objective Laws of Logic Pre-Existed Mankind
    The transcendent and timeless nature of logical laws indicates they precede our existence or ability to recognize them. Even before humans were able to understand the law of non-contradiction, “A” could not have been “Non-A”. The Laws of Logic were discovered by humans, not created by humans.
    (2) All Conceptual Laws Reflect the Mind of a Law Giver
    All laws require law givers, including conceptual laws. We know this from our common experience in the world in which we live. The laws governing our society and culture, for example, are the result and reflection of minds. But more importantly, the conceptual Laws of Logic govern rational thought processes, and for this reason, they require the existence of a mind.
    (3) The Best and Most Reasonable Explanation for the Kind of Mind Necessary for the Existence of the Transcendent, Objective, Conceptual Laws of Logic is God
    The lawgiver capable of producing the immaterial, transcendent laws preceding our existence must also be an immaterial, transcendent and pre-existent mind. This description fits what we commonly think of when we think of a Creator God.,,,
    https://coldcasechristianity.com/writings/is-god-real-evidence-from-the-laws-of-logic/

    Verse and quote:

    John 1:1
    “In the beginning was the Word, and the Word was with God, and the Word was God”

    What is the Logos?
    Logos is a Greek word literally translated as “word, speech, or utterance.” However, in Greek philosophy, Logos refers to divine reason or the power that puts sense into the world making order instead of chaos.,,,
    In the Gospel of John, John writes “In the beginning was the Word (Logos), and the Word was with God, and the Word was God” (John 1:1). John appealed to his readers by saying in essence, “You’ve been thinking, talking, and writing about the Word (divine reason) for centuries and now I will tell you who He is.”
    https://www.compellingtruth.org/what-is-the-Logos.html

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